From 3dbbbb473dbf41125999bc8f79690d4648fee045 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Fri, 21 Apr 2023 16:13:39 +0200 Subject: [PATCH 0001/2173] feat: add initial support for arm build [WIP] --- .circleci/config.yml | 116 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 116 insertions(+) create mode 100644 .circleci/config.yml diff --git a/.circleci/config.yml b/.circleci/config.yml new file mode 100644 index 0000000000000..25b514811cf09 --- /dev/null +++ b/.circleci/config.yml @@ -0,0 +1,116 @@ +# .circleci/config.yml +version: 2.1 + +executors: + osx-arm64: + macos: + xcode: 14.2.0 # indicate your selected version of Xcode + resource_class: macos.m1.large.gen1 + linux-aarch64: + machine: + image: ubuntu-2004:current + resource_class: arm.medium + +jobs: # a basic unit of work in a run + build_and_test: + parameters: + os: + type: executor + executor: << parameters.os >> + steps: + - checkout + + - run: + name: Fetch bioconda install script + command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/install-and-set-up-conda.sh + + - restore_cache: + keys: + - bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} + + - run: + name: Install bioconda-utils + command: | + bash install-and-set-up-conda.sh + + - save_cache: + key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} + paths: + - /opt/miniconda + + - run: + name: Build and test + command: | + conda activate bioconda-utils + bioconda-utils build recipes config.yml --git-range origin/master HEAD + + - run: + name: Prepare artifacts + command: | + ( + mkdir -p /tmp/artifacts/packages + cd /opt/miniconda/envs/bioconda/conda-bld || exit 0 + find -name .cache | xargs rm -rf || true + for n in index.html channeldata.json linux-64 osx-64 noarch; do + cp -rv $n /tmp/artifacts/packages || true + done + ) || true + + - store_artifacts: + path: /tmp/artifacts + + build_and_push: + parameters: + os: + type: executor + executor: << parameters.os >> + steps: + - checkout + + - run: + name: Fetch bioconda install script + command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/install-and-set-up-conda.sh + + - restore_cache: + keys: + - bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} + + - run: + name: Install bioconda-utils + command: | + bash install-and-set-up-conda.sh + + - save_cache: + key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} + paths: + - /opt/miniconda + + - run: + name: Build and push + command: | + conda activate bioconda-utils + # TODO we need to update bioconda-utils with support for retrieving circleci artifacts from above + bioconda-utils handle-merged-pr recipes config.yml \ + --repo bioconda/bioconda-recipes \ + --git-range ${CIRCLE_SHA1}~1 ${CIRCLE_SHA1} \ + --fallback build + +workflows: + build_and_test: + jobs: + - build_and_test: + filters: + branches: + ignore: master + matrix: + parameters: + os: [osx-arm64, linux-aarch64] + build_and_push: + jobs: + - build_and_push: + filters: + branches: + only: master + matrix: + parameters: + os: [osx-arm64, linux-aarch64] From a3cbc1995dce564f45ed1f06711d9ecbe95bdb84 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Fri, 21 Apr 2023 16:21:43 +0200 Subject: [PATCH 0002/2173] fix --- .circleci/config.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 25b514811cf09..280aad315526c 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -31,6 +31,7 @@ jobs: # a basic unit of work in a run - run: name: Install bioconda-utils command: | + mkdir -p /opt bash install-and-set-up-conda.sh - save_cache: @@ -78,6 +79,7 @@ jobs: # a basic unit of work in a run - run: name: Install bioconda-utils command: | + mkdir -p /opt bash install-and-set-up-conda.sh - save_cache: From 8afac37c21b1f5bd06af3b592445ae84388c9fc4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Fri, 21 Apr 2023 16:32:29 +0200 Subject: [PATCH 0003/2173] dbg --- .circleci/config.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 280aad315526c..5542891453173 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -31,7 +31,8 @@ jobs: # a basic unit of work in a run - run: name: Install bioconda-utils command: | - mkdir -p /opt + sudo mkdir -p /opt/miniconda + chown -R $USER:$USER /opt/miniconda bash install-and-set-up-conda.sh - save_cache: @@ -79,7 +80,8 @@ jobs: # a basic unit of work in a run - run: name: Install bioconda-utils command: | - mkdir -p /opt + sudo mkdir -p /opt/miniconda + chown -R $USER:$USER /opt/miniconda bash install-and-set-up-conda.sh - save_cache: From cc738bbba020869865667b94c8c9bf83edc0778e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 22 Apr 2023 11:18:24 +0200 Subject: [PATCH 0004/2173] fix --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 5542891453173..a8f3a2e6c7e86 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -32,7 +32,7 @@ jobs: # a basic unit of work in a run name: Install bioconda-utils command: | sudo mkdir -p /opt/miniconda - chown -R $USER:$USER /opt/miniconda + sudo chown -R $USER /opt/miniconda bash install-and-set-up-conda.sh - save_cache: From bc21584e5de222e3072d1c0e99117ff95469f431 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 4 Oct 2023 11:32:46 +0200 Subject: [PATCH 0005/2173] Update .circleci/config.yml Co-authored-by: Yikun Jiang --- .circleci/config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a8f3a2e6c7e86..8a3ada4a1d741 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -31,8 +31,8 @@ jobs: # a basic unit of work in a run - run: name: Install bioconda-utils command: | - sudo mkdir -p /opt/miniconda - sudo chown -R $USER /opt/miniconda + sudo mkdir -p /opt/ + sudo chown -R $USER /opt/ bash install-and-set-up-conda.sh - save_cache: From d6e1885c2f15266c58bd46ec670b2b97d65bb2e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 4 Oct 2023 11:32:55 +0200 Subject: [PATCH 0006/2173] Update .circleci/config.yml Co-authored-by: Yikun Jiang --- .circleci/config.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 8a3ada4a1d741..cca6597aff59b 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -43,7 +43,9 @@ jobs: # a basic unit of work in a run - run: name: Build and test command: | - conda activate bioconda-utils + source /opt/mambaforge/etc/profile.d/conda.sh + source /opt/mambaforge/etc/profile.d/mamba.sh + mamba activate bioconda bioconda-utils build recipes config.yml --git-range origin/master HEAD - run: From 57897c89f6ef7922ab072c6b3c061d7f4f415911 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 4 Oct 2023 11:33:04 +0200 Subject: [PATCH 0007/2173] Update .circleci/config.yml Co-authored-by: Yikun Jiang --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index cca6597aff59b..dba2f0f272c4b 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -38,7 +38,7 @@ jobs: # a basic unit of work in a run - save_cache: key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} paths: - - /opt/miniconda + - /opt/mambaforge/ - run: name: Build and test From c7591ab0db703507e12f602d05582b9c91e986db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 4 Oct 2023 11:33:12 +0200 Subject: [PATCH 0008/2173] Update .circleci/config.yml Co-authored-by: Yikun Jiang --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index dba2f0f272c4b..4ef7693a0c192 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -53,7 +53,7 @@ jobs: # a basic unit of work in a run command: | ( mkdir -p /tmp/artifacts/packages - cd /opt/miniconda/envs/bioconda/conda-bld || exit 0 + cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 find -name .cache | xargs rm -rf || true for n in index.html channeldata.json linux-64 osx-64 noarch; do cp -rv $n /tmp/artifacts/packages || true From b5b2555adb679e7df15b50c83cb848ed59f59237 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 4 Oct 2023 11:33:20 +0200 Subject: [PATCH 0009/2173] Update .circleci/config.yml Co-authored-by: Yikun Jiang --- .circleci/config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 4ef7693a0c192..7424f99d0ebfc 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -82,8 +82,8 @@ jobs: # a basic unit of work in a run - run: name: Install bioconda-utils command: | - sudo mkdir -p /opt/miniconda - chown -R $USER:$USER /opt/miniconda + sudo mkdir -p /opt + chown -R $USER:$USER /opt bash install-and-set-up-conda.sh - save_cache: From 7348a153f495fc5c678e15eb7327fb45624b85ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 4 Oct 2023 11:33:29 +0200 Subject: [PATCH 0010/2173] Update .circleci/config.yml Co-authored-by: Yikun Jiang --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 7424f99d0ebfc..a817d31c8433d 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -89,7 +89,7 @@ jobs: # a basic unit of work in a run - save_cache: key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} paths: - - /opt/miniconda + - /opt/mambaforge - run: name: Build and push From 64551a338241820ccdc3e17824a2cb58bad15d0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 4 Oct 2023 11:33:37 +0200 Subject: [PATCH 0011/2173] Update .circleci/config.yml Co-authored-by: Yikun Jiang --- .circleci/config.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a817d31c8433d..7b623adfd887c 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -94,7 +94,9 @@ jobs: # a basic unit of work in a run - run: name: Build and push command: | - conda activate bioconda-utils + source /opt/mambaforge/etc/profile.d/conda.sh + source /opt/mambaforge/etc/profile.d/mamba.sh + mamba activate bioconda # TODO we need to update bioconda-utils with support for retrieving circleci artifacts from above bioconda-utils handle-merged-pr recipes config.yml \ --repo bioconda/bioconda-recipes \ From c5549e39aa3a1c5bab57528d01c07f853eae2757 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 11:50:07 +0200 Subject: [PATCH 0012/2173] adapt script retrieval to latest changes --- .circleci/config.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 7b623adfd887c..e4f5d8128a4af 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -7,8 +7,8 @@ executors: xcode: 14.2.0 # indicate your selected version of Xcode resource_class: macos.m1.large.gen1 linux-aarch64: - machine: - image: ubuntu-2004:current + docker: + - image: cimg/base:2023.06 resource_class: arm.medium jobs: # a basic unit of work in a run @@ -22,7 +22,7 @@ jobs: # a basic unit of work in a run - run: name: Fetch bioconda install script - command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/install-and-set-up-conda.sh + command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh - restore_cache: keys: @@ -73,7 +73,7 @@ jobs: # a basic unit of work in a run - run: name: Fetch bioconda install script - command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/install-and-set-up-conda.sh + command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh - restore_cache: keys: From a39df061002220f9c7c640a18f6962155d419664 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 11:51:52 +0200 Subject: [PATCH 0013/2173] add configuration --- .circleci/config.yml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index e4f5d8128a4af..2c6df8783d3eb 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -40,6 +40,16 @@ jobs: # a basic unit of work in a run paths: - /opt/mambaforge/ + # We reconfigure conda to use the right channel setup. + # This has to be done after the cache is restored, because + # the channel setup is not cached as it resides in the home directory. + # We could use a system-wide (and therefore cached) channel setup, + # but mamba does not support that at the time of implementation + # (it ignores settings made by --system). + - run: + name: Configure conda + command: bash configure-conda.sh + - run: name: Build and test command: | @@ -91,6 +101,16 @@ jobs: # a basic unit of work in a run paths: - /opt/mambaforge + # We reconfigure conda to use the right channel setup. + # This has to be done after the cache is restored, because + # the channel setup is not cached as it resides in the home directory. + # We could use a system-wide (and therefore cached) channel setup, + # but mamba does not support that at the time of implementation + # (it ignores settings made by --system). + - run: + name: Configure conda + command: bash configure-conda.sh + - run: name: Build and push command: | From 387bc5e153e4a52d3e8afee9deefe422923fa8eb Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 11:59:44 +0200 Subject: [PATCH 0014/2173] update cache key --- .circleci/config.yml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 2c6df8783d3eb..6ea0cf84313ba 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -26,17 +26,19 @@ jobs: # a basic unit of work in a run - restore_cache: keys: - - bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} + - bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} - run: name: Install bioconda-utils command: | sudo mkdir -p /opt/ - sudo chown -R $USER /opt/ + chown -R $USER:$USER /opt + echo "installing bioconda-utils" + ls install-and-set-up-conda.sh bash install-and-set-up-conda.sh - save_cache: - key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} + key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} paths: - /opt/mambaforge/ @@ -87,7 +89,7 @@ jobs: # a basic unit of work in a run - restore_cache: keys: - - bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} + - bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} - run: name: Install bioconda-utils @@ -97,7 +99,7 @@ jobs: # a basic unit of work in a run bash install-and-set-up-conda.sh - save_cache: - key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }} + key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} paths: - /opt/mambaforge From 27b96fc8eedd9dd4d3963d2c46d66ea7bb8568b2 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 12:04:03 +0200 Subject: [PATCH 0015/2173] dbg --- .circleci/config.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 6ea0cf84313ba..9d2148b2c4997 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -35,6 +35,7 @@ jobs: # a basic unit of work in a run chown -R $USER:$USER /opt echo "installing bioconda-utils" ls install-and-set-up-conda.sh + ls -l / bash install-and-set-up-conda.sh - save_cache: From ce7efff84a26676c574a67962d395d3ce6d0943f Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 12:06:35 +0200 Subject: [PATCH 0016/2173] dbg --- .circleci/config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 9d2148b2c4997..da6406b9f2707 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -32,7 +32,7 @@ jobs: # a basic unit of work in a run name: Install bioconda-utils command: | sudo mkdir -p /opt/ - chown -R $USER:$USER /opt + sudo chown -R $USER:$USER /opt echo "installing bioconda-utils" ls install-and-set-up-conda.sh ls -l / @@ -96,7 +96,7 @@ jobs: # a basic unit of work in a run name: Install bioconda-utils command: | sudo mkdir -p /opt - chown -R $USER:$USER /opt + sudo chown -R $USER:$USER /opt bash install-and-set-up-conda.sh - save_cache: From 3a01e4ac11ea763170e86dfb949745e870737ae1 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 12:12:04 +0200 Subject: [PATCH 0017/2173] dbg --- .circleci/config.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index da6406b9f2707..c3e489873f269 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -32,7 +32,9 @@ jobs: # a basic unit of work in a run name: Install bioconda-utils command: | sudo mkdir -p /opt/ - sudo chown -R $USER:$USER /opt + echo $USER + sudo chmod o+rwx /opt + #sudo chown -R $USER:$USER /opt echo "installing bioconda-utils" ls install-and-set-up-conda.sh ls -l / From 8e29e3889f64e88ea213bbb6904a641bafc3a241 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 12:28:19 +0200 Subject: [PATCH 0018/2173] setup PATH --- .circleci/config.yml | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index c3e489873f269..cf3c6e1d0b022 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -32,18 +32,18 @@ jobs: # a basic unit of work in a run name: Install bioconda-utils command: | sudo mkdir -p /opt/ - echo $USER sudo chmod o+rwx /opt - #sudo chown -R $USER:$USER /opt - echo "installing bioconda-utils" - ls install-and-set-up-conda.sh - ls -l / bash install-and-set-up-conda.sh - save_cache: key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} paths: - /opt/mambaforge/ + + - run: + name: Setup PATH + command: + echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV" # We reconfigure conda to use the right channel setup. # This has to be done after the cache is restored, because @@ -98,7 +98,7 @@ jobs: # a basic unit of work in a run name: Install bioconda-utils command: | sudo mkdir -p /opt - sudo chown -R $USER:$USER /opt + sudo chmod o+rwx /opt bash install-and-set-up-conda.sh - save_cache: @@ -106,6 +106,11 @@ jobs: # a basic unit of work in a run paths: - /opt/mambaforge + - run: + name: Setup PATH + command: + echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV" + # We reconfigure conda to use the right channel setup. # This has to be done after the cache is restored, because # the channel setup is not cached as it resides in the home directory. From e14571be5182be17b4a8fe06a0d0444b92a761bf Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 12:50:55 +0200 Subject: [PATCH 0019/2173] disable M1, job naming --- .circleci/config.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index cf3c6e1d0b022..f2205ae6c0346 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -2,17 +2,17 @@ version: 2.1 executors: - osx-arm64: - macos: - xcode: 14.2.0 # indicate your selected version of Xcode - resource_class: macos.m1.large.gen1 + # osx-arm64: + # macos: + # xcode: 14.2.0 # indicate your selected version of Xcode + # resource_class: macos.m1.large.gen1 linux-aarch64: docker: - image: cimg/base:2023.06 resource_class: arm.medium jobs: # a basic unit of work in a run - build_and_test: + build and test (ARM): parameters: os: type: executor @@ -78,7 +78,7 @@ jobs: # a basic unit of work in a run - store_artifacts: path: /tmp/artifacts - build_and_push: + build and upload (ARM): parameters: os: type: executor From f0c837c2d21b6d8b9ec3084203d5e749602bb55e Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 12:52:36 +0200 Subject: [PATCH 0020/2173] workflow naming --- .circleci/config.yml | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index f2205ae6c0346..5723813272f7e 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -12,7 +12,7 @@ executors: resource_class: arm.medium jobs: # a basic unit of work in a run - build and test (ARM): + build_and_test: parameters: os: type: executor @@ -78,7 +78,7 @@ jobs: # a basic unit of work in a run - store_artifacts: path: /tmp/artifacts - build and upload (ARM): + build_and_upload: parameters: os: type: executor @@ -134,7 +134,7 @@ jobs: # a basic unit of work in a run --fallback build workflows: - build_and_test: + build and test (ARM): jobs: - build_and_test: filters: @@ -142,13 +142,18 @@ workflows: ignore: master matrix: parameters: - os: [osx-arm64, linux-aarch64] - build_and_push: + os: + #- osx-arm64 + - linux-aarch64 + + build and upload (ARM): jobs: - - build_and_push: + - build_and_upload: filters: branches: only: master matrix: parameters: - os: [osx-arm64, linux-aarch64] + os: + #- osx-arm64 + - linux-aarch64 From 5c9c6c394a05fcb24bba2314109ee86b01f0067f Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 12:55:36 +0200 Subject: [PATCH 0021/2173] bump abra2 for testing ARM build --- recipes/abra2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/abra2/meta.yaml b/recipes/abra2/meta.yaml index 1d5adf33ab6ae..15218a30514bc 100644 --- a/recipes/abra2/meta.yaml +++ b/recipes/abra2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: edb35fb6ff318239353a573d1abad148073b8ac0bb2cd44a18e561abe08aef32 build: - number: 2 + number: 3 skip: true # [osx] requirements: From d1baa032c2145ed63bb9affdb51da5e4ec1d9bb3 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 13:53:31 +0200 Subject: [PATCH 0022/2173] add run_exports for abra2 --- recipes/abra2/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/abra2/meta.yaml b/recipes/abra2/meta.yaml index 15218a30514bc..0ab7046f22f92 100644 --- a/recipes/abra2/meta.yaml +++ b/recipes/abra2/meta.yaml @@ -12,6 +12,8 @@ source: build: number: 3 skip: true # [osx] + run_exports: + - pin_subpackage(name, max_pin="x") requirements: build: From 2e66149abd9f1c8d3e08849657ceb71e082fcff1 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 14:35:31 +0200 Subject: [PATCH 0023/2173] dbg --- recipes/abra2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/abra2/meta.yaml b/recipes/abra2/meta.yaml index 0ab7046f22f92..1f6c21fb38f27 100644 --- a/recipes/abra2/meta.yaml +++ b/recipes/abra2/meta.yaml @@ -26,7 +26,7 @@ requirements: test: commands: - - 'abra2 2>&1 | grep "Abra version"' + - 'abra2 2>&1 | grep "Abra version" || (abra2 && exit 1)' about: home: https://github.com/mozack/abra2 From b925d5e29fa807dd79df4c2ff4cdc636aa3b86ce Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 4 Oct 2023 15:03:58 +0200 Subject: [PATCH 0024/2173] add zlib dependency --- recipes/abra2/meta.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/recipes/abra2/meta.yaml b/recipes/abra2/meta.yaml index 1f6c21fb38f27..b5ae0cb6be58c 100644 --- a/recipes/abra2/meta.yaml +++ b/recipes/abra2/meta.yaml @@ -20,9 +20,12 @@ requirements: - maven - make - {{ compiler('cxx') }} + host: + - zlib run: - openjdk >=8,<10 - coreutils + - zlib test: commands: From e38681c031a822e2f6858680f3d826d0c56fdedf Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:47:01 -0400 Subject: [PATCH 0025/2173] Copy linux-aarch64 files --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 5723813272f7e..c3060dcd6fb42 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -70,7 +70,7 @@ jobs: # a basic unit of work in a run mkdir -p /tmp/artifacts/packages cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 find -name .cache | xargs rm -rf || true - for n in index.html channeldata.json linux-64 osx-64 noarch; do + for n in index.html channeldata.json linux-aarch64 linux-64 osx-64 noarch; do cp -rv $n /tmp/artifacts/packages || true done ) || true From fd30c0065b2e254669f4d6a6a9e02381c3e0b9e6 Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Wed, 18 Oct 2023 04:05:09 -0400 Subject: [PATCH 0026/2173] Skip arm builds if no recipes request the platform (#43708) * abort job if platform not found * sudo for yq call * debug yq error * separate regex * more debugging * check yq version * more debugging * even more debugging * check shell * more debugging * isolate debug checks * trial and error * test * download correct yq version * check arch of yq * Download ARM build of yq * Add platform to recipe * dynamically get yq platform * test skip * move check to script * permissions * swap argument order --- .circleci/check-for-additional-platforms.sh | 38 +++++++++++++++++++++ .circleci/config.yml | 8 +++++ 2 files changed, 46 insertions(+) create mode 100755 .circleci/check-for-additional-platforms.sh diff --git a/.circleci/check-for-additional-platforms.sh b/.circleci/check-for-additional-platforms.sh new file mode 100755 index 0000000000000..f165332fe417e --- /dev/null +++ b/.circleci/check-for-additional-platforms.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +# arguments +git_range=$1 +job_name=$2 + +# Download ARM version of yq +yq_platform=$(uname) +yq_arch=$(uname -m) +[[ $yq_arch = "aarch64" ]] && yq_arch="arm64" +wget https://github.com/mikefarah/yq/releases/latest/download/yq_${yq_platform}_${yq_arch} -O /usr/local/bin/yq + +# Find recipes changed from this merge +files=`git diff --name-only --diff-filter AMR ${git_range} | grep -E 'meta.yaml$' ` +build=0 + +for file in $files; do + echo $file + additional_platforms=$(cat $file \ + | sed -E 's/(.*)\{%(.*)%\}(.*)/# \1\2\3/g' \ + | sed -E 's/(.*)\{\{(.*)\}\}(.*)/\1\2\3/g' \ + | yq '.extra.additional-platforms[]') + # Check if any additional platforms match this job + for additional_platform in $additional_platforms; do + if [ "${CIRCLE_JOB}" = "${job_name}-${additional_platform}" ] + then + build=1 + break + fi + done +done + +# If no changed recipes apply to this platform, skip remaining steps +if [[ build -lt 1 ]] +then + echo "No recipes using this platform, skipping rest of job." + circleci-agent step halt +fi \ No newline at end of file diff --git a/.circleci/config.yml b/.circleci/config.yml index c3060dcd6fb42..f9cbef85a5163 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -20,6 +20,10 @@ jobs: # a basic unit of work in a run steps: - checkout + - run: + name: Check for Additional Platforms + command: ./.circleci/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test" + - run: name: Fetch bioconda install script command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh @@ -86,6 +90,10 @@ jobs: # a basic unit of work in a run steps: - checkout + - run: + name: Check for Additional Platforms + command: ./.circleci/check-for-additional-platforms.sh "${CIRCLE_SHA1}~1 ${CIRCLE_SHA1}" "build_and_upload" + - run: name: Fetch bioconda install script command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh From 4077396dda9d9733aef2ed3059d2b479015af48d Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Wed, 15 Nov 2023 10:05:27 -0500 Subject: [PATCH 0027/2173] CircleCI workflow for Bulk builds on ARM (#44245) * add bulk ARM build * update image to ubuntu 22 --- .circleci/config.yml | 104 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 104 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index f9cbef85a5163..30a61b2288088 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -10,6 +10,10 @@ executors: docker: - image: cimg/base:2023.06 resource_class: arm.medium + linux-aarch64-bulk: + machine: + image: ubuntu-2204:current + resource_class: arm.medium jobs: # a basic unit of work in a run build_and_test: @@ -141,6 +145,93 @@ jobs: # a basic unit of work in a run --git-range ${CIRCLE_SHA1}~1 ${CIRCLE_SHA1} \ --fallback build + bulk_build: + parameters: + os: + type: executor + runner: + type: integer + executor: << parameters.os >> + steps: + - add_ssh_keys: + fingerprints: + - 1e:85:74:42:35:5f:c5:a2:35:c2:ec:b7:80:c0:7c:40 + + - checkout + + - run: + name: Check for [ci run] + command: | + commit_message="$(git log --format=oneline -n 1 $CIRCLE_SHA1)" + if [[ $commit_message =~ "[ci run]" ]]; then + echo "[ci run] found, continuing." + else + echo "[ci run] not found, exiting." + circleci-agent step halt + fi + + - run: + name: set git user + command: | + git config user.name bioconda-bot + git config user.email bioconda-bot@users.noreply.github.com + git branch --set-upstream-to=origin/$CIRCLE_BRANCH $CIRCLE_BRANCH + + - run: + name: Fetch bioconda install script + command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh + + - restore_cache: + keys: + - bioconda-utils-{{ arch }}-bulk--{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} + + - run: + name: Install bioconda-utils + command: | + sudo mkdir -p /opt/ + sudo chmod o+rwx /opt + bash install-and-set-up-conda.sh + + - save_cache: + key: bioconda-utils-{{ arch }}--bulk--{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} + paths: + - /opt/mambaforge/ + + - run: + name: Setup PATH + command: + echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV" + + # We reconfigure conda to use the right channel setup. + # This has to be done after the cache is restored, because + # the channel setup is not cached as it resides in the home directory. + # We could use a system-wide (and therefore cached) channel setup, + # but mamba does not support that at the time of implementation + # (it ignores settings made by --system). + - run: + name: Configure conda + command: bash configure-conda.sh + + # For now, do not upload ARM images to biocontainers: --mulled-upload-target biocontainers + # FIXME: For initial testing, the following were removed: + - run: + name: Build and upload + command: | + set -e + eval "$(conda shell.bash hook)" + conda activate bioconda + echo '============' + conda info --all + conda config --show-sources + python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' + echo '============' + bioconda-utils build recipes config.yml \ + --worker-offset << parameters.runner >> --n-workers 6 \ + --docker --mulled-test --docker-base-image quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch) \ + --anaconda-upload --record-build-failures --skiplist-leafs + conda clean -y --all + + workflows: build and test (ARM): jobs: @@ -165,3 +256,16 @@ workflows: os: #- osx-arm64 - linux-aarch64 + + Bulk branch (ARM): + jobs: + - bulk_build: + filters: + branches: + only: bulk + matrix: + parameters: + os: + #- osx-arm64-bulk + - linux-aarch64-bulk + runner: [0, 1, 2, 3, 4, 5] From 6db7e5fa6bfa33d212b9cca5a6607733dffbbe80 Mon Sep 17 00:00:00 2001 From: aliciaaevans Date: Wed, 15 Nov 2023 18:13:33 -0500 Subject: [PATCH 0028/2173] Use BiocondaBot for failure commit --- .circleci/config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 30a61b2288088..9ad9f65ce4dde 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -173,8 +173,8 @@ jobs: # a basic unit of work in a run - run: name: set git user command: | - git config user.name bioconda-bot - git config user.email bioconda-bot@users.noreply.github.com + git config user.name BiocondaBot + git config user.email biocondabot@users.noreply.github.com git branch --set-upstream-to=origin/$CIRCLE_BRANCH $CIRCLE_BRANCH - run: From 60bc977a30530a12da7121e450df730aec992b87 Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Wed, 15 Nov 2023 18:14:56 -0500 Subject: [PATCH 0029/2173] Update recipes/abra2/meta.yaml additional-platform Co-authored-by: Yikun Jiang --- recipes/abra2/meta.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/abra2/meta.yaml b/recipes/abra2/meta.yaml index b5ae0cb6be58c..342af9bad048e 100644 --- a/recipes/abra2/meta.yaml +++ b/recipes/abra2/meta.yaml @@ -31,6 +31,10 @@ test: commands: - 'abra2 2>&1 | grep "Abra version" || (abra2 && exit 1)' +extra: + additional-platforms: + - linux-aarch64 + about: home: https://github.com/mozack/abra2 license: MIT From 4985c183793fefca6b67d42a84f5fad7f12f3ac7 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 18 Nov 2023 19:56:09 -0500 Subject: [PATCH 0030/2173] add comments on sed command --- .circleci/check-for-additional-platforms.sh | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.circleci/check-for-additional-platforms.sh b/.circleci/check-for-additional-platforms.sh index f165332fe417e..a05da11215509 100755 --- a/.circleci/check-for-additional-platforms.sh +++ b/.circleci/check-for-additional-platforms.sh @@ -1,5 +1,9 @@ #!/bin/bash +# Check to see if any changed recipes have specified the key +# extra:additional-platforms, and if so, if they match the platform of the +# currently-running machine. + # arguments git_range=$1 job_name=$2 @@ -16,6 +20,8 @@ build=0 for file in $files; do echo $file + # To create a properly-formatted yaml that yq can parse, comment out jinja2 + # variable setting with {% %} and remove variable use with {{ }}. additional_platforms=$(cat $file \ | sed -E 's/(.*)\{%(.*)%\}(.*)/# \1\2\3/g' \ | sed -E 's/(.*)\{\{(.*)\}\}(.*)/\1\2\3/g' \ @@ -35,4 +41,4 @@ if [[ build -lt 1 ]] then echo "No recipes using this platform, skipping rest of job." circleci-agent step halt -fi \ No newline at end of file +fi From 6e1f8180d2fb7f29c3ba19e4ccf2ddc9c302fda6 Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Sat, 25 Nov 2023 15:15:18 -0500 Subject: [PATCH 0031/2173] ARM builds: CircleCI jobs consistency (#44447) * use machine for build-and-test and store images * remove outdated comment --- .circleci/config.yml | 27 ++++++++++++++++++--------- 1 file changed, 18 insertions(+), 9 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 9ad9f65ce4dde..1045700662f42 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -7,10 +7,6 @@ executors: # xcode: 14.2.0 # indicate your selected version of Xcode # resource_class: macos.m1.large.gen1 linux-aarch64: - docker: - - image: cimg/base:2023.06 - resource_class: arm.medium - linux-aarch64-bulk: machine: image: ubuntu-2204:current resource_class: arm.medium @@ -69,7 +65,10 @@ jobs: # a basic unit of work in a run source /opt/mambaforge/etc/profile.d/conda.sh source /opt/mambaforge/etc/profile.d/mamba.sh mamba activate bioconda - bioconda-utils build recipes config.yml --git-range origin/master HEAD + bioconda-utils build recipes config.yml \ + --docker --mulled-test \ + --docker-base-image quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch) \ + --git-range origin/master HEAD - run: name: Prepare artifacts @@ -81,6 +80,18 @@ jobs: # a basic unit of work in a run for n in index.html channeldata.json linux-aarch64 linux-64 osx-64 noarch; do cp -rv $n /tmp/artifacts/packages || true done + if command -V docker >/dev/null; then + mkdir -p /tmp/artifacts/images + cd /tmp/artifacts/images + docker image ls --format='{{.Repository}}:{{.Tag}}' | \ + { grep biocontainers || true ; } | \ + xargs -n1 -P4 bash -c ' + test -n "${1+x}" || exit 0 + echo "Start compressing docker image ${1} ..." + docker save "${1}" | gzip -c > "${1##*/}.tar.gz" + echo "Finished compressing docker image ${1} ." + ' -- + fi ) || true - store_artifacts: @@ -139,7 +150,6 @@ jobs: # a basic unit of work in a run source /opt/mambaforge/etc/profile.d/conda.sh source /opt/mambaforge/etc/profile.d/mamba.sh mamba activate bioconda - # TODO we need to update bioconda-utils with support for retrieving circleci artifacts from above bioconda-utils handle-merged-pr recipes config.yml \ --repo bioconda/bioconda-recipes \ --git-range ${CIRCLE_SHA1}~1 ${CIRCLE_SHA1} \ @@ -213,7 +223,6 @@ jobs: # a basic unit of work in a run command: bash configure-conda.sh # For now, do not upload ARM images to biocontainers: --mulled-upload-target biocontainers - # FIXME: For initial testing, the following were removed: - run: name: Build and upload command: | @@ -266,6 +275,6 @@ workflows: matrix: parameters: os: - #- osx-arm64-bulk - - linux-aarch64-bulk + #- osx-arm64 + - linux-aarch64 runner: [0, 1, 2, 3, 4, 5] From 24b46bc502cdbcfb389c28a1a6f267744ac6b796 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 25 Nov 2023 22:46:34 -0500 Subject: [PATCH 0032/2173] Arm builds circleci fixes (#44457) * remove caching for circleci * do not run regular tests on pushes to bulk * add linting * remove cache from all circleci steps --- .circleci/config.yml | 43 +++++++++++-------------------------------- 1 file changed, 11 insertions(+), 32 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 1045700662f42..141443ed4a1f0 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -28,10 +28,6 @@ jobs: # a basic unit of work in a run name: Fetch bioconda install script command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh - - restore_cache: - keys: - - bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} - - run: name: Install bioconda-utils command: | @@ -39,11 +35,6 @@ jobs: # a basic unit of work in a run sudo chmod o+rwx /opt bash install-and-set-up-conda.sh - - save_cache: - key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} - paths: - - /opt/mambaforge/ - - run: name: Setup PATH command: @@ -66,7 +57,7 @@ jobs: # a basic unit of work in a run source /opt/mambaforge/etc/profile.d/mamba.sh mamba activate bioconda bioconda-utils build recipes config.yml \ - --docker --mulled-test \ + --lint --docker --mulled-test \ --docker-base-image quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch) \ --git-range origin/master HEAD @@ -113,10 +104,6 @@ jobs: # a basic unit of work in a run name: Fetch bioconda install script command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh - - restore_cache: - keys: - - bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} - - run: name: Install bioconda-utils command: | @@ -124,11 +111,6 @@ jobs: # a basic unit of work in a run sudo chmod o+rwx /opt bash install-and-set-up-conda.sh - - save_cache: - key: bioconda-utils-{{ arch }}-{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} - paths: - - /opt/mambaforge - - run: name: Setup PATH command: @@ -191,10 +173,6 @@ jobs: # a basic unit of work in a run name: Fetch bioconda install script command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh - - restore_cache: - keys: - - bioconda-utils-{{ arch }}-bulk--{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} - - run: name: Install bioconda-utils command: | @@ -202,11 +180,6 @@ jobs: # a basic unit of work in a run sudo chmod o+rwx /opt bash install-and-set-up-conda.sh - - save_cache: - key: bioconda-utils-{{ arch }}--bulk--{{ checksum "install-and-set-up-conda.sh" }}-{{ checksum "configure-conda.sh" }}-{{ checksum "common.sh" }} - paths: - - /opt/mambaforge/ - - run: name: Setup PATH command: @@ -227,8 +200,9 @@ jobs: # a basic unit of work in a run name: Build and upload command: | set -e - eval "$(conda shell.bash hook)" - conda activate bioconda + source /opt/mambaforge/etc/profile.d/conda.sh + source /opt/mambaforge/etc/profile.d/mamba.sh + mamba activate bioconda echo '============' conda info --all conda config --show-sources @@ -237,7 +211,10 @@ jobs: # a basic unit of work in a run bioconda-utils build recipes config.yml \ --worker-offset << parameters.runner >> --n-workers 6 \ --docker --mulled-test --docker-base-image quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch) \ - --anaconda-upload --record-build-failures --skiplist-leafs + --anaconda-upload \ + --mulled-upload-target biocontainers \ + --record-build-failures \ + --skiplist-leafs conda clean -y --all @@ -247,7 +224,9 @@ workflows: - build_and_test: filters: branches: - ignore: master + ignore: + - master + - bulk matrix: parameters: os: From 5cf3f192a391e5092ace0962a59ab1cc48ab5d0b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 08:41:05 -0600 Subject: [PATCH 0033/2173] Update raptor to 3.0.1 (#43430) * Update raptor to 3.0.1 * Add run_exports * Update build command * Add dependency --------- Co-authored-by: Enrico Seiler Co-authored-by: Enrico Seiler --- recipes/raptor/build.sh | 7 ++----- recipes/raptor/meta.yaml | 10 +++++++--- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/recipes/raptor/build.sh b/recipes/raptor/build.sh index d718df2eaca8e..ae27ae77a6465 100644 --- a/recipes/raptor/build.sh +++ b/recipes/raptor/build.sh @@ -2,9 +2,6 @@ mkdir -p build cd build -cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-mavx2 -D__STDC_FORMAT_MACROS" -DRAPTOR_NATIVE_BUILD=OFF -DRAPTOR_LTO_BUILD=OFF +cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-mavx2 -D__STDC_FORMAT_MACROS" -DRAPTOR_NATIVE_BUILD=OFF -DCMAKE_INSTALL_PREFIX="${PREFIX}" make -j"${CPU_COUNT}" - -mkdir -p $PREFIX/bin -cp bin/raptor $PREFIX/bin -chmod +x $PREFIX/bin/raptor +make install diff --git a/recipes/raptor/meta.yaml b/recipes/raptor/meta.yaml index e0462b62e1c01..60599432442f1 100644 --- a/recipes/raptor/meta.yaml +++ b/recipes/raptor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "raptor" %} -{% set version = "3.0.0" %} +{% set version = "3.0.1" %} package: name: "{{ name }}" @@ -7,11 +7,13 @@ package: source: url: https://github.com/seqan/{{ name }}/releases/download/{{ name }}-v{{ version }}/{{ name }}-{{ version }}-Source.tar.xz - sha256: cb984586d249d9dcf85bc672568735c797002e319f4ce922e918837800746f06 + sha256: be44e7b2635e110c940cf40ff132956200551a2e25765d9f057e844f7a3ccebb build: - number: 1 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} requirements: build: @@ -21,9 +23,11 @@ requirements: host: - bzip2 - zlib + - yaml-cpp run: - bzip2 - zlib + - yaml-cpp test: commands: From 1934a5ebad05cb27b1a1047c1fc8be647efb3966 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 09:19:57 -0600 Subject: [PATCH 0034/2173] Update taxpasta to 0.6.1 (#43412) --- recipes/taxpasta/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxpasta/meta.yaml b/recipes/taxpasta/meta.yaml index c02c3ec442f9f..3778c68e675b9 100644 --- a/recipes/taxpasta/meta.yaml +++ b/recipes/taxpasta/meta.yaml @@ -1,6 +1,6 @@ {% set name = "taxpasta" %} -{% set version = "0.6.0" %} -{% set sha256 = "b6ee7c3432d60e2375ac1e71b03d3d961f61ff809692852466267971e1d470b5" %} +{% set version = "0.6.1" %} +{% set sha256 = "468141b00bb286e5b52fb47e7046af68d4f849eecb209a3ec77b0ce4da5dcf01" %} package: name: {{ name|lower }} From b436597414ed9a8ea566ba450ab61f529fbeb4b8 Mon Sep 17 00:00:00 2001 From: Sandra Romain <74207779+SandraLouise@users.noreply.github.com> Date: Wed, 4 Oct 2023 18:53:52 +0200 Subject: [PATCH 0035/2173] Update recipe for new version of SVJedi-graph v1.2.1 (#43395) --- recipes/svjedi-graph/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/svjedi-graph/meta.yaml b/recipes/svjedi-graph/meta.yaml index 1f53c0c85f13c..28a591a5f48b6 100644 --- a/recipes/svjedi-graph/meta.yaml +++ b/recipes/svjedi-graph/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.2.0" %} -{% set sha256 = "ec01f0fc9bc0814f1d42caf3af57f50ead8bc4b89aabd007f595c31a200a078c" %} +{% set version = "1.2.1" %} +{% set sha256 = "862b12aae1b4e12494263933d9d7cab859ac856220aec55fba01de43a2120e6e" %} package: name: svjedi-graph @@ -8,6 +8,8 @@ package: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('svjedi-graph', max_pin=None) }} source: url: https://github.com/SandraLouise/SVJedi-graph/archive/refs/tags/v{{ version }}.tar.gz From 7bde19e3303ed382d94f0864c09816ee39dcbf89 Mon Sep 17 00:00:00 2001 From: lwalpen <130650560+lwalpen@users.noreply.github.com> Date: Wed, 4 Oct 2023 19:02:00 +0200 Subject: [PATCH 0036/2173] Add Phylornn (#43327) * Add phylornn recipe * Update requirements --- recipes/phylornn/meta.yaml | 46 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/phylornn/meta.yaml diff --git a/recipes/phylornn/meta.yaml b/recipes/phylornn/meta.yaml new file mode 100644 index 0000000000000..fd87847f297f0 --- /dev/null +++ b/recipes/phylornn/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.0" %} # Remember to also update sha256 below +{% set sha256 = "3c78cff8031dff8f428c4ec2942d03404a9218cbd138cff85b4614020c531d78" %} + +package: + name: phylornn + version: {{ version }} + +source: + url: https://github.com/phyloRNN/phyloRNN/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . -vv + run_exports: + - {{ pin_subpackage('phylornn', max_pin="x") }} + +requirements: + host: + - python >=3.8 + # - setuptools + run: + - python >=3.8 + - numpy >=1.23.1,<1.24 + - seaborn >=0.11.2,<0.12 + - matplotlib-base >=3.5.2,<3.6 + - pandas >=1.4.3,<1.5 + - scipy >=1.8.1,<1.9 + - dendropy >=4.5.2,<4.6 + - tensorflow >=2.9.1,<3 + - keras >=2.9.0,<2.10 + - seq-gen >=1.3.0,<1.4 + - phyml >=3.3.0,<3.4 + - biopython >=1.81,<2 + +test: + imports: + - phyloRNN + +about: + home: https://github.com/phyloRNN/phyloRNN + license: LPGL-2.1-only + license_family: LGPL + summary: PhyloRNN + From c627f45ab1ad0d5a313cdf51369fa34656b8a5a1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 12:25:14 -0600 Subject: [PATCH 0037/2173] Update actc to 0.6.0 (#43442) --- recipes/actc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/actc/meta.yaml b/recipes/actc/meta.yaml index f59deea84b4a8..88f37c2d8dfe2 100644 --- a/recipes/actc/meta.yaml +++ b/recipes/actc/meta.yaml @@ -1,6 +1,6 @@ {% set name = "actc" %} -{% set version = "0.5.0" %} -{% set sha256 = "96354e0a7c7981e788ed33aa21cfc7efd115ba92b1494eb57b2a1a811165f049" %} +{% set version = "0.6.0" %} +{% set sha256 = "8b19414ec185b30fa1362c4aec97655a9392b98a3322a9371bdc3fc3b31a63bf" %} package: name: {{ name }} From 5e414672e454ce1079dc80e348f69dec1fe835e8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 14:51:23 -0600 Subject: [PATCH 0038/2173] Update alignoth to 0.10.0 (#43457) --- recipes/alignoth/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/alignoth/meta.yaml b/recipes/alignoth/meta.yaml index d992f7d2f3a24..e795d8fb5e4de 100644 --- a/recipes/alignoth/meta.yaml +++ b/recipes/alignoth/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.9.0" %} +{% set version = "0.10.0" %} package: name: alignoth @@ -14,7 +14,7 @@ build: source: url: https://github.com/koesterlab/alignoth/archive/v{{ version }}.tar.gz - sha256: eaaa504139956d21eea9f948684abccf0bc73dcbda84f18877844d13c3b6af58 + sha256: 0f0a2a78c8a4d840957fc91ce1d3d2d598e773b1d0df3a8af0435f6a7b9eb2bf requirements: build: From 25877702ef11d611cc2879f59563ca56e9da5ece Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:11:28 -0600 Subject: [PATCH 0039/2173] Update hiphase to 0.10.2 (#43436) * Update hiphase to 0.10.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/hiphase/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index 38b939bf9f0b8..aca9785f60d1f 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "0.10.0" %} -{% set hiphase_sha256 = "e22d3530a395bd218bd4634537f5b3c31a82cd8155849291c69d81c48f0c58fe" %} +{% set version = "0.10.2" %} +{% set hiphase_sha256 = "2a20fc437ab5c0f2437246e8a36e7590c68f5ae5caa0cecb8e85a371f5357c6c" %} package: name: {{ name }} @@ -13,6 +13,8 @@ source: build: number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('hiphase', max_pin="x") }} test: commands: From 556ba38d27fef63292e96b4ffc18f944281f1084 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:23:47 -0600 Subject: [PATCH 0040/2173] Update pandora to 0.9.2 (#43422) * Update pandora to 0.9.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/pandora/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/pandora/meta.yaml b/recipes/pandora/meta.yaml index 462abc256d677..32af134587696 100644 --- a/recipes/pandora/meta.yaml +++ b/recipes/pandora/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pandora" %} -{% set version = "0.9.1" %} +{% set version = "0.9.2" %} {% set repo_URL = "https://github.com/rmcolq/pandora" %} package: @@ -8,11 +8,13 @@ package: source: url: {{ repo_URL }}/releases/download/{{ version }}/{{ name }}-{{ version }}.tar.gz - sha256: 1dbde37526f1d2d0b36b51c5366a6ef96a975a45127dd265aec5d61ccf00caa8 - + sha256: 0e6189990dcf51eb28d175e0be76154a3ede1b602e5197f1a86ce8ba2839ba4e + build: - number: 2 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('pandora', max_pin="x") }} requirements: build: @@ -34,6 +36,7 @@ test: about: home: {{ repo_URL }} license: MIT + license_family: MIT license_file: LICENSE summary: Pan-genome inference and genotyping with long noisy or short accurate reads From 7519da9b8943e58738732dd137c48004fadef36f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:35:44 -0600 Subject: [PATCH 0041/2173] Update nextflow to 23.04.4 (#43451) --- recipes/nextflow/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nextflow/meta.yaml b/recipes/nextflow/meta.yaml index b23f56434b27d..bf48e7be6a046 100644 --- a/recipes/nextflow/meta.yaml +++ b/recipes/nextflow/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.04.3" %} -{% set sha256 = "258714c0772db3cab567267e8441c5b72102381f6bd58fc6957c2972235be7e0" %} +{% set version = "23.04.4" %} +{% set sha256 = "494b462f8f2c47e51ba6f833d818ee0c55412b88fdb526b71ec8f0c758dd8f0f" %} package: name: nextflow From 836a341460a9a5772485762d8b57afd4b4e2c1dd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:36:15 -0600 Subject: [PATCH 0042/2173] Update nthits to 1.0.2 (#43448) * Update nthits to 1.0.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/nthits/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/nthits/meta.yaml b/recipes/nthits/meta.yaml index 17a3ce06be503..7418b9891adb4 100644 --- a/recipes/nthits/meta.yaml +++ b/recipes/nthits/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nthits" %} -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: nthits @@ -7,18 +7,20 @@ package: source: url: https://github.com/bcgsc/ntHits/releases/download/v{{ version }}/{{ name|lower }}-{{ version }}.tar.gz - sha256: 1c821869bb275118c8f5638b9e823398ed9cd92c086293b2cd80c183d5a9f929 + sha256: f7b18c9d9510a44cc24cec2f24f3e87312330ea70805b559a4989ea47d530e64 build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('nthits', max_pin="x") }} requirements: build: - {{ compiler('cxx') }} + - cmake host: - meson - ninja - - cmake - btllib >=1.5.0 - llvm-openmp # [osx] - libgomp # [linux] @@ -33,5 +35,6 @@ test: about: home: https://github.com/bcgsc/ntHits license: MIT + license_family: MIT license_file: LICENSE summary: ntHits is a tool for efficiently counting and filtering k-mers based on their frequencies From ead11a580bf0cac0f5df098b664898d42081ce27 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:36:42 -0600 Subject: [PATCH 0043/2173] Update squigulator to 0.2.1 (#43446) * Update squigulator to 0.2.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/squigulator/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/squigulator/meta.yaml b/recipes/squigulator/meta.yaml index d268f694d6c60..3e77d7e68e208 100644 --- a/recipes/squigulator/meta.yaml +++ b/recipes/squigulator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "squigulator" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name }} @@ -7,10 +7,12 @@ package: source: url: https://github.com/hasindu2008/squigulator/releases/download/v{{ version }}/squigulator-v{{ version }}-release.tar.gz - sha256: 5f4ccac9cf42656789c6c2320c3b3699743cb3100caaba99ed2b638d59143f38 + sha256: c6019bb6fed55d9f4b875185b8fb12afd2052150d23d41d6fcb0f7a6149d8a80 build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('squigulator', max_pin="x") }} requirements: build: @@ -31,6 +33,7 @@ test: about: home: https://github.com/hasindu2008/squigulator license: MIT + license_family: MIT license_file: LICENSE summary: A tool for simulating nanopore raw signal data description: 'squigulator is a tool for simulating nanopore raw signal data.' From 5b7614fa4fa85e63a96c68cf7e13a0d914812b46 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:37:03 -0600 Subject: [PATCH 0044/2173] Update marti to 0.9.15 (#43454) * Update marti to 0.9.15 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/marti/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/marti/meta.yaml b/recipes/marti/meta.yaml index 6ecbeef96092b..53848307a0c89 100644 --- a/recipes/marti/meta.yaml +++ b/recipes/marti/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MARTi" %} -{% set version = "0.9.14" %} +{% set version = "0.9.15" %} package: name: {{ name|lower }} @@ -7,11 +7,13 @@ package: source: url: https://github.com/richardmleggett/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: ec840d9ac3a5c290a3c4dfeca437ea1e5d4ee505ec0eb14876576e43c508659c + sha256: 8bb5851d382ce91bda51602d6af46ace995b25520635836dcddf1e5de069e6f6 build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('marti', max_pin="x") }} requirements: host: From 1d904f9ac7e530da61ac996dd8757636a08bcaab Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:37:28 -0600 Subject: [PATCH 0045/2173] Update sem to 1.2.3 (#43441) * Update sem to 1.2.1 * Update sem to 1.2.2 * Update sem to 1.2.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/sem/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/sem/meta.yaml b/recipes/sem/meta.yaml index 02465703c233c..09d772cc3e45f 100644 --- a/recipes/sem/meta.yaml +++ b/recipes/sem/meta.yaml @@ -1,4 +1,4 @@ - {% set version = "1.2.0" %} +{% set version = "1.2.3" %} package: name: sem @@ -7,9 +7,11 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('sem', max_pin="x") }} source: - sha256: f11ea1891c2b7347d5b9155ee576d1d07ca0e3fa04cae31d4597811d9ada6a76 + sha256: ebb0d0fc303d052f62e6a1fcc2afd6df319774cbf249d603f747f48c0b624a12 url: https://github.com/YenLab/SEM/releases/download/v{{ version }}/sem-{{ version }}.tar.gz requirements: @@ -24,6 +26,7 @@ test: about: home: 'https://github.com/YenLab/SEM' license: "MIT" + license_family: MIT summary: "A nucleosome calling package for nucleosome subtype detection" extra: From 3f3fa89310adf5485c81d632ebbf1dd5b275f984 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:37:57 -0600 Subject: [PATCH 0046/2173] Update ksw to 0.2.3 (#43432) * Update ksw to 0.2.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/ksw/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/ksw/meta.yaml b/recipes/ksw/meta.yaml index 9c4f656b2e154..ef7ffc9504f45 100644 --- a/recipes/ksw/meta.yaml +++ b/recipes/ksw/meta.yaml @@ -1,15 +1,17 @@ -{% set version = "0.2.2" %} +{% set version = "0.2.3" %} package: name: ksw version: {{ version }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('ksw', max_pin="x") }} source: url: https://github.com/nh13/ksw/releases/download/{{ version }}/{{ version }}.tar.gz - sha256: 0ec3bf0da5ef85e1077e6f5b26a49eb5dd7a253369df8919e5a482543f86997e + sha256: 77c5f670e7cd1c608679fea077543d47771f48bef8b18773b9ba6ca0032815c0 requirements: build: @@ -30,6 +32,7 @@ test: about: home: https://github.com/nh13/ksw license: MIT + license_family: MIT license_file: LICENSE summary: 'Ksw: (interactive) smith-waterman in C' From 20b4305b83b5e7676374f4a0aa35e8ffd33404dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:38:22 -0600 Subject: [PATCH 0047/2173] Update cytoscape to 3.10.1 (#43444) * Update cytoscape to 3.10.0 * Update cytoscape to 3.10.1 * fix: add run_exports for cytoscape * try bumping openjdk version --------- Co-authored-by: Michael L Heuer Co-authored-by: joshuazhuang7 --- recipes/cytoscape/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/cytoscape/meta.yaml b/recipes/cytoscape/meta.yaml index d6b6a07126a1d..6fc7e23fbb204 100644 --- a/recipes/cytoscape/meta.yaml +++ b/recipes/cytoscape/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cytoscape" %} -{% set version = "3.9.1" %} -{% set sha256 = "0b20ac377dc01e6b0f7067104c2e463d8f834e50ee19dc302bb101dfcbc342a1" %} +{% set version = "3.10.1" %} +{% set sha256 = "93373f75143822a2162c4db5b0b0b614fdf2e34c1a0300ab915cadfd1b148418" %} package: name: {{ name }} @@ -11,19 +11,21 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('cytoscape', max_pin="3") }} requirements: build: - gettext host: - - openjdk >=11,<=12 + - openjdk >=17,<20 - fontconfig - freetype - font-ttf-dejavu-sans-mono run: - - openjdk >=11,<=12 + - openjdk >=17,<20 - xorg-libxtst - fontconfig - freetype From 731627449654abc206e3e2283109a1c3c60720b6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:39:13 -0600 Subject: [PATCH 0048/2173] Update hafez to 1.0.4 (#43431) * Update hafez to 1.0.4 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/hafez/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/hafez/meta.yaml b/recipes/hafez/meta.yaml index 18340ae7da713..a598e177d9895 100644 --- a/recipes/hafez/meta.yaml +++ b/recipes/hafez/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hafeZ" %} -{% set version = "1.0.3" %} +{% set version = "1.0.4" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://github.com/Chrisjrt/hafeZ/releases/download/{{ version }}/{{ name }}-{{ version }}.tar.gz" - sha256: 91572193361cf20f1dc228f16b1ab0ff70d7501b7e863e06c884a6b78d42191b + sha256: 8be39ddb827be742c824a95fb00cb86448d6d09b9a2996c0a76ca725e8eff1a6 build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('hafez', max_pin="x") }} requirements: host: @@ -31,6 +33,7 @@ requirements: - pandas >=1.2.4 - pysam >=0.16.0.1 - pyrodigal >=0.4.7 + - python - samtools >=1.11 - sambamba >=0.6.8 - scipy >=1.6.2 @@ -44,8 +47,8 @@ test: about: home: "https://github.com/Chrisjrt/hafeZ" - license: GPL-3 - license_family: GPL-3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: "A tool for identifying active prophage elements through read mapping" doc_url: "https://github.com/Chrisjrt/hafeZ/blob/master/README.md" From 796c8de8c923e60393e4db0a8cd73bdc3b862b9c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:40:28 -0600 Subject: [PATCH 0049/2173] Update gencove to 2.8.0 (#43399) --- recipes/gencove/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gencove/meta.yaml b/recipes/gencove/meta.yaml index ea6f90f7879d6..24f62927d4580 100644 --- a/recipes/gencove/meta.yaml +++ b/recipes/gencove/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.7.3" %} -{% set sha256 = "eae75e3b3fc4922883d006f177f6c5bb9269900edf429f6c85f857cc18bd7b12" %} +{% set version = "2.8.0" %} +{% set sha256 = "f738535c5366a3d17c61d1095968194ebd7a90f600a2bc7eddae47d7d53ff5eb" %} package: name: gencove From f0de422bebf0d051a3e77918c320e0c71e261436 Mon Sep 17 00:00:00 2001 From: Shou-Wen Wang Date: Thu, 5 Oct 2023 06:48:16 +0800 Subject: [PATCH 0050/2173] Add cospar (#43308) * add cospar * update maintainer * cospar * Increase matplotlib version * update version * update hash digest * update dependency version * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: raymond-u <36328498+raymond-u@users.noreply.github.com> --- recipes/cospar/meta.yaml | 65 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 recipes/cospar/meta.yaml diff --git a/recipes/cospar/meta.yaml b/recipes/cospar/meta.yaml new file mode 100644 index 0000000000000..01194971282e4 --- /dev/null +++ b/recipes/cospar/meta.yaml @@ -0,0 +1,65 @@ +{% set name = "cospar" %} +{% set version = "0.3.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cospar-{{ version }}.tar.gz + sha256: 881ee97be1b1d7ecb6e642a91cc3f2f2d569bd410cc2d48a117ea48cde0ec345 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv + number: 0 + run_exports: + - {{ pin_subpackage('cospar', max_pin='x.x') }} + +requirements: + host: + - python >=3.8 + - setuptools >=40.6.0 + - wheel + - pip + - matplotlib-base <3.8.0 + - scanpy >=1.6.0 + - fastcluster >=1.1.26 + - scikit-misc >=0.1.3 + - plotnine >=0.7.1 + - leidenalg >=0.7.0 + - ete3 >=3.1.2 + - ipywidgets + - gseapy >=0.9.13 + run: + - python >=3.8 + - numpy >=1.19.4 + - scipy >=1.5.4 + - scikit-learn >=1.1.1 + - scanpy >=1.6.0 + - pandas >=1.1.4 + - statsmodels >=0.14.0 + - plotnine >=0.7.1 + - matplotlib-base <3.8.0 + - fastcluster >=1.1.26 + - anndata >=0.7.5 + - numba >=0.52.0 + - scikit-misc >=0.1.3 + - leidenalg >=0.7.0 + - ete3 >=3.1.2 + - ipywidgets + - gseapy >=0.9.13 + +test: + imports: + - cospar + +about: + home: https://github.com/ShouWenWang-Lab/cospar + summary: 'CoSpar: integrating state and lineage information for dynamic inference' + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - ShouWenWang From e690133fe03d284e3082cff8f9ffc37b0f2acdc0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 16:48:44 -0600 Subject: [PATCH 0051/2173] Update samtools to 1.18 (#43283) --- recipes/samtools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index dc63f3dc05545..431fee4e74d1e 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "1.17" %} +{% set version = "1.18" %} package: name: samtools version: {{ version }} build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('samtools', max_pin="x.x") }} source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - sha256: 3adf390b628219fd6408f14602a4c4aa90e63e18b395dad722ab519438a2a729 + sha256: d686ffa621023ba61822a2a50b70e85d0b18e79371de5adb07828519d3fc06e1 requirements: build: From ca25b5cd60f9ddbcc719587215c223a18117de9c Mon Sep 17 00:00:00 2001 From: lemene Date: Thu, 5 Oct 2023 06:59:41 +0800 Subject: [PATCH 0052/2173] Update pecat to v0.0.3 (#43353) --- recipes/pecat/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/pecat/meta.yaml b/recipes/pecat/meta.yaml index ecb814e661e0b..1f11b5bf2cede 100644 --- a/recipes/pecat/meta.yaml +++ b/recipes/pecat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pecat" %} -{% set version = "0.0.2" %} -{% set sha256 = "e88f1e9be1de6f8c90ffb2309d8e271b541191f5d1fa5482aab48e6d5e626cbb" %} +{% set version = "0.0.3" %} +{% set sha256 = "e7a1165f5602ace31bf77a852a7b26fd640ddf0a5a55670ee6e1fb8788be2fc3" %} package: name: {{ name }} @@ -11,8 +11,10 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('pecat', max_pin="x") }} requirements: build: From 6f00a7867d2fc2d4cb6b251b294d97a95c5c3c3b Mon Sep 17 00:00:00 2001 From: Ilya Shlyakhter Date: Wed, 4 Oct 2023 19:03:58 -0400 Subject: [PATCH 0053/2173] Add pbsim3, a simulator for PacBio and Oxford Nanopore long reads (#43338) --- recipes/pbsim3/build.sh | 12 +++++++++++ recipes/pbsim3/meta.yaml | 44 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100755 recipes/pbsim3/build.sh create mode 100644 recipes/pbsim3/meta.yaml diff --git a/recipes/pbsim3/build.sh b/recipes/pbsim3/build.sh new file mode 100755 index 0000000000000..dadd7a3b4ab3b --- /dev/null +++ b/recipes/pbsim3/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +set -eux -o pipefail + +outdir=$PREFIX/data +mkdir -p $outdir +cp -R ./data/* $outdir/ + +autoreconf -fi +./configure --prefix="${PREFIX}" +make +make install diff --git a/recipes/pbsim3/meta.yaml b/recipes/pbsim3/meta.yaml new file mode 100644 index 0000000000000..36243c12f136e --- /dev/null +++ b/recipes/pbsim3/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "pbsim3" %} +{% set version = "3.0.0" %} +{% set sha256 = "949ac8bcc2832d5b775da1766de19bdbdd97bd69b1543231ccd16688b46f7972" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/yukiteruono/pbsim3/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + include-package-data: true + manifest: + - recursive-include data * + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + - autoconf + - automake + host: + +test: + commands: + - "pbsim 2>&1 | grep -q 'USAGE: pbsim'" + +about: + home: https://github.com/yukiteruono/pbsim3 + license: GPLv2 + license_file: COPYING + summary: "A simulator for all types of Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) long reads" + +extra: + recipe-maintainers: + - idfarbanecha + - notestaff + identifiers: + - doi:10.1093/nargab/lqac092 From 8f7f20c816b7575dc1f585ad6491ca5ce8bcd802 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Thu, 5 Oct 2023 14:43:26 +1300 Subject: [PATCH 0054/2173] Update to two months ago's bcftools 1.18 release (#43474) --- recipes/bcftools/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/bcftools/meta.yaml b/recipes/bcftools/meta.yaml index fcb21d9815d24..0fade8e8dac4e 100644 --- a/recipes/bcftools/meta.yaml +++ b/recipes/bcftools/meta.yaml @@ -1,15 +1,17 @@ -{% set version="1.17" %} +{% set version="1.18" %} package: name: bcftools version: {{ version }} build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage("bcftools", max_pin="x") }} source: url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 - sha256: 01f75d8e701d85b2c759172412009cc04f29b61616ace2fa75116123de4596cc + sha256: d9b9d36293e4cc62ab7473aa2539389d4e1de79b1a927d483f6e91f3c3ceac7e requirements: build: From 9c02083bdb1c90ad0d8af289cffe3454fd6bf3c9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 4 Oct 2023 23:25:09 -0600 Subject: [PATCH 0055/2173] Update varfish-server-worker to 0.10.2 (#43477) Co-authored-by: Manuel Holtgrewe --- recipes/varfish-server-worker/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/varfish-server-worker/meta.yaml b/recipes/varfish-server-worker/meta.yaml index 15840bc3b7223..c895ca635ee19 100644 --- a/recipes/varfish-server-worker/meta.yaml +++ b/recipes/varfish-server-worker/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.10.1" %} +{% set version = "0.10.2" %} package: name: varfish-server-worker @@ -7,10 +7,12 @@ package: build: number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage("varfish-server-worker", max_pin="x.x") }} source: url: https://github.com/bihealth/varfish-server-worker/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9d1b937fdab4909d70f681b719ccc52871e2d8824fabee1e6536e4a83c6f561d + sha256: d75f79952215c8be560d864adafd305e46a3694ffe6d9116243bf88c0b1465c4 requirements: build: From 9ec32bfb996d68b265af344c405c402136ee9b02 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 03:05:52 -0600 Subject: [PATCH 0056/2173] Update jbrowse2 to 2.7.0 (#43472) * Update jbrowse2 to 2.7.0 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/jbrowse2/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 10fb137fa4e42..49e10cc0085a5 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,17 +1,19 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.6.3" %} +{% set version = "2.7.0" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 123044f86a11a0d8f30fcef29444689df3fe1d6ae2fe784f862e541fc848894b + sha256: 5ef46308d17c16ac3f3f519ab1c41bd8b3aa6575e4bac24858042fd84f5843ba url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('jbrowse2', max_pin="x") }} requirements: host: From eb226287e2178ab7b5d3f42de30d3af642559dfd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 03:09:02 -0600 Subject: [PATCH 0057/2173] Update snakefmt to 0.8.5 (#43478) * Update snakefmt to 0.8.5 * add run_export --------- Co-authored-by: Michael Hall --- recipes/snakefmt/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/snakefmt/meta.yaml b/recipes/snakefmt/meta.yaml index f366db6742cdb..49a1189437a9a 100644 --- a/recipes/snakefmt/meta.yaml +++ b/recipes/snakefmt/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.4" %} +{% set version = "0.8.5" %} package: name: snakefmt @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakefmt/snakefmt-{{ version }}.tar.gz - sha256: 277eb436d4d61161d2c75c6eece44df34bcbb6299bc3f4fffafb0976e16afe40 + sha256: 5aa5182dbbbeb84d477dd0f5a9eeeba41bac1f185cfd4897a0b005d4af59ba71 build: number: 0 @@ -14,6 +14,8 @@ build: entry_points: - snakefmt = snakefmt.snakefmt:main script: {{ PYTHON }} -m pip install . -vv + run_exports: + - {{ pin_subpackage('snakefmt', max_pin="x") }} requirements: host: From 1c0a90e5bad867dd4e7c553aea60cc4c6f5fcfd7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 03:09:38 -0600 Subject: [PATCH 0058/2173] Update trgt to 0.5.0 (#43450) * Update trgt to 0.5.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/trgt/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/trgt/meta.yaml b/recipes/trgt/meta.yaml index 484af55245473..883dff1c8071c 100644 --- a/recipes/trgt/meta.yaml +++ b/recipes/trgt/meta.yaml @@ -1,7 +1,7 @@ {% set name = "trgt" %} -{% set version = "0.4.0" %} -{% set trgt_sha256 = "a76011125d553b016acded6bde532d6e40fe4e5cb4249e37c9c52f23046ddd63" %} -{% set trvz_sha256 = "1a4fa4e78a2fb75ed5ab7c44da916c830f2606e1def279a7ba480b76879ba9e2" %} +{% set version = "0.5.0" %} +{% set trgt_sha256 = "d16deb99be8cdd3bc29fee5539fa270642ed2018cdd35f3228e7061938eb923a" %} +{% set trvz_sha256 = "51c18e1bdd1221c225e477c2f2938e1269f7cbfe3d0e92681c1db34226780311" %} package: name: {{ name }} @@ -22,10 +22,12 @@ extra: recipe-maintainers: - zeeev - williamrowell - + build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('trgt', max_pin="x") }} test: commands: From c7b0d788f290bf65411c915ac04176f0f9831604 Mon Sep 17 00:00:00 2001 From: Thomas Krannich Date: Thu, 5 Oct 2023 16:44:05 +0200 Subject: [PATCH 0059/2173] Add initial commit for amplisim (#43275) * initial commit for amplisim * update recipe * update recipe * Update git_url in meta.yaml Use tarball over git repo * correct upstream url * remove lint skips * Update build.sh Github is not recursively cloning dependencies when auto-creating the tarball archive for a release. Obviously, when the Bioconda CI runner is trying to compile the code it's missing the htslib library. Let's see if I can post-hoc clone the dependency after decompression of the tarball. * Update build.sh second attempt to hack my way around changing the Makefile * Update meta.yaml added minimal working example for testing * revert test * Create run_test.sh * Update meta.yaml * Update run_test.sh * Update meta.yaml * Update run_test.sh * Update run_test.sh --------- Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com> --- recipes/amplisim/build.sh | 18 ++++++++++++++ recipes/amplisim/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++ recipes/amplisim/run_test.sh | 6 +++++ 3 files changed, 71 insertions(+) create mode 100644 recipes/amplisim/build.sh create mode 100644 recipes/amplisim/meta.yaml create mode 100644 recipes/amplisim/run_test.sh diff --git a/recipes/amplisim/build.sh b/recipes/amplisim/build.sh new file mode 100644 index 0000000000000..01537b262a0d0 --- /dev/null +++ b/recipes/amplisim/build.sh @@ -0,0 +1,18 @@ +#!/bin/sh + +ls -l -a +cd lib +git clone --recursive https://github.com/samtools/htslib.git +cd htslib +git reset --hard 7f5136f +cd htscodecs +git reset --hard 11b5007 +cd ../../.. + +make -C lib/htslib CC=${CC} CFLAGS="${CFLAGS} -g -Wall -O2 -fvisibility=hidden" LDFLAGS="${LDFLAGS} -fvisibility=hidden" lib-static + +mkdir -p build +make CXX=${CXX} CXXFLAGS="${CXXFLAGS} -O3 -DNDEBUG -Wno-missing-field-initializers -Wno-unused-function" LDLIBS="${LDFLAGS}" + +mkdir -p ${PREFIX}/bin +cp amplisim ${PREFIX}/bin diff --git a/recipes/amplisim/meta.yaml b/recipes/amplisim/meta.yaml new file mode 100644 index 0000000000000..68aa49bcbceca --- /dev/null +++ b/recipes/amplisim/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "0.2.1" %} +{% set sha256 = "3b101a7d15be0d31a43451368046a39ab04e006fa006e240b02fe6c80e6cc8eb" %} + +package: + name: amplisim + version: {{ version }} + +source: + url: https://github.com/rki-mf1/amplisim/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('amplisim', max_pin="x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - {{ compiler('c') }} + - make + host: + - zlib + - xz + - bzip2 + - libcurl + - libdeflate + run: + - zlib + - xz + - bzip2 + - libcurl + - libdeflate + +test: + source_files: + - test/MN908947.3.spike.fasta + - test/SARS-CoV-2.spike.primer.bed + commands: + - amplisim --help + +about: + home: https://github.com/rki-mf1/amplisim + license_file: LICENSE + license: Apache License 2.0 + summary: Plain simple amplicon sequence simulator for in-silico genomic sequencing assays. diff --git a/recipes/amplisim/run_test.sh b/recipes/amplisim/run_test.sh new file mode 100644 index 0000000000000..1536c294002d3 --- /dev/null +++ b/recipes/amplisim/run_test.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +amplisim \ + -o test/amplicons.spike.fasta \ + test/MN908947.3.spike.fasta \ + test/SARS-CoV-2.spike.primer.bed From 43e241e839e9fe74a08585c71bcca134286adab8 Mon Sep 17 00:00:00 2001 From: Ilya Shlyakhter Date: Thu, 5 Oct 2023 10:57:39 -0400 Subject: [PATCH 0060/2173] Add sharg, the argument parser for bio-c++ tools from the seqan3 library (#43460) * Add sharg, the argument parser for bio-c++ tools from the seqan3 library * Review The patch removes checks for zlib and bzip2. These also will be removed upstream as they are unused. More importantly, it also adds a find_package for yaml-cpp, which is otherwise not found. This issue could not be reproduced locally. --------- Co-authored-by: Enrico Seiler --- recipes/sharg/build.sh | 5 +++ recipes/sharg/meta.yaml | 50 +++++++++++++++++++++++++ recipes/sharg/patch | 77 +++++++++++++++++++++++++++++++++++++++ recipes/sharg/run_test.sh | 26 +++++++++++++ 4 files changed, 158 insertions(+) create mode 100644 recipes/sharg/build.sh create mode 100644 recipes/sharg/meta.yaml create mode 100644 recipes/sharg/patch create mode 100644 recipes/sharg/run_test.sh diff --git a/recipes/sharg/build.sh b/recipes/sharg/build.sh new file mode 100644 index 0000000000000..a68bd02c73b52 --- /dev/null +++ b/recipes/sharg/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash +set -exuo pipefail + +cmake . -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="${PREFIX}" +make install diff --git a/recipes/sharg/meta.yaml b/recipes/sharg/meta.yaml new file mode 100644 index 0000000000000..edd18ee12069b --- /dev/null +++ b/recipes/sharg/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "sharg" %} +{% set version = "1.1.1" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/seqan/sharg-parser/releases/download/{{ version }}/sharg-{{ version }}-Source.tar.xz + sha256: 7330f06501718e7871e55e5fd70d0e41472cc8b34bd0e3519f8c5547510c671c + patches: + - patch + +# osx can be enabled once clangxx_osx-64 17* is available on main channels +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + - cmake >=3.16 + host: + - yaml-cpp + run: + - yaml-cpp + +test: + requires: + - make + - {{ compiler('cxx') }} + - cmake >=3.16 + +about: + home: https://github.com/seqan/sharg-parser + summary: 'A modern argument parser for C++ tools.' + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE.md + doc_url: https://docs.seqan.de/sharg/{{ version }}/index.html + doc_source_url: https://raw.githubusercontent.com/seqan/sharg-parser/{{ version }}/README.md + dev_url: https://github.com/seqan/sharg-parser + +extra: + maintainers: + - eseiler + - notestaff diff --git a/recipes/sharg/patch b/recipes/sharg/patch new file mode 100644 index 0000000000000..bd40922f0d57d --- /dev/null +++ b/recipes/sharg/patch @@ -0,0 +1,77 @@ +diff --git a/build_system/sharg-config.cmake b/build_system/sharg-config.cmake +index 8fb33cd..62eca72 100644 +--- a/build_system/sharg-config.cmake ++++ b/build_system/sharg-config.cmake +@@ -157,15 +157,6 @@ set (CMAKE_REQUIRED_QUIET 1) + set (CMAKE_REQUIRED_INCLUDES ${CMAKE_INCLUDE_PATH} ${SHARG_INCLUDE_DIR} ${SHARG_DEPENDENCY_INCLUDE_DIRS}) + set (CMAKE_REQUIRED_FLAGS ${CMAKE_CXX_FLAGS}) + +-# ---------------------------------------------------------------------------- +-# Force-deactivate optional dependencies +-# ---------------------------------------------------------------------------- +- +-# These two are "opt-in", because detected by CMake +-# If you want to force-require these, just do find_package (zlib REQUIRED) before find_package (sharg) +-option (SHARG_NO_ZLIB "Don't use ZLIB, even if present." OFF) +-option (SHARG_NO_BZIP2 "Don't use BZip2, even if present." OFF) +- + # ---------------------------------------------------------------------------- + # Require C++20 + # ---------------------------------------------------------------------------- +@@ -217,6 +208,7 @@ endif () + # ---------------------------------------------------------------------------- + # tool description lib (tdl) dependency + # ---------------------------------------------------------------------------- ++find_package (yaml-cpp QUIET) + find_package (TDL QUIET HINTS ${SHARG_SUBMODULES_DIR}/submodules/tool_description_lib ${SHARG_HINT_TDL}) + + if (TDL_FOUND) +@@ -225,48 +217,6 @@ else () + sharg_config_error ("Dependency: TDL not found.") + endif () + +-# ---------------------------------------------------------------------------- +-# ZLIB dependency +-# ---------------------------------------------------------------------------- +- +-if (NOT SHARG_NO_ZLIB) +- find_package (ZLIB QUIET) +-endif () +- +-if (ZLIB_FOUND) +- set (SHARG_LIBRARIES ${SHARG_LIBRARIES} ${ZLIB_LIBRARIES}) +- set (SHARG_DEPENDENCY_INCLUDE_DIRS ${SHARG_DEPENDENCY_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS}) +- set (SHARG_DEFINITIONS ${SHARG_DEFINITIONS} "-DSHARG_HAS_ZLIB=1") +- sharg_config_print ("Optional dependency: ZLIB-${ZLIB_VERSION_STRING} found.") +-else () +- sharg_config_print ("Optional dependency: ZLIB not found.") +-endif () +- +-# ---------------------------------------------------------------------------- +-# BZip2 dependency +-# ---------------------------------------------------------------------------- +- +-if (NOT SHARG_NO_BZIP2) +- find_package (BZip2 QUIET) +-endif () +- +-if (NOT ZLIB_FOUND AND BZIP2_FOUND) +- # NOTE (marehr): iostream_bzip2 uses the type `uInt`, which is defined by +- # `zlib`. Therefore, `bzip2` will cause a ton of errors without `zlib`. +- message (AUTHOR_WARNING "Disabling BZip2 [which was successfully found], " +- "because ZLIB was not found. BZip2 depends on ZLIB.") +- unset (BZIP2_FOUND) +-endif () +- +-if (BZIP2_FOUND) +- set (SHARG_LIBRARIES ${SHARG_LIBRARIES} ${BZIP2_LIBRARIES}) +- set (SHARG_DEPENDENCY_INCLUDE_DIRS ${SHARG_DEPENDENCY_INCLUDE_DIRS} ${BZIP2_INCLUDE_DIRS}) +- set (SHARG_DEFINITIONS ${SHARG_DEFINITIONS} "-DSHARG_HAS_BZIP2=1") +- sharg_config_print ("Optional dependency: BZip2-${BZIP2_VERSION_STRING} found.") +-else () +- sharg_config_print ("Optional dependency: BZip2 not found.") +-endif () +- + # ---------------------------------------------------------------------------- + # System dependencies + # ---------------------------------------------------------------------------- diff --git a/recipes/sharg/run_test.sh b/recipes/sharg/run_test.sh new file mode 100644 index 0000000000000..c30624f22a5c9 --- /dev/null +++ b/recipes/sharg/run_test.sh @@ -0,0 +1,26 @@ +#!/bin/bash +set -exuo pipefail + +echo "#include + +int main(int argc, char ** argv) +{ + int val{}; + + sharg::parser parser{\"Eat-Me-App\", argc, argv}; + parser.add_subsection(\"Eating Numbers\"); + parser.add_option(val, sharg::config{.short_id = 'i', .long_id = \"int\", .description = \"Desc.\"}); + parser.parse(); + + return 0; +}" > hello_world.cpp + +echo "cmake_minimum_required(VERSION 3.12) +project(sharg_test CXX) +find_package (sharg 1.0 REQUIRED) +add_executable (hello_world hello_world.cpp) +target_link_libraries (hello_world sharg::sharg)" > CMakeLists.txt + +cmake . +make +./hello_world -h From 081db96da53da0772d09743c471271c27d13465c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 08:58:41 -0600 Subject: [PATCH 0061/2173] Update r-acidgenerics to 0.7.1 (#43329) * Update r-acidgenerics to 0.7.0 * Update r-acidgenerics to 0.7.1 --- recipes/r-acidgenerics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenerics/meta.yaml b/recipes/r-acidgenerics/meta.yaml index b111b5562c953..519137b6f6a00 100644 --- a/recipes/r-acidgenerics/meta.yaml +++ b/recipes/r-acidgenerics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.12" %} +{% set version = "0.7.1" %} {% set github = "https://github.com/acidgenomics/r-acidgenerics" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: ef2763af655670761bf4e36d4f8591e5a8be879ead414385ad3f2e283264660d + sha256: 02ee77e8aae3bc1259015360e20b0b0c037974b77360af1d6216179ccadfa955 build: number: 0 From 038d1b5d1dcf2639a72e542791333f85ba5d7824 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 08:59:30 -0600 Subject: [PATCH 0062/2173] Update r-goalie to 0.7.1 (#43398) * Update r-goalie to 0.7.0 * Update r-goalie to 0.7.1 --- recipes/r-goalie/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-goalie/meta.yaml b/recipes/r-goalie/meta.yaml index 8e5b622919432..03efca630a654 100644 --- a/recipes/r-goalie/meta.yaml +++ b/recipes/r-goalie/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.18" %} +{% set version = "0.7.1" %} {% set github = "https://github.com/acidgenomics/r-goalie" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 61f704a4313d60437407035179ffe30a93f7e8b7dd827ec98a0bae319bb41096 + sha256: a1ff8e34b772ef26dbb6ef7959ea07199fcb5881e084426cfc43a0badd5f51b2 build: number: 0 From 91a93378eeaf355a159cb07e3ec8bf9a447563d0 Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Thu, 5 Oct 2023 18:30:07 +0200 Subject: [PATCH 0063/2173] Add gogstools (#43414) * Add gogstools * lint * lint * fix tests * test * python3 * deps --- recipes/gogstools/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/gogstools/meta.yaml diff --git a/recipes/gogstools/meta.yaml b/recipes/gogstools/meta.yaml new file mode 100644 index 0000000000000..caf47a4d47b53 --- /dev/null +++ b/recipes/gogstools/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "gogstools" %} +{% set version = "0.1.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 65c94fe72ba529f9ba63f18c2a9fdc9c0ceeda350ae88faaab6f7185d5d968ae + +build: + number: 0 + noarch: generic + script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + run_exports: + - {{ pin_subpackage('gogstools', max_pin="x") }} + +requirements: + host: + - pip + - python ==3.10 + run: + - python ==3.10 + - bedops ==2.4.39 # version 2.4.40 broke the output of gff2bed + - bedtools + - gffread + - bcbio-gff + +test: + commands: + - ogs_check -h + - ogs_merge -h + +about: + home: "https://github.com/genouest/ogs-tools" + license: "GNU General Public v3 (GPLv3)" + license_family: GPL3 + license_file: LICENSE + summary: "GenOuest tools for manipulating Official Gene Sets" + doc_url: "https://github.com/genouest/ogs-tools" + dev_url: "https://github.com/genouest/ogs-tools" + +extra: + recipe-maintainers: + - abretaud From db5e0c0beb8ef65a9363ceeb2bf76616cd6d76ad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 10:31:23 -0600 Subject: [PATCH 0064/2173] Update mehari to 0.10.0 (#43495) * Update mehari to 0.9.0 * bump to v0.10.0 --------- Co-authored-by: Manuel Holtgrewe --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index ab020a47cee5d..3d3428b690b26 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.0" %} -{% set sha256 = "3d911d9ecf8662ba8d1e852488ce9f424d813a40542fc90a4512a28caadfed09" %} +{% set version = "0.10.0" %} +{% set sha256 = "bb9cbae51c9e31be2a100314429ead5d82d3cb8452140cf1da81df9f063f429f" %} package: name: mehari From 7d0d1a200858963cc58c22ea7e3f5ee320155798 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 11:24:51 -0600 Subject: [PATCH 0065/2173] Update vamos to 1.3.6 (#43358) --- recipes/vamos/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vamos/meta.yaml b/recipes/vamos/meta.yaml index 7d0d1e79015b7..0fd3c5e0d2840 100644 --- a/recipes/vamos/meta.yaml +++ b/recipes/vamos/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.5.2" %} +{% set version = "1.3.6" %} {% set name = "vamos" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/ChaissonLab/vamos/archive/refs/tags/{{ version }}.tar.gz - sha256: f13f3aa47e515e979ffe573d4fa357f23194bdf69009c4c5a798214c87d8f0fc + sha256: f5379fbb35bd664b761a08314d7cddc6d0d7ac3faa4c02273083626942755b10 build: number: 0 skip: True # [osx] From 552cfea184909425e7e1258943bb61580433cd9a Mon Sep 17 00:00:00 2001 From: Florian De Temmerman <69114541+fbdtemme@users.noreply.github.com> Date: Thu, 5 Oct 2023 19:27:58 +0200 Subject: [PATCH 0066/2173] Update pixelator to 0.14.0 (#43489) --- recipes/pixelator/meta.yaml | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/recipes/pixelator/meta.yaml b/recipes/pixelator/meta.yaml index 808f91425ad07..97266be48139f 100644 --- a/recipes/pixelator/meta.yaml +++ b/recipes/pixelator/meta.yaml @@ -1,14 +1,13 @@ {% set name = "pixelator" %} -{% set version = "0.13.1" %} -{% set pypi_name = "pixelgen-pixelator" %} +{% set version = "0.14.0" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/pixelgentechnologies/pixelator/archive/v{{ version }}.tar.gz - sha256: 495bec3347982397e4fee4aafcfb96a3e437d2ed6f630e2d4ad08c4a32fd87e4 + url: https://github.com/pixelgentechnologies/{{ name }}/archive/v{{ version }}.tar.gz + sha256: f8c251f3b50a0cd8609d1360f6caee183abf6e2c10436e4021f4a91dd918e2d3 build: noarch: python @@ -22,8 +21,8 @@ build: requirements: host: - python - - poetry-core >=1.0.0,<=1.7.0 - - poetry-dynamic-versioning >=1.0.0 + - poetry-core >=1.0.0 + - poetry-dynamic-versioning >=1.1.0 - pip run: - python >=3.8,<3.11 @@ -50,12 +49,14 @@ requirements: - cssselect - typing_extensions - scipy - - pyarrow + - pyarrow >=13.0.0 - semver >=3.0.0,<4.0.0 - ruamel.yaml >=0.17.21,<0.18.0 - pydantic >=1.10.7,<2.0.0 - polars >=0.17.12,<0.18.0 - importlib-resources >=5.12.0,<6.0.0 + - fsspec =>2023.9.0 + - fastparquet =>2023.8.0 test: imports: @@ -71,3 +72,7 @@ about: license: GPL-2.0 license_file: LICENSE license_family: GPL + +extra: + maintainers: + - fbdtemme \ No newline at end of file From c61daa914b87d8d7865429de4b0ac7001a4df173 Mon Sep 17 00:00:00 2001 From: mcfrith Date: Fri, 6 Oct 2023 02:30:17 +0900 Subject: [PATCH 0067/2173] new tandem-genotypes (#43482) --- recipes/tandem-genotypes/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/tandem-genotypes/meta.yaml b/recipes/tandem-genotypes/meta.yaml index 3823643fd0321..c9fee5ae68620 100644 --- a/recipes/tandem-genotypes/meta.yaml +++ b/recipes/tandem-genotypes/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.9.0" %} +{% set version = "1.9.1" %} package: name: tandem-genotypes @@ -6,11 +6,13 @@ package: source: url: https://github.com/mcfrith/tandem-genotypes/archive/{{ version }}.tar.gz - sha256: d2ce5726335c5849fd32c88587686ac4331c197a217d68fc8ebfab94f7182724 + sha256: e0322c1adb59d152d6dd2bc0305f1da9f7ae1769f9c5016e1cfc1cbbc459b9f4 build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage('tandem-genotypes', max_pin="x") }} script: python setup.py install --single-version-externally-managed --record=record.txt requirements: @@ -20,6 +22,7 @@ requirements: run: - python - r-base + - lamassemble test: commands: From 823bb83213608041b4a88076b0e7dc36ade79964 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 13:06:33 -0600 Subject: [PATCH 0068/2173] Update r-acidgenerics to 0.7.2 (#43496) --- recipes/r-acidgenerics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenerics/meta.yaml b/recipes/r-acidgenerics/meta.yaml index 519137b6f6a00..62e925da65bbf 100644 --- a/recipes/r-acidgenerics/meta.yaml +++ b/recipes/r-acidgenerics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.1" %} +{% set version = "0.7.2" %} {% set github = "https://github.com/acidgenomics/r-acidgenerics" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 02ee77e8aae3bc1259015360e20b0b0c037974b77360af1d6216179ccadfa955 + sha256: e9729a992bad302f51166f40dd76fc228ecaf9b01afd2c43adc3f77e883b9703 build: number: 0 From 002fecc2cfcfb8c2efdeaf0bcc00afe76261f6df Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 13:06:53 -0600 Subject: [PATCH 0069/2173] Update r-acidcli to 0.3.0 (#43400) * Update r-acidcli to 0.3.0 * Update dependencies * Add pinning --------- Co-authored-by: Michael Steinbaugh --- recipes/r-acidcli/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/r-acidcli/meta.yaml b/recipes/r-acidcli/meta.yaml index 281232d4e1a5d..3b96b51a9342c 100644 --- a/recipes/r-acidcli/meta.yaml +++ b/recipes/r-acidcli/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.8" %} +{% set version = "0.3.0" %} {% set github = "https://github.com/acidgenomics/r-acidcli" %} package: @@ -7,11 +7,13 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 01d87dfb60a7075509d9bf675777b3f599b0474e9cce48a0f3ec979d2c86c80e + sha256: 451c595aefad37abede3f37ba0b64f20d41eb3513146dc80124adf92414e9546 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('r-acidcli', max_pin="x.x") }} requirements: host: @@ -20,7 +22,7 @@ requirements: # Imports: - r-cli >=3.6.1 - r-crayon >=1.5.2 - - r-goalie >=0.6.13 + - r-goalie >=0.7.0 - r-rlang >=1.1.1 run: # Depends: @@ -28,7 +30,7 @@ requirements: # Imports: - r-cli >=3.6.1 - r-crayon >=1.5.2 - - r-goalie >=0.6.13 + - r-goalie >=0.7.0 - r-rlang >=1.1.1 test: From f61e77ff956378b571a8823c0381ed270bf908ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 14:27:34 -0600 Subject: [PATCH 0070/2173] Update physiofit to 3.1.1 (#43483) --- recipes/physiofit/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/physiofit/meta.yaml b/recipes/physiofit/meta.yaml index a3220223c1956..09d7a97a1680d 100644 --- a/recipes/physiofit/meta.yaml +++ b/recipes/physiofit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "physiofit" %} -{% set version = "3.1.0" %} +{% set version = "3.1.1" %} package: name: {{ name|lower }} @@ -7,14 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/physiofit-{{ version }}.tar.gz - sha256: a0a13d2ef193884d94c0485190d866e661062ef6e1ab6dcae6b2a1e9bcea6f5f + sha256: aa2cbccd7fc26174419a1d25eff80cf6fffe9e23b0c415b35b435a59fe0f8a2a build: entry_points: - physiofit = physiofit.__main__:main noarch: python script: {{ PYTHON }} -m pip install . -vv - number: 1 + number: 0 run_exports: - {{ pin_subpackage('physiofit', max_pin="x") }} From 9d31fc2535edd0a1eac6469437d7dc19bbf72c24 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Fri, 6 Oct 2023 10:12:46 +1300 Subject: [PATCH 0071/2173] Rebuild samtools using an up-to-date htslib (#43476) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Rebuild samtools-1.18 using htslib-1.18 Bump build number to rebuild this with the corresponding htslib, as unfortunately samtools-1.18-0 was merged using stale artifacts built months before the recent bioconda-utils htslib improvements. Probably ¯\_(ツ)_/¯ fix run_exports: samtools does not have an API, and its maintainers treat its command-line compatibility seriously (carefully managed ancient history around `sort` notwithstanding). * Remove library `run` dependencies These libraries will add appropriate dependencies themselves via their run_exports, and in particular zlib will add libzlib so we should not over-depend on zlib as well. --- recipes/samtools/meta.yaml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index 431fee4e74d1e..80c070b43d5c7 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -5,9 +5,9 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - - {{ pin_subpackage('samtools', max_pin="x.x") }} + - {{ pin_subpackage("samtools", max_pin="x") }} source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 @@ -21,10 +21,6 @@ requirements: - htslib - ncurses - zlib - run: - - htslib - - ncurses - - zlib about: home: https://github.com/samtools/samtools From 801d10ac0bd95376018e2aa421c8ff3eb17a7d6f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 16:31:31 -0600 Subject: [PATCH 0072/2173] Update seqan3 to 3.3.0 (#43415) * Update seqan3 to 3.3.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/seqan3/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/seqan3/meta.yaml b/recipes/seqan3/meta.yaml index 67a390e3f7b62..c5f14a78f7ae3 100644 --- a/recipes/seqan3/meta.yaml +++ b/recipes/seqan3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SeqAn3" %} -{% set version = "3.2.0" %} +{% set version = "3.3.0" %} package: name: {{ name|lower }} @@ -7,11 +7,13 @@ package: source: url: https://github.com/seqan/{{ name|lower }}/releases/download/{{ version }}/seqan3-{{ version }}-Source.tar.xz - sha256: 2737a9dc20c1d728674010662c0c9452aabbb3d4a64725bda24f28335468994c + sha256: da2fb621268ebc52b9cc26087e96f4a94109db1f4f28d363d19c7c9cdbd788b1 build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('seqan3', max_pin="x") }} requirements: build: From 4580a190d3bddd49450a85b76bef9956f04e6979 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 17:26:39 -0600 Subject: [PATCH 0073/2173] Update pybiolib to 1.1.1342 (#43390) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 143e1f250db5c..25de8355f08ec 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1316" %} +{% set version = "1.1.1342" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: bdded6276fcacbdfc542e54f726c811e853f0a82b42991006fc03469a61e7061 + sha256: 6afa593b8333c6ef70165cb6ffecba4e0d74cb7aa9c575c52d3aa5720df968ec build: noarch: python From 5d049bc7fd16556b431960f3643f78fd0f7add6f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 22:05:43 -0600 Subject: [PATCH 0074/2173] Update crispector2 to 2.0.6 (#43481) * Update crispector2 to 2.0.6 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/crispector2/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/crispector2/meta.yaml b/recipes/crispector2/meta.yaml index 39a4fa915fc0f..43f209d4a9b36 100644 --- a/recipes/crispector2/meta.yaml +++ b/recipes/crispector2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.4" %} +{% set version = "2.0.6" %} package: name: crispector2 @@ -9,11 +9,13 @@ build: entry_points: - crispector = crispector2.cli:main noarch: python - script: python -m pip install . --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('crispector2', max_pin="x") }} source: url: https://github.com/theAguy/crispector2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5d90bd9148931d6c905eee6e757b60d53fd7fb2da9ec3289d0ba9b57891c9308 + sha256: 4cb9a6d5b6ca5e697448613d22eae1c4791bb403200e8bced7d1dc948915dbd2 requirements: host: From 0b5b2fcf139ca5a23a022fb0da58d473543b1d63 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 6 Oct 2023 00:44:33 -0500 Subject: [PATCH 0075/2173] Update searchgui to 4.3.1 (#43501) --- recipes/searchgui/meta.yaml | 4 ++-- recipes/searchgui/searchgui.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index 8d73b27760eb1..3b30556a6c98f 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the searchgui.py file {% set name = "SearchGUI" %} -{% set version = "4.3.0" %} -{% set sha256 = "3966c8047c99aa0760510edcd1b151a376e58b6d1569f805ddb4bd8672d19567" %} +{% set version = "4.3.1" %} +{% set sha256 = "ef21ea768d5f67f4c4c6c1d592bfc68f2aa62ce1f0f69f7966918a2442918c18" %} {% set build = "0" %} package: diff --git a/recipes/searchgui/searchgui.py b/recipes/searchgui/searchgui.py index ad506d1057502..7c365e0a1105d 100755 --- a/recipes/searchgui/searchgui.py +++ b/recipes/searchgui/searchgui.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'SearchGUI-4.3.0.jar' +jar_file = 'SearchGUI-4.3.1.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] From bd4458937dcff92252c1ee7f7724f7ada0680de9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 23:58:01 -0600 Subject: [PATCH 0076/2173] Update fusion-inspector to 2.8.0 (#43435) --- recipes/fusion-inspector/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/fusion-inspector/meta.yaml b/recipes/fusion-inspector/meta.yaml index 52f380a790386..cb6f81488fffb 100644 --- a/recipes/fusion-inspector/meta.yaml +++ b/recipes/fusion-inspector/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fusion-inspector" %} -{% set version = "2.2.1" %} +{% set version = "2.8.0" %} {% set build = "0" %} package: @@ -8,11 +8,13 @@ package: source: url: https://github.com/FusionInspector/FusionInspector/releases/download/FusionInspector-v{{ version }}/FusionInspector-v{{ version }}.FULL.tar.gz - sha256: 3a6a885dceb39fdba0cfd6aa33d4298d3017aa0c18afa5d61d2e5f2328f7d432 + sha256: adfef115dffce5a9f55798fe0bd6ffdf771afe94f11883b69776d58858afc2ed build: noarch: generic number: {{ build }} + run_exports: + - {{ pin_subpackage('fusion-inspector', max_pin="x") }} # Trinity is needed for the build, because we have to set its location in an environment variable. # We need HTSLIB >=1.3, but was complaining about unpinned. CONDA_HTSLIB is 1.6. From 0db892303e3b5e8d9f247638f46b227af762543b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 23:58:47 -0600 Subject: [PATCH 0077/2173] Update seqchromloader to 0.7.3 (#43402) --- recipes/seqchromloader/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seqchromloader/meta.yaml b/recipes/seqchromloader/meta.yaml index 5bcca5768d3a9..cdc9f86de6604 100644 --- a/recipes/seqchromloader/meta.yaml +++ b/recipes/seqchromloader/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqchromloader" %} -{% set version = "0.7.1" %} +{% set version = "0.7.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8cd1236a92f74bdc579254a315e116aa923f8c590c8c90d2ace5c8c505eff7a6 + sha256: 8d9f666f3dddf4929349c8bd80586cdc2a3aac722f2cb1d2c8a1175a857f8d63 build: number: 0 From 30aaa744d4e81d2773771411a09f564f12c540be Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 5 Oct 2023 23:59:09 -0600 Subject: [PATCH 0078/2173] Update ncbi-datasets-pylib to 15.23.0 (#43403) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index ac4380bfcb218..4eeb50acad2c8 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.21.1" %} -{% set sha256 = "78c0bd3f242e0331a7044855caf45db4f2ce78d6d42429f47ca538fe7b416dae" %} +{% set version = "15.23.0" %} +{% set sha256 = "c97c33687d93cfd0b238ec74b4ac6caa7268be19ccd16f8749e5ac2649af038d" %} package: name: {{ name|lower }} From 5a35c4323e915c4109b5c6c7b3ffe8b7c401a70b Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 6 Oct 2023 03:08:32 -0500 Subject: [PATCH 0079/2173] Update peptide-shaker to 3.0.1 (#43499) * Update peptide-shaker to 3.0.1 * edit version string in peptide-shaker.py --- recipes/peptide-shaker/meta.yaml | 4 ++-- recipes/peptide-shaker/peptide-shaker.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/peptide-shaker/meta.yaml b/recipes/peptide-shaker/meta.yaml index 85e6b5c3446d2..31071e2cc8831 100644 --- a/recipes/peptide-shaker/meta.yaml +++ b/recipes/peptide-shaker/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the peptide-shaker.py file {% set name = "PeptideShaker" %} -{% set version = "3.0.0" %} -{% set sha256 = "b5f9ed12e2dfb969fedd4f5e83eebf8d0f496fd2e20c270f90ce28822c727ef2"%} +{% set version = "3.0.1" %} +{% set sha256 = "3f3f34c9b3f5640e39dbb5b4fd83549701353d0c2884c6742c5e40b54ba859f3"%} package: name: peptide-shaker diff --git a/recipes/peptide-shaker/peptide-shaker.py b/recipes/peptide-shaker/peptide-shaker.py index 7a2ca8faf1fda..ddca31961a444 100755 --- a/recipes/peptide-shaker/peptide-shaker.py +++ b/recipes/peptide-shaker/peptide-shaker.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'PeptideShaker-3.0.0.jar' +jar_file = 'PeptideShaker-3.0.1.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] From 078b8bd9439d32bc0c51b736c38c7fb43957b8c9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 02:08:58 -0600 Subject: [PATCH 0080/2173] Update bioframe to 0.5.0 (#43505) * Update bioframe to 0.5.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/bioframe/meta.yaml | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/recipes/bioframe/meta.yaml b/recipes/bioframe/meta.yaml index 48de9a1b12ad2..4444dd9d7103c 100644 --- a/recipes/bioframe/meta.yaml +++ b/recipes/bioframe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioframe" %} -{% set version = "0.4.1" %} +{% set version = "0.5.0" %} package: name: "{{ name|lower }}" @@ -7,25 +7,30 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 9ec45f8dad590e92d873d7a8fb3ca38de4b7a9382459128cacb497fcec8257b6 + sha256: b593214db918ae5d7427f947a32bdfd71a1cda4273fcab84cf8e1f2113801487 build: noarch: python number: 0 - script: "touch requirements.txt && {{ PYTHON }} -m pip install . -vv" + script: "touch requirements.txt && {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('bioframe', max_pin="x") }} requirements: host: - pip - python >=3.7 + - hatchling + - hatch-vcs run: - - numpy >=1.9 - - pandas >=0.17 + - numpy >=1.10 + - pandas >=1.3 - matplotlib-base - pyfaidx - pairix - pysam - python >=3.7 + - pyyaml - requests - six - cytoolz From 754465a57e6a76d2d17c52729c28ebd2fa0126d4 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Fri, 6 Oct 2023 09:35:33 +0000 Subject: [PATCH 0081/2173] Add khipu metabolomics (#43511) * added khipu-metabolomics * added pandas dependency * added run_exports statement * Update khipu-metabolomics/meta.yaml Co-authored-by: Nicola Soranzo * Update khipu-metabolomics/meta.yaml Co-authored-by: Nicola Soranzo * added pinning --------- Co-authored-by: Nicola Soranzo --- khipu-metabolomics/meta.yaml | 48 ++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 khipu-metabolomics/meta.yaml diff --git a/khipu-metabolomics/meta.yaml b/khipu-metabolomics/meta.yaml new file mode 100644 index 0000000000000..49c0ce79ec582 --- /dev/null +++ b/khipu-metabolomics/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "khipu-metabolomics" %} +{% set version = "0.7.5" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/khipu-metabolomics-{{ version }}.tar.gz + sha256: 5c89c28d30fccefb1e468d8fbcb3637bd452f002438291f7eb910a762ceb99f1 + +build: + entry_points: + - khipu=khipu.command_line:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv + number: 0 + run_exports: + - {{ pin_subpackage('khipu-metabolomics', max_pin="x.x") }} + +requirements: + host: + - python >=3.7 + - pip + run: + - python >=3.7 + - mass2chem + - treelib + - networkx + - pandas +test: + imports: + - khipu + commands: + - pip check + - khipu --help + requires: + - pip + +about: + home: https://github.com/shuzhao-li/khipu + summary: Python library for generalized, low-level annotation of MS metabolomics + license: BSD-3-Clause + license_file: LICENSE + +extra: + recipe-maintainers: + - hechth From 3a0a3278ed17eece1ba1c8b0bb450b29b78a2d17 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 04:42:43 -0600 Subject: [PATCH 0082/2173] Update r-acidbase to 0.7.0 (#43331) * Update r-acidbase to 0.7.0 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-acidbase/meta.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/recipes/r-acidbase/meta.yaml b/recipes/r-acidbase/meta.yaml index 8c0cf489298a9..759b3fc4cb480 100644 --- a/recipes/r-acidbase/meta.yaml +++ b/recipes/r-acidbase/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.23" %} +{% set version = "0.7.0" %} {% set github = "https://github.com/acidgenomics/r-acidbase" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 26f81108939dc4be8dd86c1ae1e4058b44296abaf94134528339b1d4c7f4e20a + sha256: ba31722ee78b25517c856c151e4a5d39392592843f2ccb105ad1736dcfd5c86b build: number: 0 @@ -22,26 +22,26 @@ requirements: # Imports: - bioconductor-biocgenerics >=0.46.0 - bioconductor-s4vectors >=0.38.0 - - r-acidgenerics >=0.6.9 - - r-goalie >=0.6.15 + - r-acidgenerics >=0.7.0 + - r-goalie >=0.7.0 # Suggests: - r-acidcli >=0.2.8 - r-memuse >=4.2.3 - r-processx >=3.8.2 - - r-withr >=2.5.0 + - r-withr >=2.5.1 run: # Depends: - r-base # Imports: - bioconductor-biocgenerics >=0.46.0 - bioconductor-s4vectors >=0.38.0 - - r-acidgenerics >=0.6.9 - - r-goalie >=0.6.15 + - r-acidgenerics >=0.7.0 + - r-goalie >=0.7.0 # Suggests: - r-acidcli >=0.2.8 - r-memuse >=4.2.3 - r-processx >=3.8.2 - - r-withr >=2.5.0 + - r-withr >=2.5.1 test: commands: From 81fd92c21ddd289ba5aab1abc9644e6b011cf8de Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 06:02:46 -0600 Subject: [PATCH 0083/2173] Update r-acidplyr to 0.5.0 (#43405) * Update r-acidplyr to 0.5.0 * Update recipe --------- Co-authored-by: Michael Steinbaugh --- recipes/r-acidplyr/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/r-acidplyr/meta.yaml b/recipes/r-acidplyr/meta.yaml index e5d126ad35a94..006a09a9ce671 100644 --- a/recipes/r-acidplyr/meta.yaml +++ b/recipes/r-acidplyr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.2" %} +{% set version = "0.5.0" %} {% set github = "https://github.com/acidgenomics/r-acidplyr" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: f477b52a73fc9640c11f2945d82c537ed7ee32e3fd2d434014de324b9ced28d6 + sha256: 25cf2f40fbde2f8cef5c2a9b36fd02864609ff759dd311b8472ac1e2913dd01b build: number: 0 @@ -22,16 +22,16 @@ requirements: # Imports: - bioconductor-biocgenerics >=0.46.0 - bioconductor-s4vectors >=0.38.0 - - r-acidgenerics >=0.6.8 - - r-goalie >=0.6.14 + - r-acidgenerics >=0.7.0 + - r-goalie >=0.7.0 run: # Depends: - r-base # Imports: - bioconductor-biocgenerics >=0.46.0 - bioconductor-s4vectors >=0.38.0 - - r-acidgenerics >=0.6.8 - - r-goalie >=0.6.14 + - r-acidgenerics >=0.7.0 + - r-goalie >=0.7.0 test: commands: From 4a261ba88436fd9aba4d2e0d93d366caccc23349 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 06:03:02 -0600 Subject: [PATCH 0084/2173] Update r-acidmarkdown to 0.3.0 (#43464) * Update r-acidmarkdown to 0.3.0 * Update recipe --------- Co-authored-by: Michael Steinbaugh --- recipes/r-acidmarkdown/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/r-acidmarkdown/meta.yaml b/recipes/r-acidmarkdown/meta.yaml index 8a15220941316..0599b28ba64c8 100644 --- a/recipes/r-acidmarkdown/meta.yaml +++ b/recipes/r-acidmarkdown/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.6" %} +{% set version = "0.3.0" %} {% set github = "https://github.com/acidgenomics/r-acidmarkdown" %} package: @@ -7,14 +7,13 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 1ed61f4d8c0da120eb74271df883fcc1212f863a76e27f0c4c57989c8e79c0e4 + sha256: 159dfee3894b5e95f8316e5ac82a812dd976b3e07d78ace9261570d0f115fe06 build: number: 0 noarch: generic - rpaths: - - lib/R/lib/ - - lib/ + run_exports: + - {{ pin_subpackage('r-acidmarkdown', max_pin="x.x") }} requirements: host: From 363b555a075162f10e4f2f9850a4900bb469566f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 07:03:58 -0600 Subject: [PATCH 0085/2173] Update r-syntactic to 0.7.0 (#43401) * Update r-syntactic to 0.7.0 * Update recipe * Simplify recipe --------- Co-authored-by: Michael Steinbaugh --- recipes/r-syntactic/meta.yaml | 22 +++++++++------------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/recipes/r-syntactic/meta.yaml b/recipes/r-syntactic/meta.yaml index a0717c3369e8c..171f4103eea44 100644 --- a/recipes/r-syntactic/meta.yaml +++ b/recipes/r-syntactic/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.6" %} +{% set version = "0.7.0" %} {% set github = "https://github.com/acidgenomics/r-syntactic" %} package: @@ -7,35 +7,31 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: a462665a69f22fe2073c030f2a1f4206487fafd96f8fdae5864ef8a61fbb8171 + sha256: d59f4019a6b0667e8e5200864f8608bc132919d153e7ab6ff2b8d3e5721c0629 build: noarch: generic - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('r-syntactic', max_pin="x.x") }} requirements: host: # Depends: - r-base # Imports: - - r-acidgenerics >=0.6.6 - - r-goalie >=0.6.8 + - r-acidgenerics >=0.7.0 + - r-goalie >=0.7.0 # Suggests: - - r-acidbase >=0.6.12 - - r-acidcli >=0.2.7 - r-stringi >=1.7.12 - - r-stringr >=1.5.0 run: # Depends: - r-base # Imports: - - r-acidgenerics >=0.6.6 - - r-goalie >=0.6.8 + - r-acidgenerics >=0.7.0 + - r-goalie >=0.7.0 # Suggests: - - r-acidbase >=0.6.12 - - r-acidcli >=0.2.7 - r-stringi >=1.7.12 - - r-stringr >=1.5.0 test: commands: From 59e50485cb9e76a253a06b43a215d145b0231b41 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 07:39:31 -0600 Subject: [PATCH 0086/2173] Update clinvar-this to 0.11.0 (#43515) --- recipes/clinvar-this/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clinvar-this/meta.yaml b/recipes/clinvar-this/meta.yaml index 02d046e259ca8..7dcb280567bf9 100644 --- a/recipes/clinvar-this/meta.yaml +++ b/recipes/clinvar-this/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.10.2" %} -{% set sha256 = "d993c46738db384baf53f1ea70f8df5f12e8a2e769f5319c96f84c4acbe04fdc" %} +{% set version = "0.11.0" %} +{% set sha256 = "110b7f7ecd8e009175a7faef3eb9e8d974fd5245adcc299007594ed93fbd2210" %} package: name: clinvar-this From 9a7c09c2ab78b8035f81365dae07461501e40af8 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 6 Oct 2023 09:00:59 -0500 Subject: [PATCH 0087/2173] Update pyspoa to 0.2.1 (#43503) * Update pyspoa to 0.2.1 * try pypi source * remove make command * edit license_file --- recipes/pyspoa/build.sh | 9 --------- recipes/pyspoa/meta.yaml | 15 +++++++-------- 2 files changed, 7 insertions(+), 17 deletions(-) delete mode 100644 recipes/pyspoa/build.sh diff --git a/recipes/pyspoa/build.sh b/recipes/pyspoa/build.sh deleted file mode 100644 index 6e19e29e964cc..0000000000000 --- a/recipes/pyspoa/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" - -make CXX="${CXX}" \ - CXXFLAGS="${CXXFLAGS} -O3" \ - INCLUDES="-I${PREFIX}/include" \ - LIBPATH="-L${PREFIX}/lib" -j4 build -${PYTHON} -m pip install . --use-pep517 --no-deps -vvv diff --git a/recipes/pyspoa/meta.yaml b/recipes/pyspoa/meta.yaml index 823bf1df995ae..94deab4fe5d7f 100644 --- a/recipes/pyspoa/meta.yaml +++ b/recipes/pyspoa/meta.yaml @@ -1,21 +1,19 @@ {% set name = "pyspoa" %} -{% set version = "0.0.10" %} -{% set sha256 = "fff007f781c0aa6c731cd7503513ad01f3773b50372e8dfdc9c09b4d8e608586" %} +{% set version = "0.2.1" %} +{% set sha256 = "a8a7b7df3faa1b5bb16d6b4e82099b1c9aca604c8288bcf8ca4960d376f7ff8c" %} package: name: {{ name }} version: {{ version }} source: -- url: https://github.com/nanoporetech/pyspoa/archive/refs/tags/v{{ version }}.tar.gz + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pyspoa-{{ version }}.tar.gz sha256: {{ sha256 }} -- url: https://github.com/rvaser/spoa/archive/refs/tags/4.1.2.tar.gz - sha256: 5619c7f1a9ebb9a04550771d1834ff61c4aa377bea44fbd99912e4137b1ac1f7 - folder: src build: - number: 1 + number: 0 skip: True # [py < 38] + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation run_exports: - {{ pin_subpackage('pyspoa', max_pin="x") }} @@ -42,7 +40,8 @@ test: about: home: https://github.com/nanoporetech/pyspoa license: MIT - license_file: LICENSE + license_family: MIT + license_file: src/LICENSE summary: Python binding to spoa library. doc_url: https://github.com/nanoporetech/spoa dev_url: https://github.com/nanoporetech/spoa From 3e46c434b0257f80aa83049de9558161dcdc38f4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 08:01:21 -0600 Subject: [PATCH 0088/2173] Update pybiolib to 1.1.1350 (#43514) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 25de8355f08ec..7548e8c25c7b1 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1342" %} +{% set version = "1.1.1350" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 6afa593b8333c6ef70165cb6ffecba4e0d74cb7aa9c575c52d3aa5720df968ec + sha256: bf5bcbbccdc2d7e781024f6605c6c0717c3f0bbc86884caf48e40f8c548cfd41 build: noarch: python From 9d1c95874356141c970fa30bd17ad762245110f6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 08:01:47 -0600 Subject: [PATCH 0089/2173] Update noise2read to 0.2.10 (#43507) * Update noise2read to 0.2.8 * Update noise2read to 0.2.9 * Update noise2read to 0.2.10 --------- Co-authored-by: Thanh Lee --- recipes/noise2read/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/noise2read/meta.yaml b/recipes/noise2read/meta.yaml index a5c5abb303e37..d2eb32e43f254 100644 --- a/recipes/noise2read/meta.yaml +++ b/recipes/noise2read/meta.yaml @@ -1,5 +1,5 @@ {% set name = "noise2read" %} -{% set version = "0.2.7" %} +{% set version = "0.2.10" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/noise2read-{{ version }}.tar.gz - sha256: 297608ea316390c87d5360335132d6bee86c39786af837378a25a38b16fa78d3 + sha256: 83815c0fad2d0869c63613b39bd70f0cdfa077bf02d0777e2861200d584e30d9 build: noarch: python From 9e8a1193f67cc8a886d92710cbe594035695c284 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 08:02:20 -0600 Subject: [PATCH 0090/2173] Update dnaio to 1.0.1 (#43519) --- recipes/dnaio/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/dnaio/meta.yaml b/recipes/dnaio/meta.yaml index a81a31fc7af71..93ac5a5829be8 100644 --- a/recipes/dnaio/meta.yaml +++ b/recipes/dnaio/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: dnaio version: {{ version }} source: - url: https://files.pythonhosted.org/packages/a2/21/75b44c3ae3ac2f31d7bd8f2a394b37f442774df306d442f13b40867cd569/dnaio-1.0.0.tar.gz - sha256: 528a5dc409f29eed947a1c86f2043bed3e8a72c1fe4f8426a8b5ab59aeaa0155 + url: https://files.pythonhosted.org/packages/45/65/29b0648880cc84906c5e66433b89cd63f1b001fe46c33761091302dd65ea/dnaio-1.0.1.tar.gz + sha256: 48cb0a8763d91aee329414f7756ee635dd78f6c059d5dbd0de78fb3b15f8a32a build: number: 0 From 304cb147fa86461c3401d9464d3d755ba98f3c04 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Fri, 6 Oct 2023 14:45:39 +0000 Subject: [PATCH 0091/2173] Add recipe for erah (#43295) * Add recipe for erah * renamed folder * added run exports * updated license * added version * added asari toolstack * added run export statements * fixed typo * added pandas dependency * fixed rmethods dependency * added build dependencies for asari * lint * lint * removed asari and deps * try disabling host merge * Update recipes/r-erah/meta.yaml Co-authored-by: Nicola Soranzo * Update recipes/r-erah/meta.yaml Co-authored-by: Nicola Soranzo * Update recipes/r-erah/meta.yaml Co-authored-by: Nicola Soranzo * Update recipes/r-erah/meta.yaml Co-authored-by: Nicola Soranzo --------- Co-authored-by: Nicola Soranzo Co-authored-by: Thanh Lee --- recipes/r-erah/meta.yaml | 63 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 recipes/r-erah/meta.yaml diff --git a/recipes/r-erah/meta.yaml b/recipes/r-erah/meta.yaml new file mode 100644 index 0000000000000..a16096f928c5f --- /dev/null +++ b/recipes/r-erah/meta.yaml @@ -0,0 +1,63 @@ +{% set name = "erah" %} +{% set posix = "m2-" if win else "" %} +{% set version = "1.1.2" %} + +package: + name: r-{{ name }} + version: '{{ version }}' + +source: + url: https://cran.r-project.org/src/contrib/erah_{{ version }}.tar.gz + sha256: db34880f99cd0338e3154462a1145c4dd09254083686a023fa2985a2a458d237 + +build: + number: 0 + merge_build_host: false + script: R CMD INSTALL --build . + run_exports: + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - cross-r-base {{ r_base }} # [build_platform != target_platform] + - autoconf # [unix] + - "{{ compiler('c') }}" # [unix] + - "{{ compiler('m2w64_c') }}" # [win] + - "{{ compiler('cxx') }}" # [unix] + - "{{ compiler('m2w64_cxx') }}" # [win] + - posix # [win] + host: + - r-XML + - r-base + - r-igraph + - r-r.methodss3 + - r-ncdf4 + - r-nnls + - r-quantreg + - r-signal + run: + - r-XML + - r-base + - r-igraph + - r-r.methodss3 + - r-ncdf4 + - r-nnls + - r-quantreg + - r-signal + +test: + commands: + - $R -e "library('erah')" # [not win] + - "\"%R%\" -e \"library('erah')\"" # [win] + +about: + home: https://CRAN.R-project.org/package=erah + summary: Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. + description: Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) . + license: 'GPL-2 | GPL-3' + +extra: + recipe-maintainers: + - hechth From af96aa541728c5e0e97d75bb7ca99a3a31198830 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 10:17:49 -0600 Subject: [PATCH 0092/2173] Update r-pipette to 0.14.1 (#43404) * Update r-pipette to 0.14.0 * Update r-pipette to 0.14.1 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-pipette/meta.yaml | 58 +++++++++++++++++-------------------- 1 file changed, 26 insertions(+), 32 deletions(-) diff --git a/recipes/r-pipette/meta.yaml b/recipes/r-pipette/meta.yaml index 930373177ea9f..119f2f93c52ee 100644 --- a/recipes/r-pipette/meta.yaml +++ b/recipes/r-pipette/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.13.0" %} +{% set version = "0.14.1" %} {% set github = "https://github.com/acidgenomics/r-pipette" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 8cc39a96ee47f5a99e9c6adac29f0a32fb2b9fe67962176124ee3502e633efa0 + sha256: 8574ee337b22eb709b19b4d661a231b04512e408e542fec985cffdeb8807722c build: number: 0 @@ -23,69 +23,63 @@ requirements: # Depends: - r-base # Imports: - - bioconductor-biocfilecache >=2.8.0 - bioconductor-biocgenerics >=0.46.0 - - bioconductor-biocio >=1.10.0 - bioconductor-genomicranges >=1.52.0 - bioconductor-iranges >=2.34.0 - - bioconductor-rtracklayer >=1.60.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.6.19 - - r-acidcli >=0.2.8 - - r-acidgenerics >=0.6.8 - - r-data.table >=1.14.8 - - r-digest >=0.6.33 - - r-goalie >=0.6.15 - - r-httr2 >=0.2.3 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidgenerics >=0.6.13 + - r-goalie >=0.7.0 - r-jsonlite >=1.8.7 - r-matrix >=1.6.1 - - r-readr >=2.1.4 - - r-syntactic >=0.6.6 + - r-syntactic >=0.7.0 - r-yaml >=2.3.7 # Suggests: + - bioconductor-biocfilecache >=2.8.0 - bioconductor-biostrings >=2.68.0 - bioconductor-maftools >=2.16.0 - bioconductor-rsamtools >=2.16.0 + - bioconductor-rtracklayer >=1.60.0 + - r-data.table >=1.14.8 + - r-digest >=0.6.33 + - r-httr2 >=0.2.3 - r-ontologyindex >=2.11 - r-pzfx >=0.3.0 - - r-rcurl >=1.98 + - r-readr >=2.1.4 - r-readxl >=1.4.3 - - r-rio >=0.5.29 - - r-stringi >=1.7.12 + - r-rio >=1.0.1 - r-tibble >=3.2.1 run: # Depends: - r-base # Imports: - - bioconductor-biocfilecache >=2.8.0 - bioconductor-biocgenerics >=0.46.0 - - bioconductor-biocio >=1.10.0 - bioconductor-genomicranges >=1.52.0 - bioconductor-iranges >=2.34.0 - - bioconductor-rtracklayer >=1.60.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.6.19 - - r-acidcli >=0.2.8 - - r-acidgenerics >=0.6.8 - - r-data.table >=1.14.8 - - r-digest >=0.6.33 - - r-goalie >=0.6.15 - - r-httr2 >=0.2.3 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidgenerics >=0.6.13 + - r-goalie >=0.7.0 - r-jsonlite >=1.8.7 - r-matrix >=1.6.1 - - r-readr >=2.1.4 - - r-syntactic >=0.6.6 + - r-syntactic >=0.7.0 - r-yaml >=2.3.7 # Suggests: + - bioconductor-biocfilecache >=2.8.0 - bioconductor-biostrings >=2.68.0 - bioconductor-maftools >=2.16.0 - bioconductor-rsamtools >=2.16.0 + - bioconductor-rtracklayer >=1.60.0 + - r-data.table >=1.14.8 + - r-digest >=0.6.33 + - r-httr2 >=0.2.3 - r-ontologyindex >=2.11 - r-pzfx >=0.3.0 - - r-rcurl >=1.98 + - r-readr >=2.1.4 - r-readxl >=1.4.3 - - r-rio >=0.5.29 - - r-stringi >=1.7.12 + - r-rio >=1.0.1 - r-tibble >=3.2.1 test: From 3b08c63eea50bd29a8f1a0ff7be2dca53dab9302 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:33:29 -0600 Subject: [PATCH 0093/2173] Update sanntis to 0.9.3.4 (#43413) --- recipes/sanntis/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sanntis/meta.yaml b/recipes/sanntis/meta.yaml index 0a97185dd1567..8924ab66247f5 100644 --- a/recipes/sanntis/meta.yaml +++ b/recipes/sanntis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sanntis" %} -{% set version = "0.9.3.3" %} -{% set sha256 = "6a9bfd4c3f9d4c41d7270555375428adccefb87653f44d8d31d38c1012129497" %} +{% set version = "0.9.3.4" %} +{% set sha256 = "a5b1fad410981e330827949699f29dd9a521bafbbef0ea2859ae33bd3add024e" %} package: name: {{ name }} From 93f14ec221b5494849dc999e27b0dac4a086c955 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:33:47 -0600 Subject: [PATCH 0094/2173] Update flashlfq to 1.2.5 (#43416) --- recipes/flashlfq/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/flashlfq/meta.yaml b/recipes/flashlfq/meta.yaml index f744fd416b1a7..55483f0779d06 100644 --- a/recipes/flashlfq/meta.yaml +++ b/recipes/flashlfq/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.2.4" %} -{% set sha256 = "bf245899da0bac8750ceede3c7da9f7264c6607b7aaa9f585ecc2e0471de4c85" %} +{% set version = "1.2.5" %} +{% set sha256 = "a86e3153bc6833317a68eba1156a88bb84c37b247da55df94e57650a77034567" %} source: url: https://github.com/smith-chem-wisc/FlashLFQ/releases/download/{{version}}/FlashLFQ.zip @@ -12,9 +12,10 @@ package: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('flashlfq', max_pin="x") }} requirements: - build: run: - openssl =1.1 - dotnet-runtime =6.0 @@ -28,7 +29,7 @@ about: license: LGPL-3.0 summary: ultrafast label-free quantification algorithm for mass-spectrometry proteomics license_family: GPL - + extra: identifiers: - doi:10.1021/acs.jproteome.7b00608 From 2125a0e6962013a11f55d7242723d7b787fd1cce Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:34:25 -0600 Subject: [PATCH 0095/2173] Update solvebio to 2.24.2 (#43490) --- recipes/solvebio/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/solvebio/meta.yaml b/recipes/solvebio/meta.yaml index 20001216343c5..28b6cf19fd69e 100644 --- a/recipes/solvebio/meta.yaml +++ b/recipes/solvebio/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.24.1" %} -{% set sha256 = "1b943db5a099dfac339724f3549f054c4a40a655a51108d518dd4e68416f70b7" %} +{% set version = "2.24.2" %} +{% set sha256 = "f3ba52bbb45c3cfc38bf186c9699c6ce1cbe3a5f56fc270794ffc854effc81f4" %} package: name: solvebio From d5e515c6d21d010f53abb20066d5da24fc8ae374 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:35:55 -0600 Subject: [PATCH 0096/2173] Update sequana to 0.15.4 (#43494) --- recipes/sequana/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/sequana/meta.yaml b/recipes/sequana/meta.yaml index 1a42454e0eefd..7d3be2bd989d7 100644 --- a/recipes/sequana/meta.yaml +++ b/recipes/sequana/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.15.3" %} -{% set sha256 = "3d893561ce3ab8db9553958f102a774c17dca9d772a494300e7adeb3a60e4471" %} +{% set version = "0.15.4" %} +{% set sha256 = "b394fc148a67de70959189b9053ef42dbb82a99857920825b8db0ed1a28097cd" %} {% set name = "sequana" %} package: @@ -56,6 +56,7 @@ requirements: - ruamel.yaml >=0.16.0 - scikit-learn - scipy + - selenium - snakemake-minimal >=7.16 - seaborn - statsmodels From bfee35810b063d985de83c3d5fa0fcc22c67c4a3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:40:40 -0600 Subject: [PATCH 0097/2173] Update r-acidgenomes to 0.6.0 (#43469) * Update r-acidgenomes to 0.6.0 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-acidgenomes/meta.yaml | 80 ++++++++++++++++----------------- 1 file changed, 40 insertions(+), 40 deletions(-) diff --git a/recipes/r-acidgenomes/meta.yaml b/recipes/r-acidgenomes/meta.yaml index 23a82a76fa98a..24e273af77b8c 100644 --- a/recipes/r-acidgenomes/meta.yaml +++ b/recipes/r-acidgenomes/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.1" %} +{% set version = "0.6.0" %} {% set github = "https://github.com/acidgenomics/r-acidgenomes" %} package: @@ -7,63 +7,63 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: a53c6535c95538c3afdddeb6118b62232f315b3c050cab9e83a7114e27614484 + sha256: ec8ae782391beaffda33fc4bb0da1567d4cde612de538a163b5d7444aaa838ee build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('r-acidgenomes', max_pin="x.x") }} requirements: host: # Depends: - r-base # Imports: - - bioconductor-biocgenerics >=0.44.0 - - bioconductor-genomeinfodb >=1.34.0 - - bioconductor-genomicranges >=1.50.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-s4vectors >=0.36.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidgenerics >=0.6.7 - - r-acidplyr >=0.3.9 - - r-goalie >=0.6.9 - - r-pipette >=0.10.9 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.5 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-genomeinfodb >=1.36.0 + - bioconductor-genomicranges >=1.52.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidgenerics >=0.7.1 + - r-acidplyr >=0.5.0 + - r-goalie >=0.7.0 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-annotationdbi >=1.60.0 - - bioconductor-annotationhub >=3.6.0 - - bioconductor-biomart >=2.54.0 - - bioconductor-ensembldb >=2.22.0 - - bioconductor-genomicfeatures >=1.50.0 - - r-rcurl >=1.98 + - bioconductor-annotationdbi >=1.62.0 + - bioconductor-annotationhub >=3.8.0 + - bioconductor-biocfilecache >=2.8.0 + - bioconductor-biomart >=2.56.0 + - bioconductor-ensembldb >=2.24.0 + - bioconductor-genomicfeatures >=1.52.0 - r-rvest >=1.0.3 - r-withr >=2.5.0 run: # Depends: - r-base # Imports: - - bioconductor-biocgenerics >=0.44.0 - - bioconductor-genomeinfodb >=1.34.0 - - bioconductor-genomicranges >=1.50.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-s4vectors >=0.36.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidgenerics >=0.6.7 - - r-acidplyr >=0.3.9 - - r-goalie >=0.6.9 - - r-pipette >=0.10.9 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.5 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-genomeinfodb >=1.36.0 + - bioconductor-genomicranges >=1.52.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidgenerics >=0.7.1 + - r-acidplyr >=0.5.0 + - r-goalie >=0.7.0 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-annotationdbi >=1.60.0 - - bioconductor-annotationhub >=3.6.0 - - bioconductor-biomart >=2.54.0 - - bioconductor-ensembldb >=2.22.0 - - bioconductor-genomicfeatures >=1.50.0 - - r-rcurl >=1.98 + - bioconductor-annotationdbi >=1.62.0 + - bioconductor-annotationhub >=3.8.0 + - bioconductor-biocfilecache >=2.8.0 + - bioconductor-biomart >=2.56.0 + - bioconductor-ensembldb >=2.24.0 + - bioconductor-genomicfeatures >=1.52.0 - r-rvest >=1.0.3 - r-withr >=2.5.0 From 841a505420e93e223bdce47c69baa9d36b2aac27 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 6 Oct 2023 19:45:57 +0100 Subject: [PATCH 0098/2173] added cascade-config (#43486) * added cascade-config * added cascade-config * added cascade-config --- recipes/cascade-config/meta.yaml | 45 ++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 recipes/cascade-config/meta.yaml diff --git a/recipes/cascade-config/meta.yaml b/recipes/cascade-config/meta.yaml new file mode 100644 index 0000000000000..b361491f3c62d --- /dev/null +++ b/recipes/cascade-config/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "cascade-config" %} +{% set version = "0.4.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cascade_config-{{ version }}.tar.gz + sha256: cb3cffd3e9899b6aa46f29e5462b413cfdd94e74e36748e977d1949c46478715 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + script: "{{ PYTHON }} -m pip install . --no-deps -vvv" + +requirements: + host: + - python >=3.6 + - flit-core + - pip + run: + - python >=3.6 + - jsonschema + +test: + imports: + - cascade_config + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/RalfG/cascade-config + summary: Cascading configuration from the CLI and config files. + license: Apache-2.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - compomics + - RalfG From 72d183910f79f023e3b7bf1d1dcb4c4b7045af94 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:20:24 -0600 Subject: [PATCH 0099/2173] Update hmftools-orange to 2.7.1 (#43424) * Update hmftools-orange to 2.6.0 * Update hmftools-orange to 2.7.0 * Update hmftools-orange to 2.7.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/hmftools-orange/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-orange/meta.yaml b/recipes/hmftools-orange/meta.yaml index 25daf8afb53d8..186fbdf7b2da9 100644 --- a/recipes/hmftools-orange/meta.yaml +++ b/recipes/hmftools-orange/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.10.2" %} -{% set sha256 = "3ecf59559f8c798fcd9ea7caa5c9baa436114fbaa85de1faf2c04068584a51f1" %} +{% set version = "2.7.1" %} +{% set sha256 = "596eb3bde589f51a6820b6a4b51bb58fdd249f5374076e923aa7d7dc8faa0a00" %} package: name: hmftools-orange @@ -12,6 +12,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-orange', max_pin="x") }} requirements: run: From 2eb30efe64b1c435a56d7329ae4d4d57696227dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:20:40 -0600 Subject: [PATCH 0100/2173] Update fiji-simple_omero_client to 5.15.0 (#43425) * Update fiji-simple_omero_client to 5.14.1 * Update fiji-simple_omero_client to 5.14.2 * Update fiji-simple_omero_client to 5.15.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fiji-simple_omero_client/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/fiji-simple_omero_client/meta.yaml b/recipes/fiji-simple_omero_client/meta.yaml index d6c0081da722f..a661de59a926b 100644 --- a/recipes/fiji-simple_omero_client/meta.yaml +++ b/recipes/fiji-simple_omero_client/meta.yaml @@ -1,17 +1,19 @@ {% set name = "fiji-simple_omero_client" %} -{% set version = "5.12.2" %} - +{% set version = "5.15.0" %} + package: name: {{ name | lower }} version: {{ version }} source: url: https://github.com/GReD-Clermont/simple-omero-client/releases/download/{{ version }}/simple-omero-client-{{ version }}.jar - sha256: 246a006152ae51ff6eb5f0a62567083fe589c1f45413a4ed4e463d31604fcbea + sha256: 14a6ee2a9f15c5e97dd37967f95ba41f45b5c29ed702ac3d2783f810d55e6298 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('fiji-simple_omero_client', max_pin="x") }} requirements: run: @@ -29,4 +31,4 @@ about: summary: Java library to simplify API to put/get objects on an OMERO server from Fiji/ImageJ. description: | This library presents a simplified API to put/get objects on an OMERO server. - dev_url: https://github.com/GReD-Clermont/simple-omero-client \ No newline at end of file + dev_url: https://github.com/GReD-Clermont/simple-omero-client From d1ee1276fa5bfddc8263412272c4b595b190d94a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:20:59 -0600 Subject: [PATCH 0101/2173] Update ena-webin-cli to 6.5.1 (#43426) * Update ena-webin-cli to 6.5.0 * Update ena-webin-cli to 6.5.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/ena-webin-cli/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index c882105ee4fcd..f9af45920ed36 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version="5.0.0" %} -{% set sha="54f6eeba22a6759f4c20ebb8c23c67c7ca178d6caac4674e380ecdbaf1ebfe18" %} +{% set version = "6.5.1" %} +{% set sha256 = "e46e0fe60e6959f3867280b8759fc7a2b4cdb71d46675d487f090d08e2bdb8ad" %} package: name: ena-webin-cli @@ -8,10 +8,12 @@ package: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('ena-webin-cli', max_pin="x") }} source: url: https://github.com/enasequence/webin-cli/releases/download/{{ version }}/webin-cli-{{ version }}.jar - sha256: {{ sha }} + sha256: {{ sha256 }} requirements: run: From 69b84b560dc4a3e35f57d705fb27ed1b0d1e312f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:21:16 -0600 Subject: [PATCH 0102/2173] Update fiji-omero_ij to 5.8.3 (#43427) * Update fiji-omero_ij to 5.8.1 * Update fiji-omero_ij to 5.8.2 * Update fiji-omero_ij to 5.8.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fiji-omero_ij/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/fiji-omero_ij/meta.yaml b/recipes/fiji-omero_ij/meta.yaml index 0f0a21f00394e..4da65026380f9 100644 --- a/recipes/fiji-omero_ij/meta.yaml +++ b/recipes/fiji-omero_ij/meta.yaml @@ -1,17 +1,19 @@ {% set name = "fiji-omero_ij" %} -{% set version = "5.8.0" %} - +{% set version = "5.8.3" %} + package: name: {{ name | lower }} version: {{ version }} source: url: https://github.com/ome/omero-insight/releases/download/v{{ version }}/omero_ij-{{ version }}-all.jar - sha256: 8d86d67503a8a39792c9e191fa0bdcc653db5bcdf53570f7b0cca88e79bfd71a + sha256: bddf2d1d6ad4621a3b00231c8661803dc276378dcecb986bf9fcb907cdb3f6fd build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('fiji-omero_ij', max_pin="x") }} requirements: run: @@ -28,4 +30,4 @@ about: summary: ImageJ / Fiji plugin to visualize and manipulate both image data and metadata maintained at an OMERO server site. description: | The OMERO.insight Project is a sub-project of the Open Microscopy Environment Project, OME that focuses on delivering a client for the visualization and manipulation of both image data and metadata maintained at an OMERO server site. - dev_url: https://github.com/ome/omero-insight \ No newline at end of file + dev_url: https://github.com/ome/omero-insight From a217e08a95990ce3ebc10c11501c16d27bd74d62 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:21:32 -0600 Subject: [PATCH 0103/2173] Update aviary to 0.8.1 (#43429) * Update aviary to 0.8.0 * Update aviary to 0.8.1 --- recipes/aviary/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/aviary/meta.yaml b/recipes/aviary/meta.yaml index 3033126522192..97ff289f65e9c 100644 --- a/recipes/aviary/meta.yaml +++ b/recipes/aviary/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.7.2" %} +{% set version = "0.8.1" %} {% set name = "aviary" %} -{% set sha256 = "b42caf3f5a809952f21a23cd61cee953d9012587db0f941edcf498bb8add8145" %} +{% set sha256 = "bc26f5547c80e851351ede2b268bab75bf7598debdc724736e28d4e6084a66b3" %} package: name: aviary From 4d94fe8681bbb4c021c6a96e4deb0aa82bd976cc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:22:56 -0600 Subject: [PATCH 0104/2173] Update tcdemux to 0.0.16 (#43506) * Update tcdemux to 0.0.16 * Add new deps (#43508) * Add new deps * fix build number * forgot viridis --------- Co-authored-by: Tom Harrop --- recipes/tcdemux/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/tcdemux/meta.yaml b/recipes/tcdemux/meta.yaml index 50b6fc2f1b2be..09687414ae7c3 100644 --- a/recipes/tcdemux/meta.yaml +++ b/recipes/tcdemux/meta.yaml @@ -1,5 +1,5 @@ --- -{% set version = "0.0.15" %} +{% set version = "0.0.16" %} package: name: tcdemux @@ -7,7 +7,7 @@ package: source: url: https://github.com/TomHarrop/tcdemux/archive/refs/tags/{{ version }}.tar.gz - sha256: a4c82803f7634020677954c003f3a5b12b00d21120c5608206423c712a7e1db5 + sha256: 5446f460c862f43d1b42e304f9d174274e7f8a2f9b95bafc690913592fcca87d build: number: 0 @@ -26,6 +26,10 @@ requirements: - pandas >=2.0.3 - pigz - python >=3.10 + - r-bit64 >=4.0.5 + - r-data.table >=1.14.8 + - r-ggplot2 >=3.4.3 + - r-viridis >=0.6.4 - snakemake >=7.31.0 test: From e4250a506e653d63bd25851c2fa2e3014345a024 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:23:16 -0600 Subject: [PATCH 0105/2173] Update cstag to 1.0.4 (#43509) --- recipes/cstag/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cstag/meta.yaml b/recipes/cstag/meta.yaml index 610c73fcb29e6..90c315706b610 100644 --- a/recipes/cstag/meta.yaml +++ b/recipes/cstag/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cstag" %} -{% set version = "1.0.3" %} +{% set version = "1.0.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cstag-{{ version }}.tar.gz - sha256: 2f9f0ae92a03abf14cb6c432c0aa334ab9649e4f974b83f2ecdb3af597b5b402 + sha256: 2772a4803a5f90814297ac7ceb3d8ee7783fd101f9e0898b6150d6f960aa6111 build: noarch: python From c6268f4b3ccd7181036eae1b513bdbe7fa5c53fa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:23:36 -0600 Subject: [PATCH 0106/2173] Update pcaone to 0.4.0 (#43513) --- recipes/pcaone/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml index 982d08263bbfa..636c605ed4401 100644 --- a/recipes/pcaone/meta.yaml +++ b/recipes/pcaone/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.9" %} -{% set sha256 = "b0db927bccd7005db212af95edb9a06de7ad988e0c66568b78b2116acb9c80d2" %} +{% set version = "0.4.0" %} +{% set sha256 = "b6bf45c20dddcc42811dcc902c7d92c5901d03fb4c69675ee8da39b3c92763a9" %} package: From fdf5c89b26e2fb2b34fc472c988cf48a6802c511 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:23:58 -0600 Subject: [PATCH 0107/2173] Update versionix to 0.2.1 (#43516) --- recipes/versionix/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/versionix/meta.yaml b/recipes/versionix/meta.yaml index f1304604bf061..1a9fc020c7240 100644 --- a/recipes/versionix/meta.yaml +++ b/recipes/versionix/meta.yaml @@ -1,5 +1,5 @@ {% set name = "versionix" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/versionix-{{ version }}.tar.gz - sha256: 3adc399700e1dceadd411b587de0cc0f6018d66c072e6946b98aaad5664cd78d + sha256: 43b21f5596774ef7bbe26357b97e511a2541c321426c79bd35d441fbd4e0e623 build: entry_points: From 1dbe42c5cd9e7764f03ee4d26105d13fe052c78d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:24:17 -0600 Subject: [PATCH 0108/2173] Update mehari to 0.11.0 (#43525) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 3d3428b690b26..ba1bd171afa48 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.10.0" %} -{% set sha256 = "bb9cbae51c9e31be2a100314429ead5d82d3cb8452140cf1da81df9f063f429f" %} +{% set version = "0.11.0" %} +{% set sha256 = "58b36ce9d7fb3e2a8a012e3d8275513f15148d05fbf5aa414ed32006a54483a5" %} package: name: mehari From 662a57e6663d6e4600aa143bc87f6f4221766056 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:24:34 -0600 Subject: [PATCH 0109/2173] Update python-bioext to 0.21.1 (#43528) --- recipes/python-bioext/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/python-bioext/meta.yaml b/recipes/python-bioext/meta.yaml index e5ee24104551d..fd43fd7e757ae 100644 --- a/recipes/python-bioext/meta.yaml +++ b/recipes/python-bioext/meta.yaml @@ -1,6 +1,6 @@ {% set name = "BioExt" %} -{% set version = "0.21.0" %} -{% set sha256 = "f4c146545f3a30f94d6cc9b1d7229205c6a16123b438bf4b3f1a5f2fbb6dbb3f" %} +{% set version = "0.21.1" %} +{% set sha256 = "c4432fcd9ac860ae3278faaf03bead3e3687df3766f82f4c1ed2d53e6fc29b10" %} package: name: python-{{ name|lower }} From 0bd4a8622cf1e924327daa0b4388b6a2b862501b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:48:54 -0600 Subject: [PATCH 0110/2173] Update r-goalie to 0.7.2 (#43530) --- recipes/r-goalie/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-goalie/meta.yaml b/recipes/r-goalie/meta.yaml index 03efca630a654..c9d4e5dbde261 100644 --- a/recipes/r-goalie/meta.yaml +++ b/recipes/r-goalie/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.1" %} +{% set version = "0.7.2" %} {% set github = "https://github.com/acidgenomics/r-goalie" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: a1ff8e34b772ef26dbb6ef7959ea07199fcb5881e084426cfc43a0badd5f51b2 + sha256: 2afc3babeb10fa9c5f45ae5fa660a996ddb2de36210ee73d54b3de72b14ac3ad build: number: 0 From 355f177dea156005cd26e32e58c4fc760bc0ad07 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 13:49:10 -0600 Subject: [PATCH 0111/2173] Update r-acidgenerics to 0.7.3 (#43529) --- recipes/r-acidgenerics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenerics/meta.yaml b/recipes/r-acidgenerics/meta.yaml index 62e925da65bbf..2be4f16d3aa84 100644 --- a/recipes/r-acidgenerics/meta.yaml +++ b/recipes/r-acidgenerics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.2" %} +{% set version = "0.7.3" %} {% set github = "https://github.com/acidgenomics/r-acidgenerics" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: e9729a992bad302f51166f40dd76fc228ecaf9b01afd2c43adc3f77e883b9703 + sha256: e7edbc1c56582b75f3eeb7e360cd91b04ed978e24cb68eb610264ad7845b3d42 build: number: 0 From 1a4252ec10f45de2c03fa2340ee1c6506e5a61e1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 14:11:13 -0600 Subject: [PATCH 0112/2173] Update r-acidexperiment to 0.5.2 (#43465) * Update r-acidexperiment to 0.5.0 * Update r-acidexperiment to 0.5.1 * Update r-acidexperiment to 0.5.2 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-acidexperiment/meta.yaml | 83 ++++++++++++++---------------- 1 file changed, 39 insertions(+), 44 deletions(-) diff --git a/recipes/r-acidexperiment/meta.yaml b/recipes/r-acidexperiment/meta.yaml index cc61d227b3d89..5c004ca3d3d0c 100644 --- a/recipes/r-acidexperiment/meta.yaml +++ b/recipes/r-acidexperiment/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.7" %} +{% set version = "0.5.2" %} {% set github = "https://github.com/acidgenomics/r-acidexperiment" %} package: @@ -7,66 +7,61 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 0dd42744cb2953550fb15fda5b4a59d87d00b12aa117f7c9f0cd6965436ed38c + sha256: da4d283bef0cc580abe09828f102091b2dc628298e3efdcf59d0c667943211d2 build: - number: 2 + number: 0 noarch: generic - rpaths: - - lib/R/lib/ - - lib/ + run_exports: + - {{ pin_subpackage('r-acidexperiment', max_pin="x.x") }} requirements: host: # Depends: - r-base # Imports: - - bioconductor-biobase >=2.58.0 - - bioconductor-biocgenerics >=0.44.0 - - bioconductor-genomicranges >=1.50.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-multiassayexperiment >=1.24.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-summarizedexperiment >=1.28.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.0 - - r-acidplyr >=0.3.10 - - r-goalie >=0.6.9 - - r-matrix >=1.5.4 - - r-pipette >=0.10.9 - - r-syntactic >=0.6.5 + - bioconductor-biobase >=2.60.0 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-genomicranges >=1.52.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidgenerics >=0.7.1 + - r-acidgenomes >=0.6.0 + - r-acidplyr >=0.5.0 + - r-goalie >=0.7.0 + - r-matrix >=1.6.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biostrings >=2.66.0 - - bioconductor-genomeinfodb >=1.34.0 + - bioconductor-biostrings >=2.68.0 + - bioconductor-genomeinfodb >=1.36.0 - r-scales >=1.2.1 - - r-stringi >=1.7.12 run: # Depends: - r-base # Imports: - - bioconductor-biobase >=2.58.0 - - bioconductor-biocgenerics >=0.44.0 - - bioconductor-genomicranges >=1.50.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-multiassayexperiment >=1.24.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-summarizedexperiment >=1.28.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.0 - - r-acidplyr >=0.3.10 - - r-goalie >=0.6.9 - - r-matrix >=1.5.4 - - r-pipette >=0.10.9 - - r-syntactic >=0.6.5 + - bioconductor-biobase >=2.60.0 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-genomicranges >=1.52.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidgenerics >=0.7.1 + - r-acidgenomes >=0.6.0 + - r-acidplyr >=0.5.0 + - r-goalie >=0.7.0 + - r-matrix >=1.6.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biostrings >=2.66.0 - - bioconductor-genomeinfodb >=1.34.0 + - bioconductor-biostrings >=2.68.0 + - bioconductor-genomeinfodb >=1.36.0 - r-scales >=1.2.1 - - r-stringi >=1.7.12 test: commands: From 6bc0f6618460eb5ccb017f5b1cb1d51445c90737 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 15:14:51 -0600 Subject: [PATCH 0113/2173] Update r-goalie to 0.7.3 (#43533) --- recipes/r-goalie/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-goalie/meta.yaml b/recipes/r-goalie/meta.yaml index c9d4e5dbde261..178c2c800f2b4 100644 --- a/recipes/r-goalie/meta.yaml +++ b/recipes/r-goalie/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.2" %} +{% set version = "0.7.3" %} {% set github = "https://github.com/acidgenomics/r-goalie" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 2afc3babeb10fa9c5f45ae5fa660a996ddb2de36210ee73d54b3de72b14ac3ad + sha256: 5b3080a674c88a470a55e68b66916f1e0212493a4ceb2ff9125eeb45d4b7241d build: number: 0 From 83e22bf36f6065e5b4d4188a1b4d8fa8d2162f6a Mon Sep 17 00:00:00 2001 From: Tim Fennell Date: Fri, 6 Oct 2023 16:01:58 -0600 Subject: [PATCH 0114/2173] Update fgsv recipe to 0.1.0. (#43537) --- recipes/fgsv/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/fgsv/meta.yaml b/recipes/fgsv/meta.yaml index 01fea8b99f1ee..3aaddfda83b58 100644 --- a/recipes/fgsv/meta.yaml +++ b/recipes/fgsv/meta.yaml @@ -1,4 +1,4 @@ -{% set version="0.0.2" %} +{% set version="0.1.0" %} package: name: fgsv @@ -6,11 +6,14 @@ package: source: url: https://github.com/fulcrumgenomics/fgsv/releases/download/{{ version }}/fgsv-{{ version }}.jar - sha256: f75c7f8dee195b7b6d7436aa88970aaf1717c8443c9d1e6a312429505e0fec0e + sha256: 4aa31c9beee050186d8d5ce4922dd385002a8a465e3656ca9947abdb268fcf99 build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage("fgsv", max_pin="x.x") }} + requirements: run: @@ -30,3 +33,4 @@ about: extra: recipe-maintainers: - nh13 + - tfenne From e4e7de520de4261717d97f21ef0f4dc35335c49b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 6 Oct 2023 20:50:48 -0600 Subject: [PATCH 0115/2173] Update cutadapt to 4.5 (#43527) --- recipes/cutadapt/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/cutadapt/meta.yaml b/recipes/cutadapt/meta.yaml index d25f79a3da2f0..2d2947af1bfe4 100644 --- a/recipes/cutadapt/meta.yaml +++ b/recipes/cutadapt/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "4.4" %} +{% set version = "4.5" %} package: name: cutadapt version: {{ version }} source: - url: https://files.pythonhosted.org/packages/0d/45/88d84af8d51310227e5c5c835946ebc059ae9156502203ce0b64c95e4550/cutadapt-4.4.tar.gz - sha256: 4554157c673022e1c433fcd6e3b803008fef60c8e71c01215e4aa04b0f09fe83 + url: https://files.pythonhosted.org/packages/36/f6/3e040d24a2a475aae2afc193957abe9bc90139b8b72b8a5317198201f2fb/cutadapt-4.5.tar.gz + sha256: 33e56678bb3ba90fd7045d03184b83e135f61e8a6b9f29aa3db8c63611a08e94 build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps -vv" skip: True # [py27 or py36] + run_exports: + - {{ pin_subpackage("cutadapt", max_pin="x") }} requirements: build: From e9232dc05d8ef85ca14d59f0b5a5bd34420799e2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 7 Oct 2023 00:02:32 -0600 Subject: [PATCH 0116/2173] Update cstag to 1.0.5 (#43540) --- recipes/cstag/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cstag/meta.yaml b/recipes/cstag/meta.yaml index 90c315706b610..056545dac83d6 100644 --- a/recipes/cstag/meta.yaml +++ b/recipes/cstag/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cstag" %} -{% set version = "1.0.4" %} +{% set version = "1.0.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cstag-{{ version }}.tar.gz - sha256: 2772a4803a5f90814297ac7ceb3d8ee7783fd101f9e0898b6150d6f960aa6111 + sha256: 69aeb279da6143a8f7b9b42a92ae1978f752890c8d475c953077c09ce918774b build: noarch: python From 5e16dbc325c34ea5dad2d7f39b879273313fed5f Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Sat, 7 Oct 2023 06:04:01 +0000 Subject: [PATCH 0117/2173] Add asari prerequisites metdatamodel, mass2chem, jms-metabolite-services (#43510) * added asari toolstack * removed asari and khipu * added run export statements * fixed typos * updated run_exports --- recipes/jms-metabolite-services/meta.yaml | 44 +++++++++++++++++++++ recipes/mass2chem/meta.yaml | 48 +++++++++++++++++++++++ recipes/metdatamodel/meta.yaml | 44 +++++++++++++++++++++ 3 files changed, 136 insertions(+) create mode 100644 recipes/jms-metabolite-services/meta.yaml create mode 100644 recipes/mass2chem/meta.yaml create mode 100644 recipes/metdatamodel/meta.yaml diff --git a/recipes/jms-metabolite-services/meta.yaml b/recipes/jms-metabolite-services/meta.yaml new file mode 100644 index 0000000000000..07ecbf6f80219 --- /dev/null +++ b/recipes/jms-metabolite-services/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "jms-metabolite-services" %} +{% set version = "0.5.7" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/jms-metabolite-services-{{ version }}.tar.gz + sha256: 39cad5a790ebd876ecce7f093769fb7495bbb44e74953c428d81055e5f7feac9 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv + number: 0 + run_exports: + - {{ pin_subpackage('jms-metabolite-services', max_pin="x.x") }} + + +requirements: + host: + - python >=3.0 + - pip + run: + - python >=3.0 + - mass2chem + +test: + imports: + - jms + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/shuzhao-li/JMS + summary: conversion, search of metabolic models and metabolomics data + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - hechth diff --git a/recipes/mass2chem/meta.yaml b/recipes/mass2chem/meta.yaml new file mode 100644 index 0000000000000..e274a6b4529f7 --- /dev/null +++ b/recipes/mass2chem/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "mass2chem" %} +{% set version = "0.4.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mass2chem-{{ version }}.tar.gz + sha256: d8033cc10646ab9dd4223dcfa3e3709e46cd29aa64498a57ff25701a6493eb21 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv + number: 0 + run_exports: + - {{ pin_subpackage('mass2chem', max_pin="x.x") }} + + +requirements: + host: + - python >=3.7 + - setuptools >=42 + - wheel + - pip + run: + - python >=3.7 + - numpy + - scipy + - treelib + +test: + imports: + - mass2chem + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/shuzhao-li/mass2chem + summary: Common utilities for interpreting mass spectrometry data + license: BSD-Protection + license_file: LICENSE + +extra: + recipe-maintainers: + - hechth diff --git a/recipes/metdatamodel/meta.yaml b/recipes/metdatamodel/meta.yaml new file mode 100644 index 0000000000000..bfd1858956799 --- /dev/null +++ b/recipes/metdatamodel/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "metdatamodel" %} +{% set version = "0.4.14" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metDataModel-{{ version }}.tar.gz + sha256: 49583289a596934204f458c4464579d3b58e18765ae97d283b32b58028de0fbc + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv + number: 0 + run_exports: + - {{ pin_subpackage('metdatamodel', max_pin="x.x") }} + +requirements: + host: + - python >=3.5 + - setuptools >=42 + - wheel + - pip + run: + - python >=3.5 + +test: + imports: + - metDataModel + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/shuzhao-li/metDataModel + summary: Data models for metabolomics + license: BSD-3-Clause + license_file: LICENSE + +extra: + recipe-maintainers: + - hechth From 4aa27b03004c669eb9c1802ea80ff2de9499f284 Mon Sep 17 00:00:00 2001 From: Lightning Auriga <8940921+lightning-auriga@users.noreply.github.com> Date: Sat, 7 Oct 2023 05:42:31 -0400 Subject: [PATCH 0118/2173] Update beagle to 5.4 (#43492) --- recipes/beagle/build.sh | 2 +- recipes/beagle/gpl_license | 674 +++++++++++++++++++++++++++++++++++++ recipes/beagle/meta.yaml | 15 +- 3 files changed, 684 insertions(+), 7 deletions(-) create mode 100644 recipes/beagle/gpl_license diff --git a/recipes/beagle/build.sh b/recipes/beagle/build.sh index b00f833c0de68..4cbcdc46d056b 100644 --- a/recipes/beagle/build.sh +++ b/recipes/beagle/build.sh @@ -8,7 +8,7 @@ outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $outdir mkdir -p $PREFIX/bin -cp beagle.21Apr21.304.jar $outdir/beagle.jar +cp beagle.22Jul22.46e.jar $outdir/beagle.jar cp $RECIPE_DIR/beagle $outdir/ chmod +x $outdir/beagle diff --git a/recipes/beagle/gpl_license b/recipes/beagle/gpl_license new file mode 100644 index 0000000000000..818433ecc0e09 --- /dev/null +++ b/recipes/beagle/gpl_license @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/beagle/meta.yaml b/recipes/beagle/meta.yaml index 67c620e4f24cf..4a7757df61383 100644 --- a/recipes/beagle/meta.yaml +++ b/recipes/beagle/meta.yaml @@ -1,19 +1,21 @@ {% set name = "beagle" %} -{% set version = "5.2_21Apr21.304" %} -{% set sha256 = "cf420d5766728d9110895651c1784b18888e24fddc4d882889390d33028d22e2" %} +{% set version = "5.4_22Jul22.46e" %} +{% set sha256 = "57226e441f4da7104df139d022ed24ad9804fa72cf754e45d04f5658dcef242b" %} package: name: {{ name }} version: {{ version }} source: - url: http://faculty.washington.edu/browning/beagle/beagle.21Apr21.304.jar + url: https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar sha256: {{ sha256 }} build: detect_binary_files_with_prefix: True number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('beagle', max_pin="x") }} requirements: run: @@ -25,10 +27,11 @@ test: about: home: http://faculty.washington.edu/browning/beagle/beagle.html - license: GPLv3 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 + license_file: gpl_license summary: "Beagle is a software package for phasing genotypes and for imputing ungenotyped markers." - doc_url: http://faculty.washington.edu/browning/beagle/beagle_5.1_12Aug19.pdf + doc_url: https://faculty.washington.edu/browning/beagle/beagle_5.4_18Mar22.pdf extra: identifiers: From 0faed07b14a9e4713a88ae6998e2ad7b533b06eb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 7 Oct 2023 04:02:45 -0600 Subject: [PATCH 0119/2173] Update mass2chem to 0.4.9 (#43544) --- recipes/mass2chem/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mass2chem/meta.yaml b/recipes/mass2chem/meta.yaml index e274a6b4529f7..7f7f765b95914 100644 --- a/recipes/mass2chem/meta.yaml +++ b/recipes/mass2chem/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mass2chem" %} -{% set version = "0.4.4" %} +{% set version = "0.4.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mass2chem-{{ version }}.tar.gz - sha256: d8033cc10646ab9dd4223dcfa3e3709e46cd29aa64498a57ff25701a6493eb21 + sha256: 5f570440aa217f2f2847f8b2d7cba06c2b46a4088921079db1ed0941b30c1e4b build: noarch: python From de5111d1e18e732be1567746fa0a69befa86d22f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 7 Oct 2023 06:16:40 -0600 Subject: [PATCH 0120/2173] Update kgwasflow to 1.3.0 (#43543) --- recipes/kgwasflow/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kgwasflow/meta.yaml b/recipes/kgwasflow/meta.yaml index 96d1be2cbcba3..45782fe06a4af 100644 --- a/recipes/kgwasflow/meta.yaml +++ b/recipes/kgwasflow/meta.yaml @@ -1,5 +1,5 @@ {% set name = "kgwasflow" %} -{% set version = "1.2.4" %} +{% set version = "1.3.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/akcorut/kGWASflow/archive/refs/tags/v{{ version }}.tar.gz" - sha256: d6e29706d75ace89d80b62df59c24f7e8dd076bb933d7a836dfe6fa68a3ec18f + sha256: bb8b01a3903f8c3700be328079cdfb2b12c9fdce5135866dc09005c2c5f0e495 build: noarch: python From a5aa00044ff0bdc561f0cb4432316bde9ab1065b Mon Sep 17 00:00:00 2001 From: Ian Fiddes Date: Sat, 7 Oct 2023 05:17:25 -0700 Subject: [PATCH 0121/2173] biocantor 1.1.0 (#43532) * biocantor 1.1.0 * update sha256 * add run exports * license file * add license file to release --- recipes/biocantor/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/biocantor/meta.yaml b/recipes/biocantor/meta.yaml index 73001a3725e94..fc55c29b506a0 100644 --- a/recipes/biocantor/meta.yaml +++ b/recipes/biocantor/meta.yaml @@ -1,6 +1,6 @@ {% set name = "biocantor" %} -{% set version = "1.0.0" %} -{% set sha256 = "93263bd000d711e401518a4de7420f21dda420b6b1c09d6c4149fea3b9a9b9be" %} +{% set version = "1.1.0" %} +{% set sha256 = "ea06f10f589d54b30dbf432a9b3f6e9c65f8f371c88c706505dfd115c05ed635" %} package: name: "{{ name|lower }}" @@ -14,6 +14,8 @@ build: noarch: python number: 0 script: "{{ PYTHON }} -m pip install .[io] --ignore-installed --no-deps -vv" + run_exports: + - {{ pin_subpackage("biocantor", max_pin="x") }} requirements: host: @@ -39,5 +41,5 @@ about: home: "https://github.com/ifiddes/BioCantor" license: MIT license_family: MIT - license_file: LICENSE.txt + license_file: LICENSE summary: "Coordinate Maniuplation and Genome Annotation Data Model" From 4cce63fbe11dfa9fca40b0f8f897af44b1aacd6c Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 7 Oct 2023 07:25:16 -0500 Subject: [PATCH 0122/2173] Update GMAP to 2023-10-01 (#43502) --- recipes/gmap/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index 4abb333764261..58e7b9a11010a 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GMAP" %} -{% set version = "2023.07.20" %} -{% set sha256 = "19e70eebd9b282d8596721812d071efed188b6d5000627b9948f0486f87fe68f" %} +{% set version = "2023.10.01" %} +{% set sha256 = "b6299f051189f1abea6976f668eb5204fdff2a4519a40931f7897f2496fec7ed" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ source: - single_quote_paths.patch build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('gmap', max_pin=None) }} From 07f5aea649e1bfae2c87d31edb620078f1b11b92 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 7 Oct 2023 09:16:47 -0600 Subject: [PATCH 0123/2173] Update raxml to 8.2.13 (#43411) * Update raxml to 8.2.13 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/raxml/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/raxml/meta.yaml b/recipes/raxml/meta.yaml index 4383489feac98..87550af90f582 100644 --- a/recipes/raxml/meta.yaml +++ b/recipes/raxml/meta.yaml @@ -1,21 +1,21 @@ package: name: raxml - version: "8.2.12" + version: "8.2.13" build: - number: 6 + number: 0 + run_exports: + - {{ pin_subpackage('raxml', max_pin="x") }} source: - url: https://github.com/stamatak/standard-RAxML/archive/v8.2.12.tar.gz - sha256: 338f81b52b54e16090e193daf36c1d4baa9b902705cfdc7f4497e3e09718533b + url: https://github.com/stamatak/standard-RAxML/archive/refs/tags/v8.2.13.tar.gz + sha256: 28e500793324bd7d330b396ef27ea49c9186fa5e1edb3d5439036dc6c33e6067 requirements: build: - make - {{ compiler('c') }} - run: - test: commands: - raxmlHPC -h > /dev/null From edd8547eedce2e8ec2d948eae55aa7c9fbae4c05 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 7 Oct 2023 09:17:04 -0600 Subject: [PATCH 0124/2173] Update varlociraptor to 8.4.1 (#43548) --- recipes/varlociraptor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varlociraptor/meta.yaml b/recipes/varlociraptor/meta.yaml index 05018db443df7..f8e05d834e0b0 100644 --- a/recipes/varlociraptor/meta.yaml +++ b/recipes/varlociraptor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.0" %} +{% set version = "8.4.1" %} package: name: varlociraptor @@ -11,7 +11,7 @@ build: source: url: https://github.com/varlociraptor/varlociraptor/archive/v{{ version }}.tar.gz - sha256: 8d20d7bf4d259d3bc04aeb6e5e2e7fa1427e218649074d725c794576a43c7b3c + sha256: bbc5ef7eeb64cf578b0271d8a8319ed6f5bf9c178a08310f4394896205e92f95 requirements: build: From 708f64d2e546be9b9454fe3df8c8d1348d071f4f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 7 Oct 2023 15:02:03 -0600 Subject: [PATCH 0125/2173] Update dimet to 0.1.4 (#43526) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update dimet to 0.1.4 * dimet: add six library (#43546) six library demanded during build_test azure pipelines. This should fix the PR blockage v 0.1.4 * six --------- Co-authored-by: johaGL Co-authored-by: Björn Grüning --- recipes/dimet/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/dimet/meta.yaml b/recipes/dimet/meta.yaml index 9762f44ce9cc5..fcc2e26a6ff37 100644 --- a/recipes/dimet/meta.yaml +++ b/recipes/dimet/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dimet" %} -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dimet-{{ version }}.tar.gz - sha256: 498a254fcbba804281b0039eb72e04c37d8577265b844469a6a88cc1992032b0 + sha256: 372537f9c9aef2035868357df2c04e5f94bf3f6bef39f69988e25d114a8009ab build: noarch: python @@ -21,6 +21,7 @@ requirements: - python >=3.9,<4.0 - poetry - pip + - six run: - python >=3.9,<4.0 - click From 0f807c6530e4e63050e58cba660c045705764388 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 7 Oct 2023 15:04:10 -0600 Subject: [PATCH 0126/2173] Update noise2read to 0.3.0 (#43522) * Update noise2read to 0.3.0 * update noise2read to 0.3.0 (#43541) --------- Co-authored-by: Jappy <36221893+Jappy0@users.noreply.github.com> --- recipes/noise2read/meta.yaml | 33 ++++++++++++++------------------- 1 file changed, 14 insertions(+), 19 deletions(-) diff --git a/recipes/noise2read/meta.yaml b/recipes/noise2read/meta.yaml index d2eb32e43f254..1563783acf521 100644 --- a/recipes/noise2read/meta.yaml +++ b/recipes/noise2read/meta.yaml @@ -1,5 +1,5 @@ {% set name = "noise2read" %} -{% set version = "0.2.10" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,54 +7,49 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/noise2read-{{ version }}.tar.gz - sha256: 83815c0fad2d0869c63613b39bd70f0cdfa077bf02d0777e2861200d584e30d9 + sha256: d259167a34cf99776cc3ad968c2d0aafb720b781854b09e33737c2927f34a713 build: noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 - # entry_points: - # noise2read = noise2read.noise2read:main run_exports: - {{ pin_subpackage('noise2read', max_pin='x.x') }} - + requirements: host: - - python + - python >=3.8 - setuptools - wheel - pip run: - - python + - python >=3.8 - biopython ==1.79 - xgboost ==1.6.1 - - xlsxwriter ==3.0.3 - - tqdm ==4.66.1 - - scikit-learn ==1.3 + - xlsxwriter >=3.0.3 + - scikit-learn >=1.1.1 - networkx ==2.8.5 - - pandas ==2.1.0 + - pandas >=1.4.3 - optuna >=3.1.1 - matplotlib-base >=3.5.2 - mpire >=2.8.0 - - editdistance ==0.6.2 - - imbalanced-learn ==0.9.1 - - seaborn >=0.12.1 - - psutil ==5.9.5 + - editdistance >=0.6.0 + - imbalanced-learn >=0.9.1 - seqtk - bcool test: commands: - - noise2read --version + - noise2read -v about: home: https://github.com/Jappy0/noise2read summary: Turn noise to read description: > - noise2read, originated in a computable rule translated from PCR erring mechanism that: a rare read is erroneous if it has a neighboring read of high abundance, turns erroneous reads into their original state without bringing up any non-existing sequences into the short read set(< 300bp) including DNA and RNA sequencing (DNA/RNA-seq), small RNA, unique molecular identifiers (UMI) and amplicon sequencing data. + noise2read, originated in a computable rule translated from PCR erring mechanism that: a rare read is erroneous if it has a neighboring read of high abundance, turns erroneous reads into their original state without bringing up any non-existing sequences into the short read set(< 300bp) including DNA and RNA sequencing (DNA/RNA-seq), small RNA, unique molecular identifiers (UMI) and amplicon sequencing data. license: MIT license_file: LICENSE extra: recipe-maintainers: - - Pengyao Ping + - Jappy0 From cb5bed70eb7d37d516026e62294bb2c36d38a46e Mon Sep 17 00:00:00 2001 From: Jappy <36221893+Jappy0@users.noreply.github.com> Date: Sun, 8 Oct 2023 14:03:49 +1100 Subject: [PATCH 0127/2173] Add deepdirect recipe (#43418) * add noise2read recipes * add noise2read recipes * add noise2read recipe * add noise2read recipe * add noise2read recipe * remove entry_points * add deepdirect recipe * add deepdirect recipe * add deepdirect recipe * add deepdirect recipe * add deepdirect recipe * add deepdirect recipe * add deepdirect recipe * change maintainer name --- recipes/deepdirect/meta.yaml | 46 ++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/deepdirect/meta.yaml diff --git a/recipes/deepdirect/meta.yaml b/recipes/deepdirect/meta.yaml new file mode 100644 index 0000000000000..3ef793cfafd93 --- /dev/null +++ b/recipes/deepdirect/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "deepdirect" %} +{% set version = "0.2.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/deepdirect-{{ version }}.tar.gz + sha256: 10feba8b3b52fbb274bdd0bdf9e8ae75df6669029d359a2ba9fae51af53a2faa + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('deepdirect', max_pin="x.x") }} + +requirements: + host: + - python + - setuptools + - wheel + - pip + run: + - python + - tensorflow >=2.4.0 + - keras >=2.4.0 + - colorlog ==6.7.0 + - tqdm >=4.64.1 + +test: + imports: + - deepdirect + commands: + - deepdirect -v + +about: + home: https://github.com/Jappy0/deepdirect + summary: In silico approach to generate mutations for protein complexes towards a specified direction (increase/decrease) in binding affinity. + license: GPL-2.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - Jappy0 From 690c5846f13e4cf01e8f1410100e17ec003e1258 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 7 Oct 2023 21:08:48 -0600 Subject: [PATCH 0128/2173] Update scanorama to 1.7.4 (#43554) * Update scanorama to 1.7.4 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/scanorama/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/scanorama/meta.yaml b/recipes/scanorama/meta.yaml index bde4076c536ed..f374f447dea3e 100644 --- a/recipes/scanorama/meta.yaml +++ b/recipes/scanorama/meta.yaml @@ -1,5 +1,5 @@ {% set name = "scanorama" %} -{% set version = "1.7.3" %} +{% set version = "1.7.4" %} package: name: "{{ name|lower }}" @@ -7,17 +7,18 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: e1d1cdd6855b3a302f6e9e3160442a9998113e5118ac48c71bf8a21760a657b7 + sha256: 67de100e63abc3028c7780d3a217e43e920a5781230bc6b6a51349d4605e005c build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed -vv ." + script: "{{ PYTHON }} -m pip install --no-deps --no-build-isolation -vvv ." + run_exports: + - {{ pin_subpackage('scanorama', max_pin="x") }} requirements: host: - python >=3.6 - - setuptools - pip run: - python >=3.6 @@ -37,6 +38,8 @@ test: about: home: https://github.com/brianhie/scanorama/ license: MIT + license_family: MIT + license_file: LICENSE summary: Panoramic stitching of heterogeneous single-cell transcriptomic data extra: From 6aea733751c2a61bff29b1a619236be2884aa294 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 7 Oct 2023 21:09:30 -0600 Subject: [PATCH 0129/2173] Update asciigenome to 1.18.0 (#43551) * Update asciigenome to 1.18.0 * add run_exports * remove license_file --------- Co-authored-by: joshuazhuang7 --- recipes/asciigenome/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/asciigenome/meta.yaml b/recipes/asciigenome/meta.yaml index baee0a3f676a9..78b047a743afc 100644 --- a/recipes/asciigenome/meta.yaml +++ b/recipes/asciigenome/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.17.0" %} -{% set sha256 = "ca241260074348fd0e7b11e7720041ea6b9679e6880689a3b69c0511b6761334" %} +{% set version = "1.18.0" %} +{% set sha256 = "e505f3551cd53dbe1cee82ef85e515ec9f80e60ab4e7bae462c43e37f415411e" %} package: name: asciigenome @@ -12,6 +12,8 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('asciigenome', max_pin="x") }} requirements: run: @@ -28,3 +30,4 @@ about: summary: Command-line genome browser running from terminal window and solely based on ASCII characters license_family: MIT + doc_url: https://asciigenome.readthedocs.io/en/latest/ From 057618a6df5ca7c62cecc75807859c5e4210f55c Mon Sep 17 00:00:00 2001 From: Xiangyang1984 <58356520+Xiangyang1984@users.noreply.github.com> Date: Sun, 8 Oct 2023 18:03:33 +0800 Subject: [PATCH 0130/2173] add pneumo-typer recipes (#43479) * add pneumo-typer recipes * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/pneumo-typer/build.sh | 4 +--- recipes/pneumo-typer/meta.yaml | 10 ++++------ 2 files changed, 5 insertions(+), 9 deletions(-) diff --git a/recipes/pneumo-typer/build.sh b/recipes/pneumo-typer/build.sh index 9688468e492ca..100fee3e5fb53 100644 --- a/recipes/pneumo-typer/build.sh +++ b/recipes/pneumo-typer/build.sh @@ -4,8 +4,6 @@ set -x -e RM_DIR=${PREFIX}/share/pneumo-typer mkdir -p ${RM_DIR} mkdir -p ${PREFIX}/bin -#cp -r ${SRC_DIR}/pneumo-typer-v1.0.1/* ${RM_DIR} -#cp -r pneumo-typer/* ${RM_DIR} cp -r pneumo-typer-v1.0.1/* ${RM_DIR} cp build_env_setup.sh ${RM_DIR} cp conda_build.sh ${RM_DIR} @@ -17,4 +15,4 @@ perl ${RM_DIR}/pneumo-typer.pl \$@ END -chmod a+x ${PREFIX}/bin/pneumo-typer \ No newline at end of file +chmod a+x ${PREFIX}/bin/pneumo-typer diff --git a/recipes/pneumo-typer/meta.yaml b/recipes/pneumo-typer/meta.yaml index a09039cdd77d0..9ef596df2b11e 100644 --- a/recipes/pneumo-typer/meta.yaml +++ b/recipes/pneumo-typer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pneumo-typer" %} {% set version = "1.0.1" %} -{% set sha256 = "84739053d9813501749ae1384d6af968c720032d920084a5c343722edf007ab3" %} +{% set sha256 = "d564fd21d79fa08f6e82e37283a8a55dddd21590d7d05bb261aa7ddf3374bf0f" %} package: name: "{{ name|lower }}" @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('pneumo-typer', max_pin="x") }} @@ -40,10 +40,8 @@ test: about: home: 'https://www.microbialgenomic.cn/Pneumo-Typer.html' - summary: 'Pneumo-Typer is a fast and simple-to-use tool for predicting serotype and determining sequence type (St/cgSt) for Streptococcus pneumoniae.' - description: 'Pneumo-Typer is a stand-alone perl application, which requires blat, prodigal, NCBI BLASt+, boat and several perl Modules (GD, GD::SVG) to be installed before use.' - doc_url: How to install and use Pneumo-Typer at 'https://www.microbialgenomic.cn/Pneumo-Typer.html' and or https://github.com/Xiangyang1984/Pneumo-Typer. - license: perl_5 + summary: 'Pneumo-Typer is a comprehensive prediction and visualization of serotype and sequence type for streptococcus pneumoniae using assembled genomes.' + license: GNU General Public License v3.0 or any later version (GPL-3.0-or-later) extra: author: From d317c01a85b04eb9feb512cfd54f252c31942e45 Mon Sep 17 00:00:00 2001 From: Carl Mathias Kobel Date: Sun, 8 Oct 2023 13:06:26 +0200 Subject: [PATCH 0131/2173] Add assemblycomparator2 (#43391) --- recipes/assemblycomparator2/build.sh | 20 ++++++++++++++ recipes/assemblycomparator2/meta.yaml | 40 +++++++++++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 recipes/assemblycomparator2/build.sh create mode 100644 recipes/assemblycomparator2/meta.yaml diff --git a/recipes/assemblycomparator2/build.sh b/recipes/assemblycomparator2/build.sh new file mode 100644 index 0000000000000..1c97f51cd74b7 --- /dev/null +++ b/recipes/assemblycomparator2/build.sh @@ -0,0 +1,20 @@ +#!/usr/bin/env bash + + +# First we put the necessary files in into the conda prefix directory: +mkdir -p ${PREFIX}/assemblycomparator2 +cp asscom2 snakefile config.yaml LICENSE ${PREFIX}/assemblycomparator2 +cp -r assets conda_definitions profiles report_subpipeline scripts tests ${PREFIX}/assemblycomparator2 + +# This is the binary that we wish to be able to run. +mkdir -p ${PREFIX}/bin +ln -s ${PREFIX}/assemblycomparator2/asscom2 ${PREFIX}/bin/asscom2 + + +# # I hope these variables are accessible when the user activates the environment that runs ac2. +# ASSCOM2_BASE=$PREFIX +# ASSCOM2_PROFILE=${ASSCOM2_BASE}/profiles/apptainer/local +# ASSCOM2_DATABASES=${ASSCOM2_BASE}/databases # The user should override this in their .bashrc if they want to use a different dir. + +# # I think it is better to use backslash-sentinel, because then the user can change the variables after having activated the PREFIX environment, and the changes will have effect +# alias asscom2='snakemake --snakefile \${ASSCOM2_BASE}/snakefile --profile \${ASSCOM2_PROFILE} --configfile \${ASSCOM2_BASE}/config.yaml' diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml new file mode 100644 index 0000000000000..953b5564f8e02 --- /dev/null +++ b/recipes/assemblycomparator2/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "2.5.6" %} + +package: + name: assemblycomparator2 + version: {{ version }} + +source: + url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz + md5: 2ffd351078346dce8de117f973df5efc + + +build: + number: 0 + run_exports: + - asscom2 + skip: True # [osx] + +requirements: + run: + - snakemake >=7.32.3 + - mamba >=1.4.9 # Necessary for snakemake to install child environments during development. + + +test: + commands: + - touch dummy.fa; asscom2 --help + + +about: + home: https://github.com/cmkobel/assemblycomparator2 + summary: 'assemblycomparator2: Compare prokaryotic genomic assemblies' + license_family: GPL + license: GPL-3.0 + license_file: LICENSE +extra: + skip-lints: + - should_be_noarch_generic + recipe-maintainers: + - cmkobel + From db736c3a23d7c8e0011d7b9c0f2088f74bfe6ea3 Mon Sep 17 00:00:00 2001 From: Lightning Auriga <8940921+lightning-auriga@users.noreply.github.com> Date: Sun, 8 Oct 2023 09:26:27 -0400 Subject: [PATCH 0132/2173] feat: update freebayes to 1.3.7 (#43550) --- ...0001-make-meson-build-conda-friendly.patch | 114 ++++++++++++++++++ .../0002-fix-intervaltree-include-path.patch | 39 ++++++ recipes/freebayes/LICENSE | 19 +++ recipes/freebayes/build.sh | 5 +- recipes/freebayes/meson.patch | 18 --- recipes/freebayes/meta.yaml | 12 +- recipes/freebayes/qcfail.diff | 37 ------ 7 files changed, 181 insertions(+), 63 deletions(-) create mode 100644 recipes/freebayes/0001-make-meson-build-conda-friendly.patch create mode 100644 recipes/freebayes/0002-fix-intervaltree-include-path.patch create mode 100644 recipes/freebayes/LICENSE delete mode 100644 recipes/freebayes/meson.patch delete mode 100644 recipes/freebayes/qcfail.diff diff --git a/recipes/freebayes/0001-make-meson-build-conda-friendly.patch b/recipes/freebayes/0001-make-meson-build-conda-friendly.patch new file mode 100644 index 0000000000000..98067c888dcb8 --- /dev/null +++ b/recipes/freebayes/0001-make-meson-build-conda-friendly.patch @@ -0,0 +1,114 @@ +From 62630d76f804c930753b0215ed09a33a02e1347e Mon Sep 17 00:00:00 2001 +From: Lightning Auriga +Date: Sat, 7 Oct 2023 12:25:42 -0400 +Subject: [PATCH 1/2] make meson build conda friendly + +--- + meson.build | 58 +++++++++-------------------------------------------- + 1 file changed, 9 insertions(+), 49 deletions(-) + +diff --git a/meson.build b/meson.build +index 2a91caf..66b8016 100644 +--- a/meson.build ++++ b/meson.build +@@ -15,7 +15,7 @@ + # meson build -Dstatic=true -Dprefer_system_deps=false --buildtype release + + project('freebayes', ['cpp', 'c'], +- version : '1.3.6', ++ version : '1.3.7', + default_options : ['warning_level=1', 'cpp_std=c++17', 'optimization=3']) + static_build = get_option('static') + +@@ -24,21 +24,16 @@ cc = meson.get_compiler('cpp') + zlib_dep = dependency('zlib', static: static_build) + lzma_dep = dependency('liblzma', static: static_build) + thread_dep = dependency('threads', static: static_build) +-tabixpp_dep = cc.find_library('tabixpp', required: false, static: static_build) + + # to compile htslib use + # meson build -Dprefer_system_deps=false + # otherwise it tries to pick up the local system libs + if get_option('prefer_system_deps') + htslib_dep = dependency('htslib', static: static_build, required: false) +- tabixpp_dep = cc.find_library('tabixpp', static: static_build, required: false) +- vcflib_dep = dependency('libvcflib', static: static_build, required: false) + seqlib_dep = dependency('libseqlib', static: static_build, required: false) + else + # uses the local git submodules + htslib_dep = dependency('', required : false) +- tabixpp_dep = dependency('', required : false) +- vcflib_dep = dependency('', required : false) + seqlib_dep = dependency('', required : false) + endif + +@@ -99,50 +94,15 @@ if not htslib_dep.found() + htslib_dep = declare_dependency(link_with : htslib_lib, + include_directories : htslib_inc) + else +- htslib_inc = [] ++ htslib_inc = [get_option('prefix') + '/include'] ++ htslib_lib = [get_option('prefix') + '/lib'] + endif + +- +-if not tabixpp_dep.found() +- tabixpp_inc = include_directories('contrib/vcflib/contrib/tabixpp/') +- tabixpp_src = files('contrib/vcflib/contrib/tabixpp/tabix.cpp') +- tabixpp_lib = static_library('custom_tabixpp', +- tabixpp_src, +- include_directories : [tabixpp_inc, htslib_inc], +- override_options : warn_quiet) +- tabixpp_dep = declare_dependency(link_with : tabixpp_lib, +- include_directories : tabixpp_inc) +-else +- tabixpp_inc = [] +-endif +- +-if not vcflib_dep.found() +- vcflib_inc = include_directories( +- 'contrib/vcflib/src', +- 'contrib/vcflib/contrib/smithwaterman', +- 'contrib/vcflib/contrib/multichoose', +- 'contrib/vcflib/contrib/filevercmp', +- 'contrib/vcflib/contrib/fastahack', +- ) +- vcflib_src = files( +- 'contrib/vcflib/src/Variant.cpp', +- 'contrib/vcflib/src/allele.cpp', +- 'contrib/vcflib/src/cigar.cpp', +- 'contrib/vcflib/src/split.cpp', +- 'contrib/vcflib/contrib/fastahack/Fasta.cpp', +- 'contrib/vcflib/contrib/smithwaterman/SmithWatermanGotoh.cpp', +- 'contrib/vcflib/contrib/smithwaterman/disorder.cpp', +- 'contrib/vcflib/contrib/smithwaterman/Repeats.cpp', +- 'contrib/vcflib/contrib/smithwaterman/LeftAlign.cpp', +- 'contrib/vcflib/contrib/smithwaterman/IndelAllele.cpp', +- ) +- vcflib_lib = static_library('custom_vcflib', +- vcflib_src, +- include_directories : [htslib_inc, tabixpp_inc, vcflib_inc], +- override_options : warn_quiet) +- vcflib_dep = declare_dependency(link_with : vcflib_lib, +- include_directories : vcflib_inc) +-endif ++tabixpp_inc = [get_option('prefix') + '/include'] ++tabixpp_dep = [] ++vcflib_inc = [get_option('prefix') + '/include'] ++vcflib_lib = [get_option('prefix') + '/lib'] ++vcflib_dep = [] + + + if not seqlib_dep.found() +@@ -227,7 +187,7 @@ freebayes_lib = static_library( + if static_build + link_arguments = '-static' + else +- link_arguments = [] ++ link_arguments = ['-ltabixpp', '-lwfa2', '-lvcflib'] + endif + + executable('freebayes', +-- +2.41.0 + diff --git a/recipes/freebayes/0002-fix-intervaltree-include-path.patch b/recipes/freebayes/0002-fix-intervaltree-include-path.patch new file mode 100644 index 0000000000000..ad42bf6a166ac --- /dev/null +++ b/recipes/freebayes/0002-fix-intervaltree-include-path.patch @@ -0,0 +1,39 @@ +From 2ce902eee1f187dab660d07d09cf11223b2c745f Mon Sep 17 00:00:00 2001 +From: Lightning Auriga +Date: Sat, 7 Oct 2023 12:26:03 -0400 +Subject: [PATCH 2/2] fix intervaltree include path + +--- + src/BedReader.cpp | 2 +- + src/BedReader.h | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/BedReader.cpp b/src/BedReader.cpp +index 9dd79c7..ea79235 100644 +--- a/src/BedReader.cpp ++++ b/src/BedReader.cpp +@@ -11,7 +11,7 @@ + #include "Utility.h" + #include "BedReader.h" + #include "Logging.h" +-#include "../intervaltree/IntervalTree.h" ++#include "IntervalTree.h" + + using namespace std; + +diff --git a/src/BedReader.h b/src/BedReader.h +index 03abb3f..8777d53 100644 +--- a/src/BedReader.h ++++ b/src/BedReader.h +@@ -9,7 +9,7 @@ + #include + #include + #include +-#include "../intervaltree/IntervalTree.h" ++#include "IntervalTree.h" + #include "split.h" + + using namespace std; +-- +2.41.0 + diff --git a/recipes/freebayes/LICENSE b/recipes/freebayes/LICENSE new file mode 100644 index 0000000000000..9e3322e991a3d --- /dev/null +++ b/recipes/freebayes/LICENSE @@ -0,0 +1,19 @@ +Copyright (c) 2010 Erik Garrison, Gabor Marth + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff --git a/recipes/freebayes/build.sh b/recipes/freebayes/build.sh index a8ef4bb394e1f..660009d1b0fc8 100644 --- a/recipes/freebayes/build.sh +++ b/recipes/freebayes/build.sh @@ -1,10 +1,7 @@ #!/bin/bash -#export C_INCLUDE_PATH=$PREFIX/include -#export CPLUS_INCLUDE_PATH=$PREFIX/include - mkdir build -meson build/ --buildtype debug --prefix "${PREFIX}" +meson setup --buildtype debug --prefix "${PREFIX}" -Dprefer_system_deps=true build/ diff --git a/recipes/freebayes/meson.patch b/recipes/freebayes/meson.patch deleted file mode 100644 index bc98faef5df12..0000000000000 --- a/recipes/freebayes/meson.patch +++ /dev/null @@ -1,18 +0,0 @@ ---- freebayes/meson.build -+++ freebayes/meson.build -@@ -18,7 +18,7 @@ - - htslib_dep = dependency('htslib', required : false) - tabixpp_dep = cc.find_library('tabixpp', required : false) --vcflib_dep = dependency('libvcflib', required : false) -+vcflib_dep = cc.find_library('vcflib', required : false) - seqlib_dep = dependency('libseqlib', required : false) - - # for setting a warning_level on the external code in custom_* targets below -@@ -113,6 +113,8 @@ - override_options : warn_quiet) - vcflib_dep = declare_dependency(link_with : vcflib_lib, - include_directories : vcflib_inc) -+else -+ vcflib_inc = [] - endif diff --git a/recipes/freebayes/meta.yaml b/recipes/freebayes/meta.yaml index 6bc169b8f85a2..150a384c7f12c 100644 --- a/recipes/freebayes/meta.yaml +++ b/recipes/freebayes/meta.yaml @@ -1,15 +1,18 @@ -{% set version = "1.3.6" %} +{% set version = "1.3.7" %} package: name: freebayes version: {{ version }} source: - url: https://github.com/freebayes/freebayes/releases/download/v{{ version }}/freebayes-{{ version }}-src.tar.gz - sha256: 6016c1e58fdf34a1f6f77b720dd8e12e13a127f7cbac9c747e47954561b437f5 + url: https://github.com/freebayes/freebayes/archive/refs/tags/v{{ version }}.tar.gz + sha256: 89c2202aaa82925bc6a49e04df593e5ef3b1547b3b514efcbd490a54d8ad200b + patches: + - 0001-make-meson-build-conda-friendly.patch + - 0002-fix-intervaltree-include-path.patch build: - number: 7 + number: 0 skip: true # [osx] run_exports: - {{ pin_subpackage("freebayes", max_pin="x") }} @@ -27,6 +30,7 @@ requirements: - htslib - tabixpp - vcflib + - simde run: - parallel - samtools diff --git a/recipes/freebayes/qcfail.diff b/recipes/freebayes/qcfail.diff deleted file mode 100644 index 31c93fe11d0af..0000000000000 --- a/recipes/freebayes/qcfail.diff +++ /dev/null @@ -1,37 +0,0 @@ -diff --git a/src/AlleleParser.cpp b/src/AlleleParser.cpp -index 72c0c14..a6b16ae 100644 ---- a/src/AlleleParser.cpp -+++ b/src/AlleleParser.cpp -@@ -2001,6 +2001,12 @@ void AlleleParser::updateAlignmentQueue(long int position, - continue; - } - -+ // skip reads that fail QC, used by VariantBam for high coverage downsampling -+ if (currentAlignment.ISFAILQC) { -+ DEBUG("skipping alignment " << currentAlignment.QNAME << " because it is fails QC"); -+ continue; -+ } -+ - // skip alignments which have no aligned bases - if (currentAlignment.ALIGNEDBASES == 0) { - DEBUG("skipping alignment " << currentAlignment.QNAME << " because it has no aligned bases"); -diff --git a/src/LeftAlign.h b/src/LeftAlign.h -index 46aa8f5..98e4539 100644 ---- a/src/LeftAlign.h -+++ b/src/LeftAlign.h -@@ -49,6 +49,7 @@ using namespace BamTools; - #define ISPAIRED IsPaired() - #define ISMATEMAPPED IsMateMapped() - #define ISPROPERPAIR IsProperPair() -+#define ISFAILQC IsFailedQC() - #define CIGLEN Length - #define CIGTYPE Type - #define BAMREADER BamMultiReader -@@ -90,6 +91,7 @@ using namespace BamTools; - #define GETCIGAR GetCigar() - #define GETREFID(name) Header().Name2ID(name) - #define ISDUPLICATE DuplicateFlag() -+#define ISFAILQC QCFailFlag() - #define CIGLEN Length() - #define CIGTYPE Type() - #define ADDCIGAR add From 9e56336ddd9a61019ee79d2bcbe5f29ee5631e64 Mon Sep 17 00:00:00 2001 From: "Michael X. Wang" <54554363+mxwang66@users.noreply.github.com> Date: Sun, 8 Oct 2023 10:05:51 -0500 Subject: [PATCH 0133/2173] Update Olivar source (#43409) --- recipes/olivar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/olivar/meta.yaml b/recipes/olivar/meta.yaml index 2348d1100437c..46b51dbf8ef1f 100644 --- a/recipes/olivar/meta.yaml +++ b/recipes/olivar/meta.yaml @@ -6,10 +6,10 @@ package: source: url: 'https://github.com/treangenlab/Olivar/archive/refs/tags/v{{version}}.tar.gz' - sha256: b5f74674ffc38cbd62ee7a0eff113e96ff84a2ea5221289d0a0f24f07f7a362d + sha256: b8d3df4ee17d364e6f8547b8c935cc41168034d712467c22f68540eab41fc087 build: - number: 2 + number: 3 noarch: python script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv && mkdir -p ${PREFIX}/bin && cp olivar ${PREFIX}/bin run_exports: From b1234635d1c61a30d0c8953a0731f2c890950351 Mon Sep 17 00:00:00 2001 From: Tunc Kayikcioglu <19364610+tuncK@users.noreply.github.com> Date: Sun, 8 Oct 2023 20:18:13 +0200 Subject: [PATCH 0134/2173] Add new tool kosudoku (#43553) * kosudoku added * shift bash to external repo --- recipes/kosudoku/LICENSE.md | 15 +++++++++++++ recipes/kosudoku/build.sh | 10 +++++++++ recipes/kosudoku/meta.yaml | 45 +++++++++++++++++++++++++++++++++++++ 3 files changed, 70 insertions(+) create mode 100644 recipes/kosudoku/LICENSE.md create mode 100644 recipes/kosudoku/build.sh create mode 100644 recipes/kosudoku/meta.yaml diff --git a/recipes/kosudoku/LICENSE.md b/recipes/kosudoku/LICENSE.md new file mode 100644 index 0000000000000..8ec1e88695ebf --- /dev/null +++ b/recipes/kosudoku/LICENSE.md @@ -0,0 +1,15 @@ +Princeton University Copyright Notice and Limited License + +Copyright 2016, Trustees of Princeton University (“Princeton”), Princeton, NJ. + +All Rights Reserved. + +Permission to use, copy, modify, and distribute this software and its documentation for any purpose in the following limited field of use: research, education and non-commercial purposes is hereby granted without fee, provided that (1) this copyright notice and limited license appear in all copies and in supporting documentation and (2) the name of Princeton University shall not be used in advertising or publicity pertaining to the use or distribution of the software without specific, written prior permission. + +THIS SOFTWARE IS PROVIDED “AS IS.” PRINCETON UNIVERSITY DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR ANY PARTICULAR PURPOSE. IN NO EVENT SHALL PRINCETON UNIVERSITY BE LIABLE FOR ANY SPECIAL, +INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, +NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + +Please be aware that Princeton has filed for one or more U.S. patents for related technology. No license is implied or granted with +respect to these patents. diff --git a/recipes/kosudoku/build.sh b/recipes/kosudoku/build.sh new file mode 100644 index 0000000000000..3283ef246f2df --- /dev/null +++ b/recipes/kosudoku/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash -e + +# Copy python scripts into somewhere in the env +mkdir -p "${PREFIX}/share/kosudoku" +cp -r ./programs/* "${PREFIX}/share/kosudoku/" + +# Copy bash wrappers to somewhere in the path +cp ./bash_wrappers/kosudoku-* "${PREFIX}/bin/" +chmod +x ${PREFIX}/bin/kosudoku* + diff --git a/recipes/kosudoku/meta.yaml b/recipes/kosudoku/meta.yaml new file mode 100644 index 0000000000000..416a75f601aa3 --- /dev/null +++ b/recipes/kosudoku/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "kosudoku" %} +{% set version = "1.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version | replace('-', '_') }}" + +source: + url: https://github.com/tuncK/kosudoku/archive/refs/tags/v{{ version }}.tar.gz + sha256: 01819d12a9e9da6fa9cb01ac817cb03a1f918ab2b6c8f83d265e931e2627c570 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('kosudoku', max_pin="x") }} + +requirements: + host: + - python + run: + - biopython + - bowtie2 + - matplotlib-base + - numpy <1.24 + - python >=3.5 + - scipy + +test: + commands: + - kosudoku-poolanalyze --help > /dev/null + - kosudoku-poolfit --help > /dev/null + - kosudoku-poolsolve --help > /dev/null + - kosudoku-seqanalyze --help > /dev/null + - kosudoku-verify --help > /dev/null + +about: + home: https://github.com/tuncK/kosudoku + license: Princeton University Copyright Notice and Limited License + license_file: LICENSE.md + summary: "kosudoku: a suite to rapidly create whole genome knockout collections for microorganisms" + +extras: + identifiers: + - doi:10.1038/nprot.2017.073 From a723db87bf7e530d1cdea36bc4f04fc15e353fa7 Mon Sep 17 00:00:00 2001 From: Michael Roach Date: Mon, 9 Oct 2023 14:04:26 +1030 Subject: [PATCH 0135/2173] Add recipe for Koverage 0.1.6 (#43562) * Add recipe for Koverage 0.1.6 * Fix for add recipe for Trimnami 0.1.1 * Fix test command for koverage --- recipes/koverage/meta.yaml | 48 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 recipes/koverage/meta.yaml diff --git a/recipes/koverage/meta.yaml b/recipes/koverage/meta.yaml new file mode 100644 index 0000000000000..951b2bf6ce1d3 --- /dev/null +++ b/recipes/koverage/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "koverage" %} +{% set version = "0.1.6" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 66da69ae446f89a30429f30437a95dccd909e8147f3260c1df88ca486a8139f4 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + number: 0 + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - snaketool-utils >=0.0.4 + - metasnek >=0.0.8 + - snakemake >=7.14.0 + - pyyaml >=6.0 + - Click >=8.1.3 + - zstandard >=0.21.0 + - numpy >=1.24.3 + - py-spy >=0.3.14 + - datapane >=0.16.7 + - plotly >=5.15.0 + +test: + commands: + - koverage --help + +about: + home: https://github.com/beardymcjohnface/Koverage + summary: Read-coverage statistics pipelines for multiple samples + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - beardymcjohnface From d1e5c6a459bad4b7f192672dfb967a1536ebd73f Mon Sep 17 00:00:00 2001 From: Michael Roach Date: Mon, 9 Oct 2023 14:57:41 +1030 Subject: [PATCH 0136/2173] Add recipe for Trimnami version 0.1.1 (#43567) * Add recipe for Trimnami version 0.1.1 * Fix license path --- recipes/trimnami/meta.yaml | 43 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 recipes/trimnami/meta.yaml diff --git a/recipes/trimnami/meta.yaml b/recipes/trimnami/meta.yaml new file mode 100644 index 0000000000000..34ec5afd44ed6 --- /dev/null +++ b/recipes/trimnami/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "trimnami" %} +{% set version = "0.1.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 594d14c9535ed21270afb3c56f146cad786e9e619c25a89b30556d2284f8f461 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + number: 0 + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - snaketool-utils >=0.0.3 + - snakemake >=7.14.0 + - pyyaml >=6.0 + - Click >=8.1.3 + - metasnek >=0.0.8 + +test: + commands: + - trimnami --help + +about: + home: https://github.com/beardymcjohnface/Trimnami + summary: Read-trimming pipelines for multiple samples + license: MIT + license_file: trimnami/trimnami.LICENSE + +extra: + recipe-maintainers: + - beardymcjohnface From 1e1ddf20e13da7022afb372998dbec74d29c25d6 Mon Sep 17 00:00:00 2001 From: Peter Diakumis Date: Mon, 9 Oct 2023 21:54:23 +1100 Subject: [PATCH 0137/2173] Update mosdepth v0.3.4 -> v0.3.5 (#43500) * bump mosdepth v0.3.4 -> v0.3.5 --- recipes/mosdepth/build.sh | 3 ++- recipes/mosdepth/meta.yaml | 8 +++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/mosdepth/build.sh b/recipes/mosdepth/build.sh index dcbb0237c2f55..ae5ff06f5f3cb 100755 --- a/recipes/mosdepth/build.sh +++ b/recipes/mosdepth/build.sh @@ -4,7 +4,8 @@ if [[ ${target_platform} == osx-64 ]] ; then curl -SL https://github.com/brentp/mosdepth/archive/refs/tags/v${PKG_VERSION}.tar.gz -o mosdepth-latest.tar.gz tar -xzf mosdepth-latest.tar.gz cd mosdepth-${PKG_VERSION} - nimble --localdeps build -y --verbose -d:release + nimble install -y "docopt@0.7.0" + nimble build -y --verbose -d:release else curl -SL https://github.com/brentp/mosdepth/releases/download/v$PKG_VERSION/mosdepth -o mosdepth chmod +x mosdepth diff --git a/recipes/mosdepth/meta.yaml b/recipes/mosdepth/meta.yaml index 5716f24daaff5..a637559a8e272 100755 --- a/recipes/mosdepth/meta.yaml +++ b/recipes/mosdepth/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.4" %} +{% set version = "0.3.5" %} package: name: mosdepth @@ -6,12 +6,14 @@ package: build: number: 0 + run_exports: + - {{ pin_subpackage("mosdepth", max_pin="x.x") }} requirements: build: - {{ compiler('c') }} - curl - - nim + - nim <=1.6.2 host: - htslib >=1.10 run: @@ -25,7 +27,7 @@ about: dev_url: https://github.com/brentp/mosdepth doc_url: https://github.com/brentp/mosdepth license: MIT - summary: 'Fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.' + summary: 'Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.' extra: identifiers: From 06dd732b8345651a6f2275e9ac9b2a6f4c56cc47 Mon Sep 17 00:00:00 2001 From: Carl Mathias Kobel Date: Mon, 9 Oct 2023 18:22:51 +0200 Subject: [PATCH 0138/2173] v2.5.7 (#43573) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index 953b5564f8e02..fe4a397a6f39b 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.6" %} +{% set version = "2.5.7" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - md5: 2ffd351078346dce8de117f973df5efc + md5: 934aa96c3027637cd53ad25ccab4004a build: From 4b320aeeb3daa741bc31678e4601723b76817eac Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Mon, 9 Oct 2023 16:24:03 +0000 Subject: [PATCH 0139/2173] moved khipu-metabolomics into recipes folder (#43569) --- {khipu-metabolomics => recipes/khipu-metabolomics}/meta.yaml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {khipu-metabolomics => recipes/khipu-metabolomics}/meta.yaml (100%) diff --git a/khipu-metabolomics/meta.yaml b/recipes/khipu-metabolomics/meta.yaml similarity index 100% rename from khipu-metabolomics/meta.yaml rename to recipes/khipu-metabolomics/meta.yaml From 7b36b0514bed0541926aa84317290a7bb8c78de9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 9 Oct 2023 16:24:46 -0600 Subject: [PATCH 0140/2173] Update pybiolib to 1.1.1360 (#43557) * Update pybiolib to 1.1.1358 * Update pybiolib to 1.1.1360 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 7548e8c25c7b1..dd87eee8a3fe8 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1350" %} +{% set version = "1.1.1360" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: bf5bcbbccdc2d7e781024f6605c6c0717c3f0bbc86884caf48e40f8c548cfd41 + sha256: d318f89a85e0281bd5eb904a89543109ab9d3106232c54dc7290523a61500d94 build: noarch: python From ea912d309a9784d6a39faf29c6feace2d581b93f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 9 Oct 2023 16:53:37 -0600 Subject: [PATCH 0141/2173] Update rseqc to 5.0.3 (#43558) * Update rseqc to 5.0.2 * Update rseqc to 5.0.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/rseqc/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/rseqc/meta.yaml b/recipes/rseqc/meta.yaml index 47534667bf70d..3249e84a80c2e 100644 --- a/recipes/rseqc/meta.yaml +++ b/recipes/rseqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "RSeQC" %} -{% set version = "5.0.1" %} +{% set version = "5.0.3" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 3c7d458784861af352d8da3f4f1cc8941934b37643164e9b74f929a32bd9ca80 + sha256: 869f542e08f50c8874280d58e4f5565857b0aebac66a8eceef3f23016175061e build: - number: 1 + number: 0 skip: True # [py2k] - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" + run_exports: + - {{ pin_subpackage('rseqc', max_pin="x") }} requirements: build: From b5318fc7183ed25329aca29d76790049361cbbc7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 9 Oct 2023 16:53:58 -0600 Subject: [PATCH 0142/2173] Update genometools-genometools to 1.6.4 (#43560) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/genometools-genometools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genometools-genometools/meta.yaml b/recipes/genometools-genometools/meta.yaml index 8ed02a201ff04..9b54e670a7a02 100644 --- a/recipes/genometools-genometools/meta.yaml +++ b/recipes/genometools-genometools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "genometools" %} -{% set version = "1.6.3" %} -{% set sha256 = "b4919a2eafaa353a69ff4e63c788faeaa95b61bdf8d6e70e9922e0c955e95ff8" %} +{% set version = "1.6.4" %} +{% set sha256 = "eda9cf3a5d63e5017f3c315c5700b0e308c08793d5795bc889350a536369a449" %} package: name: {{ name }}-{{ name }} From 7fc3e55b9c553de95cdd91df9251f64075914795 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 9 Oct 2023 16:54:36 -0600 Subject: [PATCH 0143/2173] Update ms2query to 1.2.3 (#43570) * Update ms2query to 1.2.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/ms2query/meta.yaml | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/recipes/ms2query/meta.yaml b/recipes/ms2query/meta.yaml index ed31265502cd6..9c03dfc03553a 100644 --- a/recipes/ms2query/meta.yaml +++ b/recipes/ms2query/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ms2query" %} -{% set version = "1.2.2" %} -{% set sha256 = "752f059b999f5b3e55ab098e6bd69337cf4d9b97bf9171351e3dd29f78dbb787" %} +{% set version = "1.2.3" %} +{% set sha256 = "2111d9bb6d6b35144128f396d6141ec151b4f4d14a262de0516e3673bfd9a9f1" %} package: name: {{ name|lower }} @@ -13,13 +13,17 @@ source: build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . + entry_points: + - ms2query=ms2query:command_line + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('ms2query', max_pin="x") }} requirements: host: - - python =3.8 + - python >=3.7 run: - - python =3.8 + - python >=3.7 - matchms >=0.14.0,<=0.17.0 - spec2vec >=0.6.0 - h5py >=3.8.0 @@ -45,6 +49,7 @@ about: license: Apache-2.0 license_file: LICENSE summary: "Reliable and fast MS/MS spectral-based analogue search" + extra: identifiers: - doi:https://doi.org/10.1038/s41467-023-37446-4 From ff1383abf47465857d03c8eb47943c97fd32614b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 9 Oct 2023 16:55:09 -0600 Subject: [PATCH 0144/2173] Update phables to 1.2.1 (#43572) * Update phables to 1.2.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/phables/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/phables/meta.yaml b/recipes/phables/meta.yaml index 9c35af0accb8f..8e5ccfddad8c5 100644 --- a/recipes/phables/meta.yaml +++ b/recipes/phables/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phables" %} -{% set version = "1.2.0" %} +{% set version = "1.2.1" %} package: name: "{{ name|lower }}" @@ -7,20 +7,24 @@ package: source: url: "https://github.com/Vini2/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 09702e1e9ece66e08e0cf0430febc2d543b4e3b8dbbbad04d50315ee7220a7b6 + sha256: a533c9d841f3fb3e4eb4d7faf9b734047317806f50ab1d0568291fd60bd2d464 build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + entry_points: + - phables=phables.__main__:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('phables', max_pin="x") }} requirements: host: - - python + - python >=3.9 - pip run: - - python >=3.8,<3.11 - - snakemake >=7.14.0 + - python >=3.9 + - snakemake-minimal >=7.14.0 - pyyaml >=6.0 - click >=8.1.3 - jinja2 >=3.0.2 From 9a3020f84a051428b8a13ed2380bde6169ac1dea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 9 Oct 2023 16:55:26 -0600 Subject: [PATCH 0145/2173] Update longreadsum to 1.3.1 (#43578) * Update longreadsum to 1.3.1 * add run_exports * edit entry point --------- Co-authored-by: joshuazhuang7 --- recipes/longreadsum/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/longreadsum/meta.yaml b/recipes/longreadsum/meta.yaml index 9f8560e9bab14..904211f5314b5 100644 --- a/recipes/longreadsum/meta.yaml +++ b/recipes/longreadsum/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.3.0" %} -{% set sha256 = "9b1cf814f696364b630b014ede41f675de0c6881c5600788e381c1f43a81842e" %} +{% set version = "1.3.1" %} +{% set sha256 = "eb4c7677d43d80d19ddbac11900ae3a14efd6f2a3c4cc8bbc08e063a81e0e1df" %} package: name: longreadsum @@ -10,10 +10,12 @@ source: sha256: '{{ sha256 }}' build: - number: 1 + number: 0 skip: true # [py2k] entry_points: - longreadsum = entry_point:main + run_exports: + - {{ pin_subpackage('longreadsum', max_pin="x") }} requirements: build: @@ -32,8 +34,9 @@ requirements: - plotly test: - commands: - - longreadsum --help + commands: + - longreadsum --help + about: home: https://github.com/WGLab/LongReadSum license: MIT From cad643280ee4f9a1ce6b351b5ec24664e1c0f870 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 9 Oct 2023 16:56:08 -0600 Subject: [PATCH 0146/2173] Update abismal to 3.2.2 (#43563) * Update abismal to 3.2.2 * Update abismal: fixing issues in an autobump (#43565) --------- Co-authored-by: Andrew Smith --- recipes/abismal/build.sh | 2 +- recipes/abismal/meta.yaml | 8 ++++++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/abismal/build.sh b/recipes/abismal/build.sh index 9b16c20f01c71..66d0cf72332e6 100644 --- a/recipes/abismal/build.sh +++ b/recipes/abismal/build.sh @@ -1,4 +1,4 @@ #!/bin/bash ./configure --prefix=$PREFIX -make +make CXXFLAGS="-O3 -D_LIBCPP_DISABLE_AVAILABILITY" make install diff --git a/recipes/abismal/meta.yaml b/recipes/abismal/meta.yaml index 1469005d43a19..28deeef92addb 100644 --- a/recipes/abismal/meta.yaml +++ b/recipes/abismal/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.2.0" %} +{% set version = "3.2.2" %} package: name: abismal @@ -6,10 +6,14 @@ package: build: number: 0 + run_exports: + # abismal is currently not intended to be stable between minor versions (x.x). + - {{ pin_subpackage('abismal', max_pin="x.x") }} + source: url: https://github.com/smithlabcode/abismal/releases/download/v{{ version }}/abismal-{{ version }}.tar.gz - sha256: 338a21ea32914b8ff457addafb0fe0a750f5cb099e0a9344a9dd7a4d317d2241 + sha256: c7014da2e97e8821f4d1fca4f0618dcf5433e26db7e1cae5b6efa937da5d2ff2 requirements: build: From 7301794a3a8c64b47d81335d35f3f925dfcf54fc Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Tue, 10 Oct 2023 14:52:56 +1100 Subject: [PATCH 0147/2173] Add phytest 1.4.0 (#43359) * Add phytest 1.3.0 * Add home, doc, dev URLs * Fix typo * Update to 1.4.0 * Fix name of treetime package * Add run_exports * Update run python version * Pin different Python version * Add @Wytamma to authors * Update meta.yaml --- recipes/phytest/meta.yaml | 60 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 recipes/phytest/meta.yaml diff --git a/recipes/phytest/meta.yaml b/recipes/phytest/meta.yaml new file mode 100644 index 0000000000000..eb176ebf8ed8d --- /dev/null +++ b/recipes/phytest/meta.yaml @@ -0,0 +1,60 @@ +{% set name = "phytest" %} +{% set version = "1.4.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/phytest-{{ version }}.tar.gz + sha256: ab69c042748799a5dcac45dee972a1bde9e4c7f6bf3d4d25721826355d78de05 + +build: + entry_points: + - phytest = phytest.cli:app + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + host: + - python >=3.8,<=3.11 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.8,<=3.11 + - pytest >=7.1.1 + - pytest-sugar >=0.9.4 + - pytest-html >=3.1.1 + - typer >=0.4.1 + - biopython >=1.79 + - treetime >=0.8.6 + - scipy >=1.8.0 + - numpy >=1.22.3 + - pytest-xdist >=3.2.0 + +test: + imports: + - phytest + commands: + - pip check + - phytest --help + requires: + - pip + +about: + home: https://github.com/phytest-devs/phytest + dev_url: https://github.com/phytest-devs/phytest + doc_url: https://phytest-devs.github.io/phytest/ + summary: Quality control for phylogenetic pipelines using pytest + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - vinisalazar + - rbturnbull + - Wytamma + - smutch From fc5d1c074a852710458049ddb9d621b45718614c Mon Sep 17 00:00:00 2001 From: Travis Wrightsman Date: Tue, 10 Oct 2023 00:02:06 -0400 Subject: [PATCH 0148/2173] Enable macOS builds for AnchorWave (#43452) * Enable macOS builds for AnchorWave * Bump build number and add run_exports for Anchorwave * Use lowercase name for AnchorWave in metadata * Patch in upstream macOS-x86 support * Patch CMakeLists.txt directly Because of conda/conda-build#4241, new files aren't properly patched in with conda-build, so patch the existing CMakeLists.txt instead of adding a new one and symlinking. --- recipes/anchorwave/build.sh | 103 ++++++++++-------- recipes/anchorwave/meta.yaml | 15 ++- .../patches/01-macOS-x86-build.patch | 15 +++ 3 files changed, 84 insertions(+), 49 deletions(-) create mode 100644 recipes/anchorwave/patches/01-macOS-x86-build.patch diff --git a/recipes/anchorwave/build.sh b/recipes/anchorwave/build.sh index 0925572c39366..ce5fd2834a87c 100644 --- a/recipes/anchorwave/build.sh +++ b/recipes/anchorwave/build.sh @@ -2,48 +2,61 @@ set -eux -mkdir -p build/{sse2,sse4.1,avx2,avx512} - -# SSE2 -rm CMakeLists.txt -ln -s CMakeLists_sse2.txt CMakeLists.txt -cd build/sse2 -cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../.. -make -j"${CPU_COUNT}" -make install -mv "${PREFIX}/bin/anchorwave" "${PREFIX}/bin/anchorwave_sse2" -cd ../.. - -# SSE4.1 -rm CMakeLists.txt -ln -s CMakeLists_sse4.1.txt CMakeLists.txt -cd build/sse4.1 -cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../.. -make -j"${CPU_COUNT}" -make install -mv "${PREFIX}/bin/anchorwave" "${PREFIX}/bin/anchorwave_sse4.1" -cd ../.. - -# AVX2 -rm CMakeLists.txt -ln -s CMakeLists_avx2.txt CMakeLists.txt -cd build/avx2 -cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../.. -make -j"${CPU_COUNT}" -make install -mv "${PREFIX}/bin/anchorwave" "${PREFIX}/bin/anchorwave_avx2" -cd ../.. - -# AVX512 -rm CMakeLists.txt -ln -s CMakeLists_avx512.txt CMakeLists.txt -cd build/avx512 -cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../.. -make -j"${CPU_COUNT}" -make install -mv "${PREFIX}/bin/anchorwave" "${PREFIX}/bin/anchorwave_avx512" -cd ../.. - -# wrapper script -cp "${RECIPE_DIR}/anchorwave" "${PREFIX}/bin/anchorwave" -chmod +x "${PREFIX}/bin/anchorwave" +if [ $TARGET_PLATFORM = "Linux" ]; then + mkdir -p build/{sse2,sse4.1,avx2,avx512} + + # SSE2 + rm CMakeLists.txt + ln -s CMakeLists_sse2.txt CMakeLists.txt + cd build/sse2 + cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../.. + make -j"${CPU_COUNT}" + make install + mv "${PREFIX}/bin/anchorwave" "${PREFIX}/bin/anchorwave_sse2" + cd ../.. + + # SSE4.1 + rm CMakeLists.txt + ln -s CMakeLists_sse4.1.txt CMakeLists.txt + cd build/sse4.1 + cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../.. + make -j"${CPU_COUNT}" + make install + mv "${PREFIX}/bin/anchorwave" "${PREFIX}/bin/anchorwave_sse4.1" + cd ../.. + + # AVX2 + rm CMakeLists.txt + ln -s CMakeLists_avx2.txt CMakeLists.txt + cd build/avx2 + cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../.. + make -j"${CPU_COUNT}" + make install + mv "${PREFIX}/bin/anchorwave" "${PREFIX}/bin/anchorwave_avx2" + cd ../.. + + # AVX512 + rm CMakeLists.txt + ln -s CMakeLists_avx512.txt CMakeLists.txt + cd build/avx512 + cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../.. + make -j"${CPU_COUNT}" + make install + mv "${PREFIX}/bin/anchorwave" "${PREFIX}/bin/anchorwave_avx512" + cd ../.. + + # wrapper script + cp "${RECIPE_DIR}/anchorwave" "${PREFIX}/bin/anchorwave" + chmod +x "${PREFIX}/bin/anchorwave" +elif [ $TARGET_PLATFORM = "macOS" ]; then + mkdir -p build/macOS + + # macOS (SSE4.1) + cd build/macOS + cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../.. + make -j"${CPU_COUNT}" + make install +else + echo "TARGET_PLATFORM must be Linux or macOS" >&2 + exit 1 +fi diff --git a/recipes/anchorwave/meta.yaml b/recipes/anchorwave/meta.yaml index d6e7839e1000a..6d75ce665ccbe 100644 --- a/recipes/anchorwave/meta.yaml +++ b/recipes/anchorwave/meta.yaml @@ -1,19 +1,26 @@ -{% set name = "AnchorWave" %} +{% set name = "anchorwave" %} {% set version = "1.2.1" %} {% set tag = "v1.2.1" %} {% set sha256 = "0e64f7b62579bbf9106a7a2f13330b8e16846176d6423db648d79b74b3dff2e7" %} package: - name: {{ name | lower }} + name: {{ name }} version: {{ version }} source: url: https://github.com/baoxingsong/AnchorWave/archive/refs/tags/{{ tag }}.tar.gz sha256: {{ sha256 }} + patches: + - patches/01-macOS-x86-build.patch # [osx] build: - number: 1 - skip: True # [not linux] + number: 2 + script_env: + - TARGET_PLATFORM=macOS # [osx] + - TARGET_PLATFORM=Linux # [linux] + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + skip: True # [not unix] requirements: build: diff --git a/recipes/anchorwave/patches/01-macOS-x86-build.patch b/recipes/anchorwave/patches/01-macOS-x86-build.patch new file mode 100644 index 0000000000000..1bafbaba2dc15 --- /dev/null +++ b/recipes/anchorwave/patches/01-macOS-x86-build.patch @@ -0,0 +1,15 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index f94dda8..c9f52c3 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -12,8 +12,8 @@ set(CMAKE_CXX_STANDARD 14) + + find_package(ZLIB) + +-set(CMAKE_CXX_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -msse4.1 -msse4.2 -I ./ -std=gnu++14 -pthread -lrt") # the -mavx* is for GNU compiler and xCORE* are for intel compiler +-set(CMAKE_C_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -msse4.1 -msse4.2 -I ./ -pthread -lrt") ++set(CMAKE_CXX_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -msse4.1 -msse4.2 -I ./ -std=gnu++14 -pthread") # the -mavx* is for GNU compiler and xCORE* are for intel compiler ++set(CMAKE_C_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -msse4.1 -msse4.2 -I ./ -pthread") + + + #for google unit test From 2fd020d3dae78e692314f90575b2053da3212001 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 9 Oct 2023 22:35:35 -0600 Subject: [PATCH 0149/2173] Update phytest to 1.4.1 (#43585) --- recipes/phytest/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phytest/meta.yaml b/recipes/phytest/meta.yaml index eb176ebf8ed8d..71fb8bfd5bca3 100644 --- a/recipes/phytest/meta.yaml +++ b/recipes/phytest/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phytest" %} -{% set version = "1.4.0" %} +{% set version = "1.4.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/phytest-{{ version }}.tar.gz - sha256: ab69c042748799a5dcac45dee972a1bde9e4c7f6bf3d4d25721826355d78de05 + sha256: a4083778922020f317efd02474a35dcb822df6451b6e9a6e9350bb1c1ce336a2 build: entry_points: From 80351c6826a89a0a3762ad38c53e8624ff897274 Mon Sep 17 00:00:00 2001 From: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com> Date: Tue, 10 Oct 2023 09:50:25 +0200 Subject: [PATCH 0150/2173] Add modkit (Oxford Nanopore) (#43580) * Add recipe for ONT modkit v0.2.0 * Add run_exports statement according to PR docs. --------- Co-authored-by: Matthias Zepper --- recipes/ont-modkit/build.sh | 10 +++++++++ recipes/ont-modkit/meta.yaml | 40 ++++++++++++++++++++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 recipes/ont-modkit/build.sh create mode 100644 recipes/ont-modkit/meta.yaml diff --git a/recipes/ont-modkit/build.sh b/recipes/ont-modkit/build.sh new file mode 100644 index 0000000000000..5c4efc2ca83d4 --- /dev/null +++ b/recipes/ont-modkit/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash -euo +export CFLAGS="${CFLAGS} -fcommon" +export CXXFLAGS="${CFLAGS} -fcommon" + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . \ No newline at end of file diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml new file mode 100644 index 0000000000000..98c62caaf3178 --- /dev/null +++ b/recipes/ont-modkit/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "0.2.0" %} +{% set sha256 = "bb9970c5fb9ef2387d01c92078df0b6723c331d600567a6b6b9e011bdfbbdd97" %} + +package: + name: ont-modkit + version: {{ version }} + +source: + url: https://github.com/nanoporetech/modkit/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("ont-modkit", max_pin="x") }} + +requirements: + build: + - rust >=1.40 + - cmake + - make + - autoconf + - {{ compiler('cxx') }} + - pkg-config + - zlib + host: + - zlib + run: + + +test: + commands: + - modkit --version + +about: + home: https://github.com/nanoporetech/modkit + license: Oxford Nanopore Technologies PLC. Public License Version 1.0 + license_family: PROPRIETARY + license_file: LICENCE.txt + summary: A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data. From c72a7936d3dee9963a4be277f86fe7e427a571d6 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 10 Oct 2023 02:50:43 -0500 Subject: [PATCH 0151/2173] Update rmblast to 2.14.1 (#43583) --- ...mblast.patch => isb-2.14.1+-rmblast.patch} | 74 ++++++++++--------- recipes/rmblast/meta.yaml | 12 +-- 2 files changed, 48 insertions(+), 38 deletions(-) rename recipes/rmblast/{isb-2.14.0+-rmblast.patch => isb-2.14.1+-rmblast.patch} (96%) diff --git a/recipes/rmblast/isb-2.14.0+-rmblast.patch b/recipes/rmblast/isb-2.14.1+-rmblast.patch similarity index 96% rename from recipes/rmblast/isb-2.14.0+-rmblast.patch rename to recipes/rmblast/isb-2.14.1+-rmblast.patch index 9faf2dde9d66a..89d516ae3d55f 100644 --- a/recipes/rmblast/isb-2.14.0+-rmblast.patch +++ b/recipes/rmblast/isb-2.14.1+-rmblast.patch @@ -1,5 +1,5 @@ --- a/c++/include/algo/blast/blastinput/rmblastn_args.hpp 2011-02-09 06:37:10.000000000 -0800 -+++ b/c++/include/algo/blast/blastinput/rmblastn_args.hpp 2023-05-02 11:58:12.572972917 -0700 ++++ b/c++/include/algo/blast/blastinput/rmblastn_args.hpp 2023-08-24 15:48:58.352822168 -0700 @@ -32,13 +32,44 @@ public: virtual int GetQueryBatchSize() const; @@ -46,8 +46,16 @@ END_SCOPE(blast) END_NCBI_SCOPE --- a/c++/src/algo/blast/blastinput/rmblastn_args.cpp 2016-05-04 07:59:01.000000000 -0700 -+++ b/c++/src/algo/blast/blastinput/rmblastn_args.cpp 2023-05-02 11:58:12.572972917 -0700 -@@ -88,7 +88,7 @@ CRMBlastnAppArgs::CRMBlastnAppArgs() ++++ b/c++/src/algo/blast/blastinput/rmblastn_args.cpp 2023-08-24 15:48:58.352822168 -0700 +@@ -44,6 +44,7 @@ CRMBlastnAppArgs::CRMBlastnAppArgs() + m_Args.push_back(arg); + + m_BlastDbArgs.Reset(new CBlastDatabaseArgs); ++ m_BlastDbArgs->SetDatabaseMaskingSupport(true); + arg.Reset(m_BlastDbArgs); + m_Args.push_back(arg); + +@@ -88,7 +89,7 @@ CRMBlastnAppArgs::CRMBlastnAppArgs() arg.Reset(m_FormattingArgs); m_Args.push_back(arg); @@ -56,7 +64,7 @@ arg.Reset(m_MTArgs); m_Args.push_back(arg); -@@ -101,19 +101,62 @@ CRMBlastnAppArgs::CRMBlastnAppArgs() +@@ -101,19 +102,62 @@ CRMBlastnAppArgs::CRMBlastnAppArgs() m_Args.push_back(arg); } @@ -124,9 +132,9 @@ } END_SCOPE(blast) ---- a/c++/src/algo/blast/format/blast_format.cpp 2023-03-09 08:46:25.000000000 -0800 -+++ b/c++/src/algo/blast/format/blast_format.cpp 2023-05-02 11:58:12.573972897 -0700 -@@ -2496,18 +2496,6 @@ void CBlastFormat::LogBlastSearchInfo(CB +--- a/c++/src/algo/blast/format/blast_format.cpp 2023-04-25 10:14:39.000000000 -0700 ++++ b/c++/src/algo/blast/format/blast_format.cpp 2023-08-24 15:48:58.353822148 -0700 +@@ -2494,18 +2494,6 @@ void CBlastFormat::LogBlastSearchInfo(CB } } else { @@ -146,7 +154,7 @@ report.AddParam(CBlastUsageReport::eDBNumSeqs, num_seqs); report.AddParam(CBlastUsageReport::eDBDate, m_DbInfo[0].date); --- a/c++/src/algo/blast/core/blast_stat.c 2021-06-21 12:27:23.000000000 -0700 -+++ b/c++/src/algo/blast/core/blast_stat.c 2023-05-02 11:58:12.574972876 -0700 ++++ b/c++/src/algo/blast/core/blast_stat.c 2023-08-24 15:48:58.354822127 -0700 @@ -85,7 +85,6 @@ typedef struct MatrixInfo { Int4 max_number_values; /**< number of values (e.g., BLOSUM90_VALUES_MAX). */ } MatrixInfo; @@ -339,9 +347,9 @@ /** Read in the matrix from the FILE *fp. * This function ASSUMES that the matrices are in the ncbistdaa * @param sbp the BlastScoreBlk with the matrix to be populated [in|out] ---- a/c++/src/app/blast/blast_app_util.cpp 2023-03-09 10:35:34.000000000 -0800 -+++ b/c++/src/app/blast/blast_app_util.cpp 2023-05-02 11:58:12.575972856 -0700 -@@ -950,12 +950,6 @@ void LogCmdOptions(blast::CBlastUsageRep +--- a/c++/src/app/blast/blast_app_util.cpp 2023-05-02 06:55:28.000000000 -0700 ++++ b/c++/src/app/blast/blast_app_util.cpp 2023-08-24 15:48:58.354822127 -0700 +@@ -957,12 +957,6 @@ void LogCmdOptions(blast::CBlastUsageRep args.GetBlastDatabaseArgs()->GetSearchDatabase()->GetSeqDb().NotEmpty()) { CRef db = args.GetBlastDatabaseArgs()->GetSearchDatabase()->GetSeqDb(); @@ -354,8 +362,8 @@ report.AddParam(CBlastUsageReport::eDBLength, (Int8) db->GetTotalLength()); report.AddParam(CBlastUsageReport::eDBNumSeqs, db->GetNumSeqs()); report.AddParam(CBlastUsageReport::eDBDate, db->GetDate()); ---- a/c++/src/app/blastdb/blastdbcmd.cpp 2023-01-04 06:29:24.000000000 -0800 -+++ b/c++/src/app/blastdb/blastdbcmd.cpp 2023-05-02 11:58:12.575972856 -0700 +--- a/c++/src/app/blastdb/blastdbcmd.cpp 2022-11-08 11:47:48.000000000 -0800 ++++ b/c++/src/app/blastdb/blastdbcmd.cpp 2023-08-24 15:48:58.355822107 -0700 @@ -1239,21 +1239,6 @@ void CBlastDBCmdApp::x_AddCmdOptions() m_UsageReport.AddParam(CBlastUsageReport::eOutputFmt, args["outfmt"].AsString()); } @@ -379,7 +387,7 @@ m_UsageReport.AddParam(CBlastUsageReport::eDBNumSeqs, m_BlastDb->GetNumSeqs()); m_UsageReport.AddParam(CBlastUsageReport::eDBDate, m_BlastDb->GetDate()); --- a/c++/src/app/rmblastn/CMakeLists.rmblastn.app.txt 1969-12-31 16:00:00.000000000 -0800 -+++ b/c++/src/app/rmblastn/CMakeLists.rmblastn.app.txt 2023-05-02 11:58:12.576972835 -0700 ++++ b/c++/src/app/rmblastn/CMakeLists.rmblastn.app.txt 2023-08-24 15:48:58.355822107 -0700 @@ -0,0 +1,10 @@ +# Derived from CMakeLists.blastn.app.txt 626054 2021-02-23 17:13:18Z fongah2 + @@ -392,7 +400,7 @@ +NCBI_end_app() + --- a/c++/src/app/rmblastn/Makefile.in 1969-12-31 16:00:00.000000000 -0800 -+++ b/c++/src/app/rmblastn/Makefile.in 2023-05-02 11:58:12.576972835 -0700 ++++ b/c++/src/app/rmblastn/Makefile.in 2023-08-24 15:48:58.355822107 -0700 @@ -0,0 +1,13 @@ +# Meta-makefile("APP" project) +################################# @@ -408,7 +416,7 @@ +rmblastn: lib + ${MAKE} ${MFLAGS} -f Makefile.rmblastn_app --- a/c++/src/app/rmblastn/Makefile.rmblastn.app 1969-12-31 16:00:00.000000000 -0800 -+++ b/c++/src/app/rmblastn/Makefile.rmblastn.app 2023-05-02 11:58:12.576972835 -0700 ++++ b/c++/src/app/rmblastn/Makefile.rmblastn.app 2023-08-24 15:48:58.356822087 -0700 @@ -0,0 +1,17 @@ +APP = rmblastn +SRC = rmblastn_node rmblastn_app @@ -428,7 +436,7 @@ + +PROJ_TAG = gbench --- a/c++/src/app/rmblastn/rmblastn_app.cpp 1969-12-31 16:00:00.000000000 -0800 -+++ b/c++/src/app/rmblastn/rmblastn_app.cpp 2023-05-02 11:58:12.576972835 -0700 ++++ b/c++/src/app/rmblastn/rmblastn_app.cpp 2023-08-24 15:48:58.356822087 -0700 @@ -0,0 +1,394 @@ +/* $Id: blastn_app.cpp 634685 2021-07-16 13:42:53Z fongah2 $ + * =========================================================================== @@ -825,7 +833,7 @@ +} +#endif /* SKIP_DOXYGEN_PROCESSING */ --- a/c++/src/app/rmblastn/rmblastn_node.cpp 1969-12-31 16:00:00.000000000 -0800 -+++ b/c++/src/app/rmblastn/rmblastn_node.cpp 2023-05-02 11:58:12.577972815 -0700 ++++ b/c++/src/app/rmblastn/rmblastn_node.cpp 2023-08-24 15:48:58.356822087 -0700 @@ -0,0 +1,245 @@ +/* $Id: + * =========================================================================== @@ -1073,7 +1081,7 @@ +} + --- a/c++/src/app/rmblastn/rmblastn_node.hpp 1969-12-31 16:00:00.000000000 -0800 -+++ b/c++/src/app/rmblastn/rmblastn_node.hpp 2023-05-02 11:58:12.577972815 -0700 ++++ b/c++/src/app/rmblastn/rmblastn_node.hpp 2023-08-24 15:48:58.356822087 -0700 @@ -0,0 +1,62 @@ +/* $Id: + * =========================================================================== @@ -1138,7 +1146,7 @@ + +#endif /* APP__RMBLASTN_NODE__HPP */ --- a/c++/src/connect/ncbi_usage_report.cpp 2022-07-27 20:36:37.000000000 -0700 -+++ b/c++/src/connect/ncbi_usage_report.cpp 2023-05-02 14:34:10.306661145 -0700 ++++ b/c++/src/connect/ncbi_usage_report.cpp 2023-08-24 15:48:58.357822066 -0700 @@ -46,7 +46,7 @@ BEGIN_NCBI_SCOPE // All parameters can be redefined in the configuration file. @@ -1164,8 +1172,8 @@ return "MSWIN"; // Windows #elif defined(__CYGWIN__) return "CYGWIN"; // Windows (Cygwin POSIX under Microsoft Windows) ---- a/c++/src/objtools/align_format/showalign.cpp 2021-06-10 08:55:25.000000000 -0700 -+++ b/c++/src/objtools/align_format/showalign.cpp 2023-05-02 11:58:12.579972774 -0700 +--- a/c++/src/objtools/align_format/showalign.cpp 2023-03-06 10:09:11.000000000 -0800 ++++ b/c++/src/objtools/align_format/showalign.cpp 2023-08-24 15:48:58.358822046 -0700 @@ -1787,11 +1787,31 @@ void CDisplaySeqalign::x_PrepareIdentity aln_vec_info->positive = 0; aln_vec_info->gap = 0; @@ -1448,7 +1456,7 @@ { out<<" Score = "< #include @@ -1546,8 +1554,8 @@ Blast_PerrorWithLocation(blast_message, status, kBlastMessageNoContext); return status; } ---- a/c++/src/objtools/align_format/tabular.cpp 2023-02-23 06:48:07.000000000 -0800 -+++ b/c++/src/objtools/align_format/tabular.cpp 2023-05-02 11:58:12.580972753 -0700 +--- a/c++/src/objtools/align_format/tabular.cpp 2023-04-10 11:34:52.000000000 -0700 ++++ b/c++/src/objtools/align_format/tabular.cpp 2023-08-24 15:48:58.360822005 -0700 @@ -971,7 +971,11 @@ int CBlastTabularInfo::SetFields(const C x_IsFieldRequested(eBTOP) || (x_IsFieldRequested(eNumIdentical) && !kNoFetchSequence) || @@ -1847,7 +1855,7 @@ x_PrintNumPositives(); break; case eGapOpenings: --- a/c++/include/objtools/align_format/tabular.hpp 2021-09-16 08:24:06.000000000 -0700 -+++ b/c++/include/objtools/align_format/tabular.hpp 2023-05-02 11:58:12.581972733 -0700 ++++ b/c++/include/objtools/align_format/tabular.hpp 2023-08-24 15:48:58.360822005 -0700 @@ -135,6 +135,18 @@ public: void SetCustomDelim(string customDelim) { x_SetFieldDelimiter(eCustom,customDelim); @@ -1953,7 +1961,7 @@ { m_NoFetch = nofetch; --- a/c++/src/objtools/align_format/format_flags.cpp 2018-10-23 07:28:28.000000000 -0700 -+++ b/c++/src/objtools/align_format/format_flags.cpp 2023-05-02 11:58:12.581972733 -0700 ++++ b/c++/src/objtools/align_format/format_flags.cpp 2023-08-24 15:48:58.361821984 -0700 @@ -40,7 +40,7 @@ string kDfltArgTabularOutputFmt = "evalue bitscore"; const string kDfltArgTabularOutputFmtTag("std"); @@ -1997,7 +2005,7 @@ "Number of positive-scoring matches", ePositives), --- a/c++/include/objtools/align_format/format_flags.hpp 2018-10-23 07:27:09.000000000 -0700 -+++ b/c++/include/objtools/align_format/format_flags.hpp 2023-05-02 11:58:12.581972733 -0700 ++++ b/c++/include/objtools/align_format/format_flags.hpp 2023-08-24 15:48:58.361821984 -0700 @@ -114,6 +114,16 @@ enum ETabularField { ePercentIdentical, ///< Percentage of identical matches eNumIdentical, ///< Number of identical matches @@ -2016,7 +2024,7 @@ eGapOpenings, ///< Number of gap openings eGaps, ///< Total number of gaps --- a/c++/include/algo/blast/api/blast_exception.hpp 2018-11-27 10:22:00.000000000 -0800 -+++ b/c++/include/algo/blast/api/blast_exception.hpp 2023-05-02 11:58:12.581972733 -0700 ++++ b/c++/include/algo/blast/api/blast_exception.hpp 2023-08-24 15:48:58.362821964 -0700 @@ -83,7 +83,8 @@ public: eSeqSrcInit, ///< Initialization error in BlastSeqSrc /// implementation @@ -2036,7 +2044,7 @@ } } --- a/c++/src/algo/blast/api/blast_setup.hpp 2016-10-17 12:00:07.000000000 -0700 -+++ b/c++/src/algo/blast/api/blast_setup.hpp 2023-05-02 11:58:12.582972712 -0700 ++++ b/c++/src/algo/blast/api/blast_setup.hpp 2023-08-24 15:48:58.362821964 -0700 @@ -192,7 +192,10 @@ public: TSeqPos size() const { TSeqPos retval = x_Size(); @@ -2050,7 +2058,7 @@ } return retval; --- a/c++/src/algo/blast/api/blast_setup_cxx.cpp 2021-05-07 05:10:35.000000000 -0700 -+++ b/c++/src/algo/blast/api/blast_setup_cxx.cpp 2023-05-02 11:58:12.582972712 -0700 ++++ b/c++/src/algo/blast/api/blast_setup_cxx.cpp 2023-08-24 15:48:58.362821964 -0700 @@ -628,7 +628,14 @@ SetupQueries_OMF(IBlastQuerySource& quer // s_AddMask releases the elements of frame_to_bsl that it uses; // the rest are freed by frame_to_bsl in the destructor. @@ -2077,7 +2085,7 @@ } --- a/c++/src/algo/blast/core/blast_hits.c 2019-10-09 04:00:47.000000000 -0700 -+++ b/c++/src/algo/blast/core/blast_hits.c 2023-05-02 14:01:27.637227311 -0700 ++++ b/c++/src/algo/blast/core/blast_hits.c 2023-08-24 15:48:58.363821943 -0700 @@ -3452,7 +3452,9 @@ static int s_SortHspWrapRawScore(const v if (wrap1->hsp->score < wrap2->hsp->score) return 1; diff --git a/recipes/rmblast/meta.yaml b/recipes/rmblast/meta.yaml index fbeee64e82fcb..423e85e5dfe61 100644 --- a/recipes/rmblast/meta.yaml +++ b/recipes/rmblast/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RMBlast" %} -{% set version = "2.14.0" %} -{% set sha256 = "bf477f1b0c3b82f0b7a7094bf003a9a83e37e3b0716c1df799060c4feab17500" %} +{% set version = "2.14.1" %} +{% set sha256 = "712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e" %} package: name: {{ name|lower }} @@ -11,14 +11,16 @@ source: sha256: {{ sha256 }} patches: #- isb-{{ version }}+-{{ name }}.patch # Needs the -p1 option, applied in build.sh - # patch taken from http://www.repeatmasker.org/rmblast/isb-2.14.0+-rmblast.patch.gz - - isb-2.14.0+-rmblast.patch + # patch taken from http://www.repeatmasker.org/rmblast/isb-2.14.1+-rmblast.patch.gz + - isb-2.14.1+-rmblast.patch - configurellvm.patch - get_species_taxids.patch - phonehome.patch build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('rmblast', max_pin="x") }} requirements: build: From 12112d16041d652611f015804d1a772a02b52591 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 10 Oct 2023 01:51:50 -0600 Subject: [PATCH 0152/2173] Update mehari to 0.12.0 (#43575) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index ba1bd171afa48..03f4a64f50319 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.11.0" %} -{% set sha256 = "58b36ce9d7fb3e2a8a012e3d8275513f15148d05fbf5aa414ed32006a54483a5" %} +{% set version = "0.12.0" %} +{% set sha256 = "793e5719f00faa20ce0fb4ecf8a682432e058777ff357116f9f67964c8b6dc2c" %} package: name: mehari From 63ff2e6f58023fc6ca66582438d0ed7f78729fb6 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Tue, 10 Oct 2023 11:31:03 +0100 Subject: [PATCH 0153/2173] Update dev version ms2pip (#43545) * Update dev version ms2pip Update to development version of ms2pip needed by #43487 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml remove noarch * Update meta.yaml add spectrum_utils only in linux. * Update meta.yaml --- recipes/ms2pip/meta.yaml | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/recipes/ms2pip/meta.yaml b/recipes/ms2pip/meta.yaml index b3378d4e50f80..975bda9d85d11 100644 --- a/recipes/ms2pip/meta.yaml +++ b/recipes/ms2pip/meta.yaml @@ -1,5 +1,6 @@ -{% set version = "3.11.0" %} -{% set sha256 = "38feec7962a6b56d15f310df0dbfe7bbb3c88ab8beb4f183e8048e7e2cefa7dd" %} +{% set version = "4.0.0.dev4" %} +{% set name = "ms2pip" %} +{% set sha256 = "3342bca48d5163a2fc833065ef1fc43bd349eb3ea32239fb8b74bc759b98ea3d" %} package: name: "ms2pip" @@ -10,8 +11,10 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 0 skip: True # [py < 37] + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} entry_points: - ms2pip=ms2pip.__main__:main - fasta2speclib=fasta2speclib.fasta2speclib:main @@ -27,10 +30,10 @@ requirements: - cython >=0.29.2,<1 - numpy - pip - - python + - python >=3.8 + - spectrum_utils >=0.4 # [linux] run: - - python - - biopython >=1.74 + - python >=3.8 - {{ pin_compatible('numpy') }} - pandas >=1.0 - pyteomics >=3.5 @@ -40,10 +43,12 @@ requirements: - click >=7 - xgboost >=1.3 - matplotlib-base >=3.0 - - spectrum_utils >=0.3.5 - lxml >=4 - rich >=13 - - pydantic >=1.10 + - pydantic >=1.10,<2 + - psm-utils + - werkzeug >=2 + - pyarrow test: imports: From 6baa7d0f28d0311f29a18da01720cd0780a1c8f3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 10 Oct 2023 05:02:55 -0600 Subject: [PATCH 0154/2173] Update delly to 1.1.8 (#43592) --- recipes/delly/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/delly/meta.yaml b/recipes/delly/meta.yaml index 900efd110931b..89b9485cd2e33 100644 --- a/recipes/delly/meta.yaml +++ b/recipes/delly/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.7" %} -{% set sha256 = "4e5ad12a5e31b40290c1bd732910eab18c7604de13301bc37e40238dc893e5c6" %} +{% set version = "1.1.8" %} +{% set sha256 = "f72a1143dc71449fc277fc8b3e337a4d35b2fe736f3693a14b1986efa8da4889" %} package: name: delly From a2e2df149ed32df02ed2ceb250156b8303d344ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ga=C3=ABtan=20BENOIT?= <79975313+GaetanBenoitDev@users.noreply.github.com> Date: Tue, 10 Oct 2023 21:38:03 +0200 Subject: [PATCH 0155/2173] Add metaMDBG v0.3 (#43354) * Add metaMDBG v0.3 * fix issues * fix issues * fix issues * fix issues * fix issues * fix issues * fix issues * fix issues * fix issues * fix issues * fix issues --------- Co-authored-by: GaetanBenoitDev --- recipes/metamdbg/build.sh | 14 +++++++++++++ recipes/metamdbg/meta.yaml | 41 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 recipes/metamdbg/build.sh create mode 100644 recipes/metamdbg/meta.yaml diff --git a/recipes/metamdbg/build.sh b/recipes/metamdbg/build.sh new file mode 100644 index 0000000000000..6ca4ef93a91f9 --- /dev/null +++ b/recipes/metamdbg/build.sh @@ -0,0 +1,14 @@ +#!/bin/bash + + +mkdir -p $PREFIX/bin + +export CPATH=${PREFIX}/include + +mkdir build +cd build +cmake .. + +make + +cp ./bin/metaMDBG $PREFIX/bin diff --git a/recipes/metamdbg/meta.yaml b/recipes/metamdbg/meta.yaml new file mode 100644 index 0000000000000..7316c6c86c897 --- /dev/null +++ b/recipes/metamdbg/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "0.3" %} + +package: + name: metamdbg + version: {{ version }} + +source: + url: https://github.com/GaetanBenoitDev/metaMDBG/archive/refs/tags/metaMDBG-{{ version }}.tar.gz + sha256: 24b34fcc7416b44081963a470059209c7f0592bd597a25388a94dae5edb2b09d + +build: + skip: True # [osx] + number: 0 + run_exports: + - {{ pin_subpackage('metamdbg', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - cmake + - make + host: + - zlib + - openmp + run: + - zlib + - openmp + - wfmash =0.8.2 + - samtools =1.6 + - minimap2 =2.24 + - gsl =2.7 =he838d99_0 + +test: + commands: + - metaMDBG 2>&1 | grep 'Usage' + +about: + home: https://github.com/GaetanBenoitDev/metaMDBG + license: MIT + summary: 'MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.' + From 0bee68f4a0f0dd81e1fb5358a870a35fad9d082c Mon Sep 17 00:00:00 2001 From: Adam Caprez Date: Tue, 10 Oct 2023 15:14:42 -0500 Subject: [PATCH 0156/2173] Add recipe for pythoncyc 2.0.2. (#43602) --- recipes/pythoncyc/meta.yaml | 43 +++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 recipes/pythoncyc/meta.yaml diff --git a/recipes/pythoncyc/meta.yaml b/recipes/pythoncyc/meta.yaml new file mode 100644 index 0000000000000..79bd9ac6ca10b --- /dev/null +++ b/recipes/pythoncyc/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "pythoncyc" %} +{% set version = "2.0.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/PythonCyc-{{ version }}.tar.gz + sha256: 05cb733ab7890eaf960f31cd289d59eca6f24bb154ed48052158041e68f7e4f7 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv + number: 0 + run_exports: + - {{ pin_subpackage('pythoncyc', max_pin="x") }} + +requirements: + host: + - python >=3.0 + - pip + run: + - python >=3.0 + +test: + imports: + - pythoncyc + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/networkbiolab/PythonCyc + summary: A Python interface to Pathway Tools, 2019 update + dev_url: https://github.com/networkbiolab/PythonCyc + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - acaprez From 4e2bf08c0206f82331aacfd497b4798a34883bc5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 10 Oct 2023 14:15:10 -0600 Subject: [PATCH 0157/2173] Update pybiolib to 1.1.1367 (#43598) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index dd87eee8a3fe8..3c528fb4ca9da 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1360" %} +{% set version = "1.1.1367" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: d318f89a85e0281bd5eb904a89543109ab9d3106232c54dc7290523a61500d94 + sha256: f8bd06b4e0314f4e179dbaa5a9710ebcdd82373be2987d5a32814b1ec6c51019 build: noarch: python From 62ead91374c54a75f0b2c10f7db1227a22e6a40e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 10 Oct 2023 14:19:59 -0600 Subject: [PATCH 0158/2173] Update hifiasm to 0.19.7 (#43600) * Update hifiasm to 0.19.7 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/hifiasm/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/hifiasm/meta.yaml b/recipes/hifiasm/meta.yaml index 618485fbbd2c2..13e47d1eabfc2 100644 --- a/recipes/hifiasm/meta.yaml +++ b/recipes/hifiasm/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.19.6" %} +{% set version = "0.19.7" %} package: name: hifiasm @@ -6,10 +6,12 @@ package: source: url: https://github.com/chhylp123/hifiasm/archive/{{ version }}.tar.gz - sha256: 9a0d99f80759f759f9156f506defa13125610e5a7746e8d11c20fdc95537f344 + sha256: 16d6127c7efb2d450630f25402a05e7d691b411465b304950d84d8afd53d5ee6 build: number: 0 + run_exports: + - {{ pin_subpackage('hifiasm', max_pin="x") }} requirements: build: @@ -26,4 +28,6 @@ test: about: home: https://github.com/chhylp123/hifiasm license: MIT + license_family: MIT summary: 'Haplotype-resolved assembler for accurate Hifi reads' + doc_url: https://hifiasm.readthedocs.io/en/latest/index.html From 983ffe3f84704e191dbe5297e30e5397d0afe654 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 10 Oct 2023 15:51:13 -0600 Subject: [PATCH 0159/2173] Update rrmscorer to 1.0.9 (#43595) * Update rrmscorer to 1.0.9 * add run_exports * add seaborn --------- Co-authored-by: joshuazhuang7 --- recipes/rrmscorer/meta.yaml | 30 ++++++++++++++++++------------ 1 file changed, 18 insertions(+), 12 deletions(-) diff --git a/recipes/rrmscorer/meta.yaml b/recipes/rrmscorer/meta.yaml index ffb6879b5e311..2ff2cab297ffa 100644 --- a/recipes/rrmscorer/meta.yaml +++ b/recipes/rrmscorer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "rrmscorer" %} -{% set version = "1.0.8" %} +{% set version = "1.0.9" %} package: name: "{{ name|lower }}" @@ -7,27 +7,32 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 6df8179adaf0ac0b6a6ff48cd9eab92e2e7b78df21bdc2f22cedc9db67cf8fea + sha256: 2058ec1af72ff6ed0d026a643d0358c3e06f7cdb25615bba66b05554df2d76fa build: noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" number: 0 + entry_points: + - rrmscorer=rrmscorer.__main__:main + run_exports: + - {{ pin_subpackage('rrmscorer', max_pin="x") }} requirements: host: - pip - python >=3.9 run: - - biopython ==1.79 + - biopython - hmmer - - logomaker ==0.8 + - logomaker - matplotlib-base - - numpy ==1.22.3 - - pandas ==1.4.2 + - numpy + - pandas - python >=3.9 - - requests ==2.28.2 - - scikit-learn ==1.1.1 + - requests + - scikit-learn + - seaborn test: commands: @@ -43,9 +48,9 @@ about: dev_url: https://bitbucket.org/bio2byte/rrmscorer/ doc_url: https://pypi.org/project/rrmscorer doc_source_url: https://bitbucket.org/bio2byte/rrmscorer/raw/master/readme.md - license: "GNU General Public v3 (GPLv3)" - license_family: GPL3 - license_file: + license: MIT + license_family: MIT + license_file: LICENSE summary: "RRMScorer (RRM-RNA score predictor) predicts how likely a single RRM is to bind ssRNA" description: | RRMScorer (RRM-RNA score predictor) allows the user to easily predict @@ -63,6 +68,7 @@ about: the Marie Skłodowska-Curie grant agreement No. 813239. Wim Vranken, Bio2Byte group within the RNAct project, VUB, Belgium. + extra: recipe-maintainers: - JoelRoca From fa8e607afaaff5c14fb05722fc2e7c832d28a035 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 10 Oct 2023 15:51:30 -0600 Subject: [PATCH 0160/2173] Update bayescode to 1.3.1 (#43588) * Update bayescode to 1.3.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/bayescode/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/bayescode/meta.yaml b/recipes/bayescode/meta.yaml index 3f669c693c82a..85a836c0a1394 100644 --- a/recipes/bayescode/meta.yaml +++ b/recipes/bayescode/meta.yaml @@ -1,12 +1,14 @@ -{% set version = "1.3.0" %} -{% set sha256 = "cf3a7b0541f6d79ca496ace29db3bea95f9a67f5a32ba42dde835f4c43aea72b" %} +{% set version = "1.3.1" %} +{% set sha256 = "d96b0d193eba18b5264851c5e64648bd4a4c57ffd44f14d66ef74d15408d7e8b" %} package: name: bayescode - version: {{ version }} + version: {{ version }} build: number: 0 + run_exports: + - {{ pin_subpackage('bayescode', max_pin="x") }} source: url: https://github.com/ThibaultLatrille/bayescode/archive/refs/tags/v{{ version }}.tar.gz @@ -18,13 +20,13 @@ requirements: - cmake - {{ compiler('c') }} - {{ compiler('cxx') }} - host: run: - python >=3.6 - numpy - pandas - ete3 - matplotlib-base + test: commands: - fasta_to_ali.py --help @@ -45,5 +47,6 @@ test: about: home: https://github.com/ThibaultLatrille/bayescode license: MIT + license_family: MIT license_file: License.MD summary: Mutation-Selection phylogenetic codon models to detect site-specific adaptive evolution or to infer long-term effective population size From 905defe057ef718a886b0c9c82f6fe812e176649 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 10 Oct 2023 15:58:20 -0600 Subject: [PATCH 0161/2173] Update r-acidbase to 0.7.1 (#43534) Co-authored-by: Michael Steinbaugh --- recipes/r-acidbase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidbase/meta.yaml b/recipes/r-acidbase/meta.yaml index 759b3fc4cb480..c37758af63053 100644 --- a/recipes/r-acidbase/meta.yaml +++ b/recipes/r-acidbase/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} {% set github = "https://github.com/acidgenomics/r-acidbase" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: ba31722ee78b25517c856c151e4a5d39392592843f2ccb105ad1736dcfd5c86b + sha256: 2237473f0b4577fd74266017940aeb0eb305812ba145ae7c56f1f821ebe10854 build: number: 0 From 45133625cab5534fdad9efe90478dd35ada15c31 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 10 Oct 2023 17:07:47 -0600 Subject: [PATCH 0162/2173] Update r-acidsinglecell to 0.4.0 (#43466) * Update r-acidsinglecell to 0.4.0 * Update dependencies * Add pinning info --------- Co-authored-by: Michael Steinbaugh --- recipes/r-acidsinglecell/meta.yaml | 92 ++++++++++++++---------------- 1 file changed, 44 insertions(+), 48 deletions(-) diff --git a/recipes/r-acidsinglecell/meta.yaml b/recipes/r-acidsinglecell/meta.yaml index 9353ed6e2fca6..36ad195dda0da 100644 --- a/recipes/r-acidsinglecell/meta.yaml +++ b/recipes/r-acidsinglecell/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.6" %} +{% set version = "0.4.0" %} {% set github = "https://github.com/acidgenomics/r-acidsinglecell" %} package: @@ -7,69 +7,65 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 440bf4f9c4c60fa6ef2c37de94dcbbb374d6bd383180f822dabb33b0030e1580 + sha256: 5cbcbfe093902e7a7f6b316130241b6f07f5ceb465a58b6e6801608b50b1334b build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('r-acidsinglecell', max_pin="x.x") }} requirements: host: # Depends: - r-base # Imports: - - bioconductor-biobase >=2.56.0 - - bioconductor-biocgenerics >=0.42.0 - - bioconductor-biocio >=1.6.0 - - bioconductor-iranges >=2.30.1 - - bioconductor-s4vectors >=0.34.0 - - bioconductor-singlecellexperiment >=1.18.0 - - bioconductor-summarizedexperiment >=1.26.0 - - r-acidbase >=0.6.8 - - r-acidcli >=0.2.4 - - r-acidexperiment >=0.4.4 - - r-acidgenerics >=0.6.4 - - r-acidgenomes >=0.4.4 - - r-acidplyr >=0.3.2 - - r-goalie >=0.6.6 - - r-matrix >=1.5.1 - - r-pipette >=0.10.0 - - r-stringi >=1.7.8 - - r-syntactic >=0.6.3 + - bioconductor-biobase >=2.60.0 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-singlecellexperiment >=1.22.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.7.1 + - r-acidgenomes >=0.6.0 + - r-acidplyr >=0.5.0 + - r-goalie >=0.7.1 + - r-matrix >=1.6.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biocparallel >=1.30.0 - - bioconductor-deseq2 >=1.36.0 - - bioconductor-dropletutils >=1.16.0 - - bioconductor-edger >=3.38.4 - - bioconductor-scuttle >=1.6.3 + - bioconductor-deseq2 >=1.40.0 + - bioconductor-dropletutils >=1.20.0 + - bioconductor-edger >=3.42.0 + - bioconductor-scuttle >=1.10.0 run: # Depends: - r-base # Imports: - - bioconductor-biobase >=2.56.0 - - bioconductor-biocgenerics >=0.42.0 - - bioconductor-biocio >=1.6.0 - - bioconductor-iranges >=2.30.1 - - bioconductor-s4vectors >=0.34.0 - - bioconductor-singlecellexperiment >=1.18.0 - - bioconductor-summarizedexperiment >=1.26.0 - - r-acidbase >=0.6.8 - - r-acidcli >=0.2.4 - - r-acidexperiment >=0.4.4 - - r-acidgenerics >=0.6.4 - - r-acidgenomes >=0.4.4 - - r-acidplyr >=0.3.2 - - r-goalie >=0.6.6 - - r-matrix >=1.5.1 - - r-pipette >=0.10.0 - - r-stringi >=1.7.8 - - r-syntactic >=0.6.3 + - bioconductor-biobase >=2.60.0 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-singlecellexperiment >=1.22.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.7.1 + - r-acidgenomes >=0.6.0 + - r-acidplyr >=0.5.0 + - r-goalie >=0.7.1 + - r-matrix >=1.6.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biocparallel >=1.30.0 - - bioconductor-deseq2 >=1.36.0 - - bioconductor-dropletutils >=1.16.0 - - bioconductor-edger >=3.38.4 - - bioconductor-scuttle >=1.6.3 + - bioconductor-deseq2 >=1.40.0 + - bioconductor-dropletutils >=1.20.0 + - bioconductor-edger >=3.42.0 + - bioconductor-scuttle >=1.10.0 test: commands: From 04ec3bf852520c8103e919ec3a0f4f7582a62df5 Mon Sep 17 00:00:00 2001 From: Chenlai Shi <33204827+shichenlai@users.noreply.github.com> Date: Tue, 10 Oct 2023 18:58:03 -0500 Subject: [PATCH 0163/2173] Add Seqstr (#43340) * Create build.sh * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Delete recipes/seqstr/tests directory * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Delete recipes/seqstr/build.sh * Add files via upload * Add files via upload * Add files via upload * edit maintainer field --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/seqstr/meta.yaml | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 recipes/seqstr/meta.yaml diff --git a/recipes/seqstr/meta.yaml b/recipes/seqstr/meta.yaml new file mode 100644 index 0000000000000..ce31fc8849ef6 --- /dev/null +++ b/recipes/seqstr/meta.yaml @@ -0,0 +1,38 @@ +package: + name: seqstr + version: 0.1.0 + +source: + url: https://github.com/jzhoulab/Seqstr/archive/refs/tags/v0.1.0.tar.gz + sha256: ddef0e2fce2f3c262bf23e16a45bf65886228bd20be314a05842f7f72bd9a705 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('seqstr', max_pin="x.x") }} + script: {{ PYTHON }} -m pip install . -vv + +requirements: + host: + - python >=3.7 + - pip >=21.2.2 + run: + - python >=3.7 + - requests >=2.25.0 + - pyfaidx >=0.6.3 + +about: + home: https://github.com/jzhoulab/Seqstr + license: MIT + summary: Lightweight tool to compile simple string input into long genomic sequences + description: | + Seqstr is designed to provide a concise and flexible way to specify long genomic sequences that can be used for downstream analysis. For example, it can be used by web servers to avoid transferring long genomic sequences. Seqstr is also a format specification, which can be implemented in different languages. We also provide a test suite for verifying an implementation. + +extra: + recipe-maintainers: + - shichenlai + +test: + imports: + - seqstr From 60a99085fac154f8a4f77d101f0fc479c7b7a43f Mon Sep 17 00:00:00 2001 From: George Bouras <84495559+gbouras13@users.noreply.github.com> Date: Wed, 11 Oct 2023 10:58:41 +1030 Subject: [PATCH 0164/2173] Add pypolca 0.1.1 (#43604) --- recipes/pypolca/meta.yaml | 52 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/pypolca/meta.yaml diff --git a/recipes/pypolca/meta.yaml b/recipes/pypolca/meta.yaml new file mode 100644 index 0000000000000..f2563aea92d94 --- /dev/null +++ b/recipes/pypolca/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "pypolca" %} +{% set version = "0.1.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 2e0ab4f28aa64eb1363afc7952728196d3dfbfbd5cbb2a5d61950de28164ab36 + +build: + number: 0 + noarch: python + entry_points: + - pypolca = pypolca:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('pypolca', max_pin='x') }} + +requirements: + host: + - python >=3.8,<4.0 + - poetry-core >=1.0.0 + - pip + run: + - samtools >=1.18 + - python >=3.8,<4.0 + - click >=8.0.0 + - freebayes >=1.3.1,<1.3.7 + - biopython >=1.76 + - loguru >=0.5.3 + - pandas >=1.4.2 + - pyyaml >=6.0 + - bwa >=0.7.17 + +test: + imports: + - pypolca + commands: + - pypolca --help + +about: + home: https://github.com/gbouras13/pypolca + license: MIT + license_family: MIT + license_file: LICENSE + summary: Standalone Python re-implementation of the POLCA polisher from MaSuRCA + +extra: + recipe-maintainers: + - gbouras13 From f2071590bc83b2f6ae9f9ac0af33c798d75fb0a2 Mon Sep 17 00:00:00 2001 From: Leon Rauschning <99650940+lrauschning@users.noreply.github.com> Date: Wed, 11 Oct 2023 02:36:40 +0200 Subject: [PATCH 0165/2173] Update t-coffee and merge t_coffee (#43571) * bump version to 13.46 * Revert "bump version to 13.46" This reverts commit b3d6f0b85e4796171fd0e3d2eae8a65dbbb250ce. * symlink t_coffee to t-coffee to not break workflows * bump version in proper package * fix lint issues --------- Co-authored-by: Leon Rauschning Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/t-coffee/meta.yaml | 8 +++--- recipes/t_coffee | 1 + recipes/t_coffee/build.sh | 18 ------------- recipes/t_coffee/meta.yaml | 39 --------------------------- recipes/t_coffee/t_coffee/__init__.py | 0 recipes/t_coffee/t_coffee/__main__.py | 32 ---------------------- recipes/t_coffee/t_coffee/config.py | 34 ----------------------- 7 files changed, 6 insertions(+), 126 deletions(-) create mode 120000 recipes/t_coffee delete mode 100755 recipes/t_coffee/build.sh delete mode 100644 recipes/t_coffee/meta.yaml delete mode 100644 recipes/t_coffee/t_coffee/__init__.py delete mode 100644 recipes/t_coffee/t_coffee/__main__.py delete mode 100644 recipes/t_coffee/t_coffee/config.py diff --git a/recipes/t-coffee/meta.yaml b/recipes/t-coffee/meta.yaml index 3eb499f930acc..b5cc7ac1818c2 100644 --- a/recipes/t-coffee/meta.yaml +++ b/recipes/t-coffee/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "13.45.0.4846264" %} +{% set version = "13.46.0.919e8c6b" %} package: name: t-coffee version: {{ version }} build: - number: 7 + number: 0 + run_exports: + - {{ pin_subpackage('t-coffee', max_pin="x") }} source: # The latest stable release is at http://www.tcoffee.org/Packages/Stable/Latest/ , # but is then archived at http://www.tcoffee.org/Packages/Archives/ url: https://s3.eu-central-1.amazonaws.com/tcoffee-packages/Archives/T-COFFEE_distribution_Version_{{ version }}.tar.gz - sha256: c8e5ba17de11ddf07cf2ed37f077d81c1432d55b77761f115f9374de6f8d0d03 + sha256: 31fd0ca0734974c93cb68bef6e394f463a4589c3315fd28cf2bd41b8a167db22 patches: - expose-os-detection.patch diff --git a/recipes/t_coffee b/recipes/t_coffee new file mode 120000 index 0000000000000..8e7ab1b381a35 --- /dev/null +++ b/recipes/t_coffee @@ -0,0 +1 @@ +t-coffee \ No newline at end of file diff --git a/recipes/t_coffee/build.sh b/recipes/t_coffee/build.sh deleted file mode 100755 index 8ccaf32698633..0000000000000 --- a/recipes/t_coffee/build.sh +++ /dev/null @@ -1,18 +0,0 @@ -#!/bin/bash - -export CFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" - -TCOFFEE_FOLDER_NAME="${PKG_NAME}-${PKG_VERSION}" -TCOFFEE_INSTALL_PATH="$PREFIX/lib/$TCOFFEE_FOLDER_NAME" - -chmod +x T-COFFEE_installer_Version_*_linux_x64.bin -./T-COFFEE_installer_Version_*_linux_x64.bin \ - --prefix "$TCOFFEE_INSTALL_PATH" \ - --mode unattended \ - --user_email username@hostname.com - -cp -rf "$RECIPE_DIR/t_coffee" "$TCOFFEE_INSTALL_PATH" -ln -s "$TCOFFEE_INSTALL_PATH/t_coffee" "$SP_DIR/t_coffee" -sed -i "s|{{TCOFFEE_FOLDER_NAME}}|$TCOFFEE_FOLDER_NAME|g" "$TCOFFEE_INSTALL_PATH/t_coffee/config.py" - diff --git a/recipes/t_coffee/meta.yaml b/recipes/t_coffee/meta.yaml deleted file mode 100644 index 56f78fb27a755..0000000000000 --- a/recipes/t_coffee/meta.yaml +++ /dev/null @@ -1,39 +0,0 @@ -package: - name: t_coffee - version: "13.45.0" - -source: - url: http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_installer_Version_13.45.0.4846264_linux_x64.bin - sha256: 0eb0e2b1283650ee8bf366185a350f504e82cbdb5542b3a7b85b685811b61ef5 - -build: - skip: True # [osx] - number: 0 - entry_points: - - t_coffee = t_coffee.__main__:main - -requirements: - build: - - {{ compiler('cxx') }} - host: - - curl - - openssl - - python - - zlib - run: - - curl - - openssl - - perl - - python - - zlib - -test: - commands: - - HOME=/tmp t_coffee - - HOME=/tmp t_coffee --help - - HOME=/tmp t_coffee 2>&1 |grep "mafft is Installed" >/dev/null - -about: - home: http://www.tcoffee.org/Projects/tcoffee/ - license: GNU - summary: A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures. diff --git a/recipes/t_coffee/t_coffee/__init__.py b/recipes/t_coffee/t_coffee/__init__.py deleted file mode 100644 index e69de29bb2d1d..0000000000000 diff --git a/recipes/t_coffee/t_coffee/__main__.py b/recipes/t_coffee/t_coffee/__main__.py deleted file mode 100644 index ed71679c811cb..0000000000000 --- a/recipes/t_coffee/t_coffee/__main__.py +++ /dev/null @@ -1,32 +0,0 @@ -from __future__ import absolute_import, print_function - -import sys -import subprocess - -from . import config - - -def main(): - """Run the ``t_coffee`` multiple sequence alignment tool. - - Parameters - ---------- - argv : list, optional - A list of arguments to pass on to ``t_coffee``. - """ - print("\n" + "*" * 80) - print('Command line arguments: {}'.format(sys.argv)) - print("Install folder: {}".format(config.tcoffee_install_dir)) - print("*" * 80 + "\n") - env = config.get_tcoffee_environ() - child_process = subprocess.Popen([config.tcoffee_exe_file] + sys.argv[1:], env=env) - result, error_message = child_process.communicate() - print("\n" + "*" * 80) - print("Result: {}".format(result)) - print("Error message: {}".format(error_message)) - print("*" * 80 + "\n") - return child_process.returncode - - -if __name__ == '__main__': - main() diff --git a/recipes/t_coffee/t_coffee/config.py b/recipes/t_coffee/t_coffee/config.py deleted file mode 100644 index 24b61c8b8696c..0000000000000 --- a/recipes/t_coffee/t_coffee/config.py +++ /dev/null @@ -1,34 +0,0 @@ -import os -import os.path as op -import sys -import tempfile - -tcoffee_install_dir = op.normpath(op.join(op.dirname(__file__), '..', '..', '..', '{{TCOFFEE_FOLDER_NAME}}')) -tcoffee_bin_dir = op.join(tcoffee_install_dir, 'bin') -tcoffee_exe_file = op.join(tcoffee_bin_dir, 't_coffee') -if sys.platform.startswith('linux'): - platform = 'linux' -elif sys.platform == 'darwin': - platform = 'macosx' -else: - raise Exception("Unsupported platform '%s'" % sys.platform) -tcoffee_plugins_dir = op.join(tcoffee_install_dir, 'plugins', platform) -tcoffee_perl_dir = op.join(tcoffee_install_dir, 'perl', 'lib', 'perl5') -tcoffee_default_email = 'username@example.org' - - -def get_tcoffee_environ(): - env = os.environ.copy() - if 'TMP_4_TCOFFEE' not in env: - env['TMP_4_TCOFFEE'] = tempfile.mkdtemp() - if 'PLUGINS_4_TCOFFEE' not in env: - env['PLUGINS_4_TCOFFEE'] = tcoffee_plugins_dir - if 'MAFFT_BINARIES' not in env: - env['MAFFT_BINARIES'] = tcoffee_plugins_dir - if 'PERL5LIB' not in env: - env['PERL5LIB'] = tcoffee_perl_dir - elif tcoffee_perl_dir not in env['PERL5LIB']: - env['PERL5LIB'] = tcoffee_plugins_dir + ':' + env['PERL5LIB'] - if 'EMAIL_4_TCOFFEE' not in env or not env['EMAIL_4_TCOFFEE']: - env['EMAIL_4_TCOFFEE'] = tcoffee_default_email - return env From 926a086dc421702b3b0ef225801f0193b030f4a4 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 10 Oct 2023 21:39:28 -0500 Subject: [PATCH 0166/2173] Update GMAP to 2023-10-10 (#43605) --- recipes/gmap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index 58e7b9a11010a..74c8b1a25c564 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GMAP" %} -{% set version = "2023.10.01" %} -{% set sha256 = "b6299f051189f1abea6976f668eb5204fdff2a4519a40931f7897f2496fec7ed" %} +{% set version = "2023.10.10" %} +{% set sha256 = "f76cc3d0024c6c963ea1c13e46236b62a548d965ad8e295a181f138b82aca36e" %} package: name: {{ name|lower }} From 2c71bfb29274c68a49f261759524fb7f15500941 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 10 Oct 2023 21:40:11 -0600 Subject: [PATCH 0167/2173] Update t1k to 1.0.4 (#43552) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/t1k/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/t1k/meta.yaml b/recipes/t1k/meta.yaml index d9c8351eb25f5..24f2102ec5b3a 100644 --- a/recipes/t1k/meta.yaml +++ b/recipes/t1k/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.3" %} +{% set version = "1.0.4" %} package: name: t1k @@ -11,7 +11,7 @@ build: source: url: https://github.com/mourisl/T1K/archive/v{{ version }}.tar.gz - sha256: f025a93087366d46eaddc89a4897ce6452271d38a7632478956f79577645db0d + sha256: 1ace975b9e6ab07a10d801ab783dceab534c3754c3f25805c536f34413d63ca0 requirements: build: From ced7d7c402ac445fe0d99e9e3aa481796aa028c4 Mon Sep 17 00:00:00 2001 From: Nina Murrell <63961601+ninashenker@users.noreply.github.com> Date: Wed, 11 Oct 2023 00:31:32 -0400 Subject: [PATCH 0168/2173] inital commit for TADlib package to bioconda (#43601) --- recipes/tadlib/meta.yaml | 64 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 recipes/tadlib/meta.yaml diff --git a/recipes/tadlib/meta.yaml b/recipes/tadlib/meta.yaml new file mode 100644 index 0000000000000..ecf8487e04ced --- /dev/null +++ b/recipes/tadlib/meta.yaml @@ -0,0 +1,64 @@ +{% set name = "tadlib" %} +{% set version = "0.4.5.post1" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://pypi.io/packages/source/t/tadlib/TADLib-0.4.5.post1.tar.gz + sha256: 37dd485ff97588d037a6d287cce5de152bcbd3dd607c79ff9704d5a45015961f + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - _libgcc_mutex 0.1 conda_forge + - _openmp_mutex 4.5 2_gnu + - ca-certificates 2023.7.22 hbcca054_0 + - ld_impl_linux-64 2.40 h41732ed_0 + - libffi 3.4.2 h7f98852_5 + - libgcc-ng 13.2.0 h807b86a_2 + - libgomp 13.2.0 h807b86a_2 + - ncurses 6.4 hcb278e6_0 + - openssl 3.1.3 hd590300_0 + - pip 23.2.1 pyhd8ed1ab_0 + - python 3.10.12 hd12c33a_0_cpython + - readline 8.2 h8228510_1 + - setuptools 68.2.2 pyhd8ed1ab_0 + - tk 8.6.13 h2797004_0 + - wheel 0.41.2 pyhd8ed1ab_0 + - xz 5.2.6 h166bdaf_0 + run: + - cooler + - matplotlib-base + - numpy + - pomegranate + - python >=3.5 + - python_abi + - scikit-learn + - scipy + +test: + imports: + - tadlib + - tadlib.calfea + - tadlib.domaincaller + - tadlib.hitad + - tadlib.visualize + +about: + home: https://github.com/XiaoTaoWang/TADLib/ + license: GPLv3 + license_family: GPL3 + license_file: LICENSE + summary: A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains + dev_url: https://github.com/XiaoTaoWang/TADLib/ + +extra: + recipe-maintainers: ninashenker From 04326e692771279f66f68b7a86774a8a6501e402 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 10 Oct 2023 23:07:16 -0600 Subject: [PATCH 0169/2173] Update singlem to 0.15.0 (#43564) --- recipes/singlem/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/singlem/meta.yaml b/recipes/singlem/meta.yaml index 1a1840808f0f8..66ff4e4fb31c6 100644 --- a/recipes/singlem/meta.yaml +++ b/recipes/singlem/meta.yaml @@ -1,5 +1,5 @@ {% set name = "singlem" %} -{% set version = "0.14.0" %} +{% set version = "0.15.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 55d5cbeb307e0ab49ef86bc17ac30ed3e0635c5085e801e0b6eb7552d944d82a + sha256: c13d17bcb2df0e840a8b0cf136e1433f231d8df43c519dc8a6b4a86d7e496464 build: number: 0 From 785d3ec51144aacd5b7da6f093d8bdd9da9dd593 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 04:04:36 -0600 Subject: [PATCH 0170/2173] Update varfish-annotator-cli to 0.34 (#43609) --- recipes/varfish-annotator-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varfish-annotator-cli/meta.yaml b/recipes/varfish-annotator-cli/meta.yaml index 1247c69365465..2d6713f5146eb 100644 --- a/recipes/varfish-annotator-cli/meta.yaml +++ b/recipes/varfish-annotator-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.33" %} -{% set sha256 = "76e2acf7f9a19e19139f06aedd900f5f3d85f4ff658d6f6442f987efe17b3e9f" %} +{% set version = "0.34" %} +{% set sha256 = "4dc1399e5a41564a9616474597bec4ec100478f961bb114075c507b6c19af738" %} package: name: varfish-annotator-cli From cf821c053c4df18f259bbee6695cd8e73a4eb46a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 04:35:54 -0600 Subject: [PATCH 0171/2173] Update tcdemux to 0.0.17 (#43566) --- recipes/tcdemux/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tcdemux/meta.yaml b/recipes/tcdemux/meta.yaml index 09687414ae7c3..dca6f8e300868 100644 --- a/recipes/tcdemux/meta.yaml +++ b/recipes/tcdemux/meta.yaml @@ -1,5 +1,5 @@ --- -{% set version = "0.0.16" %} +{% set version = "0.0.17" %} package: name: tcdemux @@ -7,7 +7,7 @@ package: source: url: https://github.com/TomHarrop/tcdemux/archive/refs/tags/{{ version }}.tar.gz - sha256: 5446f460c862f43d1b42e304f9d174274e7f8a2f9b95bafc690913592fcca87d + sha256: dc91a17e9f32de9f38001fee2b494aec2b50408a3f36845678ab8a9670a40cda build: number: 0 From 355daff45051c2530dcd4f8a35c127c7a3fd3349 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Wed, 11 Oct 2023 11:57:41 +0100 Subject: [PATCH 0172/2173] customtkinter dependency of ms2rescore (#43607) * customtkinter dependency of ms2rescore * customtkinter dependency of ms2rescore * customtkinter dependency of ms2rescore * customtkinter dependency of ms2rescore * customtkinter dependency of ms2rescore * Update meta.yaml * Update meta.yaml remove tk --- recipes/customtkinter/meta.yaml | 47 +++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/customtkinter/meta.yaml diff --git a/recipes/customtkinter/meta.yaml b/recipes/customtkinter/meta.yaml new file mode 100644 index 0000000000000..61dc5a5b28ba0 --- /dev/null +++ b/recipes/customtkinter/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "customtkinter" %} +{% set version = "5.2.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/customtkinter-{{ version }}.tar.gz + sha256: e93448a8d22121e20ec16e95960a8306e17cf7e0079766f5804b2e855e614937 + +build: + script: "{{ PYTHON }} -m pip install . --no-deps -vvv" + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + host: + - python + - setuptools >=42 + - wheel + - pip + run: + - python + - darkdetect + - typing-extensions # [py<=37] + - xorg-libx11 + +test: + imports: + - customtkinter + commands: + - pip check + requires: + - pip + +about: + home: https://customtkinter.tomschimansky.com + summary: Create modern looking GUIs with Python + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - ypriverol From 90e26f740a6135b55baee5f1b17dc99d01b1bb5a Mon Sep 17 00:00:00 2001 From: balajtimate <51365402+balajtimate@users.noreply.github.com> Date: Wed, 11 Oct 2023 12:58:15 +0200 Subject: [PATCH 0173/2173] Add scRNAsim-toolz (#43594) * Add scRNAsim-toolz * fix test * fix scrnasim-toolz * fix scrnasim-toolz * remove test import command * add pandas * add packages * remove cli_test_helpers * refactor scrnasim-toolz --- recipes/scrnasim-toolz/meta.yaml | 50 ++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 recipes/scrnasim-toolz/meta.yaml diff --git a/recipes/scrnasim-toolz/meta.yaml b/recipes/scrnasim-toolz/meta.yaml new file mode 100644 index 0000000000000..82412589d1d36 --- /dev/null +++ b/recipes/scrnasim-toolz/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "scrnasim-toolz" %} +{% set version = "0.1.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/zavolanlab/scRNAsim-toolz/archive/refs/tags/v0.1.0.tar.gz + sha256: 738f420e12fec1730927894debdf495953aa9e8bb288e901fde5caacac0042a9 + +build: + number: 0 + noarch: python + entry_points: + - transcript-sampler = scRNAsim_toolz.transcript_sampler.cli:main + - structure-generator = scRNAsim_toolz.structure_generator.cli:app + - sequence-extractor = scRNAsim_toolz.sequence_extractor.cli:main + - priming-site-predictor = scRNAsim_toolz.priming_site_predictor.cli:main + - cdna-generator = scRNAsim_toolz.cdna_generator.cli:main + - fragment-selector = scRNAsim_toolz.fragment_selector.cli:main + - read-sequencer = scRNAsim_toolz.read_sequencer.cli:main + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python <=3.10 + - pip + - setuptools-git >=1.2 + run: + - python <=3.10 + - biopython >=1.78 + - numpy >=1.23.3 + - pandas >=1.4.4 + - packaging + - importlib-metadata + - polars ==0.16.17 + - gtfparse + +test: + commands: + - transcript-sampler --version + +about: + home: https://github.com/zavolanlab/scRNAsim-toolz + license: MIT License + license_file: LICENSE + summary: Tools used by scRNAsim workflow. From a72186c2bf76126c255db5c3791af6ad434143e3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 06:29:47 -0600 Subject: [PATCH 0174/2173] Update nf-test to 0.8.1 (#43612) --- recipes/nf-test/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-test/meta.yaml b/recipes/nf-test/meta.yaml index 1660c69142938..dc0320369511b 100644 --- a/recipes/nf-test/meta.yaml +++ b/recipes/nf-test/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.0" %} +{% set version = "0.8.1" %} package: @@ -13,7 +13,7 @@ build: source: url: https://github.com/askimed/nf-test/releases/download/v{{version}}/nf-test-{{version}}.tar.gz - sha256: db910190b6e9f47686d56a56ea3aa9e87cf269abf469b710813dbca250a4446d + sha256: fb2e6a098c7bf16e7e849d98838651b95d1bf94ab59766e43d91d19729bcfe9e requirements: host: From 80bf1f40de5377c93bd63d05f56b2d99e53f602a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 10:47:28 -0600 Subject: [PATCH 0175/2173] Update oakvar to 2.9.43 (#43581) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index caf96e91b12ca..45f96a4ab45c6 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.41" %} -{% set sha256 = "183b387206ce354eed932261d6987218670a38bfd1e223b16175b53124ec634b" %} +{% set version = "2.9.43" %} +{% set sha256 = "47113739aceaa54f868a61b4e2214a0322efb52a462286ebdd47f21c7a4dde04" %} package: name: {{ name|lower }} From 1ec44a371ab52e3b32b740609135a115eda9cf91 Mon Sep 17 00:00:00 2001 From: Carl Mathias Kobel Date: Wed, 11 Oct 2023 20:09:45 +0200 Subject: [PATCH 0176/2173] update assemblycomparator2 v2.5.8 (#43614) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index fe4a397a6f39b..8b7f3fe701c6d 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.7" %} +{% set version = "2.5.8" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - md5: 934aa96c3027637cd53ad25ccab4004a + md5: 42d29dc011d2e057992a0801e41fa4ac build: From a3bd94b0d1abf5f4e71ac1b43f3d0050385b026c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 12:12:12 -0600 Subject: [PATCH 0177/2173] Update olivar to 1.1.3 (#43568) --- recipes/olivar/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/olivar/meta.yaml b/recipes/olivar/meta.yaml index 46b51dbf8ef1f..312f353f707f4 100644 --- a/recipes/olivar/meta.yaml +++ b/recipes/olivar/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.2" %} +{% set version = "1.1.3" %} package: name: olivar @@ -6,10 +6,10 @@ package: source: url: 'https://github.com/treangenlab/Olivar/archive/refs/tags/v{{version}}.tar.gz' - sha256: b8d3df4ee17d364e6f8547b8c935cc41168034d712467c22f68540eab41fc087 + sha256: f7a04661321a33c8c4142fcb65397e13fdbcc3be2e6f429d2a5056e3f16fb567 build: - number: 3 + number: 0 noarch: python script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv && mkdir -p ${PREFIX}/bin && cp olivar ${PREFIX}/bin run_exports: From 74121d3d59880f736ef8b7ab74a84941f3c90756 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 12:12:45 -0600 Subject: [PATCH 0178/2173] Update guidescan to 2.2.0 (#43538) --- recipes/guidescan/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/guidescan/meta.yaml b/recipes/guidescan/meta.yaml index f204d471f5357..9aea5a66ea70d 100644 --- a/recipes/guidescan/meta.yaml +++ b/recipes/guidescan/meta.yaml @@ -1,5 +1,5 @@ {% set name="guidescan" %} -{% set version="2.1.8" %} +{% set version="2.2.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/pritykinlab/guidescan-cli/releases/download/v{{ version }}/guidescan-v{{ version }}-src.tar.gz - sha256: f4b6ce2d5473d7c2e3e24056db1a0dc3205f08986f212f665a5d052cdffe5c7e + sha256: b1fd82fc65bbcd883e6006ed921762e8075edd61b693f1a4d084e1fda6305f72 build: number: 0 From 8cc18826802d457208cc14928d1d99f059f41e93 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 12:28:35 -0600 Subject: [PATCH 0179/2173] Update snakemake-interface-common to 1.12.0 (#43613) * Update snakemake-interface-common to 1.11.0 * Update snakemake-interface-common to 1.12.0 --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index ce11fe2565894..dd2e115b443c6 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 6f6b0ee1acfa7649cba7314dafd3079b4697fe80ad22bbff6b7005db249af6cf + sha256: 2a6052b4db59a5a8bc632ea832ae30eba615f63e02737bb6cd1f2691945ab91f build: noarch: python From b639b942f3506810a9d3a208b6d532ca733334ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 12:29:18 -0600 Subject: [PATCH 0180/2173] Update tbpore to 0.7.0 (#43606) * Update tbpore to 0.7.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/tbpore/meta.yaml | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/recipes/tbpore/meta.yaml b/recipes/tbpore/meta.yaml index 39c5a58d61266..0931d21a6f35f 100644 --- a/recipes/tbpore/meta.yaml +++ b/recipes/tbpore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tbpore" %} -{% set version = "0.6.0" %} +{% set version = "0.7.0" %} package: name: {{ name|lower }} @@ -7,23 +7,24 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 18f36797b172fd774dce664cdb252ffca1fa810a96777420dd04a39b1d22439d - + sha256: 9b9fd8cf7e6ec98d90ae196e4abcb7865fbb2f360c1fa1b4c6aa574cde87ec75 + build: number: 0 noarch: python entry_points: - tbpore = tbpore.tbpore:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('tbpore', max_pin="x") }} requirements: host: - - python >=3.8,<3.10 - - poetry =1.3 + - python >=3.8 + - poetry-core >=1.0.0 - pip - run: - - python >=3.8,<3.10 + - python >=3.8 - mykrobe =0.12 - rasusa - samtools =1.13 @@ -36,7 +37,7 @@ requirements: - loguru >=0.5.3,<1.0 - pyyaml >=6.0 - pandas >=1.4.2,<2.0 - - pysam =0.17 + - pysam <1.0 - networkx >=2.8,<3.0 - nanoq =0.9 @@ -49,6 +50,7 @@ test: about: home: https://github.com/mbhall88/tbpore license: MIT + license_family: MIT license_file: LICENSE summary: Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data @@ -56,3 +58,5 @@ extra: recipe-maintainers: - mbhall88 - leoisl + identifiers: + - doi:10.1016/S2666-5247(22)00301-9 From 77963ddf8e2cdd70728270de292fd8f5bd60ad3b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 12:30:26 -0600 Subject: [PATCH 0181/2173] Update influx_si to 7.0.1 (#43456) * Update influx_si to 7.0.1 * add run_exports * fix pip install command --------- Co-authored-by: joshuazhuang7 --- recipes/influx_si/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/influx_si/meta.yaml b/recipes/influx_si/meta.yaml index 1d3544d01efc5..2604d723ff941 100644 --- a/recipes/influx_si/meta.yaml +++ b/recipes/influx_si/meta.yaml @@ -1,5 +1,5 @@ {% set name = "influx_si" %} -{% set version = "7.0" %} +{% set version = "7.0.1" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "fcc201022ba64d86246ab625a3f8fe1aaa1ff490b556a9819ffcee30e78a0547" + sha256: "24756a8c4ae1882244ffb2fd1faf83fe51e0cb6bb0d81756ce2c97c816764f3d" build: number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python entry_points: - ff2ftbl = influx_si.cli:cli @@ -27,6 +27,9 @@ build: - txt2ftbl = influx_si.txt2ftbl:main - ftbl2mtf = influx_si.ftbl2mtf:main - ftbl2metxml = influx_si.ftbl2metxml:main + - ftbl2labcin = influx_si.ftbl2labcin:main + run_exports: + - {{ pin_subpackage('influx_si', max_pin="x") }} requirements: host: From 3e1c087facf75a03f0c7e35123af5968e2d9e749 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 12:33:14 -0600 Subject: [PATCH 0182/2173] Update r-acidplots to 0.7.1 (#43467) * Update r-acidplots to 0.7.0 * Update r-acidplots to 0.7.1 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-acidplots/meta.yaml | 110 +++++++++++++++++----------------- 1 file changed, 54 insertions(+), 56 deletions(-) diff --git a/recipes/r-acidplots/meta.yaml b/recipes/r-acidplots/meta.yaml index f136c64040fd5..a4217ce91b0fa 100644 --- a/recipes/r-acidplots/meta.yaml +++ b/recipes/r-acidplots/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.1" %} +{% set version = "0.7.1" %} {% set github = "https://github.com/acidgenomics/r-acidplots" %} package: @@ -7,89 +7,87 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 696d05b660a404dc73cffbe8c3e08f894f0a4740f33b89ba78483fc77a22bf4b + sha256: bda01fadcb22b2978d4aa7965e246de94e9f51b5673fdd6e5e59fe5a2a76c87f build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('r-acidplots', max_pin="x.x") }} requirements: host: # Depends: - r-base # Imports: - - bioconductor-biobase >=2.58.0 - - bioconductor-biocgenerics >=0.44.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-singlecellexperiment >=1.20.0 - - bioconductor-summarizedexperiment >=1.28.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidexperiment >=0.4.7 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.0 - - r-acidmarkdown >=0.2.5 - - r-acidplyr >=0.3.10 - - r-acidsinglecell >=0.3.5 - - r-ggplot2 >=3.4.2 - - r-goalie >=0.6.9 - - r-matrix >=1.5.4 - - r-patchwork >=1.1.2 - - r-pipette >=0.10.9 - - r-rlang >=1.1.0 + - bioconductor-biobase >=2.60.0 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-singlecellexperiment >=1.22.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.7.1 + - r-acidgenomes >=0.6.0 + - r-acidmarkdown >=0.3.0 + - r-acidplyr >=0.5.0 + - r-acidsinglecell >=0.4.0 + - r-ggplot2 >=3.4.3 + - r-goalie >=0.7.1 + - r-matrix >=1.6.1 + - r-patchwork >=1.1.3 + - r-pipette >=0.14.0 + - r-rlang >=1.1.1 - r-scales >=1.2.1 - - r-stringr >=1.5.0 - - r-syntactic >=0.6.5 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biocparallel >=1.32.0 - - bioconductor-dropletutils >=1.18.0 + - bioconductor-dropletutils >=1.20.0 - r-complexupset >=1.3.3 - - r-ggpmisc >=0.5.2 + - r-ggpmisc >=0.5.4 - r-ggrepel >=0.9.3 - r-ggridges >=0.5.4 - - r-matrixstats >=0.63.0 + - r-matrixstats >=1.0.0 - r-pheatmap >=1.0.12 - r-rcolorbrewer >=1.1.3 - - r-viridis >=0.6.2 + - r-viridis >=0.6.4 run: # Depends: - r-base # Imports: - - bioconductor-biobase >=2.58.0 - - bioconductor-biocgenerics >=0.44.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-singlecellexperiment >=1.20.0 - - bioconductor-summarizedexperiment >=1.28.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidexperiment >=0.4.7 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.0 - - r-acidmarkdown >=0.2.5 - - r-acidplyr >=0.3.10 - - r-acidsinglecell >=0.3.5 - - r-ggplot2 >=3.4.2 - - r-goalie >=0.6.9 - - r-matrix >=1.5.4 - - r-patchwork >=1.1.2 - - r-pipette >=0.10.9 - - r-rlang >=1.1.0 + - bioconductor-biobase >=2.60.0 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-singlecellexperiment >=1.22.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.7.1 + - r-acidgenomes >=0.6.0 + - r-acidmarkdown >=0.3.0 + - r-acidplyr >=0.5.0 + - r-acidsinglecell >=0.4.0 + - r-ggplot2 >=3.4.3 + - r-goalie >=0.7.1 + - r-matrix >=1.6.1 + - r-patchwork >=1.1.3 + - r-pipette >=0.14.0 + - r-rlang >=1.1.1 - r-scales >=1.2.1 - - r-stringr >=1.5.0 - - r-syntactic >=0.6.5 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biocparallel >=1.32.0 - - bioconductor-dropletutils >=1.18.0 + - bioconductor-dropletutils >=1.20.0 - r-complexupset >=1.3.3 - - r-ggpmisc >=0.5.2 + - r-ggpmisc >=0.5.4 - r-ggrepel >=0.9.3 - r-ggridges >=0.5.4 - - r-matrixstats >=0.63.0 + - r-matrixstats >=1.0.0 - r-pheatmap >=1.0.12 - r-rcolorbrewer >=1.1.3 - - r-viridis >=0.6.2 + - r-viridis >=0.6.4 test: commands: From 544ef8d7457f4517567c3730f24890aa9949a445 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 13:04:29 -0600 Subject: [PATCH 0183/2173] Update chewbbaca to 3.3.0 (#43616) * Update chewbbaca to 3.3.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/chewbbaca/meta.yaml | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index 3472ae0917946..50fe78324108b 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -1,5 +1,5 @@ -{% set name='chewBBACA' %} -{% set version='3.2.0' %} +{% set name = 'chewBBACA' %} +{% set version = '3.3.0' %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b6bc4dc5570b7bb710832f14299bcbd5fc0b356a37363e7fe35cfe60fb7e2937 + sha256: 6ca1a4971ede86ecb5e1e3e6c484fbe16e4ba87d3aebb751594480d3a674be67 build: number: 0 @@ -15,7 +15,9 @@ build: entry_points: - chewBBACA.py = CHEWBBACA.chewBBACA:main - chewie = CHEWBBACA.chewBBACA:main - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv + run_exports: + - {{ pin_subpackage('chewbbaca', max_pin="x") }} requirements: host: @@ -31,13 +33,11 @@ requirements: - requests >=2.27.1 - sparqlwrapper >=2.0.0 - blast >=2.9.0 - - prodigal >=2.6.3 + - pyrodigal >=3.0.0 - clustalw >=2.1 - mafft >=7.505 test: - requires: - - pip imports: - CHEWBBACA - CHEWBBACA.CHEWBBACA_NS @@ -47,16 +47,17 @@ test: - CHEWBBACA.CreateSchema - CHEWBBACA.utils commands: - - pip check - chewBBACA.py --help - chewie --version about: home: https://github.com/B-UMMI/chewBBACA - license: GPL-3.0-only + license: GPL-3.0-or-later license_family: GPL3 + license_file: LICENSE summary: 'A complete suite for gene-by-gene schema creation and strain identification.' description: 'chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci.' + doc_url: https://chewbbaca.readthedocs.io/en/latest/index.html extra: identifiers: From 9b1711014ffadd09c5d32063472cfdd8f25dbf42 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 14:36:00 -0600 Subject: [PATCH 0184/2173] Update metagenome-atlas to 2.18.1 (#43611) * Update metagenome-atlas to 2.18.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/metagenome-atlas/meta.yaml | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/recipes/metagenome-atlas/meta.yaml b/recipes/metagenome-atlas/meta.yaml index d662a3d4f4249..7b5d034a1fe9d 100644 --- a/recipes/metagenome-atlas/meta.yaml +++ b/recipes/metagenome-atlas/meta.yaml @@ -1,5 +1,4 @@ - -{% set version = "2.18.0" %} +{% set version = "2.18.1" %} package: name: metagenome-atlas @@ -7,24 +6,26 @@ package: source: url: https://github.com/metagenome-atlas/atlas/archive/v{{ version }}.tar.gz - sha256: 398469ed81d98872f0bcf3de34b3a405d32c7a714017ea7cf12a53b2e3fdbb92 + sha256: 225a0e34c5c7a34ab053b98c0be5fa3c6281a03144a156454deeda5588e3d774 build: number: 0 entry_points: - atlas=atlas.atlas:cli noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('metagenome-atlas', max_pin="x") }} requirements: host: - - python >=3.8, <3.11 + - python >=3.8,<3.11 - pip run: - - python >=3.8, <3.11 + - python >=3.8,<3.11 - mamba - - bbmap >=39.01, <40 - - snakemake-minimal >=7.18.1, <7.26 + - bbmap >=39.01,<40 + - snakemake-minimal >=7.18.1,<7.26 - pygments - networkx - graphviz @@ -36,7 +37,7 @@ requirements: - pathlib # optional to help conda solve - numpy =1.21 - + test: imports: - atlas From 28d2597842d49465c7a0ec944eaa212df0ba7b59 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 16:33:54 -0600 Subject: [PATCH 0185/2173] Update r-bcbiobase to 0.9.0 (#43491) * Update r-bcbiobase to 0.9.0 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-bcbiobase/meta.yaml | 43 ++++++++++++++++------------------- 1 file changed, 20 insertions(+), 23 deletions(-) diff --git a/recipes/r-bcbiobase/meta.yaml b/recipes/r-bcbiobase/meta.yaml index d8f3ade328f65..2fbc32b4e4ad2 100644 --- a/recipes/r-bcbiobase/meta.yaml +++ b/recipes/r-bcbiobase/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.8.2' %} +{% set version = '0.9.0' %} {% set github = "https://github.com/hbc/bcbioBase" %} package: @@ -7,42 +7,39 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 7e343d9e1f5da2f62a64193123a441d5f1586ea5424db978930bb4479332229a + sha256: f9c3e39f86e07d1af07838f95a0f1cae6f7c142bfb0e13ceb5dd2e16f2941cb2 build: noarch: generic number: 0 - rpaths: - - lib/R/lib/ - - lib/ + run_exports: + - {{ pin_subpackage('r-bcbiobase', max_pin="x.x") }} requirements: host: # Depends: - r-base # Imports: - - bioconductor-s4vectors >=0.36.0 - - r-acidbase >=0.6.8 - - r-acidcli >=0.2.5 - - r-acidexperiment >=0.4.4 - - r-acidplyr >=0.3.2 - - r-goalie >=0.6.6 - - r-pipette >=0.10.1 - - r-stringr >=1.4.1 - - r-syntactic >=0.6.3 + - bioconductor-s4vectors >=0.38.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidplyr >=0.5.0 + - r-goalie >=0.7.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 run: # Depends: - r-base # Imports: - - bioconductor-s4vectors >=0.36.0 - - r-acidbase >=0.6.8 - - r-acidcli >=0.2.5 - - r-acidexperiment >=0.4.4 - - r-acidplyr >=0.3.2 - - r-goalie >=0.6.6 - - r-pipette >=0.10.1 - - r-stringr >=1.4.1 - - r-syntactic >=0.6.3 + - bioconductor-s4vectors >=0.38.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidplyr >=0.5.0 + - r-goalie >=0.7.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 test: commands: From 5e2c3d83e70e605990305ab2214e007136db62b6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 16:34:02 -0600 Subject: [PATCH 0186/2173] Update r-wormbase to 0.5.0 (#43323) * Update r-wormbase to 0.5.0 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-wormbase/meta.yaml | 39 ++++++++++++++++++------------------ 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/recipes/r-wormbase/meta.yaml b/recipes/r-wormbase/meta.yaml index 60e8aff596def..bb2667d5a1a98 100644 --- a/recipes/r-wormbase/meta.yaml +++ b/recipes/r-wormbase/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.2" %} +{% set version = "0.5.0" %} {% set github = "https://github.com/acidgenomics/r-wormbase" %} package: @@ -7,14 +7,13 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 082899e136e6f58ef3d184ff2b8faf2bc7594788a7aec6ea3cb80cca1f9fe9f0 + sha256: dce59a925b8fa24c4de87747e303333eb0a9f79a0f0dde130d8f242cb17809a7 build: number: 0 noarch: generic - rpaths: - - lib/R/lib/ - - lib/ + run_exports: + - {{ pin_subpackage('r-wormbase', max_pin="x.x") }} requirements: host: @@ -24,14 +23,15 @@ requirements: - bioconductor-biocgenerics >=0.46.0 - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.6.18 + - r-acidbase >=0.7.0 - r-acidcli >=0.2.8 - - r-acidgenerics >=0.6.7 - - r-acidplyr >=0.3.11 - - r-goalie >=0.6.14 - - r-pipette >=0.11.1 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.6 + - r-acidgenerics >=0.6.13 + - r-acidplyr >=0.4.3 + - r-goalie >=0.7.0 + - r-pipette >=0.14.0 + - r-syntactic >=0.6.7 + # Suggests: + - r-httr2 >=0.2.3 run: # Depends: - r-base @@ -39,14 +39,15 @@ requirements: - bioconductor-biocgenerics >=0.46.0 - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.6.18 + - r-acidbase >=0.7.0 - r-acidcli >=0.2.8 - - r-acidgenerics >=0.6.7 - - r-acidplyr >=0.3.11 - - r-goalie >=0.6.14 - - r-pipette >=0.11.1 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.6 + - r-acidgenerics >=0.6.13 + - r-acidplyr >=0.4.3 + - r-goalie >=0.7.0 + - r-pipette >=0.14.0 + - r-syntactic >=0.6.7 + # Suggests: + - r-httr2 >=0.2.3 test: commands: From e8f62ee48905272ba57122f5ab04b091d2dfeb1a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 16:34:25 -0600 Subject: [PATCH 0187/2173] Update r-deseqanalysis to 0.7.0 (#43470) * Update r-deseqanalysis to 0.7.0 * Update dependencies * Add pinning info --------- Co-authored-by: Michael Steinbaugh --- recipes/r-deseqanalysis/meta.yaml | 102 ++++++++++++++++-------------- 1 file changed, 54 insertions(+), 48 deletions(-) diff --git a/recipes/r-deseqanalysis/meta.yaml b/recipes/r-deseqanalysis/meta.yaml index f0da1dff143ad..4f0912b12277e 100644 --- a/recipes/r-deseqanalysis/meta.yaml +++ b/recipes/r-deseqanalysis/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.12" %} +{% set version = "0.7.0" %} {% set github = "https://github.com/acidgenomics/r-deseqanalysis" %} package: @@ -7,71 +7,77 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 6c6cde768a5ba7eb78fc2b456d97902c4cc3ce5094df737d2f063b997a24eb8b + sha256: cf5b1cae6fa44e0db16cba3aab8de0d738ab26af7326f9ff24ee42ffb05574d6 build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('r-deseqanalysis', max_pin="x.x") }} requirements: host: # Depends: - r-base - - bioconductor-deseq2 >=1.40.0 # Imports: - bioconductor-biocgenerics >=0.46.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-summarizedexperiment >=1.28.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidexperiment >=0.4.7 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.0 - - r-acidmarkdown >=0.2.5 - - r-acidplots >=0.5.5 - - r-acidplyr >=0.3.10 - - r-ggplot2 >=3.4.2 - - r-goalie >=0.6.9 - - r-pipette >=0.10.9 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.5 + - bioconductor-deseq2 >=1.40.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.2.8 + - r-acidexperiment >=0.4.8 + - r-acidgenerics >=0.6.13 + - r-acidgenomes >=0.5.2 + - r-acidmarkdown >=0.2.6 + - r-acidplots >=0.6.2 + - r-acidplyr >=0.4.2 + - r-ggplot2 >=3.4.3 + - r-goalie >=0.6.19 + - r-pipette >=0.14.0 + - r-syntactic >=0.6.7 # Suggests: - - bioconductor-apeglm >=1.20.0 - - bioconductor-tximport >=1.26.0 - - r-ashr >=2.2.54 - - r-basejump >=0.16.5 - - r-knitr >=1.42 - - r-rmarkdown >=2.21 + - bioconductor-apeglm >=1.22.0 + - bioconductor-tximport >=1.28.0 + - r-ashr >=2.2.63 + - r-basejump >=0.17.0 + - r-complexupset >=1.3.3 + - r-ggrepel >=0.9.3 + - r-knitr >=1.44 + - r-pheatmap >=1.0.12 + - r-rmarkdown >=2.25 run: # Depends: - r-base - - bioconductor-deseq2 >=1.40.0 # Imports: - bioconductor-biocgenerics >=0.46.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-summarizedexperiment >=1.28.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidexperiment >=0.4.7 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.0 - - r-acidmarkdown >=0.2.5 - - r-acidplots >=0.5.5 - - r-acidplyr >=0.3.10 - - r-ggplot2 >=3.4.2 - - r-goalie >=0.6.9 - - r-pipette >=0.10.9 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.5 + - bioconductor-deseq2 >=1.40.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.2.8 + - r-acidexperiment >=0.4.8 + - r-acidgenerics >=0.6.13 + - r-acidgenomes >=0.5.2 + - r-acidmarkdown >=0.2.6 + - r-acidplots >=0.6.2 + - r-acidplyr >=0.4.2 + - r-ggplot2 >=3.4.3 + - r-goalie >=0.6.19 + - r-pipette >=0.14.0 + - r-syntactic >=0.6.7 # Suggests: - - bioconductor-apeglm >=1.20.0 - - bioconductor-tximport >=1.26.0 - - r-ashr >=2.2.54 - - r-basejump >=0.16.5 - - r-knitr >=1.42 - - r-rmarkdown >=2.21 + - bioconductor-apeglm >=1.22.0 + - bioconductor-tximport >=1.28.0 + - r-ashr >=2.2.63 + - r-basejump >=0.17.0 + - r-complexupset >=1.3.3 + - r-ggrepel >=0.9.3 + - r-knitr >=1.44 + - r-pheatmap >=1.0.12 + - r-rmarkdown >=2.25 test: commands: From 13f6052d28b824e9678c13cb33f06f5a18e23906 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 17:37:28 -0600 Subject: [PATCH 0188/2173] Update r-basejump to 0.18.0 (#43461) * Update r-basejump to 0.18.0 * Update dependencies * Fix typo --------- Co-authored-by: Michael Steinbaugh --- recipes/r-basejump/meta.yaml | 57 +++++++++++++++++------------------- 1 file changed, 27 insertions(+), 30 deletions(-) diff --git a/recipes/r-basejump/meta.yaml b/recipes/r-basejump/meta.yaml index 731fe52af6b3b..8e6d80ca32c6f 100644 --- a/recipes/r-basejump/meta.yaml +++ b/recipes/r-basejump/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.17.0" %} +{% set version = "0.18.0" %} {% set github = "https://github.com/acidgenomics/r-basejump" %} package: @@ -7,48 +7,45 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 98a0c18f37fdcff995fd98020828a3ef91a5ca1314d5968b27793ddd2975203d + sha256: 06b216c539d112468172d021ba9445b8d98918609319fb34c200093fa052cbb9 build: - number: 1 + number: 0 noarch: generic - rpaths: - - lib/R/lib/ - - lib/ + run_exports: + - {{ pin_subpackage('r-basejump', max_pin="x.x") }} requirements: host: # Depends: - r-base # Imports: - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - r-acidbase - - r-acidexperiment - - r-acidgenomes - - r-acidmarkdown - - r-acidplots - - r-acidplyr - - r-acidsinglecell - - r-magrittr - - r-pipette - - r-syntactic + - bioconductor-singlecellexperiment >=1.22.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidexperiment >=0.5.0 + - r-acidgenomes >=0.6.0 + - r-acidmarkdown >=0.3.0 + - r-acidplots >=0.7.0 + - r-acidplyr >=0.5.0 + - r-acidsinglecell >=0.4.0 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 run: # Depends: - r-base # Imports: - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - r-acidbase - - r-acidexperiment - - r-acidgenomes - - r-acidmarkdown - - r-acidplots - - r-acidplyr - - r-acidsinglecell - - r-magrittr - - r-pipette - - r-syntactic + - bioconductor-singlecellexperiment >=1.22.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidexperiment >=0.5.0 + - r-acidgenomes >=0.6.0 + - r-acidmarkdown >=0.3.0 + - r-acidplots >=0.7.0 + - r-acidplyr >=0.5.0 + - r-acidsinglecell >=0.4.0 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 test: commands: From 4754d8b083dc31ceb9fe50bd8490587249d081ce Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 17:37:47 -0600 Subject: [PATCH 0189/2173] Update r-cellosaurus to 0.8.1 (#43523) * Update r-cellosaurus to 0.8.0 * Update r-cellosaurus to 0.8.1.9000 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-cellosaurus/meta.yaml | 33 ++++++++++++++------------------- 1 file changed, 14 insertions(+), 19 deletions(-) diff --git a/recipes/r-cellosaurus/meta.yaml b/recipes/r-cellosaurus/meta.yaml index d584165ffbe84..0a6c31bd625d5 100644 --- a/recipes/r-cellosaurus/meta.yaml +++ b/recipes/r-cellosaurus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.2" %} +{% set version = "0.8.1" %} {% set github = "https://github.com/acidgenomics/r-cellosaurus" %} package: @@ -7,14 +7,11 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: f3f5dafc49800f6688e1a20526236f63790d5a41d466d9b90484a7fa5608929f + sha256: c18ed889a603e15332afdc71cd7fb1ab13701fe892e5247c55ba6fbb630c2677 build: noarch: generic number: 0 - rpaths: - - lib/R/lib/ - - lib/ run_exports: - {{ pin_subpackage('r-cellosaurus', max_pin="x.x") }} @@ -26,14 +23,13 @@ requirements: - bioconductor-biocgenerics >=0.46.0 - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.6.19 - - r-acidcli >=0.2.8 - - r-acidgenerics >=0.6.8 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidgenerics >=0.7.1 - r-acidplyr >=0.4.2 - - r-goalie >=0.6.15 - - r-pipette >=0.12.0 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.6 + - r-goalie >=0.7.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 run: # Depends: - r-base @@ -41,14 +37,13 @@ requirements: - bioconductor-biocgenerics >=0.46.0 - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.6.19 - - r-acidcli >=0.2.8 - - r-acidgenerics >=0.6.8 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidgenerics >=0.7.1 - r-acidplyr >=0.4.2 - - r-goalie >=0.6.15 - - r-pipette >=0.12.0 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.6 + - r-goalie >=0.7.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 test: commands: From 5b3b367064be1108611adc256d1c6909987b92ed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 17:38:06 -0600 Subject: [PATCH 0190/2173] Update r-panther to 0.5.0 (#43535) * Update r-panther to 0.5.0 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-panther/meta.yaml | 43 +++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 23 deletions(-) diff --git a/recipes/r-panther/meta.yaml b/recipes/r-panther/meta.yaml index 4a154083a3f82..2e919526cef60 100644 --- a/recipes/r-panther/meta.yaml +++ b/recipes/r-panther/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.0" %} +{% set version = "0.5.0" %} {% set github = "https://github.com/acidgenomics/r-panther" %} package: @@ -7,14 +7,13 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 231f84aa649b74d06a71d10196bf0b7e71c9b64c9a6e3632c499e53c485d722b + sha256: e636e0e6ec3bbaf382609f93f2b02311db3b9138a4819e777176cabd07e7a05c build: number: 0 noarch: generic - rpaths: - - lib/R/lib/ - - lib/ + run_exports: + - {{ pin_subpackage('r-panther', max_pin="x.x") }} requirements: host: @@ -24,15 +23,14 @@ requirements: - bioconductor-biocgenerics >=0.46.0 - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.6.18 - - r-acidcli >=0.2.8 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.1 - - r-acidplyr >=0.3.11 - - r-goalie >=0.6.14 - - r-pipette >=0.11.1 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.6 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidgenerics >=0.7.3 + - r-acidgenomes >=0.6.0 + - r-acidplyr >=0.5.0 + - r-goalie >=0.7.3 + - r-pipette >=0.14.1 + - r-syntactic >=0.7.0 run: # Depends: - r-base @@ -40,15 +38,14 @@ requirements: - bioconductor-biocgenerics >=0.46.0 - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.6.18 - - r-acidcli >=0.2.8 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.1 - - r-acidplyr >=0.3.11 - - r-goalie >=0.6.14 - - r-pipette >=0.11.1 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.6 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidgenerics >=0.7.3 + - r-acidgenomes >=0.6.0 + - r-acidplyr >=0.5.0 + - r-goalie >=0.7.3 + - r-pipette >=0.14.1 + - r-syntactic >=0.7.0 test: commands: From 00802c9ed9fd973ba700171908e5e91d9a10c35c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 17:38:21 -0600 Subject: [PATCH 0191/2173] Update r-eggnog to 0.3.0 (#43536) * Update r-eggnog to 0.3.0 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-eggnog/meta.yaml | 23 ++++++++++------------- 1 file changed, 10 insertions(+), 13 deletions(-) diff --git a/recipes/r-eggnog/meta.yaml b/recipes/r-eggnog/meta.yaml index cd1a8bcc35aaa..97de17d22f778 100644 --- a/recipes/r-eggnog/meta.yaml +++ b/recipes/r-eggnog/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.2" %} +{% set version = "0.3.0" %} {% set github = "https://github.com/acidgenomics/r-eggnog" %} package: @@ -7,14 +7,13 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 79540c0248a6a15c6450fe21845da6163a150f8998c761a697dd6b902f758a65 + sha256: 8c003ee0b7dd03b44b7d110eb5d45e46a98822950a8f7e75f70798d2c680cb2c build: number: 0 noarch: generic - rpaths: - - lib/R/lib/ - - lib/ + run_exports: + - {{ pin_subpackage('r-eggnog', max_pin="x.x") }} requirements: host: @@ -24,10 +23,9 @@ requirements: - bioconductor-biocgenerics >=0.46.0 - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.6.18 - - r-acidplyr >=0.3.11 - - r-goalie >=0.6.14 - - r-pipette >=0.11.1 + - r-acidbase >=0.7.1 + - r-goalie >=0.7.3 + - r-pipette >=0.14.1 run: # Depends: - r-base @@ -35,10 +33,9 @@ requirements: - bioconductor-biocgenerics >=0.46.0 - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.6.18 - - r-acidplyr >=0.3.11 - - r-goalie >=0.6.14 - - r-pipette >=0.11.1 + - r-acidbase >=0.7.1 + - r-goalie >=0.7.3 + - r-pipette >=0.14.1 test: commands: From c39429909190b72df1511a9979258aa19541a237 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 19:15:42 -0600 Subject: [PATCH 0192/2173] Update espresso to 1.4.0 (#43621) * Update espresso to 1.4.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/espresso/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/espresso/meta.yaml b/recipes/espresso/meta.yaml index c75e80df30a03..336ead6120ef1 100644 --- a/recipes/espresso/meta.yaml +++ b/recipes/espresso/meta.yaml @@ -1,16 +1,18 @@ -{% set version = "1.3.2" %} +{% set version = "1.4.0" %} package: name: espresso version: {{ version }} source: - sha256: c9d01f6e699ac9b7b781ee3726ee9c338bfd31442d3f9f25db5526f04424135e + sha256: 656a5ab152782e5bb195b25a3814a3b94c1ed9ae9c03a1692cf1bba0794d1295 url: https://github.com/Xinglab/espresso/releases/download/v{{ version }}/espresso_v_{{ version|replace(".", "_") }}.tar.gz build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('espresso', max_pin="x") }} requirements: run: From 8208a1e3699b6e57b25530622ffe2b88769612d6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 19:16:02 -0600 Subject: [PATCH 0193/2173] Update phykit to 1.11.16 (#43620) * Update phykit to 1.11.16 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/phykit/meta.yaml | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index 58f5ee435ca91..2cc69efc713ff 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.11.15" %} +{% set version = "1.11.16" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d1b6771b4226afafd37ef5b24838f90fd132a3f035eb31444c46506136f758e5 + sha256: 4bf542cfa50b70134a58bd0fe4ea63536388c781fe15902f4149d8c4aaa926c1 build: noarch: python @@ -121,7 +121,9 @@ build: - pk_thread_dna = phykit.phykit:thread_dna - pk_pal2nal = phykit.phykit:thread_dna - pk_p2n = phykit.phykit:thread_dna - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('phykit', max_pin="x") }} requirements: host: @@ -253,8 +255,12 @@ test: about: home: "https://github.com/jlsteenwyk/phykit" license: MIT + license_family: MIT summary: "PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data." + doc_url: https://jlsteenwyk.com/PhyKIT/ extra: recipe-maintainers: - pauldg + identifiers: + - doi:10.1093/bioinformatics/btab096 From bda42c633db7597d9ac91b95b1c2a0613b0a2127 Mon Sep 17 00:00:00 2001 From: Nina Murrell <63961601+ninashenker@users.noreply.github.com> Date: Wed, 11 Oct 2023 21:58:07 -0400 Subject: [PATCH 0194/2173] Add Neoloopfinder (#43584) * initial commit for neoloop package to bioconda * successful build neoloop 0.4.3 * Adding missing dependency * added run_exports --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/neoloop/meta.yaml | 78 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 recipes/neoloop/meta.yaml diff --git a/recipes/neoloop/meta.yaml b/recipes/neoloop/meta.yaml new file mode 100644 index 0000000000000..8f25df575a9bd --- /dev/null +++ b/recipes/neoloop/meta.yaml @@ -0,0 +1,78 @@ +{% set name = "neoloop" %} +{% set version = "0.4.3.post2" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://pypi.io/packages/source/n/neoloop/neoloop-0.4.3.post2.tar.gz + sha256: 2b2d2b9a807a02e4b52282a1cc0e4131f1dbbd5b386da68acdf5d4f320df740a + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - _libgcc_mutex 0.1 conda_forge + - _openmp_mutex 4.5 2_gnu + - ca-certificates 2022.12.7 ha878542_0 + - certifi 2022.12.7 pyhd8ed1ab_0 + - ld_impl_linux-64 2.40 h41732ed_0 + - libffi 3.4.2 h7f98852_5 + - libgcc-ng 12.2.0 h65d4601_19 + - libgomp 12.2.0 h65d4601_19 + - libstdcxx-ng 12.2.0 h46fd767_19 + - ncurses 6.3 h27087fc_1 + - openssl 1.1.1t h0b41bf4_0 + - pip 23.0.1 pyhd8ed1ab_0 + - python 3.10.8 h257c98d_0_cpython + - python_abi 3.10 3_cp310 + - readline 8.2 h8228510_1 + - setuptools 67.6.0 pyhd8ed1ab_0 + - tk 8.6.12 h27826a3_0 + - wheel 0.40.0 pyhd8ed1ab_0 + - xz 5.2.6 h166bdaf_0 + - zlib 1.2.13 h166bdaf_4 + run: + - cooler + - h5py + - intervaltree + - joblib 1.1.0 + - matplotlib-base + - networkx + - numpy + - pandas + - pomegranate 0.14.8 + - pybigwig + - pyensembl + - python >=3.6 + - r-base + - r-mgcv + - rpy2 + - scikit-learn 1.1.2 + - scipy + - tadlib + +test: + imports: + - neoloop + - neoloop.cnv + - neoloop.pastis + - neoloop.tadtool + - neoloop.visualize + +about: + home: https://github.com/XiaoTaoWang/NeoLoopFinder + license: https://github.com/XiaoTaoWang/NeoLoopFinder/blob/master/LICENSE + license_family: OTHER + license_file: LICENSE + summary: Predict neo-loops induced by structural variations + dev_url: 'https://github.com/XiaoTaoWang/NeoLoopFinder' + +extra: + recipe-maintainers: ninashenker From 06e5e1073abed0e6ea31f786813c47ae7f96c0e7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 11 Oct 2023 20:05:06 -0600 Subject: [PATCH 0195/2173] Update pango-designation to 1.23 (#43622) * Update pango-designation to 1.23 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/pango-designation/meta.yaml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/pango-designation/meta.yaml b/recipes/pango-designation/meta.yaml index c25d35907dab0..869455a8746fb 100644 --- a/recipes/pango-designation/meta.yaml +++ b/recipes/pango-designation/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.22" %} +{% set version = "1.23" %} package: name: pango-designation @@ -6,12 +6,16 @@ package: source: url: https://github.com/cov-lineages/pango-designation/archive/refs/tags/v{{ version }}.tar.gz - sha256: 740cbea6aa9c5305fc1c9d46478d98cc1722a32662e0e08ec686440698a6d5a9 + sha256: 5692d92d4b7ff902464552e81d71fc25dcafd0ada175af3b143246c14fc6d9c1 build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation -vvv . + entry_points: + - pango_designation = pango_designation.command:main + run_exports: + - {{ pin_subpackage('pango-designation', max_pin="x") }} requirements: host: @@ -29,7 +33,7 @@ about: license: CC-BY-NC-4.0 license_file: LICENSE.md summary: Repository for suggesting new lineages that should be added to the current - + extra: recipe-maintainers: - corneliusroemer From ccadfdbaccf195433e1084814a8006a2aeac733d Mon Sep 17 00:00:00 2001 From: Yasuhiro Tanizawa <30499043+nigyta@users.noreply.github.com> Date: Thu, 12 Oct 2023 11:06:17 +0900 Subject: [PATCH 0196/2173] Add submission_excel2xml (#43385) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * add submission-excel2xml * minor fix * submission-excel2xml added * submission-excel2xml added * Update meta.yaml * Update meta.yaml --------- Co-authored-by: 谷沢靖洋 --- recipes/submission-excel2xml/build.sh | 58 +++++++++++++++++++++++++ recipes/submission-excel2xml/meta.yaml | 37 ++++++++++++++++ recipes/submission-excel2xml/patch | 60 ++++++++++++++++++++++++++ 3 files changed, 155 insertions(+) create mode 100644 recipes/submission-excel2xml/build.sh create mode 100644 recipes/submission-excel2xml/meta.yaml create mode 100644 recipes/submission-excel2xml/patch diff --git a/recipes/submission-excel2xml/build.sh b/recipes/submission-excel2xml/build.sh new file mode 100644 index 0000000000000..e94caa89de577 --- /dev/null +++ b/recipes/submission-excel2xml/build.sh @@ -0,0 +1,58 @@ +#! /bin/bash + +gem install date -v "3.0.0" +gem install open3 -v "0.1.2" +gem install mini_portile2 -v "2.4.0" +gem install nokogiri -v "1.15.3" +gem install rubyzip -v "2.3.2" +gem install roo -v "2.10.0" +gem install builder -v "3.2.4" +gem install rexml -v "3.2.5" + +APPROOT=$PREFIX/opt/submission-excel2xml + + +mkdir -p $APPROOT + +# sed -i.bak '1 s|^.*$|#!/usr/bin/env ruby|g' *.rb + +cp excel2xml_dra.rb $APPROOT/ +cp validate_meta_dra.rb $APPROOT/ +cp excel2xml_jga.rb $APPROOT/ +cp validate_meta_jga.rb $APPROOT/ + +chmod a+x $APPROOT/excel2xml_dra.rb +chmod a+x $APPROOT/validate_meta_dra.rb +chmod a+x $APPROOT/excel2xml_jga.rb +chmod a+x $APPROOT/validate_meta_jga.rb + + +mkdir -p $APPROOT/xsd + +cd $APPROOT/xsd + +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.analysis.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.annotation.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.common.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.experiment.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.package.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.run.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.sample.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.study.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.submission.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.analysis.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.common.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.dac.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.data.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.dataset.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.experiment.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.policy.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.sample.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.study.xsd +curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.submission.xsd + +cd $PREFIX/bin +ln -s ../opt/submission-excel2xml/excel2xml_dra.rb ./ +ln -s ../opt/submission-excel2xml/validate_meta_dra.rb ./ +ln -s ../opt/submission-excel2xml/excel2xml_jga.rb ./ +ln -s ../opt/submission-excel2xml/validate_meta_jga.rb ./ diff --git a/recipes/submission-excel2xml/meta.yaml b/recipes/submission-excel2xml/meta.yaml new file mode 100644 index 0000000000000..fe1bdec983d3e --- /dev/null +++ b/recipes/submission-excel2xml/meta.yaml @@ -0,0 +1,37 @@ +package: + name: submission-excel2xml + version: "2.0.0" +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('submission-excel2xml', max_pin="x") }} + +source: + url: https://github.com/ddbj/submission-excel2xml/archive/refs/heads/master.zip + md5: 746ef9a1e1bd13f20a0b348fd080eb45 + patches: + - patch + +requirements: + build: + - make + host: + - ruby 3.2.2 + - compilers + - libxml2 + run: + - ruby 3.2.2 + - compilers + - libxml2 + +test: + commands: + - "excel2xml_jga.rb -h" + +about: + home: https://github.com/ddbj/submission-excel2xml + license: Apache License 2.0 + summary: Generate DRA metadata XML files from Excel spreadsheet + + diff --git a/recipes/submission-excel2xml/patch b/recipes/submission-excel2xml/patch new file mode 100644 index 0000000000000..59faa15a8cfa7 --- /dev/null +++ b/recipes/submission-excel2xml/patch @@ -0,0 +1,60 @@ +diff --git a/excel2xml_dra.rb b/excel2xml_dra.rb +index ff30c77..2dbf2ba 100644 +--- a/excel2xml_dra.rb ++++ b/excel2xml_dra.rb +@@ -1,4 +1,4 @@ +-#! /usr/bin/ruby ++#! /usr/bin/env ruby + # -*- coding: utf-8 -*- + + require 'rubygems' +diff --git a/excel2xml_jga.rb b/excel2xml_jga.rb +index 8bd6b32..0cdfebe 100644 +--- a/excel2xml_jga.rb ++++ b/excel2xml_jga.rb +@@ -1,4 +1,4 @@ +-#! /usr/bin/ruby ++#! /usr/bin/env ruby + # -*- coding: utf-8 -*- + + require 'rubygems' +diff --git a/validate_meta_dra.rb b/validate_meta_dra.rb +index 47d417d..8256cfb 100644 +--- a/validate_meta_dra.rb ++++ b/validate_meta_dra.rb +@@ -1,4 +1,4 @@ +-#! /usr/bin/ruby ++#! /usr/bin/env ruby + # -*- coding: utf-8 -*- + + require 'rubygems' +@@ -53,7 +53,7 @@ end + + ## Validate DRA XML against xsd + #xsd_path = "/opt/submission-excel2xml/" +-xsd_path = "xsd/" ++xsd_path = __dir__ + "/xsd/" + + puts "\n== XML validation against SRA xsd ==" + if FileTest.exist?("#{submission_id}_dra_Submission.xml") +diff --git a/validate_meta_jga.rb b/validate_meta_jga.rb +index 055bc61..1d3d2f6 100644 +--- a/validate_meta_jga.rb ++++ b/validate_meta_jga.rb +@@ -1,4 +1,4 @@ +-#! /usr/bin/ruby ++#! /usr/bin/env ruby + # -*- coding: utf-8 -*- + + require 'rexml/document' +@@ -41,8 +41,8 @@ meta_object = ['Submission', 'Study', 'Sample', 'Experiment', 'Data', 'Analysis' + ## + + ## Validate XMLs against JGA xsd +-xsd_path = "/opt/submission-excel2xml/" +-#xsd_path = "xsd/" ++#xsd_path = "/opt/submission-excel2xml/" ++xsd_path = __dir__ + "/xsd/" + + xml_a = [] + Dir.glob("#{submission_id}*xml").each{|xml| From db1ff472c955be5b22d2c93bae6d6b8dc8ae3a09 Mon Sep 17 00:00:00 2001 From: Arafat Rahman Date: Wed, 11 Oct 2023 19:08:52 -0700 Subject: [PATCH 0197/2173] Update build.sh for v0.5.2 (#43406) * Update build.sh for v0.5.2 * Update meta.yaml * Add run_exports for beav v0.5.2 * Update meta.yaml for run_exports * Update meta.yaml * Update meta.yaml for run_exports * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/beav/build.sh | 2 +- recipes/beav/meta.yaml | 13 ++++++++++--- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/recipes/beav/build.sh b/recipes/beav/build.sh index 9c4e721721705..21c585b4bf8ff 100755 --- a/recipes/beav/build.sh +++ b/recipes/beav/build.sh @@ -17,7 +17,7 @@ mv models/* $BEAV_DIR/models mv test_data/* $BEAV_DIR/test_data mv DBSCAN-SWA $BEAV_DIR/software/ - +mv PyCirclize $BEAV_DIR/software/ mv PaperBLAST $BEAV_DIR/software/ mkdir $BEAV_DIR/software/PaperBLAST/bin/blast diff --git a/recipes/beav/meta.yaml b/recipes/beav/meta.yaml index d4c1a041c1ba0..e82a265f199d3 100644 --- a/recipes/beav/meta.yaml +++ b/recipes/beav/meta.yaml @@ -1,10 +1,12 @@ {% set name = "beav" %} -{% set version = "0.5.1" %} -{% set sha256 = "0266f133815aefa62fe8e69a9f4bec3984bdb17650144345a5d03266e46390dc" %} +{% set version = "0.5.2" %} +{% set sha256 = "28b1f541725d59b28543c76a40be0f74cd0e9b763e59c2cb58a3c5658e777e09" %} {% set dbscan_git = "condabeav0.5" %} {% set dbscan_sha256 = "2fe08873026fe63a9992bfb997e59fecce7facb903778983dc6917c962573463" %} {% set gapmind_git = "Beav0.5.1conda" %} {% set gapmind_sha256 = "a5d0c4855d65355fa4675172a65b97cb03d4ec2e5098a08bece84f677e48a244" %} +{% set pycirclize_git = "v0.5.1-beav0.5.1" %} +{% set pycirclize_sha256 = "969990f486ebdb51b73cef7d8f6cea9ae34b97fe8e2de376e5599aff339aa78f" %} package: name: {{ name }} @@ -19,10 +21,15 @@ source: - url: https://github.com/weisberglab/PaperBLAST_Beav/archive/refs/tags/{{ gapmind_git }}.tar.gz folder: PaperBLAST sha256: {{ gapmind_sha256 }} + - url: https://github.com/acarafat/pyCirclize/archive/refs/tags/{{ pycirclize_git }}.tar.gz + folder: PyCirclize + sha256: {{pycirclize_sha256}} build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} requirements: run: @@ -30,7 +37,7 @@ requirements: - perl >=5.22.0 - hmmer >=3.3.2 - bakta >=1.6 - - integron_finder >=2.0.1 + - integron_finder =2.0rc6 - macsyfinder - defense-finder - fastani From adf6a51a364a76a65be1bf0ffa67d40ab561c5be Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 01:05:37 -0600 Subject: [PATCH 0198/2173] Update tcdemux to 0.0.18 (#43627) --- recipes/tcdemux/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tcdemux/meta.yaml b/recipes/tcdemux/meta.yaml index dca6f8e300868..4cf69dfd97390 100644 --- a/recipes/tcdemux/meta.yaml +++ b/recipes/tcdemux/meta.yaml @@ -1,5 +1,5 @@ --- -{% set version = "0.0.17" %} +{% set version = "0.0.18" %} package: name: tcdemux @@ -7,7 +7,7 @@ package: source: url: https://github.com/TomHarrop/tcdemux/archive/refs/tags/{{ version }}.tar.gz - sha256: dc91a17e9f32de9f38001fee2b494aec2b50408a3f36845678ab8a9670a40cda + sha256: 095a00e37638e502bdd6a185d905ca7fb177f5ef598b113ff26506581eca0cc7 build: number: 0 From 5cc2d401abfbae550550cf75764861f9ba831472 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 01:06:27 -0600 Subject: [PATCH 0199/2173] Update ont-modkit to 0.2.1 (#43625) --- recipes/ont-modkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml index 98c62caaf3178..e265a6e9485fb 100644 --- a/recipes/ont-modkit/meta.yaml +++ b/recipes/ont-modkit/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.0" %} -{% set sha256 = "bb9970c5fb9ef2387d01c92078df0b6723c331d600567a6b6b9e011bdfbbdd97" %} +{% set version = "0.2.1" %} +{% set sha256 = "5602a3dbf3c2cfc962b45743da229dbf440d91b2e0d4e50d98413e371c8c0b51" %} package: name: ont-modkit From f96a63de4e1b5f430eb27b74fafdad6aeaf265dd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 01:06:42 -0600 Subject: [PATCH 0200/2173] Update gnparser to 1.8.0 (#43624) --- recipes/gnparser/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gnparser/meta.yaml b/recipes/gnparser/meta.yaml index 7b93c5fc72c08..3833b72d233ef 100644 --- a/recipes/gnparser/meta.yaml +++ b/recipes/gnparser/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.7.5" %} -{% set sha256 = "52bb1129e26c5aafa929bde57d60c94b6fea89ac0fbeb137bdf404cdfd5d65a2" %} +{% set version = "1.8.0" %} +{% set sha256 = "4812f334d137d9aed7be9cfce874c060a3fc2833ca2595a6bce1139ff41d3495" %} package: name: "gnparser" From 50a9e41173a3a52d05dff368dc73a789e1096afe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 01:07:47 -0600 Subject: [PATCH 0201/2173] Update pxblat to 0.3.4 (#43623) --- recipes/pxblat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index 67ada24b74abd..c1b7d1b9467db 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "0.3.2" %} -{% set sha256 = "7d8e2ae09fce7ef12b8aa0f6f5a9b5343676a035ac1cbaa3cf125dba2d7573d3" %} +{% set version = "0.3.4" %} +{% set sha256 = "59ff417a0ee2e6760cb96d653ffbff2d8d76e5f0e498b2a3915bfc578b276f06" %} package: name: {{ name|lower }} From d822b344705edf5f13a5345634df0e09166c4fa9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 01:08:00 -0600 Subject: [PATCH 0202/2173] Update skani to 0.2.1 (#43626) --- recipes/skani/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skani/meta.yaml b/recipes/skani/meta.yaml index 31cc552e725ed..7c86f9a689682 100644 --- a/recipes/skani/meta.yaml +++ b/recipes/skani/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: skani @@ -11,7 +11,7 @@ build: source: url: https://github.com/bluenote-1577/skani/archive/v{{ version }}.tar.gz - sha256: 59ed7e71a57238a8e44a213e9ccb86190e1225a9aea47a0fd3bf95c7a694fe16 + sha256: 0516323d2ccc90889206b215f67e84bfa8fc9c4233608113508f27c1771bd126 requirements: build: From 711003a6574a3b8aacf5280cd386ef049c1c910d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 01:08:15 -0600 Subject: [PATCH 0203/2173] Update capcruncher to 0.3.6 (#43599) --- recipes/capcruncher/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/capcruncher/meta.yaml b/recipes/capcruncher/meta.yaml index 2e156f597dbc7..6d285b8f2bce1 100644 --- a/recipes/capcruncher/meta.yaml +++ b/recipes/capcruncher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "capcruncher" %} -{% set version = "0.3.5" %} +{% set version = "0.3.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/capcruncher-{{ version }}.tar.gz - sha256: 3f4a06c71fc7b3a6218704ecf9a01460350114b95b753a9e96303f684c6224b2 + sha256: 1f3c23b3c022b0c681f8d66d7a54463591c06632721cbe6684246df64e23015d build: number: 0 From ca6e47f51c3d20ba865bb0cf0a5a59f738b30d58 Mon Sep 17 00:00:00 2001 From: Anders Jemt Date: Thu, 12 Oct 2023 09:12:42 +0200 Subject: [PATCH 0204/2173] Add vcf2cytosure (#43577) * starting with vcf2cytosure * use pypi version of vcf2cytosure * adds run_exports to meta.yml * remove run requirements from host --- recipes/vcf2cytosure/meta.yaml | 44 ++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 recipes/vcf2cytosure/meta.yaml diff --git a/recipes/vcf2cytosure/meta.yaml b/recipes/vcf2cytosure/meta.yaml new file mode 100644 index 0000000000000..b12cd42dbb2bb --- /dev/null +++ b/recipes/vcf2cytosure/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "vcf2cytosure" %} +{% set version = "0.9.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 96e89005869cf6cfa42bba30f6063721326107a490efca150cf65cc65eb0e9d6 + +build: + noarch: python + number: 0 + entry_points: + - vcf2cytosure=vcf2cytosure.vcf2cytosure:main + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage("vcf2cytosure", max_pin="x.x") }} + +requirements: + host: + - pip + - python + run: + - cyvcf2 + - lxml + - pandas + - python + +test: + imports: + - tests + - vcf2cytosure + - vcf2cytosure.constants + commands: + - vcf2cytosure --help + +about: + home: "https://github.com/NBISweden/vcf2cytosure" + license: MIT + license_family: MIT + summary: "Convert VCF with structural variations to CytoSure format" + From c2b9267521194102c857211b38992bfbe1bbe410 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 03:05:25 -0600 Subject: [PATCH 0205/2173] Update annonars to 0.21.1 (#43629) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 6027c1035a66e..5ad2456ae0ff0 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.21.0" %} +{% set version = "0.21.1" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 21d2ef0796f9e8696b8b7e4ccaf0d199c965b9432e5af202462d4980188e9a68 + sha256: 5623bdc4fd93b9de87dbbd938260defab4d744aecb5511804d851cc0434be683 requirements: build: From af1a6d4692f622cbf2b14a8bf0fd673afb081bfe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 05:39:51 -0600 Subject: [PATCH 0206/2173] Update r-acidgsea to 0.9.0 (#43471) * Update r-acidgsea to 0.9.0 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-acidgsea/meta.yaml | 99 +++++++++++++++++------------------- 1 file changed, 48 insertions(+), 51 deletions(-) diff --git a/recipes/r-acidgsea/meta.yaml b/recipes/r-acidgsea/meta.yaml index 641a06f646cb9..557872f114317 100644 --- a/recipes/r-acidgsea/meta.yaml +++ b/recipes/r-acidgsea/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.9" %} +{% set version = "0.9.0" %} {% set github = "https://github.com/acidgenomics/r-acidgsea" %} package: @@ -7,72 +7,69 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 07be1b62a186454c5eb55cbb6995fd30744676a79940a467501e5e4b3be324a5 + sha256: 7ebe40096263d7d8ae4fd2c0ec49b2a3afcb45fb26d7ba1816d99fd16b3ff73e build: number: 0 noarch: generic - rpaths: - - lib/R/lib/ - - lib/ + run_exports: + - {{ pin_subpackage('r-acidgsea', max_pin="x.x") }} requirements: host: # Depends: - r-base # Imports: - - bioconductor-biocgenerics >=0.44.0 - - bioconductor-fgsea >=1.24.0 - - bioconductor-genomeinfodb >=1.34.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-summarizedexperiment >=1.28.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidexperiment >=0.4.7 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.0 - - r-acidmarkdown >=0.2.5 - - r-acidplots >=0.5.5 - - r-acidplyr >=0.3.10 - - r-deseqanalysis >=0.6.8 - - r-ggplot2 >=3.4.2 - - r-goalie >=0.6.9 - - r-pipette >=0.10.9 - - r-syntactic >=0.6.5 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-fgsea >=1.26.0 + - bioconductor-genomeinfodb >=1.36.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.7.1 + - r-acidgenomes >=0.6.0 + - r-acidmarkdown >=0.3.0 + - r-acidplots >=0.7.0 + - r-acidplyr >=0.5.0 + - r-deseqanalysis >=0.7.0 + - r-ggplot2 >=3.4.3 + - r-goalie >=0.7.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biocparallel >=1.32.0 - - r-basejump >=0.16.5 - - r-knitr >=1.42 - - r-rmarkdown >=2.17 + - r-basejump >=0.18.0 + - r-knitr >=1.44 + - r-rmarkdown >=2.25 run: # Depends: - r-base # Imports: - - bioconductor-biocgenerics >=0.44.0 - - bioconductor-fgsea >=1.24.0 - - bioconductor-genomeinfodb >=1.34.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-summarizedexperiment >=1.28.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidexperiment >=0.4.7 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.0 - - r-acidmarkdown >=0.2.5 - - r-acidplots >=0.5.5 - - r-acidplyr >=0.3.10 - - r-deseqanalysis >=0.6.8 - - r-ggplot2 >=3.4.2 - - r-goalie >=0.6.9 - - r-pipette >=0.10.9 - - r-syntactic >=0.6.5 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-fgsea >=1.26.0 + - bioconductor-genomeinfodb >=1.36.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.7.1 + - r-acidgenomes >=0.6.0 + - r-acidmarkdown >=0.3.0 + - r-acidplots >=0.7.0 + - r-acidplyr >=0.5.0 + - r-deseqanalysis >=0.7.0 + - r-ggplot2 >=3.4.3 + - r-goalie >=0.7.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biocparallel >=1.32.0 - - r-basejump >=0.16.5 - - r-knitr >=1.42 - - r-rmarkdown >=2.17 + - r-basejump >=0.18.0 + - r-knitr >=1.44 + - r-rmarkdown >=2.25 test: commands: From 3cd59799c0d330abfe98f55f4cd84a1cfb0d747b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 05:40:00 -0600 Subject: [PATCH 0207/2173] Update r-bcbiosinglecell to 0.7.0 (#43524) * Update r-bcbiosinglecell to 0.7.0 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-bcbiosinglecell/meta.yaml | 101 +++++++++++++--------------- 1 file changed, 48 insertions(+), 53 deletions(-) diff --git a/recipes/r-bcbiosinglecell/meta.yaml b/recipes/r-bcbiosinglecell/meta.yaml index 85567ff0f6c94..822cb5d07aea9 100644 --- a/recipes/r-bcbiosinglecell/meta.yaml +++ b/recipes/r-bcbiosinglecell/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.4" %} +{% set version = "0.7.0" %} {% set github = "https://github.com/hbc/bcbioSingleCell" %} package: @@ -7,76 +7,71 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 12b322cd4ea608dba84d1bb215c0fe9eb36f4639e6d4c3802ed4c1d25f5f4da2 + sha256: 60e4aaf76db0b307d0fec376db7d533faffce465c14e20fbbbeb981603ae8603 build: number: 0 noarch: generic - rpaths: - - lib/R/lib/ - - lib/ + run_exports: + - {{ pin_subpackage('r-bcbiosinglecell', max_pin="x.x") }} requirements: host: # Depends: - r-base - - bioconductor-singlecellexperiment >=1.18.0 # Imports: - - bioconductor-biocgenerics >=0.42.0 - - bioconductor-biocparallel >=1.30.0 - - bioconductor-iranges >=2.30.0 - - bioconductor-s4vectors >=0.34.0 - - bioconductor-summarizedexperiment >=1.26.0 - - r-acidbase >=0.6.8 - - r-acidcli >=0.2.4 - - r-acidexperiment >=0.4.4 - - r-acidgenerics >=0.6.4 - - r-acidgenomes >=0.4.4 - - r-acidmarkdown >=0.2.4 - - r-acidplots >=0.5.1 - - r-acidplyr >=0.3.2 - - r-acidsinglecell >=0.3.3 - - r-bcbiobase >=0.8.1 - - r-ggplot2 >=3.3.6 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-singlecellexperiment >=1.22.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.7.1 + - r-acidgenomes >=0.6.0 + - r-acidmarkdown >=0.3.0 + - r-acidplots >=0.7.0 + - r-acidplyr >=0.5.0 + - r-acidsinglecell >=0.4.0 + - r-bcbiobase >=0.9.0 + - r-ggplot2 >=3.4.3 - r-ggridges >=0.5.4 - - r-goalie >=0.6.6 - - r-pipette >=0.10.0 - - r-stringi >=1.7.8 - - r-syntactic >=0.6.3 + - r-goalie >=0.7.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biostrings >=2.64.0 - - r-basejump >=0.16.0 - - r-rmarkdown >=2.17 + - bioconductor-biostrings >=2.68.0 + - r-basejump >=0.18.0 + - r-rmarkdown >=2.25 run: # Depends: - r-base - - bioconductor-singlecellexperiment >=1.18.0 # Imports: - - bioconductor-biocgenerics >=0.42.0 - - bioconductor-biocparallel >=1.30.0 - - bioconductor-iranges >=2.30.0 - - bioconductor-s4vectors >=0.34.0 - - bioconductor-summarizedexperiment >=1.26.0 - - r-acidbase >=0.6.8 - - r-acidcli >=0.2.4 - - r-acidexperiment >=0.4.4 - - r-acidgenerics >=0.6.4 - - r-acidgenomes >=0.4.4 - - r-acidmarkdown >=0.2.4 - - r-acidplots >=0.5.1 - - r-acidplyr >=0.3.2 - - r-acidsinglecell >=0.3.3 - - r-bcbiobase >=0.8.1 - - r-ggplot2 >=3.3.6 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-singlecellexperiment >=1.22.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.7.1 + - r-acidgenomes >=0.6.0 + - r-acidmarkdown >=0.3.0 + - r-acidplots >=0.7.0 + - r-acidplyr >=0.5.0 + - r-acidsinglecell >=0.4.0 + - r-bcbiobase >=0.9.0 + - r-ggplot2 >=3.4.3 - r-ggridges >=0.5.4 - - r-goalie >=0.6.6 - - r-pipette >=0.10.0 - - r-stringi >=1.7.8 - - r-syntactic >=0.6.3 + - r-goalie >=0.7.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biostrings >=2.64.0 - - r-basejump >=0.16.0 - - r-rmarkdown >=2.17 + - bioconductor-biostrings >=2.68.0 + - r-basejump >=0.18.0 + - r-rmarkdown >=2.25 test: commands: From 8501e9d378eeb857ae4f0c0ba7acb4ee90ed6872 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 05:40:07 -0600 Subject: [PATCH 0208/2173] Update r-chromium to 0.3.0 (#43531) * Update r-chromium to 0.3.0 * Update dependencies * Fix typo --------- Co-authored-by: Michael Steinbaugh --- recipes/r-chromium/meta.yaml | 70 ++++++++++++++++++------------------ 1 file changed, 35 insertions(+), 35 deletions(-) diff --git a/recipes/r-chromium/meta.yaml b/recipes/r-chromium/meta.yaml index 69ff59c5adfba..323e18c9b526c 100644 --- a/recipes/r-chromium/meta.yaml +++ b/recipes/r-chromium/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.1" %} +{% set version = "0.3.0" %} {% set github = "https://github.com/acidgenomics/r-chromium" %} package: @@ -7,53 +7,53 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: ece585f9516dc760c35bea9720bcab9feff920121f0440dc5d546305bbe6c048 + sha256: e2f58a6141ce55b73d631323360d86d3713bf7870476c2505f457c61f41a3d0b build: - number: 1 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('r-chromium', max_pin="x.x") }} requirements: host: # Depends: - r-base # Imports: - - bioconductor-rhdf5 >=2.42.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-singlecellexperiment >=1.20.0 - - bioconductor-summarizedexperiment >=1.28.0 - - r-acidbase >=0.6.12 - - r-acidcli >=0.2.7 - - r-acidexperiment >=0.4.5 - - r-acidgenerics >=0.6.6 - - r-acidgenomes >=0.4.7 - - r-acidplyr >=0.3.6 - - r-acidsinglecell >=0.3.4 - - r-goalie >=0.6.8 - - r-matrix >=1.5.1 - - r-pipette >=0.10.3 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.4 + - bioconductor-rhdf5 >=2.44.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-singlecellexperiment >=1.22.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.2.8 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.6.13 + - r-acidgenomes >=0.6.0 + - r-acidplyr >=0.4.3 + - r-acidsinglecell >=0.3.7 + - r-goalie >=0.7.0 + - r-matrix >=1.6.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.6.7 run: # Depends: - r-base # Imports: - - bioconductor-rhdf5 >=2.42.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-singlecellexperiment >=1.20.0 - - bioconductor-summarizedexperiment >=1.28.0 - - r-acidbase >=0.6.12 - - r-acidcli >=0.2.7 - - r-acidexperiment >=0.4.5 - - r-acidgenerics >=0.6.6 - - r-acidgenomes >=0.4.7 - - r-acidplyr >=0.3.6 - - r-acidsinglecell >=0.3.4 - - r-goalie >=0.6.8 - - r-matrix >=1.5.1 - - r-pipette >=0.10.3 - - r-stringi >=1.7.12 - - r-syntactic >=0.6.4 + - bioconductor-rhdf5 >=2.44.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-singlecellexperiment >=1.22.0 + - bioconductor-summarizedexperiment >=1.30.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.2.8 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.6.13 + - r-acidgenomes >=0.6.0 + - r-acidplyr >=0.4.3 + - r-acidsinglecell >=0.3.7 + - r-goalie >=0.7.0 + - r-matrix >=1.6.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.6.7 test: commands: From 6ed976f62e9863f6d7dc3f5db74ecd567148a3d8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 08:04:15 -0600 Subject: [PATCH 0209/2173] Update skder to 1.0.7 (#43634) --- recipes/skder/build.sh | 4 ++-- recipes/skder/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/skder/build.sh b/recipes/skder/build.sh index 521331d75ac6a..77291308f3479 100644 --- a/recipes/skder/build.sh +++ b/recipes/skder/build.sh @@ -5,8 +5,8 @@ $PYTHON -m pip install . --ignore-installed --no-deps -vv mkdir -p ${PREFIX}/bin # (re)-compile C++ programs -${CXX} -std=c++11 -o ${PREFIX}/bin/skDERcore skDERcore.cpp -${CXX} -std=c++11 -o ${PREFIX}/bin/skDERsum skDERsum.cpp +${CXX} -std=c++11 -o ${PREFIX}/bin/skDERcore src/skDER/skDERcore.cpp +${CXX} -std=c++11 -o ${PREFIX}/bin/skDERsum src/skDER/skDERsum.cpp chmod +x ${PREFIX}/bin/skDERcore chmod +x ${PREFIX}/bin/skDERsum diff --git a/recipes/skder/meta.yaml b/recipes/skder/meta.yaml index 16b4a58dc844a..eb286dd48636b 100644 --- a/recipes/skder/meta.yaml +++ b/recipes/skder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skder" %} -{% set version = "1.0.6" %} +{% set version = "1.0.7" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/raufs/skDER/archive/refs/tags/v{{ version }}.tar.gz - sha256: 781b618a9a9b70418e3a697ffd450627ca5840cd7f367c71d7e183ed17c6e9e3 + sha256: 057483c05f5364bfaa0ee12b5f59a3272eaf3de81d6bfea8d53422ba110c840d build: number: 0 From 1648caca43ee134d2d8d3445886ed4fe98984947 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 08:19:01 -0600 Subject: [PATCH 0210/2173] Update r-bcbiornaseq to 0.6.0 (#43521) * Update r-bcbiornaseq to 0.6.0 * Update dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-bcbiornaseq/meta.yaml | 161 ++++++++++++++++---------------- 1 file changed, 78 insertions(+), 83 deletions(-) diff --git a/recipes/r-bcbiornaseq/meta.yaml b/recipes/r-bcbiornaseq/meta.yaml index ece9172e7e173..24cd7740aadd0 100644 --- a/recipes/r-bcbiornaseq/meta.yaml +++ b/recipes/r-bcbiornaseq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.5" %} +{% set version = "0.6.0" %} {% set github = "https://github.com/hbc/bcbioRNASeq" %} package: @@ -7,110 +7,105 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 8a6d837f2310bacb172133050c562bb25a590c46eb5e683c348d02b2a410e829 + sha256: 317f907519a0242892f461eb10d4cd3cd5421eedc765ffddb6435cd2186e5541 build: number: 0 noarch: generic - rpaths: - - lib/R/lib/ - - lib/ + run_exports: + - {{ pin_subpackage('r-bcbiornaseq', max_pin="x.x") }} requirements: host: # Depends: - r-base - - bioconductor-summarizedexperiment >=1.28.0 # Imports: - - bioconductor-biocgenerics >=0.44.0 - - bioconductor-deseq2 >=1.38.0 - - bioconductor-edger >=3.40.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-tximport >=1.26.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidexperiment >=0.4.7 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.0 - - r-acidplots >=0.5.5 - - r-bcbiobase >=0.8.1 - - r-ggplot2 >=3.4.2 - - r-goalie >=0.6.8 - - r-pipette >=0.10.9 - - r-syntactic >=0.6.6 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-deseq2 >=1.40.0 + - bioconductor-edger >=3.42.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-tximport >=1.28.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.7.2 + - r-acidgenomes >=0.6.0 + - r-acidplots >=0.7.1 + - r-bcbiobase >=0.9.0 + - r-ggplot2 >=3.4.3 + - r-goalie >=0.7.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biocstyle >=2.26.0 - - bioconductor-clusterprofiler >=4.6.0 - - bioconductor-degreport >=1.34.0 - - bioconductor-dose >=3.24.0 - - bioconductor-enrichplot >=1.18.0 + - bioconductor-biocstyle >=2.28.0 + - bioconductor-clusterprofiler >=4.8.0 + - bioconductor-degreport >=1.36.0 + - bioconductor-dose >=3.26.0 + - bioconductor-enrichplot >=1.20.0 - bioconductor-ensdb.hsapiens.v75 >=2.99.0 - - bioconductor-genomeinfodb >=1.34.0 - - bioconductor-org.hs.eg.db >=3.16.0 - - bioconductor-org.mm.eg.db >=3.16.0 - - bioconductor-pathview >=1.38.0 - - bioconductor-rhdf5 >=2.42.0 - - bioconductor-vsn >=3.66.0 - - r-acidgsea >=0.8.8 - - r-basejump >=0.16.5 - - r-deseqanalysis >=0.6.8 - - r-ggnewscale >=0.4.8 + - bioconductor-genomeinfodb >=1.36.0 + - bioconductor-org.hs.eg.db >=3.17.0 + - bioconductor-org.mm.eg.db >=3.17.0 + - bioconductor-pathview >=1.40.0 + - bioconductor-rhdf5 >=2.44.0 + - bioconductor-vsn >=3.68.0 + - r-acidgsea >=0.9.0 + - r-acidmarkdown >=0.3.0 + - r-basejump >=0.18.0 + - r-deseqanalysis >=0.7.0 + - r-ggnewscale >=0.4.9 - r-hexbin >=1.28.3 - - r-knitr >=1.42 + - r-knitr >=1.44 - r-pheatmap >=1.0.12 - - r-rmarkdown >=2.21 - - r-r.utils >=2.12.2 - - r-stringi >=1.7.12 - - r-viridis >=0.6.2 - - r-withr >=2.5.0 + - r-rmarkdown >=2.25 + - r-viridis >=0.6.4 + - r-withr >=2.5.1 run: # Depends: - r-base - - bioconductor-summarizedexperiment >=1.28.0 # Imports: - - bioconductor-biocgenerics >=0.44.0 - - bioconductor-deseq2 >=1.38.0 - - bioconductor-edger >=3.40.0 - - bioconductor-iranges >=2.32.0 - - bioconductor-s4vectors >=0.36.0 - - bioconductor-tximport >=1.26.0 - - r-acidbase >=0.6.15 - - r-acidcli >=0.2.7 - - r-acidexperiment >=0.4.7 - - r-acidgenerics >=0.6.7 - - r-acidgenomes >=0.5.0 - - r-acidplots >=0.5.5 - - r-bcbiobase >=0.8.1 - - r-ggplot2 >=3.4.2 - - r-goalie >=0.6.8 - - r-pipette >=0.10.9 - - r-syntactic >=0.6.6 + - bioconductor-biocgenerics >=0.46.0 + - bioconductor-deseq2 >=1.40.0 + - bioconductor-edger >=3.42.0 + - bioconductor-iranges >=2.34.0 + - bioconductor-s4vectors >=0.38.0 + - bioconductor-tximport >=1.28.0 + - r-acidbase >=0.7.0 + - r-acidcli >=0.3.0 + - r-acidexperiment >=0.5.0 + - r-acidgenerics >=0.7.2 + - r-acidgenomes >=0.6.0 + - r-acidplots >=0.7.1 + - r-bcbiobase >=0.9.0 + - r-ggplot2 >=3.4.3 + - r-goalie >=0.7.1 + - r-pipette >=0.14.0 + - r-syntactic >=0.7.0 # Suggests: - - bioconductor-biocstyle >=2.26.0 - - bioconductor-clusterprofiler >=4.6.0 - - bioconductor-degreport >=1.34.0 - - bioconductor-dose >=3.24.0 - - bioconductor-enrichplot >=1.18.0 + - bioconductor-biocstyle >=2.28.0 + - bioconductor-clusterprofiler >=4.8.0 + - bioconductor-degreport >=1.36.0 + - bioconductor-dose >=3.26.0 + - bioconductor-enrichplot >=1.20.0 - bioconductor-ensdb.hsapiens.v75 >=2.99.0 - - bioconductor-genomeinfodb >=1.34.0 - - bioconductor-org.hs.eg.db >=3.16.0 - - bioconductor-org.mm.eg.db >=3.16.0 - - bioconductor-pathview >=1.38.0 - - bioconductor-rhdf5 >=2.42.0 - - bioconductor-vsn >=3.66.0 - - r-acidgsea >=0.8.8 - - r-basejump >=0.16.5 - - r-deseqanalysis >=0.6.8 - - r-ggnewscale >=0.4.8 + - bioconductor-genomeinfodb >=1.36.0 + - bioconductor-org.hs.eg.db >=3.17.0 + - bioconductor-org.mm.eg.db >=3.17.0 + - bioconductor-pathview >=1.40.0 + - bioconductor-rhdf5 >=2.44.0 + - bioconductor-vsn >=3.68.0 + - r-acidgsea >=0.9.0 + - r-acidmarkdown >=0.3.0 + - r-basejump >=0.18.0 + - r-deseqanalysis >=0.7.0 + - r-ggnewscale >=0.4.9 - r-hexbin >=1.28.3 - - r-knitr >=1.42 + - r-knitr >=1.44 - r-pheatmap >=1.0.12 - - r-rmarkdown >=2.21 - - r-r.utils >=2.12.2 - - r-stringi >=1.7.12 - - r-viridis >=0.6.2 - - r-withr >=2.5.0 + - r-rmarkdown >=2.25 + - r-viridis >=0.6.4 + - r-withr >=2.5.1 test: commands: From 092e571586bdb2df4625363d04dbac297c567f3b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 11:17:17 -0600 Subject: [PATCH 0211/2173] Update snakemake-interface-executor-plugins to 6.0.0 (#43631) * Update snakemake-interface-executor-plugins to 6.0.0 * add configargparse --------- Co-authored-by: joshuazhuang7 --- recipes/snakemake-interface-executor-plugins/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index 8f7d15220f077..871b7ef76fc38 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "5.0.2" %} +{% set version = "6.0.0" %} package: name: {{ name|lower }} @@ -7,11 +7,11 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: c0a6755594463797dbf748ad4873e2133a9d99fa5193bdd3ea78b3a4d9898067 + sha256: 99fc3d7b056f2d410b6cbbc243927a5a671297c29916ea539bc17b131b9c471e build: noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv run_exports: - {{ pin_subpackage(name, max_pin='x') }} number: 0 @@ -24,6 +24,7 @@ requirements: run: - python >=3.9.0,<4.0.0 - argparse-dataclass >=2.0.0,<3.0.0 + - configargparse - snakemake-interface-common - throttler >=1.2.2,<2.0.0 @@ -39,6 +40,7 @@ about: summary: This package provides a stable interface for interactions between Snakemake and its executor plugins. home: https://github.com/snakemake/snakemake-interface-executor-plugins license: MIT + license_family: MIT license_file: LICENSE extra: From 9b848fa7ab804cc410546375f01a8ff13bc09885 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 11:17:33 -0600 Subject: [PATCH 0212/2173] Update virstrain to 1.14 (#43628) * Update virstrain to 1.14 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/virstrain/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/virstrain/meta.yaml b/recipes/virstrain/meta.yaml index 4cea9e5295616..6f527c19bffa1 100644 --- a/recipes/virstrain/meta.yaml +++ b/recipes/virstrain/meta.yaml @@ -1,5 +1,5 @@ {% set name = "virstrain" %} -{% set version = "1.13" %} +{% set version = "1.14" %} package: name: "{{ name|lower }}" @@ -7,15 +7,17 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 35a2cfae54083288f0565145069c9bd4daecb60eb8831d3eae5f79d22c0ba3fb + sha256: f9247a696892c75ded21e93ba60a2a4d6a63d3ecacd18b8d002fd8d7560227d5 build: number: 0 entry_points: - virstrain = VirStrain.VirStrain:main - virstrain_build = VirStrain.VirStrain_build:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('virstrain', max_pin="x.x") }} requirements: host: @@ -29,8 +31,7 @@ requirements: - pandas ==1.0.1 - plotly ==3.10.0 - python ==3.7.3 - - pip - + test: imports: - VirStrain @@ -42,6 +43,7 @@ about: home: https://github.com/liaoherui/VirStrain license: MIT license_family: MIT + license_file: LICENSE.txt summary: An RNA/DNA virus strain-level identification tool for short reads. extra: From 6c68f7c2ff96460e90caaa2388c95e760af30b53 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 11:17:54 -0600 Subject: [PATCH 0213/2173] Update fastagap to 1.0.1 (#43633) * Update fastagap to 1.0.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fastagap/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/fastagap/meta.yaml b/recipes/fastagap/meta.yaml index 82f67329fa854..c6a74612d2012 100644 --- a/recipes/fastagap/meta.yaml +++ b/recipes/fastagap/meta.yaml @@ -1,14 +1,16 @@ package: name: fastagap - version: "1.0" + version: "1.0.1" source: - url: https://github.com/nylander/fastagap/archive/refs/tags/v1.0.tar.gz - sha256: 4873e63daf735cb6932a32fcdcfc546e5448a72ade7577cff9a059317605e955 + url: https://github.com/nylander/fastagap/archive/refs/tags/v1.0.1.tar.gz + sha256: eb00b459ddb3bde4cca40ee1a3adaaa193ed089caa4e94300379f94c13004c56 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('fastagap', max_pin="x") }} requirements: run: @@ -22,6 +24,7 @@ test: about: home: https://github.com/nylander/fastagap license: MIT + license_family: MIT license_file: LICENSE summary: Count and remove missing data in fasta-formatted sequence data From f18122f092af5d44baea10d2ad359e816e0bbcdc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 13:03:12 -0600 Subject: [PATCH 0214/2173] Update oakvar to 2.9.49 (#43617) * Update oakvar to 2.9.46 * Update oakvar to 2.9.48 * edit dependencies * Update oakvar to 2.9.49 --------- Co-authored-by: joshuazhuang7 --- recipes/oakvar/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 45f96a4ab45c6..a18bc4f68f610 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.43" %} -{% set sha256 = "47113739aceaa54f868a61b4e2214a0322efb52a462286ebdd47f21c7a4dde04" %} +{% set version = "2.9.49" %} +{% set sha256 = "8626750837c865c23784e8363e20fd007640d2d5538350c479283955c78f4489" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ source: build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - ov=oakvar.__main__:main run_exports: @@ -29,7 +29,7 @@ requirements: - requests-toolbelt - liftover - markdown - - aiohttp + - aiohttp <4.0.0 - chardet >=3.0.4 - aiosqlite - oyaml @@ -65,7 +65,7 @@ about: summary: "OakVar - Genomic Variant Analysis Platform" dev_url: 'https://pypi.org/project/oakvar/' license: 'AGPL-3.0-or-later' - license_family: GPL + license_family: AGPL license_file: LICENSE doc_url: 'https://rkimoakbioinformatics.github.io/oakvar/' From 176990706dc70bc2f3a5d747c1e0f8124515b7c1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 13:29:15 -0600 Subject: [PATCH 0215/2173] Update phylofisher to 1.2.13 (#43582) --- recipes/phylofisher/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phylofisher/meta.yaml b/recipes/phylofisher/meta.yaml index a9b6fe617ec66..29979d4e64b53 100644 --- a/recipes/phylofisher/meta.yaml +++ b/recipes/phylofisher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "PhyloFisher" %} -{% set version = "1.2.12" %} +{% set version = "1.2.13" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/TheBrownLab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 8b8fa8708a3865ec812b145422e75c5893bbb4d1c9dfd943f73d0c4ff5fe6d72 + sha256: 0003e1820bbf84453edbf3cba68e01e2bd1c24a12608fe02bc01b1168efb5a1b build: noarch: python From a99691c87032d28fee40ecf757cab18209682474 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 13:29:34 -0600 Subject: [PATCH 0216/2173] Update dxpy to 0.359.1 (#43597) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index d7eec62ff287d..64b5decd8085b 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.359.0" %} +{% set version = "0.359.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: f26c520759358aaf32870ac690d20c770936a365aee8756a68d2ae33ed7f8496 + sha256: 3ea10e7e7b59634dc8514037465bdb8cedbf9988973262a4091478f3d680571e build: number: 0 From b88c9365663235323afd272d3f6dabab4dba080a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 13:42:40 -0600 Subject: [PATCH 0217/2173] Update pybiolib to 1.1.1393 (#43635) * Update pybiolib to 1.1.1374 * Update pybiolib to 1.1.1379 * Update pybiolib to 1.1.1382 * Update pybiolib to 1.1.1393 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 3c528fb4ca9da..6c491a382a251 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1367" %} +{% set version = "1.1.1393" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: f8bd06b4e0314f4e179dbaa5a9710ebcdd82373be2987d5a32814b1ec6c51019 + sha256: 743b5d4f8d83f88e1982e38363292c7381e3837e96909e11d6543ec54bc143f1 build: noarch: python From 4a2e764af9e0f7fe54a4151e0cc41eef2d108360 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 14:44:13 -0600 Subject: [PATCH 0218/2173] Update r-acidplyr to 0.5.1 (#43644) --- recipes/r-acidplyr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidplyr/meta.yaml b/recipes/r-acidplyr/meta.yaml index 006a09a9ce671..52af371705552 100644 --- a/recipes/r-acidplyr/meta.yaml +++ b/recipes/r-acidplyr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} {% set github = "https://github.com/acidgenomics/r-acidplyr" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 25cf2f40fbde2f8cef5c2a9b36fd02864609ff759dd311b8472ac1e2913dd01b + sha256: 80c9722f0c254fd7619989b8cfe06aff11e545b6598de3e73f0255c7252b04ec build: number: 0 From c030d6719741044bf9ae196926b764ea07ad50f3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 16:47:32 -0600 Subject: [PATCH 0219/2173] Update viralmsa to 1.1.36 (#43645) --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index 3fe0f4a4b7c75..948d8ae71d3f2 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.35" %} +{% set version = "1.1.36" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: 6de12888f92985610800acea8ebf345c71043c1a3c3c72221bff19b8207b5dd5 + sha256: d34ee3a12cd0cba0404519772330450f9f54de1da1f8473395f204e84cf66aea requirements: run: From ba19d3c3e773e404a05793d42781d89945c4edcd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 16:47:56 -0600 Subject: [PATCH 0220/2173] Update gnparser to 1.9.0 (#43643) --- recipes/gnparser/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gnparser/meta.yaml b/recipes/gnparser/meta.yaml index 3833b72d233ef..6c8f65f4ec4df 100644 --- a/recipes/gnparser/meta.yaml +++ b/recipes/gnparser/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.8.0" %} -{% set sha256 = "4812f334d137d9aed7be9cfce874c060a3fc2833ca2595a6bce1139ff41d3495" %} +{% set version = "1.9.0" %} +{% set sha256 = "c326fe0398fafde9048f67962064cce741996a533e48180b27c5548e4b7289ab" %} package: name: "gnparser" From 590c7fe14d91471391cb245a2edab36253f7046f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 16:48:16 -0600 Subject: [PATCH 0221/2173] Update oakvar to 2.9.51 (#43642) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index a18bc4f68f610..e58e23a171e65 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.49" %} -{% set sha256 = "8626750837c865c23784e8363e20fd007640d2d5538350c479283955c78f4489" %} +{% set version = "2.9.51" %} +{% set sha256 = "5bb1440918e27a4d5f4816fefb28b7218dfe49a79159b1582b47e06111d24fe2" %} package: name: {{ name|lower }} From 1a6ec97a7a92fe1fa5cf9e1d20e340ab93a9aa55 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 16:48:36 -0600 Subject: [PATCH 0222/2173] Update ncbi-datasets-pylib to 15.24.0 (#43641) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 4eeb50acad2c8..d972bddd85175 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.23.0" %} -{% set sha256 = "c97c33687d93cfd0b238ec74b4ac6caa7268be19ccd16f8749e5ac2649af038d" %} +{% set version = "15.24.0" %} +{% set sha256 = "7d48d95d078128736d4d2ef98408d68cfa422ae4db9897e924983224a8070b0e" %} package: name: {{ name|lower }} From 9ab61c9f144b18a710d9cde8fd7f64cc058f376c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 16:48:56 -0600 Subject: [PATCH 0223/2173] Update cptac to 1.5.4 (#43640) --- recipes/cptac/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cptac/meta.yaml b/recipes/cptac/meta.yaml index 2f69c65f0b7cb..351aa54bd1e29 100644 --- a/recipes/cptac/meta.yaml +++ b/recipes/cptac/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cptac" %} -{% set version = "1.5.3" %} +{% set version = "1.5.4" %} package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 5f9f35ee799496efb6dd297748fed5d949cb9c1facb9080d0b07f76dc130fd53 + sha256: 4d99b3f25f36626e7fe7ecd4034e262ff452fd092593bb9808a0b44cf34d688c build: number: 0 From 3e0bbee71a3bcd8a55945d808843c730a4366db2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 16:49:17 -0600 Subject: [PATCH 0224/2173] Update ena-webin-cli to 6.6.0 (#43632) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index f9af45920ed36..f0e3c950f8f47 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.5.1" %} -{% set sha256 = "e46e0fe60e6959f3867280b8759fc7a2b4cdb71d46675d487f090d08e2bdb8ad" %} +{% set version = "6.6.0" %} +{% set sha256 = "4ea1aa1b5a79052cff9628004b85689caf59556cb70a814e12f217972e13058d" %} package: name: ena-webin-cli From 77349820d4bf47dab091000fc0e120142398ee41 Mon Sep 17 00:00:00 2001 From: Fabrice Touzain <43985838+FTouzain@users.noreply.github.com> Date: Fri, 13 Oct 2023 00:50:19 +0200 Subject: [PATCH 0225/2173] Vvv2 display 0.1.10 (#43608) * clean bioconda recipe for vvv2_display 0.1.10 * correction of url (removed useless -beta at the end of url) * add LICENSE file path, because of lint not finding LICENSE * classical url * correct license terms * correct pipn_subpackage line for name variable, remove '' in script call. Everything to iprove jinja2 compatibility * remove dir for tests, change test to the minimum -h param * remove direct python call not to look for any file when calling the program * updated license:SPDX --- recipes/vvv2_display/meta.yaml | 43 ++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 recipes/vvv2_display/meta.yaml diff --git a/recipes/vvv2_display/meta.yaml b/recipes/vvv2_display/meta.yaml new file mode 100644 index 0000000000000..3ddd50e940bcd --- /dev/null +++ b/recipes/vvv2_display/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "vvv2_display" %} +{% set version = "0.1.10" %} +{% set sha256 = "8d7bd065fae64e2cfb5e9b4ca64a2b2c3a346120ec67265953ce3c21a85cf276" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + # git_rev: "0.1.10" + url: https://github.com/ANSES-Ploufragan/vvv2_display/archive/refs/tags/{{version}}.tar.gz + sha256: {{ sha256 }} + +build: + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . -vv + +requirements: + host: + - pip + - python >=3.9 + - setuptools >=57.4.0 + run: + - pip + - python >=3.9 + - r-ggplot2 >=3.3.6 + - pysam >=0.19.1 + - numpy >=1.23.3 + +test: + commands: + - vvv2_display.py -h + +about: + home: https://github.com/ANSES_Ploufragan/vvv2_display/ + license: GPL-3.0-only + license_family: GPL + license_file: LICENSE + summary: "Creates png image file with all [vardict] variants proportions along genome/assembly with annotations from [vadr]." + maintainer: FTouzain From 57b23e1c33fcf2a8490c3a1007be1f79b3c62c46 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 17:04:28 -0600 Subject: [PATCH 0226/2173] Update abromics_galaxy_json_extractor to 0.8.2 (#43630) --- recipes/abromics_galaxy_json_extractor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abromics_galaxy_json_extractor/meta.yaml b/recipes/abromics_galaxy_json_extractor/meta.yaml index 5d0cc7650ebfb..31c567989c18d 100644 --- a/recipes/abromics_galaxy_json_extractor/meta.yaml +++ b/recipes/abromics_galaxy_json_extractor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.1" %} +{% set version = "0.8.2" %} context: {} @@ -8,7 +8,7 @@ package: source: url: https://gitlab.com/ifb-elixirfr/abromics/abromics-galaxy-json-extractor/-/archive/{{ version }}/abromics-galaxy-json-extractor-{{ version }}.tar.gz - sha256: '77a35992ea34de66ff9682991d66b3b002963b211a0e8e0f8d945236fa4743da' + sha256: '0a5dc5a7101eb8d9d00a2d9d1e556eb9bad0b1b0e55306b75de5ee6769a01762' build: noarch: python From 97034f17f0291d6de55eef815ce005d9eda9d334 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 12 Oct 2023 22:47:52 -0600 Subject: [PATCH 0227/2173] Update tcdemux to 0.0.20 (#43649) --- recipes/tcdemux/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tcdemux/meta.yaml b/recipes/tcdemux/meta.yaml index 4cf69dfd97390..39bbb845e62fa 100644 --- a/recipes/tcdemux/meta.yaml +++ b/recipes/tcdemux/meta.yaml @@ -1,5 +1,5 @@ --- -{% set version = "0.0.18" %} +{% set version = "0.0.20" %} package: name: tcdemux @@ -7,7 +7,7 @@ package: source: url: https://github.com/TomHarrop/tcdemux/archive/refs/tags/{{ version }}.tar.gz - sha256: 095a00e37638e502bdd6a185d905ca7fb177f5ef598b113ff26506581eca0cc7 + sha256: 7f7df6b992c40bb5b158625b2d6b9d202af2fe14cba907c98e2f50c1550ccc7a build: number: 0 From 7c680ff29c978d2e31f24c5bdebbd3f8a40c95d8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 13 Oct 2023 05:01:32 -0600 Subject: [PATCH 0228/2173] Update annonars to 0.22.0 (#43654) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 5ad2456ae0ff0..344b583def70c 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.21.1" %} +{% set version = "0.22.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5623bdc4fd93b9de87dbbd938260defab4d744aecb5511804d851cc0434be683 + sha256: 9acc7cef3eec51da9b7854c8a88695ce062f95eb58eaa5c9c62c9d4b98e301c8 requirements: build: From d2b99725133e8086d5ec122691dac1814eef0712 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 13 Oct 2023 05:05:10 -0600 Subject: [PATCH 0229/2173] Update sdm to 2.13 (#43647) --- recipes/sdm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sdm/meta.yaml b/recipes/sdm/meta.yaml index 4a0280af894a9..a6d9470841bc6 100644 --- a/recipes/sdm/meta.yaml +++ b/recipes/sdm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sdm" %} -{% set version = "2.11" %} +{% set version = "2.13" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/hildebra/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 038abe3fc624cd7e687baa9bc75e00d18b63b2ff5899e7a6f238b57b668df894 + sha256: 9942b7190825353eeff89d0af1a269e91d71a28671bc4ec2746f2b4922781140 patches: - sdm_1.83.patch From f1e1081b4e1590147575069e97fb1d54d7986ebb Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Fri, 13 Oct 2023 14:04:16 +0200 Subject: [PATCH 0230/2173] Add missing dependency to truvari (#43656) * Add missing dependency to truvari * Update build number --- recipes/truvari/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/truvari/meta.yaml b/recipes/truvari/meta.yaml index 602d906979554..1acdd86eb2934 100644 --- a/recipes/truvari/meta.yaml +++ b/recipes/truvari/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . -vvv entry_points: @@ -35,6 +35,7 @@ requirements: - pytabix - bwapy - pandas + - mafft test: imports: From 6dcec78b6505564f4996e1063c67d5b03f9fd6ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Pontus=20H=C3=B6jer?= Date: Fri, 13 Oct 2023 20:06:47 +0200 Subject: [PATCH 0231/2173] Update naibr-plus (#43661) * bump naibr-plus * add run_exports statement * update sha256 --- recipes/naibr-plus/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/naibr-plus/meta.yaml b/recipes/naibr-plus/meta.yaml index b7f108f06edc7..886ae5ad3b0cd 100644 --- a/recipes/naibr-plus/meta.yaml +++ b/recipes/naibr-plus/meta.yaml @@ -1,5 +1,5 @@ {% set name = "naibr-plus" %} -{% set version = "0.5" %} +{% set version = "0.5.1" %} package: name: "{{ name }}" @@ -7,12 +7,14 @@ package: source: url: https://github.com/pontushojer/NAIBR/releases/download/v{{ version }}/naibr-{{ version }}.tar.gz - sha256: 6736d5a3072ee4acd4c8937b05cdb9f09ee7e54c5cff752910cf3fd26097502b + sha256: 62629ee70fb68c0299e7e5464c528b4a91c778176b86ad6abf6e1d4f00967fdb build: number: 0 noarch: python script: {{ PYTHON }} -m pip install --no-deps . + run_exports: + - {{ pin_subpackage('naibr-plus', max_pin="x.x") }} requirements: host: From 079a3f8ceb7ddc6862eeed347a68a6ea4c4709c2 Mon Sep 17 00:00:00 2001 From: Rafael Mamede Date: Fri, 13 Oct 2023 19:08:55 +0100 Subject: [PATCH 0232/2173] Updated chewbbaca recipe. (#43646) --- recipes/chewbbaca/meta.yaml | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index 50fe78324108b..412df0e410395 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 6ca1a4971ede86ecb5e1e3e6c484fbe16e4ba87d3aebb751594480d3a674be67 build: - number: 0 + number: 1 noarch: python entry_points: - chewBBACA.py = CHEWBBACA.chewBBACA:main @@ -25,26 +25,29 @@ requirements: - pip run: - python >=3.7 - - numpy >=1.23.4 - - scipy >=1.9.3 + - numpy >=1.24.3 + - scipy >=1.10.1 - biopython >=1.78 - pandas >=1.5.1 - plotly >=5.8.0 - requests >=2.27.1 - sparqlwrapper >=2.0.0 - - blast >=2.9.0 - pyrodigal >=3.0.0 - - clustalw >=2.1 + - blast >=2.9.0 - mafft >=7.505 + - fasttree >=2.1.11 test: imports: - CHEWBBACA - - CHEWBBACA.CHEWBBACA_NS - - CHEWBBACA.PrepExternalSchema - - CHEWBBACA.SchemaEvaluator - - CHEWBBACA.AlleleCall - CHEWBBACA.CreateSchema + - CHEWBBACA.AlleleCall + - CHEWBBACA.SchemaEvaluator + - CHEWBBACA.AlleleCallEvaluator + - CHEWBBACA.ExtractCgMLST + - CHEWBBACA.PrepExternalSchema + - CHEWBBACA.UniprotFinder + - CHEWBBACA.CHEWBBACA_NS - CHEWBBACA.utils commands: - chewBBACA.py --help From 5b59cd78fb4b13f7fa0f36bcca46119a4bb0826b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 13 Oct 2023 13:26:46 -0600 Subject: [PATCH 0233/2173] Update r-acidgenomes to 0.6.1 (#43657) --- recipes/r-acidgenomes/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenomes/meta.yaml b/recipes/r-acidgenomes/meta.yaml index 24e273af77b8c..c3c299fe4266e 100644 --- a/recipes/r-acidgenomes/meta.yaml +++ b/recipes/r-acidgenomes/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.0" %} +{% set version = "0.6.1" %} {% set github = "https://github.com/acidgenomics/r-acidgenomes" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: ec8ae782391beaffda33fc4bb0da1567d4cde612de538a163b5d7444aaa838ee + sha256: c69cd608fcab47ef5360bc2dd5a87b09eae5aa0a38e1689a21ae97f03958f32d build: number: 0 From e6f79efe2b6660fe7e2452ca9a45730d7f679626 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 13 Oct 2023 14:55:07 -0600 Subject: [PATCH 0234/2173] Update microhapdb to 0.10.1 (#43665) * Update microhapdb to 0.10.1 * Pin max Python version * Pin python again --------- Co-authored-by: Daniel Standage --- recipes/microhapdb/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/microhapdb/meta.yaml b/recipes/microhapdb/meta.yaml index a2713c3f81388..b9cae1ccef513 100644 --- a/recipes/microhapdb/meta.yaml +++ b/recipes/microhapdb/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.10" %} -{% set sha256 = "6b8cfeb339fa03385a8c99d0921dba0ced0a5f3443f270c68365f1bde73b75af" %} +{% set version = "0.10.1" %} +{% set sha256 = "cccc04ba440bc38dd8258c5c054ce60da80f6a37abce2cbe5247e47227743dba" %} package: name: microhapdb @@ -20,10 +20,10 @@ build: requirements: host: - - python >=3 + - python >=3.7,<3.12 - pip run: - - python >=3 + - python >=3.7,<3.12 - pandas >=1.2 - pyfaidx >=0.7 From c233d5769c7ffa007e683aa4b3d61048d31b617c Mon Sep 17 00:00:00 2001 From: farchaab <116543129+farchaab@users.noreply.github.com> Date: Sat, 14 Oct 2023 01:13:46 +0200 Subject: [PATCH 0235/2173] Add recipe for aspera-cli (#43593) --- recipes/aspera-cli/build.sh | 32 ++++++++++++++++++++++ recipes/aspera-cli/meta.yaml | 52 ++++++++++++++++++++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 recipes/aspera-cli/build.sh create mode 100644 recipes/aspera-cli/meta.yaml diff --git a/recipes/aspera-cli/build.sh b/recipes/aspera-cli/build.sh new file mode 100644 index 0000000000000..ce217e42e8955 --- /dev/null +++ b/recipes/aspera-cli/build.sh @@ -0,0 +1,32 @@ +#!/usr/bin/env bash + +gem_path=$PREFIX/${PKG_NAME}-${PKG_VERSION} +mkdir -p $gem_path +cp -r $SRC_DIR/* $gem_path +rm $gem_path/{conda_build,build_env_setup}.sh + +gem build aspera-cli.gemspec +gem install ${PKG_NAME}-${PKG_VERSION}.gem + +tail -n+3 bin/ascli > $gem_path/bin/ascli +tail -n+3 bin/asession > $gem_path/bin/asession + +cat << EOF > header.txt +#!/bin/sh +# -*- ruby -*- +_=_\\ +=begin +exec "$PREFIX/bin/ruby" "-x" "\$0" "\$@" +=end +#!$PREFIX/bin/ruby +EOF + +echo "$(cat header.txt $gem_path/bin/ascli)" > $gem_path/bin/ascli +echo "$(cat header.txt $gem_path/bin/asession)" > $gem_path/bin/asession +mv $gem_path $PREFIX/share/rubygems/gems +ln -s $PREFIX/share/rubygems/gems/${PKG_NAME}-${PKG_VERSION}/bin/* $PREFIX/bin + +export ASCLI_HOME="$PREFIX/etc/aspera" +ascli conf ascp install && ascli config ascp info +cp $ASCLI_HOME/aspera-license . +ln -s $ASCLI_HOME/{ascp,aspera-license} $PREFIX/bin diff --git a/recipes/aspera-cli/meta.yaml b/recipes/aspera-cli/meta.yaml new file mode 100644 index 0000000000000..2a69e661b65d4 --- /dev/null +++ b/recipes/aspera-cli/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "aspera-cli" %} +{% set version = "4.14.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + - url: https://github.com/IBM/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: b46df368df71ad926605e85ea4b61b9e48335cce8be31ac04d97ee6f71109f03 + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('aspera-cli', max_pin="x") }} + missing_dso_whitelist: + - /lib64/ld-linux-x86-64.so.2 + - /lib64/libutil.so.1 + - /lib64/libpthread.so.0 + - /lib64/libc.so.6 + - /lib64/libdl.so.2 + - /lib64/librt.so.1 + - /lib64/libm.so.6 + ignore_run_exports: + - ruby + +requirements: + build: + - ruby >=3 + run: + - libgcc-ng + - libstdcxx-ng + - ruby >=3 + +test: + commands: + - ascli -h + - ascp -h + +about: + home: https://github.com/IBM/aspera-cli + license: Apache-2.0 + license_file: + - LICENSE + - aspera-license + summary: "Command Line Interface for IBM Aspera products" + dev_url: https://github.com/IBM/aspera-cli + +extra: + recipe-maintainers: + - farchaab From 74dae14a7be828f8b41ae24b2a9516a9939193b1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 13 Oct 2023 17:35:24 -0600 Subject: [PATCH 0236/2173] Update pybiolib to 1.1.1395 (#43655) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 6c491a382a251..f197b0b630d2e 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1393" %} +{% set version = "1.1.1395" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 743b5d4f8d83f88e1982e38363292c7381e3837e96909e11d6543ec54bc143f1 + sha256: 690c47057afe220c10bcd63837171bc809844871ca76635559b6637d79acc321 build: noarch: python From b7b35a6d7ac7e31928618c5afc5a0a5b44de8c7b Mon Sep 17 00:00:00 2001 From: Xiangyang1984 <58356520+Xiangyang1984@users.noreply.github.com> Date: Sat, 14 Oct 2023 10:14:24 +0800 Subject: [PATCH 0237/2173] add pneumo-typer recipes (#43556) * add pneumo-typer recipes * Update meta.yaml --- recipes/pneumo-typer/build.sh | 2 +- recipes/pneumo-typer/meta.yaml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pneumo-typer/build.sh b/recipes/pneumo-typer/build.sh index 100fee3e5fb53..6f3abb816792e 100644 --- a/recipes/pneumo-typer/build.sh +++ b/recipes/pneumo-typer/build.sh @@ -15,4 +15,4 @@ perl ${RM_DIR}/pneumo-typer.pl \$@ END -chmod a+x ${PREFIX}/bin/pneumo-typer +chmod a+x ${PREFIX}/bin/pneumo-typer \ No newline at end of file diff --git a/recipes/pneumo-typer/meta.yaml b/recipes/pneumo-typer/meta.yaml index 9ef596df2b11e..4e2eefab7cb6c 100644 --- a/recipes/pneumo-typer/meta.yaml +++ b/recipes/pneumo-typer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pneumo-typer" %} {% set version = "1.0.1" %} -{% set sha256 = "d564fd21d79fa08f6e82e37283a8a55dddd21590d7d05bb261aa7ddf3374bf0f" %} +{% set sha256 = "b704a93b83c0c4292f5373228229dca4529e3be478b8d8efbac9a4f72c56255a" %} package: name: "{{ name|lower }}" @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_subpackage('pneumo-typer', max_pin="x") }} From eff3e48cf1474be3a5a52bb856761f1268845c6f Mon Sep 17 00:00:00 2001 From: Jose Figueroa Date: Fri, 13 Oct 2023 22:15:43 -0400 Subject: [PATCH 0238/2173] Update mercat2 (#43339) * Update mercat2 * Update mercat2 * Update mercat2 --- recipes/mercat2/meta.yaml | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/recipes/mercat2/meta.yaml b/recipes/mercat2/meta.yaml index dc573dcd4aef8..b987d6a8d7705 100644 --- a/recipes/mercat2/meta.yaml +++ b/recipes/mercat2/meta.yaml @@ -10,24 +10,27 @@ source: sha256: 30dd54de28e8648c83c6ed0a773934655d8b62ffc3a0541864848d9e618e4bf0 build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('mercat2', max_pin="x") }} requirements: host: - pip - - python <3.10 + - python >=3.9 - setuptools run: - - python <3.10 - - grpcio + - python >=3.9 + - grpcio ==1.43 - fastqc - fastp - prodigal - ray-core - ray-dashboard - ray-default + - ray-tune - configargparse - dominate - humanize @@ -37,10 +40,11 @@ requirements: - psutil - scikit-learn - metaomestats - - scikit-bio + - scikit-bio ==0.5.7 - scipy ==1.8.1 - python-kaleido + test: imports: - mercat2_lib From 33df291ce4a4e3f4ff1ceeed3fcc9be8aaa01e19 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Sat, 14 Oct 2023 03:17:06 +0100 Subject: [PATCH 0239/2173] added ms2rescore tool (#43487) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * added ms2rescore tool * Update meta.yaml Added dependency * Update meta.yaml * Update meta.yaml * Update recipes/ms2rescore/meta.yaml Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update meta.yaml * Update recipes/ms2rescore/meta.yaml * add flit-core to run dependencies * Update meta.yaml * Update meta.yaml * mokapot added * deeplcretrainer added * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update recipes/ms2rescore/meta.yaml Co-authored-by: Ralf Gabriels * ms2rescore update version 3.0.0b1 * ms2rescore update version 3.0.0b1 * ms2rescore update version 3.0.0b1 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Björn Grüning Co-authored-by: Ralf Gabriels --- recipes/ms2rescore/meta.yaml | 76 ++++++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 recipes/ms2rescore/meta.yaml diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml new file mode 100644 index 0000000000000..34525e62a3608 --- /dev/null +++ b/recipes/ms2rescore/meta.yaml @@ -0,0 +1,76 @@ +{% set name = "ms2rescore" %} +{% set version = "3.0.0b1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore-{{ version }}.tar.gz + sha256: d3fa5112038d2e92a916f57b47f634fec5235836260fe0949fd8cc4549cc7410 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + entry_points: + - ms2rescore = ms2rescore.__main__:main + - ms2rescore-gui = ms2rescore.gui.__main__:main + - ms2rescore-report = ms2rescore.report.__main__:main + script: "{{ PYTHON }} -m pip install . --no-deps -vvv" + +requirements: + host: + - python >=3.8 + - flit-core + - pip + run: + - python >=3.8 + - numpy >=1.16.0 + - pandas >=1.0 + - rich >=12 + - pyteomics >=4.1.0 + - lxml >=4.5 + - ms2pip >=4.0.0-dev4 + - click >=7 + - cascade-config >=0.4.0 + - deeplc >=2.2 + - deeplcretrainer ==0.1.17 + - tomli >=2 # [py<311] + - psm-utils >=0.4 + - customtkinter >=5,<6 + - mokapot >=0.9 + - pydantic >=1.8.2,<2 + - jinja2 >=3 + - plotly + - sqlalchemy <2,>=1.3 + - mokapot + - statsmodels + - matplotlib-base + - seaborn + +test: + imports: + - ms2rescore + commands: + - pip check + - ms2rescore --help +# - ms2rescore-gui --help + - ms2rescore-report --help + requires: + - pip + +about: + home: https://compomics.github.io/projects/ms2rescore/ + summary: 'MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and retention times.' + dev_url: https://github.com/compomics/ms2rescore + license: Apache-2.0 + license_file: LICENSE + +extra: + container: + # Click requires the extended container + extended-base: true + recipe-maintainers: + - compomics From da54e2a4cca8f2b4f438d8520595bcd7cceff741 Mon Sep 17 00:00:00 2001 From: Ray <851836818@qq.com> Date: Sat, 14 Oct 2023 10:18:13 +0800 Subject: [PATCH 0240/2173] add GDmicro recipes (#43325) * add strainscan recipes * add gdmicro recipes * Delete recipes/strainscan/meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * add gdmicro recipes * Update meta.yaml --- recipes/gdmicro/meta.yaml | 52 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/gdmicro/meta.yaml diff --git a/recipes/gdmicro/meta.yaml b/recipes/gdmicro/meta.yaml new file mode 100644 index 0000000000000..40a50c63209e4 --- /dev/null +++ b/recipes/gdmicro/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "gdmicro" %} +{% set version = "1.0.5" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 4a2709dc921a5a323f9a189ad2084034654e49fb3a3cdce26109f9b70032ac9f + +build: + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + run_exports: + - {{ pin_subpackage('gdmicro', max_pin="x") }} + noarch: python + +requirements: + host: + - pip + - python ==3.7.3 + run: + - python ==3.7.3 + - numpy + - pandas + - scipy + - scikit-learn + - pytorch ==1.12.0 + - networkx + - matplotlib-base + - ipython + - r-base ==3.6.1 + - bioconductor-siamcat ==1.6.0 + - r-yaml ==2.2.1 + - r-tidyverse ==1.2.1 + + +test: + imports: + - GDmicro + commands: + - gdmicro --help + +about: + home: https://github.com/liaoherui/GDmicro + license: MIT + summary: GDmicro - Use GCN and Deep adaptation network to classify host disease status based on human gut microbiome data + +extra: + recipe-maintainers: + - liaoherui From a89a67aab281b9a44c77ee8dbc0da9519bbd4431 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 13 Oct 2023 20:50:23 -0600 Subject: [PATCH 0241/2173] Update anchorwave to 1.2.2 (#43586) * Update anchorwave to 1.2.2 * Drop upstreamed macOS build patch * Delete the patch file --------- Co-authored-by: Travis Wrightsman --- recipes/anchorwave/build.sh | 2 ++ recipes/anchorwave/meta.yaml | 10 ++++------ .../anchorwave/patches/01-macOS-x86-build.patch | 15 --------------- 3 files changed, 6 insertions(+), 21 deletions(-) delete mode 100644 recipes/anchorwave/patches/01-macOS-x86-build.patch diff --git a/recipes/anchorwave/build.sh b/recipes/anchorwave/build.sh index ce5fd2834a87c..238861d1d49cb 100644 --- a/recipes/anchorwave/build.sh +++ b/recipes/anchorwave/build.sh @@ -52,6 +52,8 @@ elif [ $TARGET_PLATFORM = "macOS" ]; then mkdir -p build/macOS # macOS (SSE4.1) + rm CMakeLists.txt + ln -s CMakeLists_MACOSX86.txt CMakeLists.txt cd build/macOS cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../.. make -j"${CPU_COUNT}" diff --git a/recipes/anchorwave/meta.yaml b/recipes/anchorwave/meta.yaml index 6d75ce665ccbe..2480797be239b 100644 --- a/recipes/anchorwave/meta.yaml +++ b/recipes/anchorwave/meta.yaml @@ -1,7 +1,7 @@ {% set name = "anchorwave" %} -{% set version = "1.2.1" %} -{% set tag = "v1.2.1" %} -{% set sha256 = "0e64f7b62579bbf9106a7a2f13330b8e16846176d6423db648d79b74b3dff2e7" %} +{% set version = "1.2.2" %} +{% set tag = "v1.2.2" %} +{% set sha256 = "db951e2fc8e493ce29e8c6e4f0226a68dc2fdc62631c1fe65077988647e98d01" %} package: name: {{ name }} @@ -10,11 +10,9 @@ package: source: url: https://github.com/baoxingsong/AnchorWave/archive/refs/tags/{{ tag }}.tar.gz sha256: {{ sha256 }} - patches: - - patches/01-macOS-x86-build.patch # [osx] build: - number: 2 + number: 0 script_env: - TARGET_PLATFORM=macOS # [osx] - TARGET_PLATFORM=Linux # [linux] diff --git a/recipes/anchorwave/patches/01-macOS-x86-build.patch b/recipes/anchorwave/patches/01-macOS-x86-build.patch deleted file mode 100644 index 1bafbaba2dc15..0000000000000 --- a/recipes/anchorwave/patches/01-macOS-x86-build.patch +++ /dev/null @@ -1,15 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index f94dda8..c9f52c3 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -12,8 +12,8 @@ set(CMAKE_CXX_STANDARD 14) - - find_package(ZLIB) - --set(CMAKE_CXX_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -msse4.1 -msse4.2 -I ./ -std=gnu++14 -pthread -lrt") # the -mavx* is for GNU compiler and xCORE* are for intel compiler --set(CMAKE_C_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -msse4.1 -msse4.2 -I ./ -pthread -lrt") -+set(CMAKE_CXX_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -msse4.1 -msse4.2 -I ./ -std=gnu++14 -pthread") # the -mavx* is for GNU compiler and xCORE* are for intel compiler -+set(CMAKE_C_FLAGS " -lm -lz -Wall -g3 -O3 -funroll-all-loops -msse4.1 -msse4.2 -I ./ -pthread") - - - #for google unit test From 985a1142e7024e93c12495a141f6c5c5e7cde7e9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 01:04:09 -0600 Subject: [PATCH 0242/2173] Update baredsc to 1.1.2 (#43668) * Update baredsc to 1.1.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/baredsc/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/baredsc/meta.yaml b/recipes/baredsc/meta.yaml index cbbbbd8963439..d9b7c9290d414 100644 --- a/recipes/baredsc/meta.yaml +++ b/recipes/baredsc/meta.yaml @@ -1,18 +1,20 @@ {% set name = "baredSC" %} -{% set version = "1.1.1" %} - +{% set version = "1.1.2" %} + package: name: {{ name | lower }} version: {{ version }} source: url: https://github.com/lldelisle/baredSC/archive/v{{ version }}.tar.gz - sha256: 0c1f488ccd5f276813477dcadc0a844d00702901c34a2e758ada06db59f58c4f + sha256: 9c1ac38cebdb6e9183ee208f86021e3c80bbd98a3bff8a078327c4c8420f4fba build: number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('baredsc', max_pin="x") }} requirements: host: @@ -39,7 +41,8 @@ test: about: home: https://github.com/lldelisle/baredSC/ - license: GPL3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. From a2a177f646a79f810167b0bbddbec029b1ebcbc9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 01:05:20 -0600 Subject: [PATCH 0243/2173] Update bowtie2 to 2.5.2 (#43672) * Update bowtie2 to 2.5.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/bowtie2/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/bowtie2/meta.yaml b/recipes/bowtie2/meta.yaml index 41f8c61665cb0..0d332684fac38 100644 --- a/recipes/bowtie2/meta.yaml +++ b/recipes/bowtie2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.1" %} +{% set version = "2.5.2" %} package: name: bowtie2 @@ -6,11 +6,13 @@ package: source: url: https://github.com/BenLangmead/bowtie2/archive/v{{ version }}.tar.gz - sha256: 3fe00f4f89b5dd85fd9317e2168ec93f30dbb75d7950a08516c767d21eca7c27 + sha256: 2f86dbfbf3dcb8521d559f830594fe28ac6e4c40d81313a8c2bfb17c82a501e0 build: - number: 2 + number: 0 skip: True # [py2k] + run_exports: + - {{ pin_subpackage('bowtie2', max_pin="x") }} requirements: build: @@ -47,6 +49,7 @@ test: about: home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' license: GPL-3.0-only + license_family: GPL3 license_file: LICENSE summary: Fast and sensitive gapped read alignment From d3de6d698b90f63ef1dbb252d8c741d5b0829521 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 01:05:44 -0600 Subject: [PATCH 0244/2173] Update psims to 1.2.8 (#43670) * Update psims to 1.2.8 * edit dependencies --------- Co-authored-by: joshuazhuang7 --- recipes/psims/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/psims/meta.yaml b/recipes/psims/meta.yaml index da8bafbf56b05..d53e581dd81ee 100644 --- a/recipes/psims/meta.yaml +++ b/recipes/psims/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.2.7" %} -{% set sha256 = "d1645a85411df88872865541745a2d4ad5aee2ccd8f6915b9c1d94bbb8cc3a81" %} +{% set version = "1.2.8" %} +{% set sha256 = "74d1905fc9b0cb506e3ccb33937c4f7609f97379ad41bf107603f1d4494fd6af" %} package: name: "psims" @@ -11,7 +11,7 @@ source: build: number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python run_exports: - {{ pin_subpackage('psims', max_pin='x') }} @@ -19,8 +19,9 @@ build: requirements: host: - pip - - python + - python >=3.9 run: + - python >=3.9 - lxml - six - sqlalchemy From b9a177c3917e928bfe0c524a590decd395be5fb0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 01:31:19 -0600 Subject: [PATCH 0245/2173] Update cromshell to 2.1.0 (#43669) * Update cromshell to 2.1.0 * add run_exports --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cromshell/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/cromshell/meta.yaml b/recipes/cromshell/meta.yaml index ab752e4671bc6..aac99a74ff3fe 100644 --- a/recipes/cromshell/meta.yaml +++ b/recipes/cromshell/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cromshell" %} -{% set version = "2.0.0" %} -{% set sha256 = "7e85a7e9c48c0bfa3bd395d055ff3062267933d76cde14be750fe339b50d5e09" %} +{% set version = "2.1.0" %} +{% set sha256 = "4aaa30d1e7449577fae3322271c1c0661fa5195b58aad868a2cf891cae74f6a3" %} package: name: {{ name }} @@ -9,6 +9,8 @@ package: build: noarch: python number: 0 + run_exports: + - {{ pin_subpackage('cromshell', max_pin="x") }} source: url: https://github.com/broadinstitute/{{ name }}/archive/{{ version }}.tar.gz From f2bc80d3146223aaa766921c5d454a926916b7e4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 01:31:36 -0600 Subject: [PATCH 0246/2173] Update abromics_galaxy_json_extractor to 0.8.2.1 (#43663) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/abromics_galaxy_json_extractor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abromics_galaxy_json_extractor/meta.yaml b/recipes/abromics_galaxy_json_extractor/meta.yaml index 31c567989c18d..69a27b8c03a23 100644 --- a/recipes/abromics_galaxy_json_extractor/meta.yaml +++ b/recipes/abromics_galaxy_json_extractor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.2" %} +{% set version = "0.8.2.1" %} context: {} @@ -8,7 +8,7 @@ package: source: url: https://gitlab.com/ifb-elixirfr/abromics/abromics-galaxy-json-extractor/-/archive/{{ version }}/abromics-galaxy-json-extractor-{{ version }}.tar.gz - sha256: '0a5dc5a7101eb8d9d00a2d9d1e556eb9bad0b1b0e55306b75de5ee6769a01762' + sha256: 'c179bb49d6ddfa2b05c903d669f9d91f43e13c63c354466d810b07b77cb32261' build: noarch: python From acdfeb6d53231307c526840111220d9575df5828 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 01:31:50 -0600 Subject: [PATCH 0247/2173] Update beagle-lib to 4.0.1 (#43659) * Update beagle-lib to 4.0.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/beagle-lib/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/beagle-lib/meta.yaml b/recipes/beagle-lib/meta.yaml index f83c772208a1e..082568e5e77b7 100644 --- a/recipes/beagle-lib/meta.yaml +++ b/recipes/beagle-lib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "beagle-lib" %} -{% set version = "4.0.0" %} +{% set version = "4.0.1" %} package: name: {{ name }} @@ -7,10 +7,12 @@ package: source: url: https://github.com/beagle-dev/{{ name }}/archive/v{{ version }}.tar.gz - sha256: d197eeb7fe5879dfbae789c459bcc901cb04d52c9cf5ef14fb07ff7a6b74560b + sha256: 9d258cd9bedd86d7c28b91587acd1132f4e01d4f095c657ad4dc93bd83d4f120 build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('beagle-lib', max_pin="x") }} requirements: build: @@ -32,6 +34,6 @@ test: about: home: https://github.com/beagle-dev/beagle-lib - license: GPL-3.0+ - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 summary: general purpose library for evaluating the likelihood of sequence evolution on trees From 5ad2d3d9fed637ad495dddbb714322c33fdd2ddc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 01:33:49 -0600 Subject: [PATCH 0248/2173] Update scrnasim-toolz to 0.1.1 (#43653) * Update scrnasim-toolz to 0.1.1 * Update scrnasim-toolz to 0.1.1 * edit dependencies * remove cli_test_helpers --------- Co-authored-by: joshuazhuang7 --- recipes/scrnasim-toolz/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/scrnasim-toolz/meta.yaml b/recipes/scrnasim-toolz/meta.yaml index 82412589d1d36..065e125121da5 100644 --- a/recipes/scrnasim-toolz/meta.yaml +++ b/recipes/scrnasim-toolz/meta.yaml @@ -1,13 +1,13 @@ {% set name = "scrnasim-toolz" %} -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/zavolanlab/scRNAsim-toolz/archive/refs/tags/v0.1.0.tar.gz - sha256: 738f420e12fec1730927894debdf495953aa9e8bb288e901fde5caacac0042a9 + url: https://github.com/zavolanlab/scRNAsim-toolz/archive/refs/tags/v0.1.1.tar.gz + sha256: a78f44d1e5a9d996b7648a59703a743f2038671c83100f42b3df8e244a472096 build: number: 0 @@ -20,7 +20,7 @@ build: - cdna-generator = scRNAsim_toolz.cdna_generator.cli:main - fragment-selector = scRNAsim_toolz.fragment_selector.cli:main - read-sequencer = scRNAsim_toolz.read_sequencer.cli:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -38,6 +38,7 @@ requirements: - importlib-metadata - polars ==0.16.17 - gtfparse + - pyarrow test: commands: @@ -45,6 +46,7 @@ test: about: home: https://github.com/zavolanlab/scRNAsim-toolz - license: MIT License + license: MIT + license_family: MIT license_file: LICENSE summary: Tools used by scRNAsim workflow. From 2b9088cd14bedcf30ef3c0643124642caa223cf2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 01:34:06 -0600 Subject: [PATCH 0249/2173] Update strainscan to 1.0.14 (#43651) --- recipes/strainscan/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/strainscan/meta.yaml b/recipes/strainscan/meta.yaml index 767dda9b33753..e4bb6caf0e437 100644 --- a/recipes/strainscan/meta.yaml +++ b/recipes/strainscan/meta.yaml @@ -1,5 +1,5 @@ {% set name = "strainscan" %} -{% set version = "1.0.13" %} +{% set version = "1.0.14" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: cd98a73e3e76f601ad95c763bd6cc1ea4ff2a327c5bd3ecedf81f4342793d41e + sha256: 2d927c5ac4d9b89a166afeca2aabaf4086d49b097e357ed0feb34181295cf243 build: number: 0 From 1ce2d536da1b95f91a967f4e7e07c11ce1b00ad5 Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Sat, 14 Oct 2023 18:35:02 +1100 Subject: [PATCH 0250/2173] Add corgi v0.4.0 (#43648) * Add recipe draft * Remove pip from test requirements * Add run_exports * Fix url field * Add PyPI name variable --- recipes/corgi/meta.yaml | 66 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 recipes/corgi/meta.yaml diff --git a/recipes/corgi/meta.yaml b/recipes/corgi/meta.yaml new file mode 100644 index 0000000000000..ae7dc2274df25 --- /dev/null +++ b/recipes/corgi/meta.yaml @@ -0,0 +1,66 @@ +{% set name = "corgi" %} +{% set version = "0.4.0" %} +{% set pypiname = "bio-corgi" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ pypiname[0] }}/{{ pypiname }}/bio_corgi-{{ version }}.tar.gz + sha256: bd1a00bc3fc6c407da8727575b98dc32b52df7b4f5f43297a62172112f74d74e + +build: + entry_points: + - corgi-train = corgi.apps:Corgi.main + - corgi = corgi.apps:Corgi.inference_only_main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + host: + - python >=3.8,<3.12 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.8,<3.12 + - biopython >=1.79.0,<2.0.0 + - fastai >=2.4.1,<3.0.0 + - dask-core >=2021.7.1,<2022.0.0 + - progressbar2 >=3.53.1,<4.0.0 + - h5py >=3.1.0,<4.0.0 + - humanize >=3.10.0,<4.0.0 + - pyarrow >=5.0.0 + - plotly >=5.3.1,<6.0.0 + - appdirs >=1.4.4,<2.0.0 + - beautifulsoup4 >=4.10.0,<5.0.0 + - httpx >=0.20.0,<0.21.0 + - wandb >=0.12.9,<0.13.0 + - optuna >=2.10.0,<3.0.0 + - cryptography >=36.0.1,<37.0.0 + - pymysql >=1.0.2,<2.0.0 + - termgraph >=0.5.3,<0.6.0 + - torchapp >=0.3.1 + +test: + imports: + - corgi + commands: + - corgi-train --help + - corgi --help + +about: + home: https://pypi.org/project/bio-corgi/ + dev_url: https://github.com/rbturnbull/corgi + doc_url: https://rbturnbull.github.io/corgi/ + summary: Classifier for ORganelle Genomes Inter alia + license: Apache-2.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - rbturnbull + - vinisalazar From 029eb5de0b759e61c77a6c55063b0242d2c06cf3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 01:36:45 -0600 Subject: [PATCH 0251/2173] Update r-pathfindr to 2.3.0 (#43561) * Update r-pathfindr to 2.3.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/r-pathfindr/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/r-pathfindr/meta.yaml b/recipes/r-pathfindr/meta.yaml index d938531ccff29..7b75c815daaee 100644 --- a/recipes/r-pathfindr/meta.yaml +++ b/recipes/r-pathfindr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '2.2.0' %} +{% set version = '2.3.0' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -11,17 +11,17 @@ source: url: - {{ cran_mirror }}/src/contrib/pathfindR_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/pathfindR/pathfindR_{{ version }}.tar.gz - sha256: fa0a736e80e3d3a8354bf1fd9feeb137de4feb94c58d3be5fb62826c640d82c0 + sha256: e7fc4f10859890af5ab17cc7870efac64614f234059f5734ddd7af705f67281b build: merge_build_host: True # [win] number: 0 - noarch: generic - rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage("r-pathfindr", max_pin="x") }} requirements: build: From bbc3c3cd0f072640bc9fe0485f8c9615d439137f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 01:37:00 -0600 Subject: [PATCH 0252/2173] Update zdb to 1.2.0 (#43667) * Update zdb to 1.2.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/zdb/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/zdb/meta.yaml b/recipes/zdb/meta.yaml index 0dfed1fc3b44d..1791f812922a3 100644 --- a/recipes/zdb/meta.yaml +++ b/recipes/zdb/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.1" %} +{% set version = "1.2.0" %} package: name: zdb @@ -7,10 +7,12 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('zdb', max_pin="x") }} source: url: https://github.com/metagenlab/zDB/archive/refs/tags/v{{ version }}.tar.gz - sha256: 56d1cd7ec82b45d015a0d0323adc72271152ee363506c7f1cfc1593c6acb8d8d + sha256: 19611b62cf591f03697259748e9aae8d8f82541885879d2f3a8c3d69e9bb72ab requirements: run: @@ -23,6 +25,7 @@ test: about: home: https://github.com/metagenlab/zDB/ license: MIT + license_family: MIT license_file: LICENSE summary: zDB is both a bacterial comparative genomics pipeline and a tool to visualize the results dev_url: https://github.com/metagenlab/zDB/ From dcf360530e69968917fdd6c019ccc6aa917773cb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 03:08:33 -0600 Subject: [PATCH 0253/2173] Update dbcanlight to 1.0.2 (#43673) --- recipes/dbcanlight/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dbcanlight/meta.yaml b/recipes/dbcanlight/meta.yaml index e0d8766cb5214..feb9db4e3aac6 100644 --- a/recipes/dbcanlight/meta.yaml +++ b/recipes/dbcanlight/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dbcanLight" %} -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/chtsai0105/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 8d43e78320f4a02f6853fd21deb6c41ff5c9b28813b95087767a2e183670cbdd + sha256: da8a46553010e625e0a8c5db218876b1b339a153750341f110f7883dd961c340 build: number: 0 From cf78f8cfad8fd3aa1da263fdc3d50995f165d324 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 03:08:49 -0600 Subject: [PATCH 0254/2173] Update snakemake-interface-common to 1.13.0 (#43674) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index dd2e115b443c6..5eae71378b102 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.12.0" %} +{% set version = "1.13.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 2a6052b4db59a5a8bc632ea832ae30eba615f63e02737bb6cd1f2691945ab91f + sha256: daef8b14b919062c199ddc63c0e7e8a95252c2e687322b43136afdab297e3708 build: noarch: python From cc1fd129a201c6e42c6c5e0824def15ec61e387f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 04:04:36 -0600 Subject: [PATCH 0255/2173] Update ska2 to 0.3.3 (#43675) * Update ska2 to 0.3.3 * Add run exports to ska2 --------- Co-authored-by: John Lees --- recipes/ska2/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ska2/meta.yaml b/recipes/ska2/meta.yaml index 54ce3e8f3be19..5b5657fd452c4 100644 --- a/recipes/ska2/meta.yaml +++ b/recipes/ska2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ska2" %} -{% set version = "0.3.2" %} +{% set version = "0.3.3" %} package: name: {{ name|lower}} @@ -7,11 +7,13 @@ package: source: url: https://github.com/bacpop/ska.rust/archive/v{{ version }}.tar.gz - sha256: 53ac7e43e55b589fda5891b3b87d18ef580d83214189f090a1a00d1d028e4dd3 + sha256: a44325c01060cbc9a6724a081747bd2d75e11a8bf83aa03db1f40f9399128214 build: number: 0 script: "cargo install --no-track --locked --verbose --root \"${PREFIX}\" --path ." + run_exports: + - {{ pin_subpackage("ska2", max_pin="x.x") }} requirements: build: From 21b61509d0e0e106514a8ab28653d3f5fe914702 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 16:39:02 -0600 Subject: [PATCH 0256/2173] Update gtotree to 1.8.3 (#43676) * Update gtotree to 1.8.3 * Update meta.yaml - was failing linting check due to (i think) relatively recent addition of run_export check, with this error: "ERROR: recipes/gtotree/meta.yaml:0: missing_run_exports: Recipe should have a run_export statement that ensures correct pinning in downstream packages" - so added a run_exports section to build in Case 1 format as described here: https://bioconda.github.io/contributor/linting.html#missing-run-exports * Update meta.yaml - pin_subpackage gave this error, so trying pin_compatible as suggested: "ValueError: Didn't find subpackage version info for 'GToTree', which is used in a pin_subpackage expression. Is it actually a subpackage? If not, you want pin_compatible instead." --------- Co-authored-by: Mike Lee --- recipes/gtotree/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/gtotree/meta.yaml b/recipes/gtotree/meta.yaml index 385abd9f09751..8b35139659846 100644 --- a/recipes/gtotree/meta.yaml +++ b/recipes/gtotree/meta.yaml @@ -1,5 +1,5 @@ {% set name = "GToTree" %} -{% set version = "1.8.2" %} +{% set version = "1.8.3" %} package: name: "{{ name|lower }}" @@ -7,10 +7,12 @@ package: source: url: https://github.com/AstrobioMike/GToTree/archive/v{{ version }}.tar.gz - sha256: e8abe8ef1daa6683d7351f8dab5c3126786c5a6589a48e70aa3140af3a9d9013 + sha256: 432fdfd735cca427a10033c6edd75123e42a5be02f456524760eed6a76f6906b build: number: 0 + run_exports: + - {{ pin_compatible(name, max_pin='x') }} requirements: build: From 62f4c24ef22e2007479bfcead9bdc1718975be13 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 16:53:41 -0600 Subject: [PATCH 0257/2173] Update r-signac to 1.11.0 (#43650) * Update r-signac to 1.11.0 * add run_exports --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/r-signac/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/r-signac/meta.yaml b/recipes/r-signac/meta.yaml index 43c37ca08929b..0427c385daf88 100644 --- a/recipes/r-signac/meta.yaml +++ b/recipes/r-signac/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.10.0' %} +{% set version = '1.11.0' %} package: name: r-signac @@ -8,13 +8,15 @@ source: url: - {{ cran_mirror }}/src/contrib/Signac_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/Signac/Signac_{{ version }}.tar.gz - sha256: 75c274dfc49b0f1478adfdd85e9acbf04d3fae38f2ebe31658a1ba17a7880994 + sha256: 0daac539a4ca6d7f4c779fc06e77ffed4faca3e0689d3fb47d960edb4032f1c5 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage("r-signac", max_pin="x") }} requirements: build: From cef0132d416733f644753288f6155d185fa37d95 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 14 Oct 2023 21:03:20 -0600 Subject: [PATCH 0258/2173] Update tcdemux to 0.0.21 (#43678) --- recipes/tcdemux/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tcdemux/meta.yaml b/recipes/tcdemux/meta.yaml index 39bbb845e62fa..44f2acd15d07e 100644 --- a/recipes/tcdemux/meta.yaml +++ b/recipes/tcdemux/meta.yaml @@ -1,5 +1,5 @@ --- -{% set version = "0.0.20" %} +{% set version = "0.0.21" %} package: name: tcdemux @@ -7,7 +7,7 @@ package: source: url: https://github.com/TomHarrop/tcdemux/archive/refs/tags/{{ version }}.tar.gz - sha256: 7f7df6b992c40bb5b158625b2d6b9d202af2fe14cba907c98e2f50c1550ccc7a + sha256: bfcfc349577ba94c436b36fb8fca8ba2ac563fd11feeb5923c311992c502dd55 build: number: 0 From 81c5ec6efe47f4ad7dc5a210701e8923368a4abb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 15 Oct 2023 03:58:04 -0600 Subject: [PATCH 0259/2173] Update tcdemux to 0.0.22 (#43682) --- recipes/tcdemux/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tcdemux/meta.yaml b/recipes/tcdemux/meta.yaml index 44f2acd15d07e..915c758a92ef3 100644 --- a/recipes/tcdemux/meta.yaml +++ b/recipes/tcdemux/meta.yaml @@ -1,5 +1,5 @@ --- -{% set version = "0.0.21" %} +{% set version = "0.0.22" %} package: name: tcdemux @@ -7,7 +7,7 @@ package: source: url: https://github.com/TomHarrop/tcdemux/archive/refs/tags/{{ version }}.tar.gz - sha256: bfcfc349577ba94c436b36fb8fca8ba2ac563fd11feeb5923c311992c502dd55 + sha256: 3d6b62b93de25a977ab4f28876d1bbd5edf821980f85efc6606461b3f0270c2a build: number: 0 From 9ccbd407e10463b666431d974a24329687d5c3f7 Mon Sep 17 00:00:00 2001 From: Paimon Goulart Date: Sun, 15 Oct 2023 08:45:28 -0700 Subject: [PATCH 0260/2173] Add vcfsim (#43350) * Adding vcfsim * Adding vcfsim * Adding vcfsim * Adding vcfsim * Adding vcfsim * Removed redundant statement * Test * Removed redundant statement * Undid change * Delete recipes/vcfsim/.ipynb_checkpoints directory --- recipes/vcfsim/meta.yaml | 69 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 recipes/vcfsim/meta.yaml diff --git a/recipes/vcfsim/meta.yaml b/recipes/vcfsim/meta.yaml new file mode 100644 index 0000000000000..4123c6047645d --- /dev/null +++ b/recipes/vcfsim/meta.yaml @@ -0,0 +1,69 @@ +{% set name = "vcfsim" %} +{% set version = "1.0.5.alpha" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/Pie115/VCFSimulator-SamukLab/archive/{{ version }}.tar.gz + sha256: 3930958c2e52f62e5dd9e685307ff03e5387ae80158339806152da7f7aaa57ac + +build: + entry_points: + - vcfsim=vcfsim.__main__:main + script: {{ PYTHON }} -m pip install . -vv + number: 0 + skip: True + run_exports: + - {{ pin_subpackage('vcfsim', max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - cross-python_{{ target_platform }} + - python + - pybind11 + - numpy + + host: + - python >=3.8 + - cython + - pip + - setuptools + - numpy + - setuptools_scm + - gsl + + run: + - python >=3.8 + - pandas >=1.5.2 + - numpy + - msprime >=1.0.1 + - tskit >=0.4 + - demes >=0.2 + - gsl + - scikit-allel >=1.3.5 + - scikit-learn >=1.2.0 + - scipy >=1.9.3 + +test: + imports: + - vcfsim + commands: + - pip check + - vcfsim --help + requires: + - pip + +about: + home: https://github.com/Pie115/VCFSimulator-SamukLab + license: MIT + license_file: LICENSE.txt + summary: "Script for generating simulated VCF's" + description: | + "vcfsim is a new command-line tool for generating simulated VCF's(variant call format files for encoding genetic data). Leveraging a coalescent simulating backend and providing an interface from Msprime coalescent simulating package to pandas. VCF's can now be easily simulated with just a few command line arguments!" + +extra: + recipe-maintainers: + - Pie115 From 5d4ef32b10fefc2f7f8dea50548eeca10d59a60b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 15 Oct 2023 09:46:00 -0600 Subject: [PATCH 0261/2173] Update gdmicro to 1.0.6 (#43683) --- recipes/gdmicro/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gdmicro/meta.yaml b/recipes/gdmicro/meta.yaml index 40a50c63209e4..08fce531d0ecf 100644 --- a/recipes/gdmicro/meta.yaml +++ b/recipes/gdmicro/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gdmicro" %} -{% set version = "1.0.5" %} +{% set version = "1.0.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4a2709dc921a5a323f9a189ad2084034654e49fb3a3cdce26109f9b70032ac9f + sha256: 8b890f8e609c854726ed294044fe2daaf56c69d5b25f01c2f4440fffa46903a7 build: number: 0 From e11eef69497b9d1680da961c949f98c14b895776 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sun, 15 Oct 2023 13:33:40 -0500 Subject: [PATCH 0262/2173] Add recipe for hybracter v0.1.2 (#43677) * Add recipe for hybracter v0.1.2 * Update meta.yaml deps and maintainer --------- Co-authored-by: George Bouras <84495559+gbouras13@users.noreply.github.com> --- recipes/hybracter/meta.yaml | 49 +++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/hybracter/meta.yaml diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml new file mode 100644 index 0000000000000..49ec79deaab36 --- /dev/null +++ b/recipes/hybracter/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "hybracter" %} +{% set version = "0.1.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz + sha256: 38bf79da71f8d4ae609ab4b9521443e5ad5d19e2ce5e969b44ada2e91ae8aebe + +build: + number: 0 + noarch: python + entry_points: + - hybracter=hybracter.__main__:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('hybracter', max_pin="x") }} + +requirements: + host: + - python >=3.9 + - pip + run: + - python >=3.9 + - snakemake-minimal >=7.14.0 + - pyyaml >=6.0 + - click >=8.1.3 + - attrmap >=0.0.5 + - biopython >=1.76 + +test: + imports: + - hybracter + commands: + - hybracter --help + +about: + home: https://github.com/gbouras13/hybracter + summary: An automated long-read first bacterial genome assembly pipeline. + license: MIT + license_family: MIT + license_file: LICENSE + doc_url: https://hybracter.readthedocs.io/en/latest/ + +extra: + recipe-maintainers: + - gbouras13 From 942879c7cd0aaec40f86150876d5468fc3d3ee0f Mon Sep 17 00:00:00 2001 From: Jack Eakle <41701236+jaeakle@users.noreply.github.com> Date: Sun, 15 Oct 2023 14:36:01 -0400 Subject: [PATCH 0263/2173] Add Rabies 0.5.1 (#43638) * Add rabies 0.5.1 * Add Rabies 0.5.1 * Added explicit request for etelemetry>=0.2.0 * Fixed typo found by linter * Removing pip check etelmetry is being tagged incorrectly by pip check, removing to complete upload. * Add explicit python version Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/rabies/meta.yaml | 53 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 recipes/rabies/meta.yaml diff --git a/recipes/rabies/meta.yaml b/recipes/rabies/meta.yaml new file mode 100644 index 0000000000000..e3f692a761b32 --- /dev/null +++ b/recipes/rabies/meta.yaml @@ -0,0 +1,53 @@ +{% set name = "rabies" %} +{% set version = "0.5.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/rabies-{{ version }}.tar.gz + sha256: 8ae93c1b8c5ba00c21a42a23f39cc36f365e5962596fdbe9760c0f504cea3a36 + +build: + noarch: python + run_exports: + - {{ pin_subpackage('rabies', max_pin="x.x") }} + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + +requirements: + host: + - python >=3.9 + - pip + run: + - python >=3.9 + - matplotlib-base ==3.3.4 + - nibabel ==3.2.1 + - nilearn ==0.7.1 + - nipype ==1.6.1 + - numpy ==1.20.1 + - pandas ==1.2.4 + - pathos ==0.2.7 + - pybids ==0.16.3 + - scikit-learn ==0.24.1 + - scipy ==1.8.1 + - seaborn ==0.11.1 + - simpleitk ==2.0.2 + - qbatch ==2.3 + - networkx <3 + - etelemetry >=0.2.0 + +test: + imports: + - rabies + +about: + home: https://github.com/CoBrALab/RABIES + summary: 'RABIES: Rodent Automated Bold Improvement of EPI Sequences.' + license: GPL-2.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - jaeakle From e260f9e2fa91c551cdb8b12d40a7e34057d443f4 Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Mon, 16 Oct 2023 05:37:05 +1100 Subject: [PATCH 0264/2173] Add orthoflow (#43587) * Add orthoflow v0.2.0 * Fix description key * Fix description * Relax Python version requirements * Remove pip check Pin Pandas <2.0.0 * Remove pip from test requirements Remove pytest command (tests directory is not bundled with the PyPI distribution) * depend on snakemake-minimal --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/orthoflow/meta.yaml | 66 +++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 recipes/orthoflow/meta.yaml diff --git a/recipes/orthoflow/meta.yaml b/recipes/orthoflow/meta.yaml new file mode 100644 index 0000000000000..8f8d2b203e7d3 --- /dev/null +++ b/recipes/orthoflow/meta.yaml @@ -0,0 +1,66 @@ +{% set name = "orthoflow" %} +{% set version = "0.2.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/orthoflow-{{ version }}.tar.gz + sha256: 60e5c8bf6ba3f5d3b6d2e3fa9953f4196c117b4e656c9e5c709a28a397451d93 + +build: + entry_points: + - orthoflow = orthoflow.main:app + noarch: python + script: {{ PYTHON }} -m pip install . -vv + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + host: + - python + - setuptools + - poetry-core >=1.0.0 + - pip + run: + - python + - snakemake-minimal >=7.0.0 + - pandas >=1.2.5,<2.0.0 + - typer >=0.4.1 + - flask >=2.1.2 + - biopython >=1.79.0 + - jinja2 >=3.1.2 + - pydot >=1.4.2 + - appdirs >=1.4.4 + - joblib >=1.2.0 + - toml >=0.10.2 + - phytest >=1.2.0 + - rich >=13.3.3 + +test: + imports: + - orthoflow + commands: + - orthoflow --help + +about: + home: https://github.com/rbturnbull/orthoflow + summary: Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes. + license: Apache-2.0 + license_file: LICENSE + dev_url: https://github.com/rbturnbull/orthoflow + doc_url: https://rbturnbull.github.io/orthoflow/ + description: | + + # Orthoflow - end-to-end phylogenomic inference + + Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes. + + For more information, visit the GitHub or the documentation page. + +extra: + recipe-maintainers: + - rbturnull + - vinisalazar From 1e9f03b728c34224a8df3071d98c764b7cbeb395 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 15 Oct 2023 18:17:03 -0600 Subject: [PATCH 0265/2173] Update zol to 1.3.10 (#43685) * Update zol to 1.3.10 * Update build.sh --------- Co-authored-by: Rauf Salamzade --- recipes/zol/build.sh | 1 + recipes/zol/meta.yaml | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/zol/build.sh b/recipes/zol/build.sh index 5911ede1d4bcc..09a586f99e46e 100644 --- a/recipes/zol/build.sh +++ b/recipes/zol/build.sh @@ -14,6 +14,7 @@ cp zol/orthologs/runRBH ${PREFIX}/bin/ cp zol/orthologs/splitDiamondResults ${PREFIX}/bin/ cp zol/splitDiamondResultsForFai ${PREFIX}/bin/ cp zol/clusterHeatmap.R ${PREFIX}/bin/ +cp zol/plotTinyAAI.R ${PREFIX}/bin/ cp zol/plotSegments.R ${PREFIX}/bin/ cp zol/njTree.R ${PREFIX}/bin/ cp zol/phyloHeatmap.R ${PREFIX}/bin/ diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index 74af5ac2891d3..931dcd8b5d621 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.9" %} +{% set version = "1.3.10" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 884f5a559d5c6e159ee74fa72c2d6ee7712943e8de46d7b363ab2adb2d74bf69 + sha256: 990fe4e49c6ca3f3a008ca93dd0e2ecbf97151d45ad550190b908c3343d8668c build: number: 0 From ce82a9eed84fad1d43a875caa141e54ffaa25d74 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 15 Oct 2023 21:46:01 -0600 Subject: [PATCH 0266/2173] Update tcdemux to 0.0.24 (#43686) --- recipes/tcdemux/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tcdemux/meta.yaml b/recipes/tcdemux/meta.yaml index 915c758a92ef3..b424f8dcdc1fb 100644 --- a/recipes/tcdemux/meta.yaml +++ b/recipes/tcdemux/meta.yaml @@ -1,5 +1,5 @@ --- -{% set version = "0.0.22" %} +{% set version = "0.0.24" %} package: name: tcdemux @@ -7,7 +7,7 @@ package: source: url: https://github.com/TomHarrop/tcdemux/archive/refs/tags/{{ version }}.tar.gz - sha256: 3d6b62b93de25a977ab4f28876d1bbd5edf821980f85efc6606461b3f0270c2a + sha256: ab40fd9230e126e4691a9d7c0799cfe52baac0a7e86230f22aefa42206609fda build: number: 0 From 68e9351f4dc92a4a6937c38bcb26b16658e86ac5 Mon Sep 17 00:00:00 2001 From: Paolo Di Tommaso Date: Mon, 16 Oct 2023 09:12:39 +0200 Subject: [PATCH 0267/2173] nextflow 23.10.0 (#43689) --- recipes/nextflow/meta.yaml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/recipes/nextflow/meta.yaml b/recipes/nextflow/meta.yaml index bf48e7be6a046..ccb24e6cfbb15 100644 --- a/recipes/nextflow/meta.yaml +++ b/recipes/nextflow/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.04.4" %} -{% set sha256 = "494b462f8f2c47e51ba6f833d818ee0c55412b88fdb526b71ec8f0c758dd8f0f" %} +{% set version = "23.10.0" %} +{% set sha256 = "4b7fba61ecc6d53a6850390bb435455a54ae4d0c3108199f88b16b49e555afdd" %} package: name: nextflow @@ -17,13 +17,13 @@ source: requirements: host: - - openjdk >=11,<=20 - - coreutils - - curl + - conda-forge::openjdk >=11,<=21 + - conda-forge::coreutils + - conda-forge::curl run: - - openjdk >=11,<=20 - - coreutils - - curl + - conda-forge::openjdk >=11,<=21 + - conda-forge::coreutils + - conda-forge::curl test: commands: @@ -36,4 +36,5 @@ about: extra: recipe-maintainers: + - pditommaso - mjsteinbaugh From dc52e6dfabae4e56ddee6d2ace127028147ecdb9 Mon Sep 17 00:00:00 2001 From: Ray <851836818@qq.com> Date: Mon, 16 Oct 2023 15:15:49 +0800 Subject: [PATCH 0268/2173] Update meta.yaml (#43688) * Update meta.yaml Change networkx version to 2.6.3 * Update meta.yaml --- recipes/gdmicro/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gdmicro/meta.yaml b/recipes/gdmicro/meta.yaml index 08fce531d0ecf..f4c29f068e691 100644 --- a/recipes/gdmicro/meta.yaml +++ b/recipes/gdmicro/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8b890f8e609c854726ed294044fe2daaf56c69d5b25f01c2f4440fffa46903a7 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " run_exports: - {{ pin_subpackage('gdmicro', max_pin="x") }} @@ -27,7 +27,7 @@ requirements: - scipy - scikit-learn - pytorch ==1.12.0 - - networkx + - networkx ==2.6.3 - matplotlib-base - ipython - r-base ==3.6.1 From 435e5a4f1b5f62615234333cbea5827983ab8fba Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 01:16:34 -0600 Subject: [PATCH 0269/2173] Update aviary to 0.8.2 (#43687) --- recipes/aviary/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/aviary/meta.yaml b/recipes/aviary/meta.yaml index 97ff289f65e9c..7e5d8bbcd7ace 100644 --- a/recipes/aviary/meta.yaml +++ b/recipes/aviary/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.8.1" %} +{% set version = "0.8.2" %} {% set name = "aviary" %} -{% set sha256 = "bc26f5547c80e851351ede2b268bab75bf7598debdc724736e28d4e6084a66b3" %} +{% set sha256 = "0f3299acc2586a1cca5a1c6588d63bc1bcf613a1feac91534ea9b532957f0ba1" %} package: name: aviary From 26a72d94130e28494b6e250ba1d046062b426475 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 07:15:55 -0600 Subject: [PATCH 0270/2173] Update annonars to 0.23.1 (#43693) * Update annonars to 0.23.0 * Update annonars to 0.23.1 --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 344b583def70c..5bc6d91f18878 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.22.0" %} +{% set version = "0.23.1" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9acc7cef3eec51da9b7854c8a88695ce062f95eb58eaa5c9c62c9d4b98e301c8 + sha256: 378a874690d0fee27ca18e471bf06e327c825714d7229dd87cbf53f97990b0fb requirements: build: From 44b0bdde1c7ca543bde5ebbdfc8ea6fc99121998 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 07:47:58 -0600 Subject: [PATCH 0271/2173] Update genmod to 3.8.0 (#43695) * Update genmod to 3.8.0 * Update meta.yaml --------- Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> --- recipes/genmod/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/genmod/meta.yaml b/recipes/genmod/meta.yaml index 51dbf72fb873b..fd4a3b92d4cb6 100644 --- a/recipes/genmod/meta.yaml +++ b/recipes/genmod/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genmod" %} -{% set version = "3.7.4" %} +{% set version = "3.8.0" %} package: name: "{{ name|lower }}" @@ -7,11 +7,13 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a45d0a197ac5cfa5d3df50cf415a0c9e91e7ab4cd5778077779eb8f6c29664e8 + sha256: e057cb2e630a3e16eeb63735ab604cc5315998a4a89993d57f03680c3fd8c9f3 build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage('genmod', max_pin="x") }} entry_points: - genmod = genmod.commands.base:cli script: "{{ PYTHON }} -m pip install . --no-deps -vv" From 137a23e79e08165951e16963172ef5f285ff8d90 Mon Sep 17 00:00:00 2001 From: Jakob Nybo Nissen Date: Mon, 16 Oct 2023 19:47:52 +0200 Subject: [PATCH 0272/2173] Update Vamb to v4.1.3 (#43684) * Bump Vamb to v4.1.3 * Update * Try again * Try to fix line 27 --- recipes/vamb/meta.yaml | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/recipes/vamb/meta.yaml b/recipes/vamb/meta.yaml index ab4448831fbde..a2362c80db0c2 100644 --- a/recipes/vamb/meta.yaml +++ b/recipes/vamb/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "3.0.2" %} +{% set version = "4.1.3" %} package: name: vamb version: {{ version }} source: - url: https://github.com/RasmussenLab/vamb/archive/{{ version }}.tar.gz - sha256: fb63011a89ec7fe1052983973dda6cdcdd796938cdf80ed1013f253c7ded8c67 + url: https://github.com/RasmussenLab/vamb/archive/refs/tags/v{{ version }}.tar.gz + sha256: 3b82a36138ebbebf6efe5203da4f9dfae9d0335137bac9775d5b427021aa5645 build: - number: 2 + number: 0 # Skipping py>=38 since no pytorch-cpu builds for Py3.8 are available. skip: True # [py27] skip: True # [py<30 or py>=38] entry_points: - vamb=vamb.__main__:main script: {{ PYTHON }} -m pip install . --no-deps -vv + run_exports: + - {{ pin_subpackage('vamb', max_pin="x") }} requirements: build: - {{ compiler('c') }} host: - - python + - python >=3.9.0,<3.12 - pip - - cython >=0.25.2 + - cython >=3.0.0 run: - - python - - numpy >=1.15 - - pytorch-cpu >=0.4 - - pysam >=0.14 + - python >=3.9.0,<3.12 + - numpy ==1.24.2 + - torch ==1.13.1 + - pycoverm ==0.6.0 test: imports: From 97a4fbdafdb449828ddb02d861a5d91366f6faec Mon Sep 17 00:00:00 2001 From: Florian De Temmerman <69114541+fbdtemme@users.noreply.github.com> Date: Mon, 16 Oct 2023 19:48:40 +0200 Subject: [PATCH 0273/2173] update pixelator to 0.15.0 (#43698) --- recipes/pixelator/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pixelator/meta.yaml b/recipes/pixelator/meta.yaml index 97266be48139f..1c5af2c8c9cc6 100644 --- a/recipes/pixelator/meta.yaml +++ b/recipes/pixelator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pixelator" %} -{% set version = "0.14.0" %} +{% set version = "0.15.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/pixelgentechnologies/{{ name }}/archive/v{{ version }}.tar.gz - sha256: f8c251f3b50a0cd8609d1360f6caee183abf6e2c10436e4021f4a91dd918e2d3 + sha256: 78ffabc98868679773b3a17f4dee7da9413f76353c253973108dbc72dafb4203 build: noarch: python @@ -25,7 +25,7 @@ requirements: - poetry-dynamic-versioning >=1.1.0 - pip run: - - python >=3.8,<3.11 + - python >=3.8,<3.12 - igraph >=0.10.2,<=0.11.0 - louvain >=0.8.0,<=0.9.0 - click From a071800ec0c760c8d75745183418e2c3380c4598 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 11:49:10 -0600 Subject: [PATCH 0274/2173] Update skder to 1.0.8 (#43705) --- recipes/skder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skder/meta.yaml b/recipes/skder/meta.yaml index eb286dd48636b..4dd0dfc2b7538 100644 --- a/recipes/skder/meta.yaml +++ b/recipes/skder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skder" %} -{% set version = "1.0.7" %} +{% set version = "1.0.8" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/raufs/skDER/archive/refs/tags/v{{ version }}.tar.gz - sha256: 057483c05f5364bfaa0ee12b5f59a3272eaf3de81d6bfea8d53422ba110c840d + sha256: 5d48666d6c7db738777c3bbe2601b01707c2c961b987aecde0f4210154605254 build: number: 0 From 2219ffd47f4979a65ce913238fd96526c6c590f0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 13:37:46 -0600 Subject: [PATCH 0275/2173] Update pybiolib to 1.1.1412 (#43691) * Update pybiolib to 1.1.1402 * Update pybiolib to 1.1.1412 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index f197b0b630d2e..5cfc12fb3becd 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1395" %} +{% set version = "1.1.1412" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 690c47057afe220c10bcd63837171bc809844871ca76635559b6637d79acc321 + sha256: 94936309ddb08f0bb133c9ea4e652b0683598856f50c7dc775946a3735f40425 build: noarch: python From f2a179f7cc38aba92f8d08bab9094d76b2f4e1b6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 14:56:57 -0600 Subject: [PATCH 0276/2173] Update ncbi-amrfinderplus to 3.11.26 (#43707) * Update ncbi-amrfinderplus to 3.11.26 * Update meta.yaml add --print_node option Fix tests to add --print_node option * Update meta.yaml fix build # should have been 0 --------- Co-authored-by: Arjun Prasad --- recipes/ncbi-amrfinderplus/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ncbi-amrfinderplus/meta.yaml b/recipes/ncbi-amrfinderplus/meta.yaml index ac4edfa8cc401..a1c878034c0f5 100644 --- a/recipes/ncbi-amrfinderplus/meta.yaml +++ b/recipes/ncbi-amrfinderplus/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.11.20" %} -{% set sha256 = "698462c4fa688a91130b72e44756d21faf406e186a02da914982044332419ef6" %} +{% set version = "3.11.26" %} +{% set sha256 = "49d98d0f66e121d3ed5a3d9a817089ee69399b0bd06af52f79d796bfe8b2d8b2" %} package: name: ncbi-amrfinderplus @@ -43,7 +43,7 @@ test: -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.fa \ -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.gff \ -O https://raw.githubusercontent.com/ncbi/amr/master/test_both.expected - amrfinder --plus -n test_dna.fa -p test_prot.fa -g test_prot.gff -O Escherichia > test_both.got + amrfinder --plus -n test_dna.fa -p test_prot.fa -g test_prot.gff -O Escherichia --print_node > test_both.got diff test_both.expected test_both.got about: From f98d50ab83dd775e55326357d6f8fc14e45a3a83 Mon Sep 17 00:00:00 2001 From: farchaab <116543129+farchaab@users.noreply.github.com> Date: Mon, 16 Oct 2023 22:57:21 +0200 Subject: [PATCH 0277/2173] Add recipe for assembly finder (#43696) * added assembly finder recipe * Update meta.yaml Use SPDX identifier for license --------- Co-authored-by: Thanh Lee --- recipes/assembly_finder/meta.yaml | 49 +++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/assembly_finder/meta.yaml diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml new file mode 100644 index 0000000000000..abf2e09e7e64e --- /dev/null +++ b/recipes/assembly_finder/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "assembly_finder" %} +{% set version = "0.3.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + - url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 07db574ce4edbf66e38a892c0012bed0e3d358ce2b88d8f8e98726925cd181a1 +build: + number: 0 + entry_points: + - assembly_finder = assembly_finder.assembly_finder:cli + noarch: python + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv + run_exports: + - {{ pin_subpackage('assembly_finder', max_pin="x.x") }} + +requirements: + host: + - python >=3.9 + - pip + + run: + - python >=3.9 + - snakemake-minimal >=7.32.4 + - click >=7 + - biopython >=1.78 + - pandas >=2.0.3 + - ete3 >=3.1.3 + - aspera-cli >=4.14.0 +test: + commands: + - assembly_finder -h + - assembly_finder -v +about: + home: https://github.com/metagenlab/assembly_finder + license: GPL-3.0-or-later + license_file: LICENSE + summary: Snakemake pipeline to download assemblies from NCBI. + +extra: + container: + extended-base: true + recipe-maintainers: + - idfarbanecha + - tpillone + From 6e4bcf601ee34e23caeefbdd06f60689cda79b22 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 14:57:47 -0600 Subject: [PATCH 0278/2173] Update mehari to 0.13.0 (#43697) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 03f4a64f50319..4026f0c727cbd 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.12.0" %} -{% set sha256 = "793e5719f00faa20ce0fb4ecf8a682432e058777ff357116f9f67964c8b6dc2c" %} +{% set version = "0.13.0" %} +{% set sha256 = "90cca92ae67de5c86f3bb5b40668e8558f11318d2de1ac5fbb72866521b6d133" %} package: name: mehari From 5285512d1cf86e9af8c38f5284b6689005fc2a5b Mon Sep 17 00:00:00 2001 From: Eric Kutschera Date: Mon, 16 Oct 2023 16:58:41 -0400 Subject: [PATCH 0279/2173] Update rmats2sashimiplot to v3.0.0 (#43702) * v3.0.0 stops using a deprecated matplotlib import --- .../build_failure.linux-64.yaml | 104 ------------------ .../build_failure.osx-64.yaml | 104 ------------------ recipes/rmats2sashimiplot/meta.yaml | 10 +- 3 files changed, 6 insertions(+), 212 deletions(-) delete mode 100644 recipes/rmats2sashimiplot/build_failure.linux-64.yaml delete mode 100644 recipes/rmats2sashimiplot/build_failure.osx-64.yaml diff --git a/recipes/rmats2sashimiplot/build_failure.linux-64.yaml b/recipes/rmats2sashimiplot/build_failure.linux-64.yaml deleted file mode 100644 index 0048cbb0afd57..0000000000000 --- a/recipes/rmats2sashimiplot/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 818b19264e031ab0aafc69a65856602ab4de67b68aed3fe7e3117d898e0765f6 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - pip: 23.1.2-pyhd8ed1ab_0 conda-forge - python: 3.10.11-he550d4f_0_cpython conda-forge - readline: 8.2-h8228510_1 conda-forge - setuptools: 67.7.2-pyhd8ed1ab_0 conda-forge - tk: 8.6.12-h27826a3_0 conda-forge - tzdata: 2023c-h71feb2d_0 conda-forge - wheel: 0.40.0-pyhd8ed1ab_0 conda-forge - xz: 5.2.6-h166bdaf_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - [34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 1.5kB @ 11.4MB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.6MB/s 0.0s - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0Gopt/conda/conda-bld/linux-64 1.5kB @ 19.5MB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 3.3MB/s 0.0s - [?25hMamba failed to solve: - - python_abi 3.10.* *_cp310 - - numpy - - python >=3.10,<3.11.0a0 - - scipy - - pysam - - bedtools - - matplotlib 3.3.* - - samtools - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package matplotlib-3.3.2-h06a4308_0 requires matplotlib-base >=3.3.2,<3.3.3.0a0, but none of the providers can be installed - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 230, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 220, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - python_abi 3.10.* *_cp310 - - numpy - - python >=3.10,<3.11.0a0 - - scipy - - pysam - - bedtools - - matplotlib 3.3.* - - samtools - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package matplotlib-3.3.2-h06a4308_0 requires matplotlib-base >=3.3.2,<3.3.3.0a0, but none of the providers can be installed - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2115, in build - create_build_envs(top_level_pkg, notest) - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1993, in create_build_envs - raise e - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1972, in create_build_envs - environ.get_install_actions(m.config.test_prefix, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("matplotlib==3.3.2=h06a4308_0"), MatchSpec("matplotlib-base[version='>=3.3.2,<3.3.3.0a0']")} -# Last 100 lines of the build log. diff --git a/recipes/rmats2sashimiplot/build_failure.osx-64.yaml b/recipes/rmats2sashimiplot/build_failure.osx-64.yaml deleted file mode 100644 index 8ac86c6c647cc..0000000000000 --- a/recipes/rmats2sashimiplot/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 818b19264e031ab0aafc69a65856602ab4de67b68aed3fe7e3117d898e0765f6 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - libffi: 3.4.2-h0d85af4_5 conda-forge - libsqlite: 3.42.0-h58db7d2_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - ncurses: 6.3-h96cf925_1 conda-forge - openssl: 3.1.1-h8a1eda9_1 conda-forge - pip: 23.1.2-pyhd8ed1ab_0 conda-forge - python: 3.10.11-he7542f4_0_cpython conda-forge - readline: 8.2-h9e318b2_1 conda-forge - setuptools: 67.7.2-pyhd8ed1ab_0 conda-forge - tk: 8.6.12-h5dbffcc_0 conda-forge - tzdata: 2023c-h71feb2d_0 conda-forge - wheel: 0.40.0-pyhd8ed1ab_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - Mamba failed to solve: - - bedtools - - numpy - - scipy - - samtools - - matplotlib 3.3.* - - python_abi 3.10.* *_cp310 - - pysam - - python >=3.10,<3.11.0a0 - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package matplotlib-3.3.1-0 requires matplotlib-base >=3.3.1,<3.3.2.0a0, but none of the providers can be installed - - - - Leaving build/test directories: - Work: - /opt/mambaforge/envs/bioconda/conda-bld/work - Test: - /opt/mambaforge/envs/bioconda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - Build: - source activate /opt/mambaforge/envs/bioconda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 230, in solve_for_action - t = self.solve(specs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 220, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - bedtools - - numpy - - scipy - - samtools - - matplotlib 3.3.* - - python_abi 3.10.* *_cp310 - - pysam - - python >=3.10,<3.11.0a0 - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package matplotlib-3.3.1-0 requires matplotlib-base >=3.3.1,<3.3.2.0a0, but none of the providers can be installed - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2115, in build - create_build_envs(top_level_pkg, notest) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 1993, in create_build_envs - raise e - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 1972, in create_build_envs - environ.get_install_actions(m.config.test_prefix, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("matplotlib==3.3.1=0"), MatchSpec("matplotlib-base[version='>=3.3.1,<3.3.2.0a0']")} -# Last 100 lines of the build log. diff --git a/recipes/rmats2sashimiplot/meta.yaml b/recipes/rmats2sashimiplot/meta.yaml index dddf30862ec4f..372775d61638b 100644 --- a/recipes/rmats2sashimiplot/meta.yaml +++ b/recipes/rmats2sashimiplot/meta.yaml @@ -1,5 +1,5 @@ {% set name = "rmats2sashimiplot" %} -{% set version = "2.0.4" %} +{% set version = "3.0.0" %} package: name: "{{ name|lower }}" @@ -7,14 +7,16 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 2bd76cc2e95a6b3dcd81e0ff212261cd2891d28e4ac314b5211489a6b426a9d3 + sha256: 5d8e0fa3e7c5db2e595dc08e4cdb652385c18d7f2b70468d81a0fb3d957d03ce build: - number: 3 + number: 0 entry_points: - rmats2sashimiplot=rmats2sashimiplot.rmats2sashimiplot:main - index_gff=MISO.misopy.index_gff:main - sashimi_plot=MISO.misopy.sashimi_plot.sashimi_plot:main + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: @@ -22,7 +24,7 @@ requirements: - python run: - bedtools - - matplotlib =3.3 + - matplotlib-base - numpy - pysam - python From b66ffadf64004981e05146a1bcb5b38da9462e73 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 14:59:04 -0600 Subject: [PATCH 0280/2173] Update zdb to 1.2.1 (#43700) --- recipes/zdb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zdb/meta.yaml b/recipes/zdb/meta.yaml index 1791f812922a3..16d0ff70edc24 100644 --- a/recipes/zdb/meta.yaml +++ b/recipes/zdb/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.0" %} +{% set version = "1.2.1" %} package: name: zdb @@ -12,7 +12,7 @@ build: source: url: https://github.com/metagenlab/zDB/archive/refs/tags/v{{ version }}.tar.gz - sha256: 19611b62cf591f03697259748e9aae8d8f82541885879d2f3a8c3d69e9bb72ab + sha256: 621146aa73de7bf04dd05da4e226eb558d07eb1f79e04760456c84e00ae9be0c requirements: run: From 356afcb24ee3fa4a06960e52b1c00b2fcc297fee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 15:03:09 -0600 Subject: [PATCH 0281/2173] Update dxpy to 0.361.0 (#43703) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 64b5decd8085b..2aa768cf2e5fe 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.359.1" %} +{% set version = "0.361.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 3ea10e7e7b59634dc8514037465bdb8cedbf9988973262a4091478f3d680571e + sha256: 455c2a63764e7a1158cdb48abcf987e80d186fb92c23c539d8e6f2e4cc0368c7 build: number: 0 From a0fb8c4cffcfcc263981ac819444ed552d7fbf18 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 16:45:07 -0600 Subject: [PATCH 0282/2173] Update checkqc to 3.8.2 (#43694) * Update checkqc to 3.8.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/checkqc/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/checkqc/meta.yaml b/recipes/checkqc/meta.yaml index 437ec826db435..fc9fb550cbfc4 100644 --- a/recipes/checkqc/meta.yaml +++ b/recipes/checkqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "checkQC" %} -{% set version = "3.8.1" %} +{% set version = "3.8.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 05581afe99b37d3c1ee5a383b92fd9381e7a20caa54fe43f7e9f6b5a325a9058 + sha256: 3aeb234d64aede3377f33b7573eb4719d7c665d68985e8713b16159a1be87988 build: number: 0 @@ -15,7 +15,9 @@ build: entry_points: - checkqc = checkQC.app:start - checkqc-ws = checkQC.web_app:start - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('checkqc', max_pin="x") }} requirements: host: @@ -41,7 +43,7 @@ test: about: home: "https://www.github.com/Molmed/checkQC" - license: GPLv3 + license: GPL-3.0-or-later license_family: GPL3 license_file: LICENSE summary: "A simple program to parse Illumina NGS data and check it for quality criteria." From be7297ae7edb4cfda7859aa91fcb15f80a6127b7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 16:54:45 -0600 Subject: [PATCH 0283/2173] Update fiji-morpholibj to 1.6.1 (#43692) * Update fiji-morpholibj to 1.6.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fiji-morpholibj/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/fiji-morpholibj/meta.yaml b/recipes/fiji-morpholibj/meta.yaml index ca549e2629e2c..349e228f08be3 100644 --- a/recipes/fiji-morpholibj/meta.yaml +++ b/recipes/fiji-morpholibj/meta.yaml @@ -1,17 +1,19 @@ {% set name = "fiji-morpholibj" %} -{% set version = "1.5.1" %} - +{% set version = "1.6.1" %} + package: name: {{ name | lower }} version: {{ version }} source: url: https://github.com/ijpb/MorphoLibJ/releases/download/v{{ version }}/MorphoLibJ_-{{ version }}.jar - sha256: fd6e010fb94b49d1b12786274deae4e6be57fb5a0113f36c2cf7d14dbeb6b4e6 + sha256: e6b3b3ee1355a0286d6fb09d8059ef49475d3cbad6a735037e0edd47d9d1d97d build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('fiji-morpholibj', max_pin="x") }} requirements: host: From acfce309e463d8b9f4cf2f389002241240e50749 Mon Sep 17 00:00:00 2001 From: Xiangyang1984 <58356520+Xiangyang1984@users.noreply.github.com> Date: Tue, 17 Oct 2023 06:57:14 +0800 Subject: [PATCH 0284/2173] add pneumo-typer recipes (#43679) * add pneumo-typer recipes * Update meta.yaml --- recipes/pneumo-typer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pneumo-typer/meta.yaml b/recipes/pneumo-typer/meta.yaml index 4e2eefab7cb6c..b5265377333d4 100644 --- a/recipes/pneumo-typer/meta.yaml +++ b/recipes/pneumo-typer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pneumo-typer" %} {% set version = "1.0.1" %} -{% set sha256 = "b704a93b83c0c4292f5373228229dca4529e3be478b8d8efbac9a4f72c56255a" %} +{% set sha256 = "26ff14bc8bd48588e6b2332dfa25fcae2239a89d981a00622b16818a926cf194" %} package: name: "{{ name|lower }}" @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 noarch: generic run_exports: - {{ pin_subpackage('pneumo-typer', max_pin="x") }} From c7222153b05dbcbab554cc94c65f80a58725296d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 16 Oct 2023 17:01:23 -0600 Subject: [PATCH 0285/2173] Update talon to 6.0 (#43709) * Update talon to 6.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/talon/meta.yaml | 36 +++++++++++++++++++++++++++--------- 1 file changed, 27 insertions(+), 9 deletions(-) diff --git a/recipes/talon/meta.yaml b/recipes/talon/meta.yaml index c13fd4bec353e..397bb96dabf1a 100644 --- a/recipes/talon/meta.yaml +++ b/recipes/talon/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "5.0" %} +{% set version = "6.0" %} package: name: talon @@ -6,30 +6,46 @@ package: source: url: https://github.com/mortazavilab/TALON/archive/v{{ version }}.zip - sha256: d64cf0f602be5e8cac989e7ddaa6d82c0455f94f29368782348adf36feaf0a24 - + sha256: f0e1f9e48a99f18bbfadfbacf6b31913508bdc4932e08fd0ea8ac78f2b459fd4 build: noarch: python number: 0 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps -vvv + entry_points: + - talon=talon.talon:main + - talon_label_reads=talon.talon_label_reads:main + - talon_initialize_database=talon.initialize_talon_database:main + - talon_filter_transcripts=talon.post.filter_talon_transcripts:main + - talon_abundance=talon.post.create_abundance_file_from_database:main + - talon_create_GTF=talon.post.create_GTF_from_database:main + - talon_create_adata=talon.post.create_anndata_from_database:main + - talon_reformat_gtf=talon.reformat_gtf:main + - talon_generate_report=talon.post.generate_talon_report:main + - talon_summarize=talon.post.summarize_datasets:main + - talon_fetch_reads=talon.post.get_read_annotations:main + - talon_get_sjs=talon.post.get_transcript_sjs:main + - talon_longest_end=talon.post.call_longest_ends:main + run_exports: + - {{ pin_subpackage('talon', max_pin="x.x") }} requirements: host: - - python >=3.6,<=3.7 + - python >=3.6,<3.8 - pip - run: - - python >=3.6,<=3.7 + - python >=3.6,<3.8 + - bamread >=0.0.11 - pandas - pybedtools + - pyranges - pysam >=0.15.4 - pyfaidx - + - scanpy test: commands: - - talon --help 2>&1 | grep usage + - talon --help 2>&1 | grep usage - talon_label_reads --help - talon_initialize_database --help - talon_filter_transcripts --help @@ -38,6 +54,8 @@ test: about: home: https://github.com/mortazavilab/TALON license: MIT + license_family: MIT + license_file: LICENSE summary: | TALON is a Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets. TALON is From a6356a99c0ad26b08d38cafddf291b6eea7435de Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 02:09:25 -0600 Subject: [PATCH 0286/2173] Update snakemake-interface-common to 1.14.0 (#43714) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 5eae71378b102..59989304ebb89 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.13.0" %} +{% set version = "1.14.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: daef8b14b919062c199ddc63c0e7e8a95252c2e687322b43136afdab297e3708 + sha256: 45835174fda3d3528b522637721ceb58c00c30dbd48e9c0791365cb0ec494afd build: noarch: python From fa8063f7365907c6ef78accc5b4722f1cceebca5 Mon Sep 17 00:00:00 2001 From: Stas <5831286+Dantistnfs@users.noreply.github.com> Date: Tue, 17 Oct 2023 06:08:26 -0300 Subject: [PATCH 0287/2173] Use updated download urls for SnpEff (#43701) --- recipes/snpeff/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/snpeff/meta.yaml b/recipes/snpeff/meta.yaml index 523a0584f97a9..aefeb88088b8c 100644 --- a/recipes/snpeff/meta.yaml +++ b/recipes/snpeff/meta.yaml @@ -1,8 +1,8 @@ -{% set snpeff_ver = "v5_1d" %} +{% set snpeff_ver = "v5_2" %} # NOTE: if the version contains a trailing letter, use the ..1 format # Please update recipes/snpsift as well! -{% set version = "5.1d" %} -{% set sha256 = "919e0595c08e86d1dd82279723c83cb872070244ee4ce0cb3167bde2b272893b" %} +{% set version = "5.2" %} +{% set sha256 = "60ad2eec66c4f086b8cc7812e5654dce2dd500dd218774da490326e6a4e585f7" %} about: home: 'http://snpeff.sourceforge.net/' @@ -16,6 +16,10 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_compatible('python', max_pin="3.9.*") }} + - {{ pin_compatible('perl', max_pin="5.32.*") }} + - {{ pin_compatible('openjdk', max_pin="11.*") }} source: url: https://snpeff.blob.core.windows.net/versions/snpEff_{{ snpeff_ver }}_core.zip From 3458764c59385afd86b8a533cf0e35b4b846771e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 03:37:52 -0600 Subject: [PATCH 0288/2173] Update r-ldweaver to 1.2 (#43711) * Update r-ldweaver to 1.2 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-ldweaver/meta.yaml | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/recipes/r-ldweaver/meta.yaml b/recipes/r-ldweaver/meta.yaml index b5c1b655bc510..0eaa2453f417b 100644 --- a/recipes/r-ldweaver/meta.yaml +++ b/recipes/r-ldweaver/meta.yaml @@ -1,6 +1,6 @@ {% set name = "r-ldweaver" %} -{% set version = "1.1.1" %} -{% set sha256 = "4369b95bafd128a63f10b2288fbce66deb685e22d0b7be307baaefe5005a3356" %} +{% set version = "1.2" %} +{% set sha256 = "66a51a318be2029ae163f2cd70ae0f66a925bc2313aea070d34d25b72efdc528" %} package: name: {{ name }} @@ -12,18 +12,16 @@ source: build: number: 0 - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ run_exports: - - {{ pin_subpackage('r-ldweaver', max_pin="x") }} + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: - {{ compiler('c') }} # [not win] - {{ compiler('cxx') }} # [not win] - host: - r-base 4.* - bioconductor-genomicranges @@ -48,7 +46,6 @@ requirements: - r-phytools - r-plyr - r-stringi - run: - r-base 4.* - bioconductor-genomicranges @@ -76,7 +73,6 @@ requirements: test: commands: - # You can put additional test commands to be run here. - $R -e "library('LDWeaver')" # [not win] about: From 097af7d72a4d2962907e55e2240db6f901b7f612 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 17 Oct 2023 11:49:55 +0200 Subject: [PATCH 0289/2173] Ensure that Snakemake uses at most Python 3.11 because of breaking changes in Python 3.12 (#43716) * Ensure that Snakemake uses at most Python 3.11 because of breaking changes in Python 3.12 * Update meta.yaml * Update meta.yaml --- recipes/snakemake/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 54c50d0b91ded..5b8327aee4bdc 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -9,8 +9,10 @@ source: sha256: fdc3f15dd7b06fabb7da30d460e0a3b1fba08e4ea91f9c32c47a83705cdc7b6e build: - number: 0 + number: 1 noarch: generic + run_exports: + - {{ pin_subpackage("snakemake", max_pin="x") }} requirements: run: @@ -86,6 +88,8 @@ outputs: entry_points: - snakemake = snakemake:main - snakemake-bash-completion = snakemake:bash_completion + run_exports: + - {{ pin_subpackage("snakemake-minimal", max_pin="x") }} requirements: host: @@ -94,7 +98,7 @@ outputs: - setuptools run: # Keep in sync with snakemake/setup.cfg - - python >=3.7 + - python >=3.7,<3.12 - appdirs - configargparse - connection_pool >=0.0.3 From 1f740f4921b109f28038c01c25b6a538b04a219d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 03:56:32 -0600 Subject: [PATCH 0290/2173] Update customtkinter to 5.2.1 (#43717) * Update customtkinter to 5.2.1 * Update meta.yaml packaging added as dependency --------- Co-authored-by: Yasset Perez-Riverol --- recipes/customtkinter/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/customtkinter/meta.yaml b/recipes/customtkinter/meta.yaml index 61dc5a5b28ba0..0dbc3d2ed778d 100644 --- a/recipes/customtkinter/meta.yaml +++ b/recipes/customtkinter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "customtkinter" %} -{% set version = "5.2.0" %} +{% set version = "5.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/customtkinter-{{ version }}.tar.gz - sha256: e93448a8d22121e20ec16e95960a8306e17cf7e0079766f5804b2e855e614937 + sha256: eddc1c416063e1ce1aa2793959b0814e95e22d3de3f2a940bd84828f7301f555 build: script: "{{ PYTHON }} -m pip install . --no-deps -vvv" @@ -27,6 +27,7 @@ requirements: - darkdetect - typing-extensions # [py<=37] - xorg-libx11 + - packaging test: imports: From d15e9bea27d995cbe4ce64b62f9484e1811b6641 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 05:59:28 -0600 Subject: [PATCH 0291/2173] Update whatshap to 2.1 (#43724) * Update whatshap to 2.1 * Update meta.yaml --------- Co-authored-by: Marcel Martin --- recipes/whatshap/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/whatshap/meta.yaml b/recipes/whatshap/meta.yaml index 0a939672f0d50..7c3aeef9ad35c 100644 --- a/recipes/whatshap/meta.yaml +++ b/recipes/whatshap/meta.yaml @@ -1,14 +1,16 @@ package: name: whatshap - version: "2.0" + version: "2.1" source: - url: https://files.pythonhosted.org/packages/c3/10/b53674fa02c1d5b23887f5a6b0fbf6936ce35dcd08f65e994c18601b20cb/whatshap-2.0.tar.gz - sha256: a23949e692047ab0549ea3309c2b70d95de17a01d00cbc8b2f4c8baf467f8e6a + url: https://files.pythonhosted.org/packages/35/1a/d6fedb787eac8d616ec598f6a42cf2289bcc11dbbfdeae65afdf1dcb7bfc/whatshap-2.1.tar.gz + sha256: 9b61812eda1dd5251ba8d02db16d7ddda152ccc813cb3db6a1ec796f1865fe8d build: - script: python -m pip install --no-deps --ignore-installed . number: 0 + script: python -m pip install --no-deps --ignore-installed . + run_exports: + - {{ pin_subpackage('whatshap', max_pin="x") }} requirements: build: From 1700ea99847d89d2d5e51dee11284e7f240a7de5 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 17 Oct 2023 13:06:04 +0100 Subject: [PATCH 0292/2173] bump shinyngs (#43660) Co-authored-by: Thanh Lee --- recipes/r-shinyngs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-shinyngs/meta.yaml b/recipes/r-shinyngs/meta.yaml index 5dc3321d9b9f9..8d5a2da09f423 100644 --- a/recipes/r-shinyngs/meta.yaml +++ b/recipes/r-shinyngs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.8.2' %} +{% set version = '1.8.3' %} {% set d3heatmap_version = '0.6.1.2' %} package: @@ -7,7 +7,7 @@ package: source: - url: https://github.com/pinin4fjords/shinyngs/archive/refs/tags/v{{ version }}.tar.gz - sha256: "a28b53be9d27108e80ffd13d1ef70730186b2bef159bf79983550e403535af81" + sha256: "119f0642e5c2eaf9ce17c94739be1a069ab6c1a40336d0d8369b5e03a5091650" folder: shinyngs - url: https://github.com/cran/d3heatmap/archive/refs/tags/{{ d3heatmap_version }}.tar.gz sha256: "bda213c4d335b199c38a48cb8e60027c929a8ba8ef6e14dc7de692967777c25a" From c4ee9ccf0976651c1befb66f527e08fc720c7bf6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 08:18:05 -0600 Subject: [PATCH 0293/2173] Update ska2 to 0.3.4 (#43719) --- recipes/ska2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ska2/meta.yaml b/recipes/ska2/meta.yaml index 5b5657fd452c4..53d1b819c1333 100644 --- a/recipes/ska2/meta.yaml +++ b/recipes/ska2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ska2" %} -{% set version = "0.3.3" %} +{% set version = "0.3.4" %} package: name: {{ name|lower}} @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/ska.rust/archive/v{{ version }}.tar.gz - sha256: a44325c01060cbc9a6724a081747bd2d75e11a8bf83aa03db1f40f9399128214 + sha256: 65a60e74ac061ab15d8c982cfd446e0b39d01deca353f52d978d811a412e9834 build: number: 0 From 84ed885587bb7d4476bf95dddd9ac7e29f9c8bcd Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 17 Oct 2023 16:19:17 +0200 Subject: [PATCH 0294/2173] bump stacks (#43723) * bump stacks * add run_exorts * add patch to fix include hopefully fixing ``` src/models.cc:736:30: error: 'numeric_limits' is not a member of 'std' 736 | if (weighted_sum >= std::numeric_limits::min()) { ``` --- recipes/stacks/limits.patch | 12 ++++++++++++ recipes/stacks/meta.yaml | 9 ++++++--- 2 files changed, 18 insertions(+), 3 deletions(-) create mode 100644 recipes/stacks/limits.patch diff --git a/recipes/stacks/limits.patch b/recipes/stacks/limits.patch new file mode 100644 index 0000000000000..18b4ca0761ec6 --- /dev/null +++ b/recipes/stacks/limits.patch @@ -0,0 +1,12 @@ +diff -ruN stacks-2.65-org/src/models.h stacks-2.65/src/models.h +--- stacks-2.65-org/src/models.h 2023-10-17 11:57:14.093372152 +0200 ++++ stacks-2.65/src/models.h 2023-10-17 11:57:54.645444150 +0200 +@@ -21,6 +21,8 @@ + #ifndef __MODELS_H__ + #define __MODELS_H__ + ++#include ++ + #include "constants.h" + #include "utils.h" + #include "DNASeq4.h" diff --git a/recipes/stacks/meta.yaml b/recipes/stacks/meta.yaml index 98b7f47ce85e9..d8c7d2a6d53c9 100644 --- a/recipes/stacks/meta.yaml +++ b/recipes/stacks/meta.yaml @@ -1,12 +1,14 @@ -{% set version="2.64" %} -{% set hash="5ea34f6081d6977f205d3c3943aef5f5374375a1b440dc44fe39836e860c3839" %} +{% set version="2.65" %} +{% set hash="ffd6bd3d6295ab9c89cc451f385d37cd1d47a77019c3d305f31202a2b895e2ea" %} package: name: stacks version: {{ version }} build: - number: 1 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage("stacks", max_pin="x") }} source: sha256: {{ hash }} @@ -14,6 +16,7 @@ source: patches: - at.patch - kmer_exit.patch + - limits.patch requirements: build: From ae06589b4d883703ae7cfbf510e603fb93a3d6f8 Mon Sep 17 00:00:00 2001 From: Stas <5831286+Dantistnfs@users.noreply.github.com> Date: Tue, 17 Oct 2023 13:13:25 -0300 Subject: [PATCH 0295/2173] Update SnpSift (#43710) * Use updated download url for SnpSift * Updated snpeff recipie to use correct run_exports --- recipes/snpsift/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/snpsift/meta.yaml b/recipes/snpsift/meta.yaml index e15d60db42487..fafb8edb71ec8 100644 --- a/recipes/snpsift/meta.yaml +++ b/recipes/snpsift/meta.yaml @@ -1,8 +1,8 @@ -{% set snpeff_ver = "v5_1d" %} +{% set snpeff_ver = "v5_2" %} # NOTE: if the version contains a trailing letter, use the ..1 format # Please update recipes/snpeff as well -{% set version = "5.1d" %} -{% set sha256 = "919e0595c08e86d1dd82279723c83cb872070244ee4ce0cb3167bde2b272893b" %} +{% set version = "5.2" %} +{% set sha256 = "60ad2eec66c4f086b8cc7812e5654dce2dd500dd218774da490326e6a4e585f7" %} about: home: 'http://snpeff.sourceforge.net/SnpSift.html' @@ -17,6 +17,8 @@ build: noarch: generic number: 0 skip: False + run_exports: + - {{ pin_compatible('snpsift', max_pin="x.x") }} source: url: https://snpeff.blob.core.windows.net/versions/snpEff_{{ snpeff_ver }}_core.zip From deb56594d32b6867c2e25fa4c9031eddd418d795 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 11:24:19 -0600 Subject: [PATCH 0296/2173] Update phykit to 1.12.0 (#43732) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index 2cc69efc713ff..0f98b1f2d4dda 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.11.16" %} +{% set version = "1.12.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 4bf542cfa50b70134a58bd0fe4ea63536388c781fe15902f4149d8c4aaa926c1 + sha256: 8dfc084780ce4c9a37ee49952ef9d86c617359d8cec5ef97b98ff63b0b95a486 build: noarch: python From 8ebbaae360204872f4f0d89d0367dc0aedfcb18a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 11:25:16 -0600 Subject: [PATCH 0297/2173] Update multiqc to 1.17 (#43733) --- recipes/multiqc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index 20bc3cc2abc62..f8d70ecd88c2a 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.16" %} +{% set version = "1.17" %} package: name: multiqc @@ -6,7 +6,7 @@ package: source: url: https://github.com/ewels/MultiQC/archive/v{{ version }}.tar.gz - sha256: d5a916497dfc8e09a581b8e5e0e3484a616ee499b34577daaf576e4b0f69ffa4 + sha256: f28268e50ef57dbc330ba40eb8dcbb2b86029bc4542dd420fe180c914c284d34 build: number: 0 From d32940cdc74fa6ea67965f4f939aa2a8318b17f4 Mon Sep 17 00:00:00 2001 From: llegregam <75795040+llegregam@users.noreply.github.com> Date: Tue, 17 Oct 2023 19:32:50 +0200 Subject: [PATCH 0298/2173] Bump/physiofit (#43729) * Update physiofit to 3.2.0 * removed openpyxl dependency --------- Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> --- recipes/physiofit/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/physiofit/meta.yaml b/recipes/physiofit/meta.yaml index 09d7a97a1680d..7e680d53051f0 100644 --- a/recipes/physiofit/meta.yaml +++ b/recipes/physiofit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "physiofit" %} -{% set version = "3.1.1" %} +{% set version = "3.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/physiofit-{{ version }}.tar.gz - sha256: aa2cbccd7fc26174419a1d25eff80cf6fffe9e23b0c415b35b435a59fe0f8a2a + sha256: 3b6257586da62c80ba33a5f302833da200f1d3a09c576139cc97a581c1b38132 build: entry_points: @@ -30,7 +30,6 @@ requirements: - scipy >=1.10.1 - streamlit >=1.20.0 - matplotlib-base >=3.7.1 - - openpyxl >=3.0.9 - pyyaml >=6.0.0 test: From 76af7e02f4076a660176aa2e738be9fff55f5e02 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 12:51:54 -0600 Subject: [PATCH 0299/2173] Update varvamp to 0.9.4 (#43731) --- recipes/varvamp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varvamp/meta.yaml b/recipes/varvamp/meta.yaml index f0d062aa7f1a2..c523c95c14113 100644 --- a/recipes/varvamp/meta.yaml +++ b/recipes/varvamp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varvamp" %} -{% set version = "0.9.3" %} +{% set version = "0.9.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/varvamp-{{ version }}.tar.gz - sha256: 946118079a043de4bb8394bab388665c014f95946160d93fd7bfc66b2d70fb0c + sha256: 1b5a0a40235ab295a961c7136a5eb3127e1e70f96887dc70ca7b7b7614bcf4b0 build: entry_points: From 200a881977e3eeb07e0b4ec69d112d8038a05dc8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 12:52:17 -0600 Subject: [PATCH 0300/2173] Update pybiolib to 1.1.1423 (#43721) * Update pybiolib to 1.1.1420 * Update pybiolib to 1.1.1423 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 5cfc12fb3becd..e38bdd87898b0 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1412" %} +{% set version = "1.1.1423" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 94936309ddb08f0bb133c9ea4e652b0683598856f50c7dc775946a3735f40425 + sha256: 1701e2974cd742fb8c40ee604c6312bc46767489c4cab3644d2853bf1872d6ac build: noarch: python From 2dd2c1aca10c425f2190ae65cb00e65e93dfd0da Mon Sep 17 00:00:00 2001 From: Trestan Pillonel <33416812+tpillone@users.noreply.github.com> Date: Tue, 17 Oct 2023 20:53:14 +0200 Subject: [PATCH 0301/2173] Update zdb to v1.2.1 (#43727) * update to v1.2.1 * Update meta.yaml update build number --- recipes/zdb/build.sh | 2 +- recipes/zdb/meta.yaml | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/zdb/build.sh b/recipes/zdb/build.sh index 7314ffce65edc..a61c80dfcb6b0 100644 --- a/recipes/zdb/build.sh +++ b/recipes/zdb/build.sh @@ -9,4 +9,4 @@ sed "s=version=$PKG_VERSION=" bin/zdb > ${PREFIX}/bin/zdb chmod u+x ${PREFIX}/bin/zdb -mv bin/ annotation_pipeline.nf nextflow.config db_setup.nf zdb/ conda/ webapp FAQ.txt README.md ${ZDB_DIR} \ No newline at end of file +mv bin/ annotation_pipeline.nf zdb_base nextflow.config db_setup.nf zdb/ conda/ webapp FAQ.txt README.md ${ZDB_DIR} diff --git a/recipes/zdb/meta.yaml b/recipes/zdb/meta.yaml index 16d0ff70edc24..d410159bdd9f4 100644 --- a/recipes/zdb/meta.yaml +++ b/recipes/zdb/meta.yaml @@ -5,18 +5,19 @@ package: version: {{ version }} build: - number: 0 noarch: generic + number: 1 run_exports: - - {{ pin_subpackage('zdb', max_pin="x") }} + - {{ pin_subpackage('zdb', max_pin="x.x") }} source: - url: https://github.com/metagenlab/zDB/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.2.1.tar.gz sha256: 621146aa73de7bf04dd05da4e226eb558d07eb1f79e04760456c84e00ae9be0c requirements: run: - - nextflow >=21.04.0 + - nextflow >=21.04.0,<=22.10.8 + - mamba test: commands: @@ -25,7 +26,6 @@ test: about: home: https://github.com/metagenlab/zDB/ license: MIT - license_family: MIT license_file: LICENSE summary: zDB is both a bacterial comparative genomics pipeline and a tool to visualize the results dev_url: https://github.com/metagenlab/zDB/ From e2bbbbd6eb190682f6f037eae7f12dfc975d504a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 12:53:51 -0600 Subject: [PATCH 0302/2173] Update fcsparser to 0.2.8 (#43728) --- recipes/fcsparser/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fcsparser/meta.yaml b/recipes/fcsparser/meta.yaml index 264c2839b70ec..98ca491275e3f 100644 --- a/recipes/fcsparser/meta.yaml +++ b/recipes/fcsparser/meta.yaml @@ -1,6 +1,6 @@ {% set name = "fcsparser" %} -{% set version = "0.2.7" %} -{% set sha256 = "6905871c9a6314f4ca79d11f48d84a88d725cdbfb72d3ccb7b4f617a7512270d" %} +{% set version = "0.2.8" %} +{% set sha256 = "df0436bf678df1f4ad3274e55fa06773f884fa45d8329015913a6178d10c73ea" %} package: name: {{ name|lower }} From 3eeb2865543347c09c3b478d9d505f1ab8be2332 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 15:10:54 -0600 Subject: [PATCH 0303/2173] Update cromshell to 2.1.1 (#43735) --- recipes/cromshell/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cromshell/meta.yaml b/recipes/cromshell/meta.yaml index aac99a74ff3fe..050ac19669f61 100644 --- a/recipes/cromshell/meta.yaml +++ b/recipes/cromshell/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cromshell" %} -{% set version = "2.1.0" %} -{% set sha256 = "4aaa30d1e7449577fae3322271c1c0661fa5195b58aad868a2cf891cae74f6a3" %} +{% set version = "2.1.1" %} +{% set sha256 = "2dac45dd457f057304f848fd031355aedeb142bbdf8a57cce3ed43257c706a41" %} package: name: {{ name }} From 74e52488cb80bcbffedd426d3cf4217a1dcd9ffd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 17 Oct 2023 16:43:01 -0600 Subject: [PATCH 0304/2173] Update snakemake-interface-executor-plugins to 7.0.1 (#43718) --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index 871b7ef76fc38..661b0777ce7e4 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "6.0.0" %} +{% set version = "7.0.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: 99fc3d7b056f2d410b6cbbc243927a5a671297c29916ea539bc17b131b9c471e + sha256: 40bbf9e562e20fc3eaa241ac1927e613fc52c22d9453c922a165c7ab2092cbd8 build: noarch: python From 6aab1c0b3eae68235398b477a76faaa01244e12f Mon Sep 17 00:00:00 2001 From: Adam Caprez Date: Tue, 17 Oct 2023 20:06:14 -0500 Subject: [PATCH 0305/2173] Add recipe for nii2dcm 0.1.2. (#43738) --- recipes/nii2dcm/001-version_info.patch | 14 +++++++ recipes/nii2dcm/LICENSE | 23 +++++++++++ recipes/nii2dcm/meta.yaml | 54 ++++++++++++++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 recipes/nii2dcm/001-version_info.patch create mode 100644 recipes/nii2dcm/LICENSE create mode 100644 recipes/nii2dcm/meta.yaml diff --git a/recipes/nii2dcm/001-version_info.patch b/recipes/nii2dcm/001-version_info.patch new file mode 100644 index 0000000000000..b2c1cd02888fa --- /dev/null +++ b/recipes/nii2dcm/001-version_info.patch @@ -0,0 +1,14 @@ +--- setup.py.org 2023-10-17 17:35:14.702458316 -0500 ++++ setup.py 2023-10-17 17:46:27.269258824 -0500 +@@ -1,7 +1,8 @@ ++import os + from setuptools import setup + from dunamai import Version, Style + + setup( + name="nii2dcm", +- version=Version.from_git().serialize(metadata=False, style=Style.SemVer), +-) +\ No newline at end of file ++ version=Version.parse(os.getenv('PKG_VERSION')).serialize(metadata=False, style=Style.SemVer), ++) diff --git a/recipes/nii2dcm/LICENSE b/recipes/nii2dcm/LICENSE new file mode 100644 index 0000000000000..dc300fc34755d --- /dev/null +++ b/recipes/nii2dcm/LICENSE @@ -0,0 +1,23 @@ +BSD 3-Clause License + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the +following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following +disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following +disclaimer in the documentation and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, +INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF +THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +Copyright (c) 2021-2022 Tom Roberts. All rights reserved. \ No newline at end of file diff --git a/recipes/nii2dcm/meta.yaml b/recipes/nii2dcm/meta.yaml new file mode 100644 index 0000000000000..225058d98c41c --- /dev/null +++ b/recipes/nii2dcm/meta.yaml @@ -0,0 +1,54 @@ +{% set name = "nii2dcm" %} +{% set version = "0.1.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nii2dcm-{{ version }}.tar.gz + sha256: 49630e1ec1ee0ce3f999158e8da68c8492e27593d5742ed826b7ce88c1d42be0 + patches: + - 001-version_info.patch + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv + number: 0 + run_exports: + - {{ pin_subpackage('nii2dcm', max_pin="x") }} + +requirements: + host: + - python <3.11 + - setuptools + - dunamai + - pip + run: + - python <3.11 + - numpy ==1.23.2 + - matplotlib-base ==3.6.2 + - nibabel ==5.0.0 + - pydicom ==2.3.0 + - twine ==4.0.2 + - dunamai ==1.18.0 + +test: + imports: + - nii2dcm + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/tomaroberts/nii2dcm + dev_url: https://github.com/tomaroberts/nii2dcm + summary: 'nii2dcm: NIfTI to DICOM creation with Python' + license: BSD-3 + license_family: BSD + license_file: LICENSE + +extra: + recipe-maintainers: + - acaprez From 78f40478ba22fadab07140749fcf5d59dfee77ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 00:47:40 -0600 Subject: [PATCH 0306/2173] Update pathogen-profiler to 3.1.0 (#43737) * Update pathogen-profiler to 3.1.0 * add run_exports * update freebayes * update joblib --------- Co-authored-by: Jody Phelan --- recipes/pathogen-profiler/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/pathogen-profiler/meta.yaml b/recipes/pathogen-profiler/meta.yaml index 1a6fd70f6ca55..a6d852663c109 100644 --- a/recipes/pathogen-profiler/meta.yaml +++ b/recipes/pathogen-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pathogen-profiler" %} -{% set version = "3.0.0" %} -{% set sha256 = "5af4cf87a103cc96bdb005fc214c20dede7c32cba253c89b8df7d8870351bece" %} +{% set version = "3.1.0" %} +{% set sha256 = "638f27205f20632624b98b4e11e176455f772f5ae35a9d7b09ab79373a324472" %} package: name: {{name}} @@ -14,6 +14,8 @@ build: script: python -m pip install --no-deps --ignore-installed . noarch: python number: 0 + run_exports: + - { pin_subpackage('pathogen-profiler', max_pin="x") } requirements: host: @@ -32,7 +34,7 @@ requirements: - delly >=0.8.7 - gatk4 - bedtools - - freebayes >=1.3.5 + - freebayes >=1.3.5,<1.3.7 - samclip - snpeff >=5.1 - requests @@ -43,7 +45,7 @@ requirements: - dsk >=2.2 - cryptography >=39.0.1 - rich-argparse - - joblib + - joblib >=1.3.0 - pysam test: From e5678cc90241e3220561348c7ab40e436f89169b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 02:14:09 -0600 Subject: [PATCH 0307/2173] Update clinvar-this to 0.12.0 (#43740) --- recipes/clinvar-this/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clinvar-this/meta.yaml b/recipes/clinvar-this/meta.yaml index 7dcb280567bf9..c2c2405ee7076 100644 --- a/recipes/clinvar-this/meta.yaml +++ b/recipes/clinvar-this/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.11.0" %} -{% set sha256 = "110b7f7ecd8e009175a7faef3eb9e8d974fd5245adcc299007594ed93fbd2210" %} +{% set version = "0.12.0" %} +{% set sha256 = "af2bc01c9b5a761e0e26ee6d4fcea80692943dc790cb52f2e60ba1db644ecc49" %} package: name: clinvar-this From f07a3866be3e4535cd03bc2929217a518d4c44f4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 02:32:14 -0600 Subject: [PATCH 0308/2173] Update matchms to 0.23.1 (#43741) * Update matchms to 0.23.1 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Helge Hecht --- recipes/matchms/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 80c4e679ed1dd..967e9e49a80c5 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.22.0" %} +{% set version = "0.23.1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 35fc16dc5ff3d6ee3d017ed3f028efdb6dc57b4709d695636b1eb7749544a65a + sha256: 0cee3013e6f6fd09dd4b9d41d96130c9e2273b31bc6b36d2cea666dcfdbf6f2e build: number: 0 script: "{{ PYTHON }} -m pip install . --no-deps -vvv" noarch: python + run_exports: + - {{ pin_subpackage('matchms', max_pin="x") }} requirements: host: @@ -37,6 +39,7 @@ requirements: - tqdm - pillow =9.5 - pandas + - pubchempy test: From c77bea7d01a5795e82017b9a10d1b4aa8e424e30 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 18 Oct 2023 09:56:22 +0100 Subject: [PATCH 0309/2173] Bump shinyngs version to 1.8.4 (#43743) --- recipes/r-shinyngs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-shinyngs/meta.yaml b/recipes/r-shinyngs/meta.yaml index 8d5a2da09f423..1f77aa4ab7e77 100644 --- a/recipes/r-shinyngs/meta.yaml +++ b/recipes/r-shinyngs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.8.3' %} +{% set version = '1.8.4' %} {% set d3heatmap_version = '0.6.1.2' %} package: @@ -7,7 +7,7 @@ package: source: - url: https://github.com/pinin4fjords/shinyngs/archive/refs/tags/v{{ version }}.tar.gz - sha256: "119f0642e5c2eaf9ce17c94739be1a069ab6c1a40336d0d8369b5e03a5091650" + sha256: "b30a615b38b4804d580695130ee28dedc823aca7fc957ab8f073e1454f090c10" folder: shinyngs - url: https://github.com/cran/d3heatmap/archive/refs/tags/{{ d3heatmap_version }}.tar.gz sha256: "bda213c4d335b199c38a48cb8e60027c929a8ba8ef6e14dc7de692967777c25a" From d7f11d2c55f84aa55ada6bcb0ad7ac8052a0219e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 02:59:36 -0600 Subject: [PATCH 0310/2173] Update annonars to 0.24.0 (#43744) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 5bc6d91f18878..4991df75d191f 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.23.1" %} +{% set version = "0.24.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 378a874690d0fee27ca18e471bf06e327c825714d7229dd87cbf53f97990b0fb + sha256: 1680b651e1a0932d2b329991e6451963095489c7cec011d64000cf45d44e9744 requirements: build: From e496a9c51fc16381157d4c07563f085c510c4e90 Mon Sep 17 00:00:00 2001 From: Ankit Arni <124198259+ama249@users.noreply.github.com> Date: Wed, 18 Oct 2023 10:14:01 +0100 Subject: [PATCH 0311/2173] Expanded docs and updated version (#43745) --- recipes/t1dgrs2/meta.yaml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/recipes/t1dgrs2/meta.yaml b/recipes/t1dgrs2/meta.yaml index e67155ea93b90..b6a3554ebe3e0 100644 --- a/recipes/t1dgrs2/meta.yaml +++ b/recipes/t1dgrs2/meta.yaml @@ -1,6 +1,6 @@ {% set org = "t2diabetesgenes" %} {% set pkg_name = "t1dgrs2" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} {% set build_num = 0 %} package: @@ -9,7 +9,7 @@ package: source: url: "https://github.com/{{ org }}/{{ pkg_name }}/archive/refs/tags/{{ version }}.tar.gz" - sha256: 439bb4bab8910a688607cb8516445c2a5cc162f0b316b4bf343d3e17bdca5adf + sha256: 1e9b91d92ec8e14726da308a1c9f73522d25ce7d0097de9bd0180fb4391b6c48 build: number: "{{ build_num }}" @@ -47,7 +47,14 @@ about: license_family: GPL license_file: LICENSE summary: Generate a Type 1 Diabetes Genetic Risk Score (T1D GRS) that accounts for interactions between HLA DR-DQ risk haplotypes. - description: "An improved T1D GRS (by Sharp et al., 2019) that incorporates both non-HLA and HLA risk components in discriminating between cases and controls, by accounting for interactions between HLA DR-DQ haplotype combinations. This uses 67 T1D-associated variants in either GRCh37 or GRCh38 to perform both a linear scoring of the genetic risk, with the added HLA DR-DQ interaction effect for the final GRS.\nThis Python package can be used on both imputed genotyping array and next generation sequencing (e.g., whole genome sequencing) input datasets, but will require quality control procedures to be applied beforehand.\nRequired: PLINK 1.9 fileset (.bed, .bim, .fam).\n\ + description: "An improved T1D GRS (by Sharp et al., 2019) that incorporates both non-HLA and HLA risk components in discriminating between cases and controls, by accounting for interactions between HLA DR-DQ haplotype combinations. This uses 67 T1D-associated variants in either GRCh37 or GRCh38 to perform both a linear scoring of the genetic risk, with the added HLA DR-DQ interaction effect for the final GRS.\n\nThis Python package can be used on both imputed genotyping array and next generation sequencing (e.g., whole genome sequencing) input datasets, but will require quality control procedures to be applied beforehand.\n\nRequired: PLINK 1.9 fileset (.bed, .bim, .fam).\n\nPlease download all configuration files under the 'data' directory from the [Github page](https://github.com/t2diabetesgenes/t1dgrs2) and adjust paths in 't1dgrs2_setttings.yml' accordingly.\n\ + \n### Authors\n\ + * Diane P Fraser ([email](mailto:d.p.fraser@exeter.ac.uk))\n\ + * Seth A Sharp ([email](mailto:ssharp@stanford.edu))\n\ + * Ankit M Arni ([email](mailto:a.m.arni@exeter.ac.uk))\n\ + * Richard A Oram ([email](mailto:r.oram@exeter.ac.uk))\n\ + * Michael N Weedon ([email](mailto:m.n.weedon@exeter.ac.uk))\n\ + * Kashyap A Patel ([email](mailto:k.a.patel@exeter.ac.uk))\n\ \n### References\n\ 1. Oram RA, Patel K, Hill A, et al. (2016) A Type 1 Diabetes Genetic Risk Score Can Aid Discrimination Between Type 1 and Type 2 Diabetes in Young Adults. Diabetes Care 39(3): 337-344. [10.2337/dc15-1111](https://doi.org/10.2337/dc15-1111).\n\ 2. Patel KA, Oram RA, Flanagan SE, et al. (2016) Type 1 Diabetes Genetic Risk Score: A Novel Tool to Discriminate Monogenic and Type 1 Diabetes. Diabetes 65(7): 2094-2099. [10.2337/db15-1690](https://doi.org/10.2337/db15-1690).\n\ From 7e3b3a98159aa442f9c0d295d7185398555e18cf Mon Sep 17 00:00:00 2001 From: Thanh Lee Date: Wed, 18 Oct 2023 10:33:17 +0100 Subject: [PATCH 0312/2173] Revert "Update SnpEff" (#43722) * Revert "Use updated download urls for SnpEff (#43701)" This reverts commit 9eeac472e2cb688cd9c8a77a6ec6fc8165b13a99. * Update meta.yaml revert some incorrect run_exports --- recipes/snpeff/meta.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/recipes/snpeff/meta.yaml b/recipes/snpeff/meta.yaml index aefeb88088b8c..51e7473e002ef 100644 --- a/recipes/snpeff/meta.yaml +++ b/recipes/snpeff/meta.yaml @@ -17,9 +17,7 @@ build: number: 0 noarch: generic run_exports: - - {{ pin_compatible('python', max_pin="3.9.*") }} - - {{ pin_compatible('perl', max_pin="5.32.*") }} - - {{ pin_compatible('openjdk', max_pin="11.*") }} + - {{ pin_compatible('snpeff', max_pin="x.x") }} source: url: https://snpeff.blob.core.windows.net/versions/snpEff_{{ snpeff_ver }}_core.zip From ce42d0bbd5247f2f828159c84dd62a4276d64045 Mon Sep 17 00:00:00 2001 From: Jappy <36221893+Jappy0@users.noreply.github.com> Date: Wed, 18 Oct 2023 20:37:31 +1100 Subject: [PATCH 0313/2173] update deepdirect to 0.2.5 (#43713) * add noise2read recipes * add noise2read recipes * add noise2read recipe * add noise2read recipe * add noise2read recipe * remove entry_points * add deepdirect recipe * add deepdirect recipe * add deepdirect recipe * add deepdirect recipe * add deepdirect recipe * add deepdirect recipe * add deepdirect recipe * change maintainer name * update deepdirect to 0.2.5 * update deepdirect to 0.2.5 * update deepdirect to 0.2.5 --- recipes/deepdirect/meta.yaml | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/recipes/deepdirect/meta.yaml b/recipes/deepdirect/meta.yaml index 3ef793cfafd93..4c7991b115f74 100644 --- a/recipes/deepdirect/meta.yaml +++ b/recipes/deepdirect/meta.yaml @@ -1,5 +1,5 @@ {% set name = "deepdirect" %} -{% set version = "0.2.4" %} +{% set version = "0.2.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/deepdirect-{{ version }}.tar.gz - sha256: 10feba8b3b52fbb274bdd0bdf9e8ae75df6669029d359a2ba9fae51af53a2faa + sha256: ab41f3f53161193146681d477f2412ebdb663bbf76c350e195a05efbb9f032dc build: noarch: python @@ -15,25 +15,21 @@ build: number: 0 run_exports: - {{ pin_subpackage('deepdirect', max_pin="x.x") }} - + requirements: host: - - python + - python >=3.8 - setuptools - wheel - pip run: - - python + - python >=3.8 - tensorflow >=2.4.0 - keras >=2.4.0 - - colorlog ==6.7.0 - - tqdm >=4.64.1 test: imports: - deepdirect - commands: - - deepdirect -v about: home: https://github.com/Jappy0/deepdirect @@ -43,4 +39,4 @@ about: extra: recipe-maintainers: - - Jappy0 + - Jappy0 \ No newline at end of file From 8ad08300e72b1846c069ce83411ae0f29588b34a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 04:18:28 -0600 Subject: [PATCH 0314/2173] Update mehari to 0.14.0 (#43747) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 4026f0c727cbd..16be7446d295c 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.13.0" %} -{% set sha256 = "90cca92ae67de5c86f3bb5b40668e8558f11318d2de1ac5fbb72866521b6d133" %} +{% set version = "0.14.0" %} +{% set sha256 = "b235b56a2b8a497e513621f4e6c58391cc4f43790f6fc357bf2daa7a73475a85" %} package: name: mehari From 487271dc1125571162c625ec77d61f8a22b4c40a Mon Sep 17 00:00:00 2001 From: llegregam <75795040+llegregam@users.noreply.github.com> Date: Wed, 18 Oct 2023 12:19:05 +0200 Subject: [PATCH 0315/2173] Update physiofit to 3.2.0 (#43725) * Update physiofit to 3.2.0 * Fixed sha256 From 44ce7b679be9ffb245003f741754562ba28dc2b0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 07:57:49 -0600 Subject: [PATCH 0316/2173] Update annonars to 0.24.1 (#43754) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 4991df75d191f..4782490dba970 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.24.0" %} +{% set version = "0.24.1" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 1680b651e1a0932d2b329991e6451963095489c7cec011d64000cf45d44e9744 + sha256: 2ee0ebeb1d58faa96a96cc93779670919ceedd9a227138b1c950862257c7ff58 requirements: build: From 79a0262b4ef9ab21d06d5f36ec961592dc4f248d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 08:11:07 -0600 Subject: [PATCH 0317/2173] Update quatradis to 1.1.0 (#43748) --- recipes/quatradis/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/quatradis/meta.yaml b/recipes/quatradis/meta.yaml index 677cee043a7a9..3696f0501a2d7 100644 --- a/recipes/quatradis/meta.yaml +++ b/recipes/quatradis/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.0.2" %} +{% set version="1.1.0" %} package: name: quatradis @@ -6,12 +6,14 @@ package: source: url: https://github.com/quadram-institute-bioscience/QuaTradis/archive/refs/tags/{{ version }}.tar.gz - sha256: 0ad217dc1bd0bd09e4294248ac473b9e38c3b0bf9e2b9f30215552c71ce7b192 + sha256: 10a49ec364f8ca9d86fd882f6186679fc9ce5932b4552381cc6d5a8a9b525be2 build: number: 0 script: python -m pip install -v --no-deps --ignore-installed . - + run_exports: + - {{ pin_subpackage('quatradis', max_pin="x.x") }} + requirements: build: - {{ compiler('c') }} From 9fd7ebe9f0761a3fcb04e9e1ab675cdbb7ae8ad4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 10:41:42 -0600 Subject: [PATCH 0318/2173] Update pysam to 0.22.0 (#43485) * Update pysam to 0.22.0 * Add run_exports --------- Co-authored-by: Brandon Seah Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Thanh Lee --- recipes/pysam/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/pysam/meta.yaml b/recipes/pysam/meta.yaml index 2ddf3c240ec6e..cb8678b99147c 100644 --- a/recipes/pysam/meta.yaml +++ b/recipes/pysam/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.21.0" %} +{% set version = "0.22.0" %} package: name: pysam @@ -6,12 +6,14 @@ package: source: url: https://github.com/pysam-developers/pysam/archive/v{{ version }}.tar.gz - sha256: 8b0c0d1d621892a0acea3d3dbf27564353b088d5bf6ee68852b1b8f3a408ccdf + sha256: 61b3377c5f889ddc6f6979912c3bb960d7e08407dada9cb38f13955564ea036f build: - number: 1 + number: 0 skip: True # [py2k] binary_relocation: False # [linux] + run_exports: + - {{ pin_subpackage('pysam', max_pin="x.x") }} requirements: build: From 5050539e366d5a226227688e25c834b745bee007 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 11:11:52 -0600 Subject: [PATCH 0319/2173] Update hamronization to 1.1.4 (#43739) --- recipes/hamronization/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/hamronization/meta.yaml b/recipes/hamronization/meta.yaml index 787c47c3d54cc..95cc66558b7cf 100644 --- a/recipes/hamronization/meta.yaml +++ b/recipes/hamronization/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hAMRonization" %} -{% set version = "1.1.1" %} +{% set version = "1.1.4" %} package: name: "{{ name|lower }}" @@ -7,23 +7,25 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c2eedf2e7fba995b8eb22fad77e486212882a676a4ad274b304a6cee0bfacc2d + sha256: 2f70bdf9ea2bd1faee59c99979cf14928bfb18015e9237a9790fe72fe3bf8544 build: noarch: python number: 0 entry_points: - hamronize = hAMRonization.hamronize:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('hamronization', max_pin="x") }} requirements: host: - pandas - pip - - python>=3.7 + - python >=3.7 run: - pandas - - python>=3.7 + - python >=3.7 test: imports: @@ -35,6 +37,7 @@ about: home: "https://github.com/pha4ge/hAMRonization" license: "GNU Lesser General Public v3 (LGPLv3)" license_family: LGPL + license_file: LICENSE.txt summary: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification" doc_url: "https://github.com/pha4ge/hAMRonization/blob/master/README.md" dev_url: "https://github.com/pha4ge/hAMRonization" From 857a68096661a2d91964a8c59f0c2d3a3a78f4ce Mon Sep 17 00:00:00 2001 From: Eric Kutschera Date: Wed, 18 Oct 2023 13:48:13 -0400 Subject: [PATCH 0320/2173] Update rmats to v4.2.0 (#43759) * 4.2.0 includes old patch and fixes for osx build * LD_LIBRARY_PATH fixes issue of dyld not finding libLLVM --- recipes/rmats/build.sh | 1 + recipes/rmats/build_failure.osx-64.yaml | 104 ------------------------ recipes/rmats/meta.yaml | 14 ++-- recipes/rmats/rmats_c_myfunc.patch | 10 --- 4 files changed, 8 insertions(+), 121 deletions(-) delete mode 100644 recipes/rmats/build_failure.osx-64.yaml delete mode 100644 recipes/rmats/rmats_c_myfunc.patch diff --git a/recipes/rmats/build.sh b/recipes/rmats/build.sh index 7d66e49fab05b..95408039e33d0 100644 --- a/recipes/rmats/build.sh +++ b/recipes/rmats/build.sh @@ -6,6 +6,7 @@ GSL_LDFLAGS="$(gsl-config --libs)" GSL_CFLAGS="$(gsl-config --cflags)" export GSL_LDFLAGS export GSL_CFLAGS +export LD_LIBRARY_PATH=${PREFIX}/lib make diff --git a/recipes/rmats/build_failure.osx-64.yaml b/recipes/rmats/build_failure.osx-64.yaml deleted file mode 100644 index 1837edf6c6301..0000000000000 --- a/recipes/rmats/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: bce4578c2ff87e46fffb99dfaa0533e17c948dde09a54ae99f00df2ca77f1139 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/toolkit/bamtools_merge.cpp:12: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamMultiReader.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamReader.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamAlignment.h:15: - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion] - const char GZIP_ID2 = 139; - ~~~~~~~~ ^~~ - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion] - const char OS_UNKNOWN = 255; - ~~~~~~~~~~ ^~~ - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/toolkit/bamtools_merge.cpp:12: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamMultiReader.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamReader.h:14: - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable] - int elementLength = 0; - ^ - 3 warnings generated. - [ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/toolkit/bamtools_random.cpp:12: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamMultiReader.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamReader.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamAlignment.h:15: - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion] - const char GZIP_ID2 = 139; - ~~~~~~~~ ^~~ - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion] - const char OS_UNKNOWN = 255; - ~~~~~~~~~~ ^~~ - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/toolkit/bamtools_random.cpp:12: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamMultiReader.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamReader.h:14: - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable] - int elementLength = 0; - ^ - 3 warnings generated. - [ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/toolkit/bamtools_resolve.cpp:12: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamReader.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamAlignment.h:15: - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion] - const char GZIP_ID2 = 139; - ~~~~~~~~ ^~~ - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion] - const char OS_UNKNOWN = 255; - ~~~~~~~~~~ ^~~ - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/toolkit/bamtools_resolve.cpp:12: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamReader.h:14: - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable] - int elementLength = 0; - ^ - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/toolkit/bamtools_resolve.cpp:413:36: error: no matching function for call to 'make_pair' - resolver.ReadNames.insert( make_pair(fields[1], true) ) ; - ^~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/_build_env/bin/../include/c/v1/__utility/pair.h:542:1: note: candidate function template not viable: expects an rvalue for 1st argument - make_pair(_T1&& __t1, _T2&& __t2) - ^ - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/toolkit/bamtools_resolve.cpp:610:24: error: no matching function for call to 'make_pair' - readGroups.insert( make_pair(name, resolver) ); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/_build_env/bin/../include/c/v1/__utility/pair.h:542:1: note: candidate function template not viable: 1st argument ('const std::string' (aka 'const basic_string')) would lose const qualifier - make_pair(_T1&& __t1, _T2&& __t2) - ^ - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/toolkit/bamtools_resolve.cpp:1017:41: error: no matching function for call to 'make_pair' - else resolver.ReadNames.insert( make_pair(al.Name, isCurrentMateUnique) ); - ^~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/_build_env/bin/../include/c/v1/__utility/pair.h:542:1: note: candidate function template not viable: expects an rvalue for 1st argument - make_pair(_T1&& __t1, _T2&& __t2) - ^ - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/bamtools/src/toolkit/bamtools_resolve.cpp:1049:30: error: no matching function for call to 'make_pair' - m_readGroups.insert( make_pair(rg.ID, ReadGroupResolver()) ); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/_build_env/bin/../include/c/v1/__utility/pair.h:542:1: note: candidate function template not viable: 1st argument ('const std::string' (aka 'const basic_string')) would lose const qualifier - make_pair(_T1&& __t1, _T2&& __t2) - ^ - 3 warnings and 4 errors generated. - make[3]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make:188: src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o] Error 1 - make[2]: *** [CMakeFiles/Makefile2:452: src/toolkit/CMakeFiles/bamtools_cmd.dir/all] Error 2 - make[3]: Leaving directory '$SRC_DIR/bamtools/build' - make[2]: Leaving directory '$SRC_DIR/bamtools/build' - make[1]: Leaving directory '$SRC_DIR/bamtools/build' - make[1]: *** [Makefile:136: all] Error 2 - make: *** [Makefile:3: build] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/rmats_1685395181419/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/rmats/meta.yaml b/recipes/rmats/meta.yaml index 84dcbf4381df5..fb7233b0e8977 100644 --- a/recipes/rmats/meta.yaml +++ b/recipes/rmats/meta.yaml @@ -1,18 +1,18 @@ -{% set version = "4.1.2" %} +{% set name = "rmats" %} +{% set version = "4.2.0" %} package: - name: rmats + name: {{ name }} version: {{ version }} source: - sha256: 13c558b06a0dd89463c6975b4cc244a59ad69069c897e61dc57a1906a1d7a36a + sha256: 7d5b56623e684c460a33b1709e0e2dc3ad13288d7db2be6c55c61f4fef880444 url: https://github.com/Xinglab/rmats-turbo/releases/download/v{{ version }}/rmats_turbo_v{{ version|replace(".","_") }}.tar.gz - patches: - # remove patch when new version includes: https://github.com/Xinglab/rmats-turbo/pull/169 - - rmats_c_myfunc.patch build: - number: 5 + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: diff --git a/recipes/rmats/rmats_c_myfunc.patch b/recipes/rmats/rmats_c_myfunc.patch deleted file mode 100644 index 7c9c468f29c38..0000000000000 --- a/recipes/rmats/rmats_c_myfunc.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- rMATS_C/src/myfunc.c 2021-12-21 12:53:44.229207000 -0500 -+++ rMATS_C/src/myfunc.c 2021-12-21 12:53:44.229207000 -0500 -@@ -14,7 +14,6 @@ - - extern double rho; - extern double cutoff; --extern clock_t dur; - - - #define ITER_CUTOFF 0.01 From a737a59f0f7b082130d7997b96b3486846876cf9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 12:16:37 -0600 Subject: [PATCH 0321/2173] Update dysgu to 1.6.2 (#43753) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/dysgu/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dysgu/meta.yaml b/recipes/dysgu/meta.yaml index 45ec03f933687..2837afb3d0291 100644 --- a/recipes/dysgu/meta.yaml +++ b/recipes/dysgu/meta.yaml @@ -1,6 +1,6 @@ {% set name = "dysgu" %} -{% set version = "1.6.1" %} -{% set sha256hash = "cbee02075f8d00dd65f06e974c57a220887058ffd23cb08f6ce4023978e86670" %} +{% set version = "1.6.2" %} +{% set sha256hash = "6db67f3abd45ca60f768adc9e154a879e604496909e9d243efd55513d6009910" %} package: name: {{ name|lower }} From 426f68173f9dd889beb2492b4dbd82bd27b9c6c5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 12:16:52 -0600 Subject: [PATCH 0322/2173] Update fasten to 0.6 (#43757) * Update fasten to 0.6 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fasten/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/fasten/meta.yaml b/recipes/fasten/meta.yaml index 90ebe8adbde32..09c047247e57b 100644 --- a/recipes/fasten/meta.yaml +++ b/recipes/fasten/meta.yaml @@ -1,12 +1,14 @@ -{% set version = "0.5.0" %} -{% set sha256 = "4c24431ad59d4583b95b71e26584329be12632f55b9d4cca0b7ab0567276219d" %} +{% set version = "0.6" %} +{% set sha256 = "677af7d67dba83695a3c11b096514d69439ed322c50d6315321885871c09bead" %} package: name: fasten version: {{ version }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('fasten', max_pin="x.x") }} source: url: https://github.com/lskatz/fasten/archive/v{{ version }}.tar.gz @@ -16,7 +18,6 @@ requirements: build: - rust - {{ compiler('c') }} - host: test: commands: @@ -39,5 +40,6 @@ test: about: home: https://github.com/lskatz/fasten license: MIT + license_family: MIT license_file: LICENSE summary: "Perform random operations on fastq files, using unix streaming. Secure your analysis with Fasten!" From 4f86d227e7ca9cd79f67abfb735557ee1277ee73 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 12:20:39 -0600 Subject: [PATCH 0323/2173] Update metapi to 3.0.0 (#43758) * Update metapi to 3.0.0 * add run_exports * add executor --------- Co-authored-by: joshuazhuang7 --- recipes/metapi/meta.yaml | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/recipes/metapi/meta.yaml b/recipes/metapi/meta.yaml index c15e4c6cb408d..6e9325fc6956b 100644 --- a/recipes/metapi/meta.yaml +++ b/recipes/metapi/meta.yaml @@ -1,6 +1,6 @@ {% set name = "metapi" %} -{% set version = "2.5.0" %} -{% set sha256 = "0c72c8367e934119db99c15c7f1c6aff3b99eed207598be1bff1bd8771dfa084" %} +{% set version = "3.0.0" %} +{% set sha256 = "ee0b2cedc9c5e42e9dfe015c85167b859be96cbd673e2396f0df8c027e096752" %} package: name: {{ name|lower }} @@ -13,9 +13,11 @@ source: build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: - metapi = metapi.corer:main + run_exports: + - {{ pin_subpackage('metapi', max_pin="x") }} requirements: host: @@ -31,12 +33,13 @@ requirements: - biopython >=1.73 - natsort - ruamel.yaml - - snakemake >=7.0 + - snakemake-minimal >=7.0 - seqtk - seqkit - pigz - fd-find - sra-tools >=2.11.0 + - executor test: imports: @@ -51,7 +54,8 @@ about: home: https://github.com/ohmeta/metapi summary: 'A general metagenomics data mining system focus on robust microbiome research' license: GPL-3.0-only - license_family: GPL + license_family: GPL3 + license_file: LICENSE extra: identifiers: From 18cdb88aa9137b8a268c030d3c2f0f51d7dfccc0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 12:20:57 -0600 Subject: [PATCH 0324/2173] Update tb-profiler to 5.0.1 (#43755) * Update tb-profiler to 5.0.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/tb-profiler/meta.yaml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml index b78fc17afdb0d..5c08e8e29e831 100644 --- a/recipes/tb-profiler/meta.yaml +++ b/recipes/tb-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "tb-profiler" %} -{% set version = "5.0.0" %} -{% set sha256 = "286bc21944c1129b171b5f61ed055732dafbb1105155b5bc66ff2ee41e56680d" %} +{% set version = "5.0.1" %} +{% set sha256 = "71da60ab38cd3c11f1951bac8e26e7cfe2c91700afa8132cf9001e73a2bae252" %} package: name: {{name}} @@ -13,10 +13,12 @@ source: build: noarch: python number: 0 + run_exports: + - {{ pin_subpackage('tb-profiler', max_pin="x") }} requirements: host: - - python + - python >=3.8 - pip - gatk4 - samtools >=1.10 @@ -35,6 +37,7 @@ requirements: - tqdm - pysam - rich-argparse + test: imports: - tbprofiler @@ -44,7 +47,8 @@ test: about: home: https://github.com/jodyphelan/TBProfiler - license: GPL3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data From a3f3c76be39e7bc283d812bf7e270d016209a2ce Mon Sep 17 00:00:00 2001 From: Diego Fuentes Palacios <43205584+Dfupa@users.noreply.github.com> Date: Wed, 18 Oct 2023 21:00:53 +0200 Subject: [PATCH 0325/2173] Add redundans (#43292) * Added redundans * Added run_exports to meta.yaml * Added a skip of OSX and a change to build.sh * Update meta.yaml Added specific versions for numpy and matplotlib-base to avoid dependency errors due to inference of dependencies * Update meta.yaml Changed the matplotlib version to avoid dependency conflicts due to the Python version * Update meta.yaml Enforce Python version to 3.10 for dependency issues during the build process * Changes to deal with bioconda recipes requirements for versioning software * Added missing test, ups! * Update recipes/redundans/meta.yaml Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update recipes/redundans/meta.yaml Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update recipes/redundans/meta.yaml Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update recipes/redundans/meta.yaml Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update recipes/redundans/meta.yaml Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * edit version string * try sed i.bak for macOS compatibility * try not skipping OSX build * revert back to skipping OSX build --------- Co-authored-by: dfupa Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/redundans/build.sh | 30 +++++++++++++++++ recipes/redundans/meta.yaml | 66 +++++++++++++++++++++++++++++++++++++ 2 files changed, 96 insertions(+) create mode 100644 recipes/redundans/build.sh create mode 100644 recipes/redundans/meta.yaml diff --git a/recipes/redundans/build.sh b/recipes/redundans/build.sh new file mode 100644 index 0000000000000..6c4142e6a3d24 --- /dev/null +++ b/recipes/redundans/build.sh @@ -0,0 +1,30 @@ +#!/bin/bash +export CPATH=${PREFIX}/include +#Define the install folder and binary folder and create them +INSTALL_FOLDER=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +BIN_FOLDER=$PREFIX/bin +mkdir -p $INSTALL_FOLDER && mkdir -p $BIN_FOLDER + +#Copying files to proper installation folder +chmod u+x redundans.py #To avoid permission issues + +#Avoid pathing issues with SSPACE pl script +sed -i.bak 's|bin/SSPACE/SSPACE_Standard_v3.0.pl|SSPACE/SSPACE_Standard_v3.0.pl|g' redundans.py + +###### Copying files to proper installation directory and some to the binary directory ###### +cp redundans.py $INSTALL_FOLDER/ && cp redundans.py $BIN_FOLDER && cp README.md $INSTALL_FOLDER/ +cp -r test/ $INSTALL_FOLDER/ && cp -r test/ $BIN_FOLDER && cp -r docs/ $INSTALL_FOLDER/ && cp LICENSE $INSTALL_FOLDER/ + +#We create a bin folder in the installation directory where we copy all binaries and scripts +mkdir -p $INSTALL_FOLDER/bin && cp -r bin/SSPACE $INSTALL_FOLDER/bin && cp bin/*.py $INSTALL_FOLDER/bin && cp bin/k8-Linux $INSTALL_FOLDER/bin +cp bin/platanus $INSTALL_FOLDER/bin && cp bin/GapCloser $INSTALL_FOLDER/bin && cp -r bin/last $INSTALL_FOLDER/bin && cp -r bin/merqury $INSTALL_FOLDER/bin + +#Cleaning up and copying from install folder to binary folder +cp -r $INSTALL_FOLDER/bin/* $BIN_FOLDER/ + +#Compile last and copy its binaries to BIN_FOLDER +cd $BIN_FOLDER/last/ && make clean && make -j ${CPU_COUNT} && cd .. +cp -t $BIN_FOLDER $BIN_FOLDER/last/bin/* + +#Give permissions to test folder in order to run tests if required +chmod -R 777 $BIN_FOLDER/test/ && cd .. diff --git a/recipes/redundans/meta.yaml b/recipes/redundans/meta.yaml new file mode 100644 index 0000000000000..b7192980da0b6 --- /dev/null +++ b/recipes/redundans/meta.yaml @@ -0,0 +1,66 @@ +{% set name = "Redundans" %} +{% set version = "2.01" %} +{% set sha256hash = "85a1937015aa0af44a5402761356c4098b085ee7233fb1b7cf8254e2ca0f0e54" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/Gabaldonlab/redundans/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256hash }} + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('redundans', max_pin="x") }} + no_link: + - bin/*.py + +requirements: + build: + - make + - {{ compiler('cxx') }} + - {{ compiler('c') }} + + host: + - python >=3.8,<3.11 + - pip + - zlib + - pillow + - perl + + run: + - perl + - numpy >=1.24.0 + - matplotlib-base >=3.7.3 + - python >=3.8,<3.11 + - minimap2 >=2.24 + - miniasm >=0.3 + - gfastats >=1.3.6 + - meryl =1.3 + - bwa >=0.7.12 + - snap-aligner >=2.0.3 + - r-base >=4 + - r-argparse >=2.0.1 + - r-ggplot2 >=3.3.2 + - r-scales >=1.1.1 + +test: + commands: + - redundans.py --version + + +about: + home: https://github.com/Gabaldonlab/redundans/ + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: 'Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.' + +extra: + identifiers: + - biotools:redundans + recipe-maintainers: + - Dfupa From 8f1ada46e42841e7826c7345541d386eff7f7f5b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 18 Oct 2023 13:50:46 -0600 Subject: [PATCH 0326/2173] Update talon to 6.0.1 (#43761) --- recipes/talon/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/talon/meta.yaml b/recipes/talon/meta.yaml index 397bb96dabf1a..fa0473fb78ea8 100644 --- a/recipes/talon/meta.yaml +++ b/recipes/talon/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "6.0" %} +{% set version = "6.0.1" %} package: name: talon @@ -6,7 +6,7 @@ package: source: url: https://github.com/mortazavilab/TALON/archive/v{{ version }}.zip - sha256: f0e1f9e48a99f18bbfadfbacf6b31913508bdc4932e08fd0ea8ac78f2b459fd4 + sha256: 62f5681c1d067c451a6879c927c62ca47bf640745cdc24e9529e7ef0ac01d689 build: noarch: python From 7d76f8c34f1e6ecca6eff2f842525f5cfa76992d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 01:36:00 -0600 Subject: [PATCH 0327/2173] Update ntm-profiler to 0.3.0 (#43766) * Update ntm-profiler to 0.3.0 * add run_exports * update deps --------- Co-authored-by: joshuazhuang7 Co-authored-by: Jody Phelan --- recipes/ntm-profiler/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/ntm-profiler/meta.yaml b/recipes/ntm-profiler/meta.yaml index ef14c5c1eb195..55ce1e0cf751b 100644 --- a/recipes/ntm-profiler/meta.yaml +++ b/recipes/ntm-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ntm-profiler" %} -{% set version = "0.2.2" %} -{% set sha256 = "37f11f9c56cccc158207a40eced19f94b4d1e6d35afefcc878c938cbcb5a580d" %} +{% set version = "0.3.0" %} +{% set sha256 = "1617d07625cce501980ed93146e520d5eea41c6beae5093da69accac48479f07" %} package: name: {{name}} @@ -12,8 +12,10 @@ source: build: noarch: python - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv number: 0 + run_exports: + - {{ pin_subpackage('ntm-profiler', max_pin="x") }} requirements: host: @@ -26,18 +28,19 @@ requirements: run: - python >=3.7 - mash =2.3 - - pathogen-profiler =2.0.4 + - pathogen-profiler =3.1.0 - jinja2 + - sourmash >=4.8.3 test: imports: - ntm_profiler - commands: - ntm-profiler -h about: home: https://github.com/jodyphelan/NTM-Profiler - license: GPL3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Profiling tool for NTM to detect species and resistance from WGS data From 57e787a8a9e62bb0a8d42090a45a7036649caf6f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 01:56:13 -0600 Subject: [PATCH 0328/2173] Update oakvar to 2.9.52 (#43769) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index e58e23a171e65..edfdfe20dd5ef 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.51" %} -{% set sha256 = "5bb1440918e27a4d5f4816fefb28b7218dfe49a79159b1582b47e06111d24fe2" %} +{% set version = "2.9.52" %} +{% set sha256 = "babb89ef7c1019950e5e61e050cca8d8067789e287c759867696592b4e1e288d" %} package: name: {{ name|lower }} From 8938924ef1664286ab8ea98dd04e9d7357f9d34f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 01:56:33 -0600 Subject: [PATCH 0329/2173] Update cptac to 1.5.5 (#43772) --- recipes/cptac/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cptac/meta.yaml b/recipes/cptac/meta.yaml index 351aa54bd1e29..877c6c133951f 100644 --- a/recipes/cptac/meta.yaml +++ b/recipes/cptac/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cptac" %} -{% set version = "1.5.4" %} +{% set version = "1.5.5" %} package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4d99b3f25f36626e7fe7ecd4034e262ff452fd092593bb9808a0b44cf34d688c + sha256: 8f68c964443bf9774905e909930207ea0f203e6efa48433a92cafc9b3a39f19f build: number: 0 From a3ef93f40654982e89f6fcd063b7f8ff1a9fd44f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 01:56:51 -0600 Subject: [PATCH 0330/2173] Update ms-entropy to 1.0.2 (#43770) --- recipes/ms-entropy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms-entropy/meta.yaml b/recipes/ms-entropy/meta.yaml index 33e6d744a196e..ed54619e1658b 100644 --- a/recipes/ms-entropy/meta.yaml +++ b/recipes/ms-entropy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms-entropy" %} -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms_entropy-{{ version }}.tar.gz - sha256: 0f3bcad4cb96cdcb7297e5068a38104f3f25128f533c38389293b97485ab629a + sha256: 8780b4af0a19c2054b689095ebf99b0a6fc895dbad891b99703ea889088fbbaa build: skip: true # [py<37] From 17057ffd9a7cbbe4067ce60aa3e1c322d072cc3f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 01:57:51 -0600 Subject: [PATCH 0331/2173] Update mhcflurry to 2.1.0 (#43768) * Update mhcflurry to 2.1.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/mhcflurry/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/mhcflurry/meta.yaml b/recipes/mhcflurry/meta.yaml index 2bb64e852c5a2..b69f1d8f20efe 100644 --- a/recipes/mhcflurry/meta.yaml +++ b/recipes/mhcflurry/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mhcflurry" %} -{% set version = "2.0.6" %} +{% set version = "2.1.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 06f68b39a4d8cfd181bccbc8d1ef1b961658e5fb1068a5fc174f1dadd8ddc741 + sha256: a4129922db5b662e248e066e73e12be74c3d08c7c0a9f1de4776b7e5aafa42bb build: number: 0 @@ -25,7 +25,9 @@ build: - mhcflurry-calibrate-percentile-ranks = mhcflurry.calibrate_percentile_ranks_command:run - mhcflurry-class1-train-presentation-models = mhcflurry.train_presentation_models_command:run - mhcflurry-cluster-worker-entry-point = mhcflurry.cluster_parallelism:worker_entry_point - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('mhcflurry', max_pin="x") }} requirements: host: @@ -40,7 +42,7 @@ requirements: - pyyaml - scikit-learn - six - - tensorflow >=2.2.0 + - tensorflow >=2.12.0 - tqdm test: @@ -62,8 +64,9 @@ test: about: home: "https://github.com/openvax/mhcflurry" - license: Apache Software + license: Apache-2.0 license_family: APACHE + license_file: LICENSE summary: "MHC Binding Predictor" extra: From df6995bfedaae5915596a361efef6ac864d893d4 Mon Sep 17 00:00:00 2001 From: Jody Phelan Date: Thu, 19 Oct 2023 09:01:23 +0100 Subject: [PATCH 0332/2173] updpate build (#43767) --- recipes/tb-profiler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml index 5c08e8e29e831..c98196104add1 100644 --- a/recipes/tb-profiler/meta.yaml +++ b/recipes/tb-profiler/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 run_exports: - {{ pin_subpackage('tb-profiler', max_pin="x") }} @@ -28,7 +28,7 @@ requirements: - python >=3.8 - git - jinja2 - - pathogen-profiler =3.0.0 + - pathogen-profiler =3.1.0 - filelock - docxtpl - iqtree From ff919c27a03a0f64a175754c61dfaf5901597467 Mon Sep 17 00:00:00 2001 From: Tim Fennell Date: Thu, 19 Oct 2023 02:01:52 -0600 Subject: [PATCH 0333/2173] Bump fgsv to 0.1.1 (#43765) --- recipes/fgsv/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/fgsv/meta.yaml b/recipes/fgsv/meta.yaml index 3aaddfda83b58..ddf5a0053b873 100644 --- a/recipes/fgsv/meta.yaml +++ b/recipes/fgsv/meta.yaml @@ -1,4 +1,6 @@ -{% set version="0.1.0" %} +{% set version="0.1.1" %} +{% set sha256="e39b24710d80278b7528545b43ce8084e166614054bed55ca898fa79d4be0af9" %} + package: name: fgsv @@ -6,7 +8,7 @@ package: source: url: https://github.com/fulcrumgenomics/fgsv/releases/download/{{ version }}/fgsv-{{ version }}.jar - sha256: 4aa31c9beee050186d8d5ce4922dd385002a8a465e3656ca9947abdb268fcf99 + sha256: {{ sha256 }} build: noarch: generic From dcbe1e94adfb29a09da13dde0b13d3926fe9d9c3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 02:03:32 -0600 Subject: [PATCH 0334/2173] Update jbrowse2 to 2.7.1 (#43763) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 49e10cc0085a5..dc27517914864 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.7.0" %} +{% set version = "2.7.1" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 5ef46308d17c16ac3f3f519ab1c41bd8b3aa6575e4bac24858042fd84f5843ba + sha256: 478dacd55070f37a28ea3788d4aeec66a809512613a02481efc29f1591b10ea8 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From 3aec88f54377326b80c65435ebf01fb87fdc9b31 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 07:21:50 -0600 Subject: [PATCH 0335/2173] Update mehari to 0.14.1 (#43773) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 16be7446d295c..6b5a52e698801 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.14.0" %} -{% set sha256 = "b235b56a2b8a497e513621f4e6c58391cc4f43790f6fc357bf2daa7a73475a85" %} +{% set version = "0.14.1" %} +{% set sha256 = "bfe62708394f412dda67044d21fd5649a26e2c30c304f53cda6b9fc83b869b64" %} package: name: mehari From 326c87c00a4bbffd61713b70df5a67d58b3beef0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 08:07:46 -0600 Subject: [PATCH 0336/2173] Update assembly_finder to 0.3.2 (#43776) --- recipes/assembly_finder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index abf2e09e7e64e..c1c25c1406c57 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "assembly_finder" %} -{% set version = "0.3.1" %} +{% set version = "0.3.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: - url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 07db574ce4edbf66e38a892c0012bed0e3d358ce2b88d8f8e98726925cd181a1 + sha256: 9c6a59842c3e5bf19284dee0cec65e65cd61c897d6bf6127e2929088b051fbbc build: number: 0 entry_points: From 2b9633ed3b5811d71253afbce51f400806d5539f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 08:08:16 -0600 Subject: [PATCH 0337/2173] Update r-oncopharmadb to 1.4.6 (#43775) --- recipes/r-oncopharmadb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-oncopharmadb/meta.yaml b/recipes/r-oncopharmadb/meta.yaml index f94fa12a99718..58e8fc471ae38 100644 --- a/recipes/r-oncopharmadb/meta.yaml +++ b/recipes/r-oncopharmadb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "r-oncopharmadb" %} -{% set version = "1.4.4" %} +{% set version = "1.4.6" %} {% set github = "https://github.com/sigven/oncoPharmaDB" %} package: @@ -8,7 +8,7 @@ package: source: url: https://github.com/sigven/pharmOncoX/archive/refs/tags/{{ version }}.tar.gz - sha256: 35614d77d32f10f2b9886f0e4dd324be86759a4b2faf94fdedb8ffa82e06fa59 + sha256: 5c0c708828cc91f032018e5ff2c42a391a9f98bb411038b1fa431ef6992d3095 build: number: 0 From 9ba91853198389789ff81d22acb85992e66bb4eb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 09:27:06 -0600 Subject: [PATCH 0338/2173] Update planemo to 0.75.14 (#43750) * Update planemo to 0.75.13 * Update planemo to 0.75.14 --------- Co-authored-by: Thanh Lee --- recipes/planemo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 11c268c2d46cf..a799baa098e11 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "planemo" %} -{% set version = "0.75.12" %} -{% set sha256 = "23f41d16ae4aa97e5b4c694a78a837b33ee1c9b339bc9b7118da73031d311034" %} +{% set version = "0.75.14" %} +{% set sha256 = "d317157d1a68ef9ea6a6dfce101de7861a414bb8abe719c0c23188d503fdb984" %} package: name: {{ name|lower }} From e32d9df9088acdea5350727247a741a4d5a3a78c Mon Sep 17 00:00:00 2001 From: Saliha ZENBOUDJI-BEDDEK <72068091+SalihaZ@users.noreply.github.com> Date: Thu, 19 Oct 2023 18:52:13 +0200 Subject: [PATCH 0339/2173] Add RapGreen (#41727) * add rap-green recipe use a python wrapper script for Java Conda packages and get inspired from biotransformer for the build.sh to make this wrapper working properly. --------- Co-authored-by: Saliha Zen Co-authored-by: Jacques Dainat Co-authored-by: Devon Ryan --- recipes/rapgreen/LICENSE | 674 +++++++++++++++++++++++++++++++++++ recipes/rapgreen/build.sh | 21 ++ recipes/rapgreen/meta.yaml | 41 +++ recipes/rapgreen/rapgreen.py | 101 ++++++ 4 files changed, 837 insertions(+) create mode 100644 recipes/rapgreen/LICENSE create mode 100644 recipes/rapgreen/build.sh create mode 100644 recipes/rapgreen/meta.yaml create mode 100644 recipes/rapgreen/rapgreen.py diff --git a/recipes/rapgreen/LICENSE b/recipes/rapgreen/LICENSE new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/rapgreen/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/rapgreen/build.sh b/recipes/rapgreen/build.sh new file mode 100644 index 0000000000000..a37108bb7683c --- /dev/null +++ b/recipes/rapgreen/build.sh @@ -0,0 +1,21 @@ +#!/bin/bash +set -eux -o pipefail + +# Prepare share folder +RAPGREEN_DIR=${PREFIX}/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p ${RAPGREEN_DIR} + +# take care of the jar and copy it into the share folder +mkdir -p "$PREFIX/bin" +cp -rf ${SRC_DIR}/bin/* ${RAPGREEN_DIR} + +# Handle python wrapper script that will call the jar file +cp ${RECIPE_DIR}/rapgreen.py ${RAPGREEN_DIR}/ +printf '#!/bin/bash\n' > ${RAPGREEN_DIR}/rapgreen +printf "cd ${RAPGREEN_DIR} \n" >> ${RAPGREEN_DIR}/rapgreen +printf 'python rapgreen.py "$@"\n' >> ${RAPGREEN_DIR}/rapgreen +ln -s ${RAPGREEN_DIR}/rapgreen ${PREFIX}/bin/ + +# Make executable in the share folder +chmod +x ${RAPGREEN_DIR}/* + diff --git a/recipes/rapgreen/meta.yaml b/recipes/rapgreen/meta.yaml new file mode 100644 index 0000000000000..305ec6feadb67 --- /dev/null +++ b/recipes/rapgreen/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "rapgreen" %} +{% set version = "1.0" %} +{% set sha256 = "6fffe70e950123715b22b49564f49f05d3c0b6193c765b96776eaee8394aabae" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/SouthGreenPlatform/rap-green/archive/refs/tags/v{{version}}.tar.gz + sha256: {{ sha256 }} + +build: + run_exports: + - {{ pin_subpackage('rapgreen', max_pin="x") }} + number: 0 + noarch: generic + +requirements: + run: + - openjdk + - python >=3.8 + +test: + commands: + - rapgreen --help + - rapgreen --help -Xms512m -Xmx1g + +about: + home: https://github.com/SouthGreenPlatform/rap-green + license: GPLv3 + license_family: GPL + license_file: LICENSE + summary: "Manipulate and annotate phylogenetic trees" + doc_url: http://southgreenplatform.github.io/rap-green/ + +extra: + maintainers: + - dereeper + identifiers: + - biotools:rap-green diff --git a/recipes/rapgreen/rapgreen.py b/recipes/rapgreen/rapgreen.py new file mode 100644 index 0000000000000..34ca99d94b201 --- /dev/null +++ b/recipes/rapgreen/rapgreen.py @@ -0,0 +1,101 @@ +#!/usr/bin/env python +# +# Wrapper script for Java Conda packages that ensures that the java runtime +# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). + +# +# Program Parameters +# +import os +import subprocess +import sys +import shutil +from os import access +from os import getenv +from os import X_OK +jar_file = 'RapGreen.jar' + +default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] + +# !!! End of parameter section. No user-serviceable code below this line !!! + + +def real_dirname(path): + """Return the symlink-resolved, canonicalized directory-portion of path.""" + return os.path.dirname(os.path.realpath(path)) + + +def java_executable(): + """Return the executable name of the Java interpreter.""" + java_home = getenv('JAVA_HOME') + java_bin = os.path.join('bin', 'java') + + if java_home and access(os.path.join(java_home, java_bin), X_OK): + return os.path.join(java_home, java_bin) + else: + return 'java' + + +def jvm_opts(argv): + """Construct list of Java arguments based on our argument list. + The argument list passed in argv must not include the script name. + The return value is a 3-tuple lists of strings of the form: + (memory_options, prop_options, passthrough_options) + """ + mem_opts = [] + prop_opts = [] + pass_args = [] + exec_dir = None + + for arg in argv: + if arg.startswith('-D'): + prop_opts.append(arg) + elif arg.startswith('-XX'): + prop_opts.append(arg) + elif arg.startswith('-Xm'): + mem_opts.append(arg) + elif arg.startswith('--exec_dir='): + exec_dir = arg.split('=')[1].strip('"').strip("'") + if not os.path.exists(exec_dir): + shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None) + else: + pass_args.append(arg) + + # In the original shell script the test coded below read: + # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] + # To reproduce the behaviour of the above shell code fragment + # it is important to explictly check for equality with None + # in the second condition, so a null envar value counts as True! + + if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: + mem_opts = default_jvm_mem_opts + + return (mem_opts, prop_opts, pass_args, exec_dir) + + +def main(): + java = java_executable() + """ + PeptideShaker updates files relative to the path of the jar file. + In a multiuser setting, the option --exec_dir="exec_dir" + can be used as the location for the peptide-shaker distribution. + If the exec_dir dies not exist, + we copy the jar file, lib, and resources to the exec_dir directory. + """ + (mem_opts, prop_opts, pass_args, exec_dir) = jvm_opts(sys.argv[1:]) + jar_dir = exec_dir if exec_dir else real_dirname(sys.argv[0]) + + if pass_args != [] and pass_args[0].startswith('eu'): + jar_arg = '-cp' + else: + jar_arg = '-jar' + + jar_path = os.path.join(jar_dir, jar_file) + + java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args + + sys.exit(subprocess.call(java_args)) + + +if __name__ == '__main__': + main() From b022d118962deb22b5f0e9da22acab457b32d119 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 17:35:11 -0600 Subject: [PATCH 0340/2173] Update immuneml to 2.2.6 (#43779) * Update immuneml to 2.2.6 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/immuneml/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/immuneml/meta.yaml b/recipes/immuneml/meta.yaml index a22f12301c126..14e8479833ac0 100644 --- a/recipes/immuneml/meta.yaml +++ b/recipes/immuneml/meta.yaml @@ -1,5 +1,5 @@ {% set name = "immuneML" %} -{% set version = "2.2.5" %} +{% set version = "2.2.6" %} package: name: "{{ name|lower }}" @@ -7,16 +7,18 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8fb17ccefe18649a77e8fded8f1b91005b92d79e6775d6fc4bc37826a2e70843 + sha256: 29dcfdeeaf561a1878631aa235b0d6dcb7205a206bb1cbd981c299fa658d9d99 build: - number: 1 + number: 0 # gensim pinning doesn't work for python >=3.10 skip: true [py2k or py <= 36 or py > 39] entry_points: - immune-ml = immuneML.app.ImmuneMLApp:main - immune-ml-quickstart = immuneML.workflows.instructions.quickstart:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('immuneml', max_pin="x") }} requirements: build: @@ -71,6 +73,6 @@ extra: skip-lints: - cython_must_be_in_host recipe-maintainers: - - knutwa-ext + - knutwa-ext - BlueBasilisk - pavlovicmilena From 735ab55b30ff14e587dc6a5b7b200103f991f2ab Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 22:38:00 -0600 Subject: [PATCH 0341/2173] Update semibin to 2.0.0 (#43781) * Update semibin to 2.0.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/semibin/meta.yaml | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/recipes/semibin/meta.yaml b/recipes/semibin/meta.yaml index b6082301bee3c..8c9b67c6803c4 100644 --- a/recipes/semibin/meta.yaml +++ b/recipes/semibin/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SemiBin" %} -{% set version = "1.5.1" %} +{% set version = "2.0.0" %} package: name: "{{ name|lower }}" @@ -7,8 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 25e627d2908210b48545c682bdd0f9ab647f119071902215a0e21f4a26e56608 - + sha256: 2b4ceec197b0ea2817c4e3cf6d131dd312e5605057732bfee141bbdd7025100f build: noarch: python @@ -16,7 +15,9 @@ build: entry_points: - SemiBin=SemiBin.main:main1 - SemiBin2=SemiBin.main:main2 - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv + run_exports: + - {{ pin_subpackage('semibin', max_pin="x") }} requirements: host: @@ -51,9 +52,14 @@ about: home: "https://github.com/BigDataBiology/SemiBin" license: MIT license_family: MIT - summary: "Metagenomic binning with siamese neural networks" + summary: "Metagenomic binning with semi-supervised siamese neural networks" + doc_url: https://semibin.readthedocs.io/en/latest/ extra: recipe-maintainers: - luispedro - psj1997 + identifiers: + - doi:10.1038/s41467-022-29843-y + - doi:10.1101/2023.01.09.523201 + - biotools:semibin From 59f6fe66f75c770e79b72b99eea6299d6960b347 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 19 Oct 2023 23:17:30 -0600 Subject: [PATCH 0342/2173] Update knock-knock to 0.4.2 (#39565) * Update knock-knock to 0.3.3 * Update meta.yaml * Update knock-knock to 0.3.4 * Update knock-knock to 0.3.5 * Update knock-knock to 0.3.6 * Update knock-knock to 0.3.8 * Update knock-knock to 0.4.2 * Update meta.yaml * add run_exports * loosen blast version dep * add nbconvert --------- Co-authored-by: Vivek Rai <3218617+raivivek@users.noreply.github.com> Co-authored-by: Christian Brueffer Co-authored-by: joshuazhuang7 --- recipes/knock-knock/meta.yaml | 38 +++++++++++++++++++---------------- 1 file changed, 21 insertions(+), 17 deletions(-) diff --git a/recipes/knock-knock/meta.yaml b/recipes/knock-knock/meta.yaml index 074c03b9ef2da..dcdc88a74d912 100644 --- a/recipes/knock-knock/meta.yaml +++ b/recipes/knock-knock/meta.yaml @@ -1,43 +1,46 @@ {% set name = "knock-knock" %} -{% set version = "0.2.1" %} +{% set version = "0.4.2" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: "https://files.pythonhosted.org/packages/1e/77/86a1a3047b15380ed26ae0754cf7870a572e4893d7e359e5bf4c4b9a932f/knock_knock-0.2.1.tar.gz" - sha256: "466250fe26904c347a64a8a2707eb8cb8c1f2184e7364ff028f4700341525f61" + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/knock_knock-{{ version }}.tar.gz" + sha256: "69128026055c1b8aa7e7b6e2947f108b21795a406687199e1689bd9815197d5f" build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('knock-knock', max_pin="x") }} requirements: host: - pip - - python >=3.6 + - python >=3.7 run: - - biopython >=1.70 - - blast ==2.7.1 - - bokeh >=0.12.14 - - hits >=0.1 + - python >=3.7 + - bokeh >=2.4.2 + - biopython >=1.80 + - h5py >=3.1.0 - ipywidgets >=7.1.2 - - matplotlib >=2.1.2 - - minimap2 ==2.16 - - nbconvert >=5.3.1 + - matplotlib-base >=2.1.2 + - nbconvert >=6.0.7 - nbformat >=4.4.0 - numpy >=1.14.2 - pandas >=0.22.0 - - parallel >=20190522 - pillow >=5.0.0 - pysam >=0.14 - - python >=3.6 - pyyaml >=3.12 + - hits >=0.4.0 + - tqdm >=4.31.1 + - blast >=2.7.1 + - minimap2 ==2.16 - samtools >=1.9 - star >=2.7.1 - - tqdm >=4.31.1 + - parallel >=20190522 test: imports: @@ -49,10 +52,11 @@ test: - samtools --version - STAR --version - about: home: "https://github.com/jeffhussmann/knock-knock" - license: "GPL-3" + license: "GPL-3.0-or-later" + license_family: GPL3 + license_file: LICENSE summary: "toolkit for analyzing CRISPR knock-in experiments" extra: From ae56e8265f49e6aac388dd5d8404fe6820044e70 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 20 Oct 2023 03:06:15 -0600 Subject: [PATCH 0343/2173] Update panacus to 0.2.3 (#43785) --- recipes/panacus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/panacus/meta.yaml b/recipes/panacus/meta.yaml index 69a20fc81a5f5..d5ada5ff55534 100644 --- a/recipes/panacus/meta.yaml +++ b/recipes/panacus/meta.yaml @@ -1,5 +1,5 @@ {% set name = "panacus" %} -{% set version = "0.2.2" %} +{% set version = "0.2.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/marschall-lab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: 761c69c138d6d7ec02c60d72571b4bcc057ec210c77a8fb988073275eb73db21 + sha256: 969eaed515a9679f5a74632986240f7afd0558b2a2914281dc783ac1fa1b6f9e build: number: 0 From 597a576446f3e37d25a1f181b3a17c5302d48faa Mon Sep 17 00:00:00 2001 From: Luis Pedro Coelho Date: Fri, 20 Oct 2023 23:56:12 +1000 Subject: [PATCH 0344/2173] Update SemiBin metadata (#43784) * Update SemiBin metadata - Update DOI to point to final manuscript (not preprint) * Update meta.yaml Updated build number since the original PR is for DOI update --------- Co-authored-by: Thanh Lee --- recipes/semibin/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/semibin/meta.yaml b/recipes/semibin/meta.yaml index 8c9b67c6803c4..333a87552662b 100644 --- a/recipes/semibin/meta.yaml +++ b/recipes/semibin/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - SemiBin=SemiBin.main:main1 - SemiBin2=SemiBin.main:main2 @@ -61,5 +61,5 @@ extra: - psj1997 identifiers: - doi:10.1038/s41467-022-29843-y - - doi:10.1101/2023.01.09.523201 + - doi:10.1093/bioinformatics/btad209 - biotools:semibin From 618246c374d971f557de7a4238852eed5a54a5dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 20 Oct 2023 08:19:06 -0600 Subject: [PATCH 0345/2173] Update medaka to 1.10.0 (#41417) * Update medaka to 1.8.1 * Update medaka to 1.8.2 * Update medaka to 1.9.0 * Update medaka to 1.9.1 * Update TF in medaka reqs * Explicitly use tensorflow-cpu * add run_exports * try tensorflow-base * debugging python version * more debugging * Update meta.yaml * debugging out of spec tensorflow * minor edits to the pip install command according to new grayskull release * more debugging * more debugging * Update meta.yaml * fix missing brace * More testing * use cuda not gpu * Update meta.yaml * Update build.sh * update tensorflow pinning * Update meta.yaml * remove extra dot in build.sh * add post-link noting non-support * Update medaka to 1.10.0 * match requirements for v1.10 * force cpu * make linter happy * Create conda_build_config.yaml * Update meta.yaml * Update recipes/medaka/conda_build_config.yaml Co-authored-by: Marcel Bargull * pin htslib to match samtools and bcftools * loosen pinnings to match docs * add recommendation to review config yaml in future releases * fix typo --------- Co-authored-by: Christian Brueffer Co-authored-by: Chris Wright Co-authored-by: joshuazhuang7 Co-authored-by: Robert A. Petit III Co-authored-by: Marcel Bargull --- recipes/medaka/build.sh | 4 ++-- recipes/medaka/conda_build_config.yaml | 9 +++++++++ recipes/medaka/meta.yaml | 28 +++++++++++++++----------- 3 files changed, 27 insertions(+), 14 deletions(-) create mode 100644 recipes/medaka/conda_build_config.yaml diff --git a/recipes/medaka/build.sh b/recipes/medaka/build.sh index a817fd95cb411..a17d134c7c243 100644 --- a/recipes/medaka/build.sh +++ b/recipes/medaka/build.sh @@ -2,7 +2,7 @@ export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" -export LDFLAGS="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="-I${PREFIX}/include ${LDFLAGS}" @@ -13,4 +13,4 @@ sed -i.bak "s/'build_ext': HTSBuild//" setup.py sed -i.bak 's/extra_objects.*//' build.py sed -i.bak 's/^libraries=\[/libraries=\["hts",/' build.py -$PYTHON -m pip install . -vv +$PYTHON -m pip install . --no-deps --ignore-installed -vvv diff --git a/recipes/medaka/conda_build_config.yaml b/recipes/medaka/conda_build_config.yaml new file mode 100644 index 0000000000000..f45b292d8ac64 --- /dev/null +++ b/recipes/medaka/conda_build_config.yaml @@ -0,0 +1,9 @@ +# Required to support Tensorflow v2.10, which is the only version +# supported by Medaka. The pinning of older versions of libcurl and +# openssl will cause installation of outdated packages and likely +# lead solver conflicts in the future. Please review this on future +# releases, especially if support for TensorFlow 2.11+ is added. +libcurl: + - 7 +openssl: + - 1.1.1 diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 34e6600a20be8..f1c60199cd8d3 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -1,6 +1,6 @@ {% set name = "Medaka" %} -{% set version = "1.8.0" %} -{% set sha256 = "bc6c10058d3cad662b8bccdc0af4f1e17424cf117299dce8e44ec8c87c4472ec" %} +{% set version = "1.10.0" %} +{% set sha256 = "864b6303b0b262e5e81acba7b0da003420906db123a5072adc82458d650a8b70" %} # Bot PRs - Always review requirements.txt for new release package: @@ -15,12 +15,13 @@ source: build: number: 0 - skip: True # [py < 38] entry_points: - medaka = medaka.medaka:main - medaka_counts = medaka.medaka_counts:main - medaka_data_path = medaka.common:print_data_path - medaka_version_report = medaka:report_binaries + run_exports: + - {{ pin_subpackage('medaka', max_pin='x') }} requirements: build: @@ -29,8 +30,8 @@ requirements: host: - python - pip - - cffi ==1.15.0 - - htslib + - cffi >=1.15.0 + - htslib >=1.14 - libcurl - openssl - bzip2 @@ -38,24 +39,27 @@ requirements: - zlib run: - python - - cffi ==1.15.0 + - cffi >=1.15.0 - grpcio - h5py - intervaltree - - tensorflow >=2.8.0,<2.9.dev0 + # Please review the need for the conda_build_config.yaml + # if a more recent version of Tensorflow is supported. + - tensorflow >=2.10,<2.11 - numpy >=1.21.6 - nomkl # [osx] - mappy - ont-fast5-api - parasail-python - - pyspoa >=0.0.3 + - pyabpoa + - pyspoa >=0.2.1 - pysam >=0.16.0.1 - python-edlib - requests - - samtools >=1.17 - - bcftools >=1.17 - - minimap2 >=2.26 - - htslib + - samtools >=1.14 + - bcftools >=1.14 + - minimap2 >=2.17 + - htslib >=1.14 - libcurl - openssl From 27bd705d8c4119f411d60118616b167890bab31b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 20 Oct 2023 10:55:22 -0600 Subject: [PATCH 0346/2173] Update genoboo to 0.4.8 (#43789) --- recipes/genoboo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genoboo/meta.yaml b/recipes/genoboo/meta.yaml index 8f6e34ba53f5b..1dccadf084b90 100644 --- a/recipes/genoboo/meta.yaml +++ b/recipes/genoboo/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'genoboo' %} -{% set version = '0.4.7' %} -{% set sha256 = 'e963e67261911ed91f15b447e222ba2e116efcbdfcc236ae30bc6dbbcb59ac6f' %} +{% set version = '0.4.8' %} +{% set sha256 = '09a3a5e520aae725eb7bf428490668dce02e89433dcd989f603d4393ad82b127' %} package: name: {{ name|lower }} From 0b9599bf3a4be801cd72a3dc82473b11c1eca2ec Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 20 Oct 2023 13:52:52 -0600 Subject: [PATCH 0347/2173] Update oakvar to 2.9.53 (#43794) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index edfdfe20dd5ef..929115cd483f2 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.52" %} -{% set sha256 = "babb89ef7c1019950e5e61e050cca8d8067789e287c759867696592b4e1e288d" %} +{% set version = "2.9.53" %} +{% set sha256 = "d2cc4f1762fd90afc3b7a0721b5be04a5bae6530cf8849fbf1fd7831daa63acf" %} package: name: {{ name|lower }} From 62d9a9706bbdee1602643175cb10464b3f8565c6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 20 Oct 2023 13:55:49 -0600 Subject: [PATCH 0348/2173] Update piranha-polio to 1.1 (#43792) * Update piranha-polio to 1.1 * run_exportw --------- Co-authored-by: Thanh Lee --- recipes/piranha-polio/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/piranha-polio/meta.yaml b/recipes/piranha-polio/meta.yaml index 107d82f0fee73..94c7f80c937ed 100644 --- a/recipes/piranha-polio/meta.yaml +++ b/recipes/piranha-polio/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.13" %} +{% set version = "1.1" %} package: name: piranha-polio @@ -6,12 +6,14 @@ package: source: url: https://github.com/polio-nanopore/piranha/archive/refs/tags/{{ version }}.tar.gz - sha256: 25ec27229eb36548a169adb2c9652bb6c1df9a9b3738525d6d5d5b9758f73322 + sha256: 9fb5c04786c9f05bcb362e9d7073e95d51b3e00d0c49558a7b9fa7d52cf55622 build: number: 0 noarch: python script: python -m pip install --no-deps --ignore-installed . + run_exports: + - {{ pin_subpackage("piranha-polio", max_pin="x.x") }} requirements: host: From 72f0c30a3809ac9d81d3c439414d6d41487faed2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 20 Oct 2023 17:50:58 -0600 Subject: [PATCH 0349/2173] Update r-ramclustr to 1.3.1 (#43793) * Update r-ramclustr to 1.3.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/r-ramclustr/meta.yaml | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/recipes/r-ramclustr/meta.yaml b/recipes/r-ramclustr/meta.yaml index 7706f138a70e8..bdaafa9cc6768 100644 --- a/recipes/r-ramclustr/meta.yaml +++ b/recipes/r-ramclustr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.3.0' %} +{% set version = '1.3.1' %} package: name: r-ramclustr @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/RAMClustR_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/RAMClustR/RAMClustR_{{ version }}.tar.gz - sha256: 2900206033fcbca4a74e82a76144d7186a4842783c462efa0f92aa4f5b7c8082 + sha256: cd1154bb1411346a5426a919b2d374daedaabc08ce094b6ebed5a897c1fc9156 build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-ramclustr', max_pin="x") }} requirements: host: @@ -23,18 +25,16 @@ requirements: - r-biocmanager - r-interpretmsspectrum - bioconductor-msnbase - - r-readxl + - r-readxl - r-rcurl - r-dynamictreecut - r-e1071 - r-fastcluster - - r-ff - r-ggplot2 - r-gplots - r-httr - r-jsonlite - bioconductor-pcamethods - - bioconductor-preprocesscore - r-stringi - r-stringr - r-webchem @@ -44,18 +44,16 @@ requirements: - r-biocmanager - r-interpretmsspectrum - bioconductor-msnbase - - r-readxl + - r-readxl - r-rcurl - r-dynamictreecut - r-e1071 - r-fastcluster - - r-ff - r-ggplot2 - r-gplots - r-httr - r-jsonlite - bioconductor-pcamethods - - bioconductor-preprocesscore - r-stringi - r-stringr - r-webchem From 9db679329693736f47b4b8a50b61423e483f5861 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 20 Oct 2023 17:51:12 -0600 Subject: [PATCH 0350/2173] Update psm-utils to 0.6.0 (#43782) * Update psm-utils to 0.6.0 * Update meta.yaml update run_exports * add quotes to run_exports --------- Co-authored-by: Thanh Lee Co-authored-by: joshuazhuang7 --- recipes/psm-utils/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index ccec0fab3146e..052c9e1582c18 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.5.0" %} -{% set sha256 = "8a727a7fc1ea6ecd4391512bb9cfb39346af7272c8e1e0957fa3c3f4829fe630" %} +{% set version = "0.6.0" %} +{% set sha256 = "2e4d43033b04ee3502d8f54417893d6b2f3b0967ff80bbc1c0f301ae2f8cac65" %} package: name: {{ name|lower }} @@ -14,10 +14,10 @@ build: number: 0 entry_points: - psm-utils=psm-utils.__main__:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python run_exports: - - {{ pin_subpackage(name, max_pin="x") }} + - {{ pin_subpackage('psm-utils', max_pin="x") }} requirements: host: From cb421a276a111c113a3439fa3a305127b26d028a Mon Sep 17 00:00:00 2001 From: Samvkes <44610150+Samvkes@users.noreply.github.com> Date: Sat, 21 Oct 2023 03:35:42 +0200 Subject: [PATCH 0351/2173] Update Clair3 to use extended base image (#43786) * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/clair3/meta.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/clair3/meta.yaml b/recipes/clair3/meta.yaml index 5bdcd44842662..7994450c7be40 100644 --- a/recipes/clair3/meta.yaml +++ b/recipes/clair3/meta.yaml @@ -10,8 +10,10 @@ source: sha256: aa7b7d7db44488c58122f12fec73ea0ca1feea0c6bd10199ca18a00b9308330d build: - number: 2 + number: 3 skip: True # [osx] + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: @@ -47,6 +49,9 @@ test: - longphase --version - which clair3.py - run_clair3.sh -v +extra: + container: + extended-base: true about: home: 'https://github.com/HKU-BAL/Clair3' From 952685e5fdfaa378a929af96d6faccf459d546fa Mon Sep 17 00:00:00 2001 From: farchaab <116543129+farchaab@users.noreply.github.com> Date: Sat, 21 Oct 2023 03:43:54 +0200 Subject: [PATCH 0352/2173] Update assembly_finder recipe (#43788) * restrict python version * remove whitespace --------- Co-authored-by: Robert A. Petit III --- recipes/assembly_finder/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index c1c25c1406c57..1e56d64487862 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -9,7 +9,7 @@ source: - url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz sha256: 9c6a59842c3e5bf19284dee0cec65e65cd61c897d6bf6127e2929088b051fbbc build: - number: 0 + number: 1 entry_points: - assembly_finder = assembly_finder.assembly_finder:cli noarch: python @@ -19,11 +19,11 @@ build: requirements: host: - - python >=3.9 + - python >=3.9,<3.12 - pip run: - - python >=3.9 + - python >=3.9,<3.12 - snakemake-minimal >=7.32.4 - click >=7 - biopython >=1.78 From ca94b8cb750ee699f63178acf74e0bd1d39cf232 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 20 Oct 2023 20:50:48 -0600 Subject: [PATCH 0353/2173] Update pangolin-data to 1.23 (#43795) * Update pangolin-data to 1.23 * run_exports * add entry_points --------- Co-authored-by: Thanh Lee Co-authored-by: joshuazhuang7 --- recipes/pangolin-data/meta.yaml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/recipes/pangolin-data/meta.yaml b/recipes/pangolin-data/meta.yaml index d5dbd0a04bce2..63aa7e7f4c2dd 100644 --- a/recipes/pangolin-data/meta.yaml +++ b/recipes/pangolin-data/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.22" %} +{% set version = "1.23" %} package: name: pangolin-data @@ -6,12 +6,16 @@ package: source: url: https://github.com/cov-lineages/pangolin-data/archive/refs/tags/v{{ version }}.tar.gz - sha256: b19e8db9070956dfcddf302b154bf1b1f648ccabcca4169aadc8c6f493ed0301 + sha256: b739d9275a6164e6acd7127a323e55463345cea652d9ad0c1f5ed31dcd256d9b build: number: 0 noarch: python - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv + entry_points: + - pangolin_data = pangolin_data.command:main + run_exports: + - {{ pin_subpackage("pangolin-data", max_pin="x.x") }} requirements: host: @@ -27,5 +31,6 @@ test: about: home: https://github.com/cov-lineages/pangolin-data license: GPL-3.0-only + license_family: GPL3 license_file: LICENSE summary: Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments From e4a6537354827f8d7baf598988b1129b8c8393ec Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 20 Oct 2023 23:49:23 -0600 Subject: [PATCH 0354/2173] Update semibin to 2.0.1 (#43797) --- recipes/semibin/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/semibin/meta.yaml b/recipes/semibin/meta.yaml index 333a87552662b..c56e56d7083b8 100644 --- a/recipes/semibin/meta.yaml +++ b/recipes/semibin/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SemiBin" %} -{% set version = "2.0.0" %} +{% set version = "2.0.1" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 2b4ceec197b0ea2817c4e3cf6d131dd312e5605057732bfee141bbdd7025100f + sha256: 835743d810012b2edf33274d335adfced5b861a6bb61d945572a88af469f3506 build: noarch: python - number: 1 + number: 0 entry_points: - SemiBin=SemiBin.main:main1 - SemiBin2=SemiBin.main:main2 From b3d732ba3f36756c2051ccc6a8388c51982ba002 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Sat, 21 Oct 2023 10:52:17 +0200 Subject: [PATCH 0355/2173] Update OpenMS to 3.1.0 (#43774) * bump version number * Update build.sh * add sage to thirdparty * update sirius * update msgfplus * Update meta.yaml * Update meta.yaml * Update meta.yaml * fix * add run export * afix name in run export * Update recipes/openms-meta/meta.yaml * revert pyopenms OpenMS needs to build first * attempts to fix disconnects: reduce threads * Update recipes/openms-meta/meta.yaml Co-authored-by: M Bernt * Update meta.yaml --------- Co-authored-by: Julianus Pfeuffer Co-authored-by: M Bernt --- recipes/openms-meta/build.sh | 2 +- recipes/openms-meta/meta.yaml | 16 +++++++++------- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/recipes/openms-meta/build.sh b/recipes/openms-meta/build.sh index 3ab476e843b98..54dd40136fce4 100644 --- a/recipes/openms-meta/build.sh +++ b/recipes/openms-meta/build.sh @@ -46,6 +46,6 @@ cmake .. \ -DBUILD_EXAMPLES=OFF # limit concurrent build jobs due to memory usage on CI -make -j4 OpenMS TOPP UTILS +make -j2 OpenMS TOPP # The subpackages will do the installing of the parts #make install diff --git a/recipes/openms-meta/meta.yaml b/recipes/openms-meta/meta.yaml index df66ab0487368..98834890ba05b 100644 --- a/recipes/openms-meta/meta.yaml +++ b/recipes/openms-meta/meta.yaml @@ -1,5 +1,5 @@ {% set name = "OpenMS" %} -{% set version = "3.0.0" %} +{% set version = "3.1.0" %} # if ends with 'dev' it is considered a development release and pulled from GitHub package: name: {{ name|lower }}-meta version: {{ version }} @@ -11,12 +11,13 @@ source: git_depth: 1 # (Defaults to -1/not shallow) {% else %} source: - url: https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/{{ version }}/OpenMS-{{ version }}-src.tar.gz - md5: 2b7ee0f4d8f42eb3c17384347df2dba4 + url: https://github.com/OpenMS/OpenMS/releases/download/Release{{ version }}/OpenMS-{{ version }}-src.tar.gz + md5: 6a60ef1a95c7ce915cc3a02e5bccd593 {% endif %} build: number: 1 + skip: True # [osx] # Try this when building with GUI #extra: @@ -143,14 +144,14 @@ outputs: run: - {{ pin_subpackage('openms', exact=True) }} - comet-ms ==2023010 - - fido ==1.0 - luciphor2 ==2020_04_03 - - msgf_plus ==2021.03.22 + - msgf_plus ==2023.01.1202 - pepnovo ==20101117 - percolator ==3.5 - - sirius-csifingerid =4.9 - - thermorawfileparser ==1.3.4 + - conda-forge::sirius-ms ==5.8.2 + - thermorawfileparser ==1.4.3 - xtandem ==15.12.15.2 + - sage-proteomics ==0.14.3 - gnuplot - r-gplots test: @@ -167,6 +168,7 @@ about: extra: skip-lints: - build_number_needs_reset # our linter has some issues with multi-package recipes as it seems + - missing_run_exports # linter seems expect run_export keyword for meta-package in multi-package {% if 'dev' in version %} - uses_vcs_url - missing_hash From feb331711042c16bb95fc41052c88f07653e960f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 21 Oct 2023 06:10:16 -0600 Subject: [PATCH 0356/2173] Update python-bioext to 0.21.2 (#43542) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/python-bioext/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/python-bioext/meta.yaml b/recipes/python-bioext/meta.yaml index fd43fd7e757ae..84edecf3c34ce 100644 --- a/recipes/python-bioext/meta.yaml +++ b/recipes/python-bioext/meta.yaml @@ -1,6 +1,6 @@ {% set name = "BioExt" %} -{% set version = "0.21.1" %} -{% set sha256 = "c4432fcd9ac860ae3278faaf03bead3e3687df3766f82f4c1ed2d53e6fc29b10" %} +{% set version = "0.21.2" %} +{% set sha256 = "bd3ae29e1dfc4e543b6b6acdd26d073157365233c690a31793d2924055999568" %} package: name: python-{{ name|lower }} From d03b9f24e3c3add6f5d9b28045747e96e6a40478 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 21 Oct 2023 12:38:24 -0600 Subject: [PATCH 0357/2173] Update mehari to 0.14.2 (#43798) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 6b5a52e698801..ebb7859faec88 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.14.1" %} -{% set sha256 = "bfe62708394f412dda67044d21fd5649a26e2c30c304f53cda6b9fc83b869b64" %} +{% set version = "0.14.2" %} +{% set sha256 = "4a3223b2ccf57850ede583d0f3049368a2253ac53944d2bebec67188d2dc44e1" %} package: name: mehari From 92b9bbd3314594e19497764e4594d13c8670b2f3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 21 Oct 2023 13:03:23 -0600 Subject: [PATCH 0358/2173] Update annonars to 0.24.2 (#43801) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 4782490dba970..bf93462d3c7a3 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.24.1" %} +{% set version = "0.24.2" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 2ee0ebeb1d58faa96a96cc93779670919ceedd9a227138b1c950862257c7ff58 + sha256: c6bd5a0d1a49a337c24c0185390c081040fa136690fe16f7d9c7c30dbbcdf8f5 requirements: build: From d60579f33f5f3bc3ba451898798f97cdc64a40b9 Mon Sep 17 00:00:00 2001 From: Rlibouban <127295521+rlibouba@users.noreply.github.com> Date: Sat, 21 Oct 2023 22:58:17 +0200 Subject: [PATCH 0359/2173] Update tsebra - New version (#43778) * Update tsebra * Update meta.yaml add run_exports * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/tsebra/meta.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/tsebra/meta.yaml b/recipes/tsebra/meta.yaml index dbb0e492a48b1..52af2306ddd96 100644 --- a/recipes/tsebra/meta.yaml +++ b/recipes/tsebra/meta.yaml @@ -1,20 +1,21 @@ -{% set version = "1.1.1" %} +{% set version = "1.1.2" %} {% set name = "tsebra" %} -{% set sha256 = "0426c243888135ee3fd6ea0ca9f37eb4af03dd117498165257fa756f59d49ce9" %} +{% set sha256 = "d2fcf571890a70f9c3b60c1ffdbf6e60fd6c7b3c7c71bc78462ba0a52aca6300" %} package: name: "{{ name }}" version: "{{ version }}" source: - url: "https://github.com/Gaius-Augustus/TSEBRA/archive/refs/tags/v.{{ version }}.tar.gz" + url: "https://github.com/Gaius-Augustus/TSEBRA/archive/refs/tags/v{{ version }}.tar.gz" sha256: "{{ sha256 }}" folder: tsebra build: number: 0 noarch: python - + run_exports: + - {{ pin_subpackage("tsebra", max_pin="x.x") }} requirements: build: - python >=3.5.2 @@ -32,4 +33,4 @@ about: license: Artistic-2.0 license_family: Other summary: | - TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. \ No newline at end of file + TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. From 03cdb393a0b38cfe22bf72408fad5dab25c7b57f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 22 Oct 2023 08:53:50 -0600 Subject: [PATCH 0360/2173] Update mehari to 0.14.3 (#43810) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index ebb7859faec88..dd251e5533ae4 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.14.2" %} -{% set sha256 = "4a3223b2ccf57850ede583d0f3049368a2253ac53944d2bebec67188d2dc44e1" %} +{% set version = "0.14.3" %} +{% set sha256 = "6c1c343bca1b5be9e07d131996dbffe286f59ee6171b52c452134032d9a8af1f" %} package: name: mehari From e62a066efce31083f1b1f0bf2f441d067422de89 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 22 Oct 2023 14:12:26 -0600 Subject: [PATCH 0361/2173] Update uropa to 4.0.3 (#43813) * Update uropa to 4.0.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/uropa/build.sh | 3 --- recipes/uropa/meta.yaml | 12 +++++++++--- 2 files changed, 9 insertions(+), 6 deletions(-) delete mode 100644 recipes/uropa/build.sh diff --git a/recipes/uropa/build.sh b/recipes/uropa/build.sh deleted file mode 100644 index e45c73d5420b0..0000000000000 --- a/recipes/uropa/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/usr/bin/env bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/uropa/meta.yaml b/recipes/uropa/meta.yaml index 18ebd85966662..8a5b1d0dea359 100644 --- a/recipes/uropa/meta.yaml +++ b/recipes/uropa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "uropa" %} -{% set version = "4.0.2" %} +{% set version = "4.0.3" %} package: name: "{{ name|lower }}" @@ -7,16 +7,21 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3d4288055fb60e0b58380c31524cca7f6352b46117f1644645f603655da04438 + sha256: e0b648881b95f301e3f3ecc924314995312f10b0cbabf96d5a5ce2fb18c53a59 build: number: 0 noarch: python + entry_points: + - uropa = uropa.uropa:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('uropa', max_pin="x") }} requirements: host: - python >=3.6 - - setuptools + - pip run: - numpy - psutil @@ -44,6 +49,7 @@ about: home: "https://github.com/loosolab/UROPA" license: MIT license_family: MIT + license_file: LICENSE summary: | UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for genomic region annotation from e.g. peak calling. It detects the most appropriate annotation by taking parameters such as feature type, anchor, direction and strand into account. From d44519e29ee8a330a580689c3d2425c342656a05 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 22 Oct 2023 14:12:44 -0600 Subject: [PATCH 0362/2173] Update pyhmmer to 0.10.3 (#43809) * Update pyhmmer to 0.10.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/pyhmmer/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index 670eaa702c8a5..f77198d955447 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.2" %} +{% set version = "0.10.3" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a72421f603e5010ff97cc39770b998909b243c36927678f36cfdcadd3cbd94c2 + sha256: 761eaa5b4ea2054f926f5638c5bee4cf595841bed7ee3b14d548c27951602bad build: number: 0 skip: True #[py2k or win] - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" + run_exports: + - {{ pin_subpackage('pyhmmer', max_pin="x") }} requirements: build: @@ -34,6 +36,7 @@ test: about: home: https://github.com/althonos/pyhmmer license: MIT + license_family: MIT license_file: COPYING summary: Cython bindings and Python interface to HMMER3. doc_url: https://pyhmmer.readthedocs.io From 3189a1a41a8a4adeb44d752ede3a33c599284214 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 22 Oct 2023 14:13:14 -0600 Subject: [PATCH 0363/2173] Update pyrodigal to 3.1.0 (#43807) * Update pyrodigal to 3.1.0 * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/pyrodigal/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pyrodigal/meta.yaml b/recipes/pyrodigal/meta.yaml index 55d06f50e290f..4a6a010947372 100644 --- a/recipes/pyrodigal/meta.yaml +++ b/recipes/pyrodigal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrodigal" %} -{% set version = "3.0.1" %} +{% set version = "3.1.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 10f1d15090780c79d53c72b25e707dddae840081d27b4e37ec500feca2312736 + sha256: efc01ca72e798efd07a8e79209c92b518f9f403e98012d01eca37fe2416487df build: number: 0 @@ -16,7 +16,7 @@ build: entry_points: - pyrodigal = pyrodigal.cli:main run_exports: - - {{ pin_subpackage(name, max_pin="x") }} + - {{ pin_subpackage("pyrodigal", max_pin="x.x") }} requirements: build: From c97c886b9f222ee2b62370d2d4abf64f4fae4fa9 Mon Sep 17 00:00:00 2001 From: Dirk-Jan <72025902+dirkjanvw@users.noreply.github.com> Date: Sun, 22 Oct 2023 22:59:06 +0200 Subject: [PATCH 0364/2173] Update post-link.sh script for RepeatMasker (#43288) * replace zcat by gunzip -c * bump build number repeatmasker * add run_exports to repeatmasker recipe adding max_pin x.x.x because dependencies can differ even for the x.x.x version updates * don't download dfam database when in docker --- recipes/repeatmasker/meta.yaml | 4 +++- recipes/repeatmasker/post-link.sh | 16 +++++++++++++--- 2 files changed, 16 insertions(+), 4 deletions(-) diff --git a/recipes/repeatmasker/meta.yaml b/recipes/repeatmasker/meta.yaml index 3d176290714eb..c837404507fa1 100644 --- a/recipes/repeatmasker/meta.yaml +++ b/recipes/repeatmasker/meta.yaml @@ -11,8 +11,10 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic + run_exports: + - {{ pin_subpackage('repeatmasker', max_pin='x.x.x') }} requirements: host: diff --git a/recipes/repeatmasker/post-link.sh b/recipes/repeatmasker/post-link.sh index b357c667894e7..ac28ed8558b30 100755 --- a/recipes/repeatmasker/post-link.sh +++ b/recipes/repeatmasker/post-link.sh @@ -1,7 +1,17 @@ #!/bin/bash -echo "Downloading Dfam_curatedonly.h5.gz from www.dfam.org" -wget -O Dfam_curatedonly.h5.gz https://www.dfam.org/releases/Dfam_3.7/families/Dfam_curatedonly.h5.gz +if [ -f /.dockerenv ]; then + cat >> "$PREFIX/.messages.txt" < ${PREFIX}/share/RepeatMasker/Libraries/Dfam.h5 +wget -O Dfam_curatedonly.h5.gz https://www.dfam.org/releases/Dfam_3.7/families/Dfam_curatedonly.h5.gz +gunzip -c Dfam_curatedonly.h5.gz > ${PREFIX}/share/RepeatMasker/Libraries/Dfam.h5 rm Dfam_curatedonly.h5.gz + +EOF +else + echo "Downloading Dfam_curatedonly.h5.gz from www.dfam.org" + wget -O Dfam_curatedonly.h5.gz https://www.dfam.org/releases/Dfam_3.7/families/Dfam_curatedonly.h5.gz + gunzip -c Dfam_curatedonly.h5.gz > ${PREFIX}/share/RepeatMasker/Libraries/Dfam.h5 + rm Dfam_curatedonly.h5.gz +fi From 6a67721b5df0acbe90ca80623173aa3425df5293 Mon Sep 17 00:00:00 2001 From: Boas van der Putten <32385917+boasvdp@users.noreply.github.com> Date: Sun, 22 Oct 2023 23:13:52 +0200 Subject: [PATCH 0365/2173] Add auriclass (#43800) * add auriclass meta.yaml * add run export * try to fix pip * rm double python listing * add import * use v0.5.1 * add maintainers --- recipes/auriclass/meta.yaml | 53 +++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 recipes/auriclass/meta.yaml diff --git a/recipes/auriclass/meta.yaml b/recipes/auriclass/meta.yaml new file mode 100644 index 0000000000000..fc1e06b476aaa --- /dev/null +++ b/recipes/auriclass/meta.yaml @@ -0,0 +1,53 @@ +{% set name = "AuriClass" %} +{% set version = "0.5.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/RIVM-bioinformatics/auriclass/archive/v{{ version }}.tar.gz + sha256: 2588c1ca2bdd566eb20ec424e2f5e8e7e72e05436e539a2932a214bb851d6273 + +build: + noarch: python + entry_points: + - auriclass = auriclass.main:main + script: {{ PYTHON }} -m pip install . --no-deps -vv + number: 0 + run_exports: + - {{ pin_subpackage('auriclass', max_pin='x.x') }} + +requirements: + host: + - python >=3.10 + - pip + run: + - python >=3.10 + - mash >=2 + - mypy + - pandas >=2 + - pandas-stubs + - pyfastx + - pytest + - pip + + +test: + imports: + - auriclass + commands: + - auriclass --help + +about: + home: https://rivm-bioinformatics.github.io/auriclass/ + summary: "AuriClass is a tool for quickly predicting the clade of a Candida auris genome." + dev_url: https://github.com/RIVM-bioinformatics/auriclass + license: GNU Affero General Public v3 + license_family: AGPL + license_file: LICENSE + +extra: + recipe-maintainers: + - boasvdp + - ids-bioinformatics \ No newline at end of file From 43461f6021e1155972b87a2d90b8910c7e468218 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 00:46:41 -0600 Subject: [PATCH 0366/2173] Update repeatmodeler to 2.0.5 (#43463) * Update repeatmodeler to 2.0.5 * add run_exports --------- Co-authored-by: joshuazhuang7 Co-authored-by: worku005 --- recipes/repeatmodeler/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/repeatmodeler/meta.yaml b/recipes/repeatmodeler/meta.yaml index 3e655e02cce92..ebcbe17e9442e 100644 --- a/recipes/repeatmodeler/meta.yaml +++ b/recipes/repeatmodeler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RepeatModeler" %} -{% set version = "2.0.4" %} -{% set sha256 = "94aad46cc70911d48de3001836fc3165adb95b2b282b5c53ab0d1da98c27a6b6" %} +{% set version = "2.0.5" %} +{% set sha256 = "4c005ada7e88ff944116832349580a0dc3db762dc1c91235fa574b32ea9a8452" %} package: name: "{{ name|lower }}" @@ -15,6 +15,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('repeatmodeler', max_pin="x") }} requirements: host: @@ -43,7 +45,7 @@ requirements: - ucsc-twobitinfo - ucsc-twobittofa - ucsc-fatotwobit - - ninja-nj # [not osx] + - ninja-nj test: files: From ad435d6e17eace667422d1f9b4d5621e6082549b Mon Sep 17 00:00:00 2001 From: Remi Denise Date: Mon, 23 Oct 2023 10:19:08 +0200 Subject: [PATCH 0367/2173] Add taxmyPHAGE recipe (#43812) * Creating the conda package for taxmyphage * Creating the conda package for taxmyphage add run_export * :bug: Wrong backend for pyproject.toml * :bug: Wrong sha256 in conda recipe --- recipes/taxmyphage/meta.yaml | 57 ++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 recipes/taxmyphage/meta.yaml diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml new file mode 100644 index 0000000000000..d415e5c9e9a1a --- /dev/null +++ b/recipes/taxmyphage/meta.yaml @@ -0,0 +1,57 @@ +{% set name = "taxmyphage" %} +{% set version = "0.1.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz + sha256: c9e6ef4fd9d1ccf677f268654c15571ef7f2d3ba955f20c08a21aafc4788bc30 + +build: + entry_points: + - taxmyphage = taxmyphage.__main__:main + noarch: python + script: "{{ PYTHON }} -m pip install . -vv" + number: 0 + run_exports: + - {{ pin_subpackage('taxmyphage', max_pin="x.x") }} + +requirements: + host: + - python >=3.9,<3.13 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.9,<3.13 + - biopython >=1.81.0,<2.0.0 + - pandas >=2.1.1,<3.0.0 + - numpy >=1.26.0,<2.0.0 + - matplotlib-base >=3.8.0,<4.0.0 + - seaborn >=0.13.0,<0.14.0 + - python-wget >=3.2.0,<4.0.0 + - scipy >=1.11.3,<2.0.0 + - tqdm >=4.66.1,<5.0.0 + - openpyxl >=3.1.2,<4.0.0 + - networkx >=3.1.0,<4.0.0 + - icecream >=2.1.3,<3.0.0 + - importlib-metadata >=6.8.0,<7.0.0 + - zipp >=3.17.0,<4.0.0 + - blast >=2.14.0,<3.0.0 + - mash >=2.3,<3.0.0 + +test: + commands: + - taxmyphage --help + + +about: + home: https://github.com/amillard/tax_myPHAGE + summary: Script to assign taxonomy to a bacteriophage at the genus and species level + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - rdenise From d0e582bcfc88b5b1517d3758b73fbceee3a16abb Mon Sep 17 00:00:00 2001 From: yanyew <90335707+yanyew@users.noreply.github.com> Date: Mon, 23 Oct 2023 18:08:00 +0800 Subject: [PATCH 0368/2173] add syngap recipes (#43804) --- recipes/syngap/build.sh | 10 +++++ recipes/syngap/meta.yaml | 89 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 99 insertions(+) create mode 100644 recipes/syngap/build.sh create mode 100644 recipes/syngap/meta.yaml diff --git a/recipes/syngap/build.sh b/recipes/syngap/build.sh new file mode 100644 index 0000000000000..bc4aec66a541f --- /dev/null +++ b/recipes/syngap/build.sh @@ -0,0 +1,10 @@ +mkdir -p $PREFIX/bin +cp -rf $SRC_DIR/bin $PREFIX/bin +cp -rf $SRC_DIR/scripts $PREFIX/bin +cp $SRC_DIR/SynGAP.py $PREFIX/bin +cp $SRC_DIR/dual.py $PREFIX/bin +cp $SRC_DIR/triple.py $PREFIX/bin +cp $SRC_DIR/custom.py $PREFIX/bin +cp $SRC_DIR/genepair.py $PREFIX/bin +cp $SRC_DIR/evi.py $PREFIX/bin +cp $SRC_DIR/eviplot.py $PREFIX/bin diff --git a/recipes/syngap/meta.yaml b/recipes/syngap/meta.yaml new file mode 100644 index 0000000000000..e1144f23bfe1b --- /dev/null +++ b/recipes/syngap/meta.yaml @@ -0,0 +1,89 @@ +{% set name = "syngap" %} +{% set version = "1.0.0" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/yanyew/SynGAP/releases/download/v{{ version }}/{{ name }}_v{{ version }}.tar.gz + sha256: a2848c925d8df49872ba23f4e0afbc176ff1688b60b04ee3c5f318d41dcc6c69 + +build: + number: 0 + entry_points: + - syngap = SynGAP:main + noarch: generic + run_exports: + - python + - biopython + - jcvi + - bedtools + - last + - emboss + - gffread + - seqkit + - diamond + - perl-bioperl + - kneed + - numpy + - pandas + - matplotlib-base + +requirements: + bulid: + - python >=3.10 + run: + - python >=3.10 + - biopython >=1.81 + - jcvi >=1.3.6 + - bedtools >=2.31.0 + - last >=1454 + - emboss >=6.6.0 + - gffread >=0.12.7 + - seqkit >=2.4.0 + - diamond >=2.1.8 + - perl-bioperl >=1.7.8 + - kneed >=0.8.3 + - numpy >=1.26.0 + - pandas >=2.1.1 + - matplotlib-base >=3.8.0 + - scikit-image >=0.22.0 + - pybedtools >=0.9.0 + - deap >=1.4.1 + - more-itertools + - crossmap + - graphviz + - webcolors + - ortools-python + pip: + - ftpretty + +test: + source_files: + - run_test.sh + - SynGAP.py + - dual.py + - triple.py + - custom.py + - genepair.py + - evi.py + - eviplot.py + - bin/* + - scripts/* + imports: + - SynGAP + commands: + - syngap -h + - syngap dual -h + - syngap triple -h + - syngap custom -h + - syngap genepair -h + - syngap evi -h + - syngap eviplot -h + +about: + home: https://github.com/yanyew/SynGAP + license: CC-BY-NC-SA-4.0 + summary: "SynGAP: Synteny-based Genome Annotations Polisher" + dev_url: https://github.com/yanyew/SynGAP From d7b4677b0baa7062e5364040e0b69380d7c3a4ac Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 04:09:35 -0600 Subject: [PATCH 0369/2173] Update taxmyphage to 0.1.4 (#43819) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index d415e5c9e9a1a..d2acad12c11ae 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: c9e6ef4fd9d1ccf677f268654c15571ef7f2d3ba955f20c08a21aafc4788bc30 + sha256: 09dc32220e190a3404df5e5dda0082df3641479a510094bbed3b5c935b1f2b6a build: entry_points: From 963a0b09897a7d0d6d3ff115368be971f11b5e9d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 04:10:17 -0600 Subject: [PATCH 0370/2173] Update auriclass to 0.5.2 (#43817) --- recipes/auriclass/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/auriclass/meta.yaml b/recipes/auriclass/meta.yaml index fc1e06b476aaa..f095e4e7d4b8e 100644 --- a/recipes/auriclass/meta.yaml +++ b/recipes/auriclass/meta.yaml @@ -1,5 +1,5 @@ {% set name = "AuriClass" %} -{% set version = "0.5.1" %} +{% set version = "0.5.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/RIVM-bioinformatics/auriclass/archive/v{{ version }}.tar.gz - sha256: 2588c1ca2bdd566eb20ec424e2f5e8e7e72e05436e539a2932a214bb851d6273 + sha256: 448569c7896aa27dd60628682db7c14aad29575cb0e92ae758f01c175865634b build: noarch: python @@ -50,4 +50,4 @@ about: extra: recipe-maintainers: - boasvdp - - ids-bioinformatics \ No newline at end of file + - ids-bioinformatics From 712006039c78ceff2d6056f0a0ffc46ca9c8e8a9 Mon Sep 17 00:00:00 2001 From: Jonas Fuchs <78491186+jonas-fuchs@users.noreply.github.com> Date: Mon, 23 Oct 2023 16:22:50 +0200 Subject: [PATCH 0371/2173] Add bamdash (#43822) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * added bamdash yaml * added run exports * fixed pin * use kaleido-core * added licence manually * added python-kaleido and plotly --------- Co-authored-by: Björn Grüning --- recipes/bamdash/LICENSE | 674 ++++++++++++++++++++++++++++++++++++++ recipes/bamdash/meta.yaml | 50 +++ 2 files changed, 724 insertions(+) create mode 100644 recipes/bamdash/LICENSE create mode 100644 recipes/bamdash/meta.yaml diff --git a/recipes/bamdash/LICENSE b/recipes/bamdash/LICENSE new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/bamdash/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/bamdash/meta.yaml b/recipes/bamdash/meta.yaml new file mode 100644 index 0000000000000..41d2eb08cdfca --- /dev/null +++ b/recipes/bamdash/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "bamdash" %} +{% set version = "0.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/bamdash-{{ version }}.tar.gz + sha256: 563b6fd7a0362dffd57a5affb57acccf672bc8a6153e9e84d79eb2b1ca593b13 + +build: + entry_points: + - bamdash = bamdash.command:main + noarch: python + script: {{ PYTHON }} -m pip install . --no-deps -vv + number: 0 + run_exports: + - {{ pin_subpackage('bamdash', max_pin="x.x") }} + +requirements: + host: + - python >=3.9 + - pip + run: + - python >=3.9 + - biopython >=1.79 + - pandas >=1.4.4 + - plotly >=5.17.0 + - python-kaleido >=0.2.1 + - pysam >=0.21.0 + +test: + imports: + - bamdash + commands: + - pip check + - bamdash --help + requires: + - pip + +about: + home: https://github.com/jonas-fuchs/BAMdash + summary: Aggregate pathogen NGS results into an interactive plot + license: GPL-3.0-or-later + license_file: LICENSE + +extra: + recipe-maintainers: + - jonas-fuchs From e737cf7a3953a754bf6f79441b3a1661eb846d24 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 09:42:41 -0600 Subject: [PATCH 0372/2173] Update regenie to 3.3 (#43300) * Update regenie to 3.3 * add run_exports * remove run_export * run_exports * rm build fail --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joelle Mbatchou <65199080+joellembatchou@users.noreply.github.com> Co-authored-by: root --- recipes/regenie/build.sh | 2 +- recipes/regenie/build_failure.linux-64.yaml | 104 -------------------- recipes/regenie/meta.yaml | 10 +- 3 files changed, 7 insertions(+), 109 deletions(-) delete mode 100644 recipes/regenie/build_failure.linux-64.yaml diff --git a/recipes/regenie/build.sh b/recipes/regenie/build.sh index fc79b249cc054..1b8a8269d4876 100644 --- a/recipes/regenie/build.sh +++ b/recipes/regenie/build.sh @@ -25,7 +25,7 @@ cmake \ -S "${SRC_DIR}" \ -B build -make -C build -j${CPU_COUNT:=1} regenie +make -C build -j1 regenie make -C build install # bash test/test_conda.sh --path "${SRC_DIR}" diff --git a/recipes/regenie/build_failure.linux-64.yaml b/recipes/regenie/build_failure.linux-64.yaml deleted file mode 100644 index 83c34bc1cdd6d..0000000000000 --- a/recipes/regenie/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 79124a9aa8c8c4bfc4ac1b2a6d10a5fa7bbc0886136237cccdac70de0b0ca6bc # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - opt/conda/conda-bld/noarch - [?25hMamba failed to solve: - - libgfortran-ng - - bgenix >=1.1.7 - - zstd 1.5.* - - zlib 1.2.* - - mkl-include - - libgfortran5 >=12.2.0 - - boost-cpp 1.78.0.* - - _openmp_mutex >=4.5 - - mkl >=2020.4 - - liblapack * *mkl - - libstdcxx-ng >=12 - - libgcc-ng >=12 - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package bgenix-1.1.7-h00c1625_0 requires libgfortran4 >=7.5.0, but none of the providers can be installed - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 230, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 220, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - libgfortran-ng - - bgenix >=1.1.7 - - zstd 1.5.* - - zlib 1.2.* - - mkl-include - - libgfortran5 >=12.2.0 - - boost-cpp 1.78.0.* - - _openmp_mutex >=4.5 - - mkl >=2020.4 - - liblapack * *mkl - - libstdcxx-ng >=12 - - libgcc-ng >=12 - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package bgenix-1.1.7-h00c1625_0 requires libgfortran4 >=7.5.0, but none of the providers can be installed - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bgenix==1.1.7=h00c1625_0"), MatchSpec("libgfortran4[version='>=7.5.0']")} -# Last 100 lines of the build log. diff --git a/recipes/regenie/meta.yaml b/recipes/regenie/meta.yaml index 41ee1ef6f69af..bb864e50ed545 100644 --- a/recipes/regenie/meta.yaml +++ b/recipes/regenie/meta.yaml @@ -1,6 +1,6 @@ {% set name = "regenie" %} -{% set version = "3.2.9" %} -{% set sha256 = "a268de7cd159fac5b94ac1da94d39a12bc922bf7b67f64a98172fc10511438a6" %} +{% set version = "3.3" %} +{% set sha256 = "ee5ccffa89c5ae37b4d89c367da0d0d47d808f1e157152d4d60bcbe1ab3e5f53" %} package: name: {{ name|lower }} @@ -25,8 +25,9 @@ source: build: number: 0 - - + run_exports: + - {{ pin_subpackage('regenie', max_pin="x") }} + requirements: build: - {{ compiler('c') }} @@ -61,6 +62,7 @@ test: about: home: https://rgcgithub.github.io/regenie/ license: MIT + license_family: MIT license_file: LICENSE summary: 'Regenie is a C++ program for whole genome regression modelling of large genome-wide association studies (GWAS).' dev_url: https://github.com/rgcgithub/regenie From f773bb4ca7eadb224e40c0f6e5127f17940f2db6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 10:12:26 -0600 Subject: [PATCH 0373/2173] Update graphanalyzer to 1.6.0 (#43821) * Update graphanalyzer to 1.6.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/graphanalyzer/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/graphanalyzer/meta.yaml b/recipes/graphanalyzer/meta.yaml index 766e16d6837c5..4971952796cdd 100644 --- a/recipes/graphanalyzer/meta.yaml +++ b/recipes/graphanalyzer/meta.yaml @@ -1,17 +1,19 @@ -{% set name="graphanalyzer" %} -{% set version="1.5.1" %} +{% set name = "graphanalyzer" %} +{% set version = "1.6.0" %} package: name: {{ name }} version: {{ version }} build: - noarch: generic - number: 1 + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('graphanalyzer', max_pin="x") }} source: url: https://github.com/lazzarigioele/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 9e6b327cb8b69be2a5fc6f1407920a6de1a79a3d67bdfd45d4f7f5ec6c5af316 + sha256: e2b4b6eda06cb98ee17c398be1168cb5f083caa246a5507339bc01b384994258 requirements: run: @@ -32,7 +34,9 @@ test: about: home: https://github.com/lazzarigioele/graphanalyzer - license: 'GPLv3' + license: 'GPL-3.0-or-later' + license_family: GPL3 + license_file: 'LICENSE.txt' summary: 'A tool to automatically interpret the outputs generated by vConTACT2 when using the INPHARED database' extra: From 8196bfd45f8002a1744bc589aa8a9b4a59b76b08 Mon Sep 17 00:00:00 2001 From: Dirk-Jan <72025902+dirkjanvw@users.noreply.github.com> Date: Mon, 23 Oct 2023 18:14:04 +0200 Subject: [PATCH 0374/2173] Add earlgrey v3.1 (#43762) * adding recipe for Earl Grey * fixing basic mistakes in meta.yaml * add instructions to build.sh from docker configure file on github * shortening build.sh * setting earlgrey to noarch python * setting earl grey to linux only * trying to fix the recipe * fix build for earl grey * earl grey recipe works for linux * anticipate ninja-nj availability for osx * fix paths for earlgrey recipe * some minor fixes to bash specific things in earlgrey * remove check for specific conda environment name from earl grey * add SA-SSR according to configure instructions * put sa-ssr installation not in scripts directory to prevent conflict with binary * make logging bioconda-utils more verbose and correctly install sa-ssrr and trf now * fixing sed for macos * make sure sed commands work on both linux and macos * pinning repeatmodeler because of specific parameter settings used in earlgrey * adding mreps to earlgrey and fixing -pa parameter for repeatclassifier * setting perl5lib * fix sa-ssr for earlgrey by disabling multithreading * update earlgrey to 3.1 * remove a couple lines that fixed v3.0 but are no longer needed for v3.1 --- recipes/earlgrey/build.sh | 77 ++++++++++++++++++++++++++++++++++++++ recipes/earlgrey/meta.yaml | 63 +++++++++++++++++++++++++++++++ 2 files changed, 140 insertions(+) create mode 100644 recipes/earlgrey/build.sh create mode 100644 recipes/earlgrey/meta.yaml diff --git a/recipes/earlgrey/build.sh b/recipes/earlgrey/build.sh new file mode 100644 index 0000000000000..53c799b942cb2 --- /dev/null +++ b/recipes/earlgrey/build.sh @@ -0,0 +1,77 @@ +#!/bin/bash +#Based on https://github.com/TobyBaril/EarlGrey/blob/main/configure +set -x + +# Define paths +PACKAGE_HOME=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM} +SCRIPT_DIR="${PACKAGE_HOME}/scripts/" + + +# Create directories +mkdir -p ${PREFIX}/bin +mkdir -p ${PACKAGE_HOME} + + +# Put package in share directory +cp -r * ${PACKAGE_HOME}/ + + +# Install SA-SSR (has to be done here because SA-SSR is an ancient repository without releases) +git clone https://github.com/ridgelab/SA-SSR +cd SA-SSR +make +cp bin/sa-ssr ${PREFIX}/bin/ + + +# Fixes to earlGrey executable +sed -i.bak "/CONDA_DEFAULT_ENV/,+4d" ${PACKAGE_HOME}/earlGrey #remove check that conda environment has a specific name + + +# Fixes sed command for executables so that it works on both linux and macos +sed -i.bak "s|sed -i |sed -i.bak |g" ${PACKAGE_HOME}/earlGrey ${SCRIPT_DIR}/rcMergeRepeat* ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh + + +# Remove -pa from RepeatClassifier +sed -i.bak 's/RepeatClassifier -pa ${THREADS} /RepeatClassifier /' ${SCRIPT_DIR}/TEstrainer/TEstrainer + + +# Remove -t parameter from sa-ssr (since multithreading doesn't work on OSX) +sed -i.bak 's/-t ${THREADS} / /' ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh +sed -i.bak 's/-t ${THREADS} / /' ${SCRIPT_DIR}/TEstrainer/TEstrainer + + +# Add SCRIPT_DIR to correct path +sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${PACKAGE_HOME}/earlGrey +sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/rcMergeRepeat* +sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/headSwap.sh +sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/autoPie.sh +sed -i.bak "s|INSERT_FILENAME_HERE|${SCRIPT_DIR}/TEstrainer/scripts/|g" ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh + + +# Set permissions to files +chmod +x ${PACKAGE_HOME}/earlGrey +chmod +x ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh +chmod +x ${SCRIPT_DIR}/* > /dev/null 2>&1 +chmod +x ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7/ltr_finder +chmod a+w ${SCRIPT_DIR}/repeatCraft/example + + +# Extract tRNAdb +tar -zxf ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7/tRNAdb.tar.gz --directory ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7 + + +# Set PERL5LIB upon activate/deactivate +for CHANGE in "activate" "deactivate"; +do + mkdir -p "${PREFIX}/etc/conda/${CHANGE}.d" +done +echo "#!/bin/sh" > "${PREFIX}/etc/conda/activate.d/${PKG_NAME}_activate.sh" +echo "export PERL5LIB=${PREFIX}/share/RepeatMasker/:${PREFIX}/share/RepeatModeler/" >> "${PREFIX}/etc/conda/activate.d/${PKG_NAME}_activate.sh" +echo "#!/bin/sh" > "${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}_deactivate.sh" +echo "unset PERL5LIB" >> "${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}_deactivate.sh" + + +# Put earlGrey executable in bin +cd ${PREFIX}/bin +ln -s ${PACKAGE_HOME}/earlGrey . + diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml new file mode 100644 index 0000000000000..394a1630e30cb --- /dev/null +++ b/recipes/earlgrey/meta.yaml @@ -0,0 +1,63 @@ +{% set name = "EarlGrey" %} +{% set version = "3.1" %} +{% set sha256 = "ae448b2f7edcb484a6cfd5b41be95e589c74e8c18eada391a3a87c81f19ed06b" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/TobyBaril/EarlGrey/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('earlgrey', max_pin='x') }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + run: + - python =3.8 + - hmmer + - trf + - cd-hit + - genometools-genometools + - pandas + - ncls =0.0.64 + - pyfaidx + - pyranges + - parallel + - repeatmasker >=4.1.4 + - ltr_retriever + - mafft + - mreps + - ninja-nj + - repeatscout + - recon + - repeatmodeler >=2.0.4 + - bioconductor-genomeinfodb + - bioconductor-genomeinfodbdata + - bioconductor-bsgenome + - bioconductor-plyranges + - r-ape + - r-optparse + - r-tidyverse + - r-plyr + +test: + commands: + - earlGrey -h + +about: + home: https://github.com/TobyBaril/EarlGrey + dev_url: https://github.com/TobyBaril/EarlGrey + license: OSL-2.1 + summary: "Earl Grey: A fully automated TE curation and annotation pipeline" + description: | + Earl Grey is a full-automated transposable element (TE) annotation pipeline, + leveraging the most widely-used tools and combining these with a consensus + elongation process to better define de novo consensus sequences when + annotating new genome assemblies. From 596ea71a0e93a4ed2ea988fcb97553d0b36e5251 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 10:15:29 -0600 Subject: [PATCH 0375/2173] Update abromics_galaxy_json_extractor to 0.8.3 (#43824) --- recipes/abromics_galaxy_json_extractor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abromics_galaxy_json_extractor/meta.yaml b/recipes/abromics_galaxy_json_extractor/meta.yaml index 69a27b8c03a23..9b20f38f812b2 100644 --- a/recipes/abromics_galaxy_json_extractor/meta.yaml +++ b/recipes/abromics_galaxy_json_extractor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.2.1" %} +{% set version = "0.8.3" %} context: {} @@ -8,7 +8,7 @@ package: source: url: https://gitlab.com/ifb-elixirfr/abromics/abromics-galaxy-json-extractor/-/archive/{{ version }}/abromics-galaxy-json-extractor-{{ version }}.tar.gz - sha256: 'c179bb49d6ddfa2b05c903d669f9d91f43e13c63c354466d810b07b77cb32261' + sha256: '81fc614902567dfe83d57fc978bf98cc22e26a58f0e25e359c9d647df6f05bb9' build: noarch: python From c0cb9da96c8e55a01ec421641a64e070236f5e1a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 10:28:04 -0600 Subject: [PATCH 0376/2173] Update medaka to 1.11.0 (#43823) --- recipes/medaka/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index f1c60199cd8d3..d572bdf270026 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -1,6 +1,6 @@ {% set name = "Medaka" %} -{% set version = "1.10.0" %} -{% set sha256 = "864b6303b0b262e5e81acba7b0da003420906db123a5072adc82458d650a8b70" %} +{% set version = "1.11.0" %} +{% set sha256 = "a763d3eb35a3fcee97012ac92357f7ff9cefe3bf7511020152bd2bb1faeb4b1d" %} # Bot PRs - Always review requirements.txt for new release package: From 659c3b33b0d6b200a26c0ee3ba0d95256b393a0f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 13:06:12 -0600 Subject: [PATCH 0377/2173] Update galaxy-files to 23.0.6 (#43825) * Update galaxy-files to 23.0.6 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/galaxy-files/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml index c3239a4785363..ae647f8852cfb 100644 --- a/recipes/galaxy-files/meta.yaml +++ b/recipes/galaxy-files/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.0.5" %} -{% set sha256 = "8133b8ce27cf7e89c966f5c06e52911b8fa714c5f125edbd9642fc4c209c4bcd" %} +{% set version = "23.0.6" %} +{% set sha256 = "0636fb9e8acad5826a4538500d97b80b591a1ce322459023332072956679db0a" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: @@ -13,7 +13,9 @@ source: build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + -{{ pin_subpackage('galaxy-files', max_pin="x") }} requirements: host: From c1d70e5f558677a90bceff0ef2e423e5cb94d13e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 13:06:23 -0600 Subject: [PATCH 0378/2173] Update galaxy-objectstore to 23.0.6 (#43826) * Update galaxy-objectstore to 23.0.6 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/galaxy-objectstore/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml index aecfc3d793e28..4c0885af14ee7 100644 --- a/recipes/galaxy-objectstore/meta.yaml +++ b/recipes/galaxy-objectstore/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.0.5" %} -{% set sha256 = "90efe2740c0c0251d68fa76e0f79938bade798128140e7d67d63bf572cebcb64" %} +{% set version = "23.0.6" %} +{% set sha256 = "8c749ac6d52297e3116949c5195071969b5d962cac14f4b84e7bd051ad8e2347" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: @@ -13,17 +13,19 @@ source: build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('galaxy-objectstore', max_pin="x") }} requirements: host: - pip - - python >=3.6 + - python >=3.7 - galaxy-util >={{ galaxy_version }} run: - galaxy-util >={{ galaxy_version }} - pyyaml - - python >=3.6 + - python >=3.7 - six >=1.9.0 test: From b6f3bc40a31229c4e541c5fcf7eb7664431c90af Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 13:59:18 -0600 Subject: [PATCH 0379/2173] Update mehari to 0.15.0 (#43828) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index dd251e5533ae4..4046538d4e754 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.14.3" %} -{% set sha256 = "6c1c343bca1b5be9e07d131996dbffe286f59ee6171b52c452134032d9a8af1f" %} +{% set version = "0.15.0" %} +{% set sha256 = "6f81bc682820139d859db26c2e4020284b6cae35422798774cf67bc263426a83" %} package: name: mehari From 72711f688e38400fc979b4b195e5fa4205791a93 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 14:17:48 -0600 Subject: [PATCH 0380/2173] Update pxblat to 0.3.6 (#43827) * Update pxblat to 0.3.5 * Update pxblat to 0.3.6 --- recipes/pxblat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index c1b7d1b9467db..fb077b8cf6926 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "0.3.4" %} -{% set sha256 = "59ff417a0ee2e6760cb96d653ffbff2d8d76e5f0e498b2a3915bfc578b276f06" %} +{% set version = "0.3.6" %} +{% set sha256 = "d83a1dc414789f7da59d1bf490d20f6544c7ddaa41df5da6d751cc8189c94b2f" %} package: name: {{ name|lower }} From be4082f7bcbaa4218e667eba0b1f66d2976f0d30 Mon Sep 17 00:00:00 2001 From: Andrew Smith Date: Mon, 23 Oct 2023 14:46:46 -0700 Subject: [PATCH 0381/2173] Update dnmtools: new version 1.4.2 (#43833) --- recipes/dnmtools/build.sh | 3 ++- recipes/dnmtools/meta.yaml | 6 +++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/dnmtools/build.sh b/recipes/dnmtools/build.sh index 9b16c20f01c71..dd8b881bae132 100644 --- a/recipes/dnmtools/build.sh +++ b/recipes/dnmtools/build.sh @@ -1,4 +1,5 @@ #!/bin/bash + ./configure --prefix=$PREFIX -make +make CXXFLAGS="-O3 -DNDEBUG -D_LIBCPP_DISABLE_AVAILABILITY" make install diff --git a/recipes/dnmtools/meta.yaml b/recipes/dnmtools/meta.yaml index 359c1b934654e..ed044213442b9 100644 --- a/recipes/dnmtools/meta.yaml +++ b/recipes/dnmtools/meta.yaml @@ -1,18 +1,18 @@ -{% set version = "1.3.0" %} +{% set version = "1.4.2" %} package: name: dnmtools version: {{ version }} build: - number: 1 + number: 0 run_exports: # dnmtools is currently not intended to be stable between minor versions (x.x). - {{ pin_subpackage('dnmtools', max_pin="x.x") }} source: url: https://github.com/smithlabcode/dnmtools/releases/download/v{{ version }}/dnmtools-{{ version }}.tar.gz - sha256: 8af29cb43f4eb42722bcdfdf39e37499f72733ab6e32514fcf65ace40badf9f2 + sha256: 0b712d4635a6924f0f230206b999db3d6e3a98b0d330640f3fd5cf4930eaf127 requirements: build: From 3424ba4a3d1175352d48d22a5ab017a6f94f417f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 16:04:21 -0600 Subject: [PATCH 0382/2173] Update dragonflye to 1.1.2 (#43835) * Update dragonflye to 1.1.2 * Update meta.yaml * add run_exports --------- Co-authored-by: Robert A. Petit III --- recipes/dragonflye/meta.yaml | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/recipes/dragonflye/meta.yaml b/recipes/dragonflye/meta.yaml index 6df5e41a4a32b..e69873f01afb6 100644 --- a/recipes/dragonflye/meta.yaml +++ b/recipes/dragonflye/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dragonflye" %} -{% set version = "1.1.1" %} +{% set version = "1.1.2" %} package: name: {{ name }} @@ -8,22 +8,24 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} source: url: https://github.com/rpetit3/{{ name }}/archive/v{{ version }}.tar.gz - sha256: bd2e5710d90e5472d5086c8bbff0f2ab77212d697ffd5de9361bfe07cb39fb4d + sha256: 0175f72233c2aa5b4f398fee8f1c17ae69ff04a17dd81ca5e105ec3b3fb4d0ab requirements: run: - - assembly-scan >=0.4.0 + - assembly-scan >=1.0.0 - any2fasta >=0.4.2 - bwa - fastp - flye >=2.9.2 - kmc >=3.1 - - medaka >=1.8.0 + - medaka >=1.11.0 - miniasm >=0.3_r179 - - nanoq >=0.8.1 + - nanoq >=0.10.0 - perl >=5.26 - perl-file-spec - perl-findbin @@ -31,12 +33,12 @@ requirements: - pilon - polypolish - porechop - - racon >=1.4.20 - - rasusa >=0.6 - - raven-assembler >=1.6.1 + - racon >=1.5.0 + - rasusa >=0.7.1 + - raven-assembler >=1.8.3 - samclip - samtools - - seqtk >=1.3 + - seqtk >=1.4 test: commands: From 17ba692556c0a7ef2704474e475bbe1748e0c437 Mon Sep 17 00:00:00 2001 From: LorenzoMerotto <91564922+LorenzoMerotto@users.noreply.github.com> Date: Tue, 24 Oct 2023 00:49:50 +0200 Subject: [PATCH 0383/2173] Add immucell ai (#43658) * Update of immunedeconv version * immunedeconv update packages * Update of DWLS recipe * Update DWLS name in omnideconv * Update of DWLS sha256 * Addition of immucellai_mouse * Removed a modified file from pull request * Small edits * Small edits * Add rnu_exports * Add rnu_exports * typo * build number * typo * Update recipes/r-immucellaimouse/meta.yaml Co-authored-by: Gregor Sturm --------- Co-authored-by: Merotto Co-authored-by: Gregor Sturm --- recipes/r-immucellaimouse/build.sh | 1 + recipes/r-immucellaimouse/meta.yaml | 52 +++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 recipes/r-immucellaimouse/build.sh create mode 100644 recipes/r-immucellaimouse/meta.yaml diff --git a/recipes/r-immucellaimouse/build.sh b/recipes/r-immucellaimouse/build.sh new file mode 100644 index 0000000000000..5bf492ab9fc06 --- /dev/null +++ b/recipes/r-immucellaimouse/build.sh @@ -0,0 +1 @@ +$R CMD INSTALL --build . diff --git a/recipes/r-immucellaimouse/meta.yaml b/recipes/r-immucellaimouse/meta.yaml new file mode 100644 index 0000000000000..26e04ad0e5e3d --- /dev/null +++ b/recipes/r-immucellaimouse/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.0" %} + +package: + name: r-immucellaimouse + version: {{ version }} + +source: + url: + https://github.com/lydiaMyr/ImmuCellAI-mouse/archive/refs/heads/main.zip + sha256: f83fb931ca2dc401d8d569f96620c709613934e4817ef12193b13f5cdf60d154 + +build: + run_exports: + - {{ pin_subpackage('r-immucellaimouse', max_pin="2") }} + number: 0 + noarch: generic + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-roxygen2 >=6.0.1 + - r-rcpp >=0.12.14 + - bioconductor-gsva + - r-dplyr + run: + - r-base + - r-rcpp >=0.12.14 + - bioconductor-gsva + - r-dplyr + - r-mass + +test: + commands: + - $R -e "library(ImmuCellAImouse)" + +about: + home: https://github.com/lydiaMyr/ImmuCellAI-mouse + license: GPL + summary: "ImmuCellAI-mouse is a tool to estimate the abundance of 36 immune cells based on gene expression profile from RNA-Seq or microarray data." + license_family: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + +extra: + recipe-maintainers: + - LorenzoMerotto + identifiers: + - doi:10.1093/bioinformatics/btab711 + container: + extended-base: true From cc611bf093ac46a6e911c0865a5787cf640b86fb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 17:08:06 -0600 Subject: [PATCH 0384/2173] Update genometools-genometools to 1.6.5 (#43834) --- recipes/genometools-genometools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genometools-genometools/meta.yaml b/recipes/genometools-genometools/meta.yaml index 9b54e670a7a02..dff4e1626ad6e 100644 --- a/recipes/genometools-genometools/meta.yaml +++ b/recipes/genometools-genometools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "genometools" %} -{% set version = "1.6.4" %} -{% set sha256 = "eda9cf3a5d63e5017f3c315c5700b0e308c08793d5795bc889350a536369a449" %} +{% set version = "1.6.5" %} +{% set sha256 = "f71b95c84761847223cd52a17d30ad9e6d55854448c2139fcd0aac437f73fbbe" %} package: name: {{ name }}-{{ name }} From d6309d59a2d1f0c783b843342cc06c9206352d98 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 23 Oct 2023 18:24:53 -0500 Subject: [PATCH 0385/2173] Add recipe for mavis-config v1.2.2 (#43832) --- recipes/mavis-config/meta.yaml | 37 ++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 recipes/mavis-config/meta.yaml diff --git a/recipes/mavis-config/meta.yaml b/recipes/mavis-config/meta.yaml new file mode 100644 index 0000000000000..2673b80300283 --- /dev/null +++ b/recipes/mavis-config/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "mavis-config" %} +{% set version = "1.2.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mavis_config-{{ version }}.tar.gz + sha256: b44e24d8b0ef2d406cdbc3e6c82bb6e6d26d1056d80c10bc5deda8b2b223a9e5 + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --use-pep517 + run_exports: + - {{ pin_subpackage('mavis-config', max_pin="x") }} + +requirements: + host: + - python >=3.7 + - pip + run: + - python >=3.7 + - snakemake-minimal >=7.18.1 + - braceexpand + +test: + imports: + - mavis_config + +about: + home: https://github.com/bcgsc/mavis_config.git + summary: Config validation for running MAVIS via Snakemake + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE From 7b8c93a5a779219656ff41887691584e1bd26393 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 23 Oct 2023 23:43:56 -0600 Subject: [PATCH 0386/2173] Update vg to 1.52.0 (#43831) --- recipes/vg/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml index ccd1584d543ad..c8e20fce3bf63 100644 --- a/recipes/vg/meta.yaml +++ b/recipes/vg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vg" %} -{% set version = "1.51.0" %} +{% set version = "1.52.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg - sha256: 4a6bf5f6a611648e6a90e70ad7289d39bff40f961af82e793f5da599663d3f0d + sha256: 07776b51aa6494b45982e4134eb84005ddc743e81c67e61fa52bff211d81777c build: number: 0 From fbdf917771bafd3e3f8fa427a08166d0f6ab63ee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 01:26:09 -0600 Subject: [PATCH 0387/2173] Update plassembler to 1.3.0 (#43838) --- recipes/plassembler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/plassembler/meta.yaml b/recipes/plassembler/meta.yaml index ef4d8b271a7ea..242a3302891e2 100644 --- a/recipes/plassembler/meta.yaml +++ b/recipes/plassembler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "plassembler" %} -{% set version = "1.2.0" %} +{% set version = "1.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: ae61880e66f096932e4748666cd99c6926d134c3b15e62d70154db4673ff8c88 + sha256: ec6b0e4056e170b71dfc281f70f331ff4538a8f4c61c09a10b1e77b4733d9499 build: number: 0 From 5c4b565bdc2bcd0752c07246e99ef273c6937291 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 01:30:45 -0600 Subject: [PATCH 0388/2173] Update melon to 0.1.0 (#43836) * Update melon to 0.1.0 * summary change from other pr --------- Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com> --- recipes/melon/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/melon/meta.yaml b/recipes/melon/meta.yaml index 056865f282278..ce8a8b5bd87cd 100644 --- a/recipes/melon/meta.yaml +++ b/recipes/melon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "melon" %} -{% set version = "0.0.1" %} +{% set version = "0.1.0" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/xinehc/melon/archive/refs/tags/v{{ version }}.tar.gz - sha256: bcc9c78a2321be2e84c97381fdbf737584aa3f1d2ff582ade0484b476c29ce24 + sha256: 4532d2a618e72adc235fde46945983cc7581f1917c8ceb82a1b65d6c1df9cc70 build: noarch: python @@ -38,8 +38,8 @@ about: home: https://github.com/xinehc/melon license: MIT license_family: MIT - summary: 'Melon: long-read targeting taxonomic profiling and genome copies estimation using phylogenetic marker genes' + summary: 'Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes' extra: recipe-maintainers: - - xinehc \ No newline at end of file + - xinehc From 95a868d16d74bf1803e927649b97e07d911832cd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 03:41:11 -0600 Subject: [PATCH 0389/2173] Update mehari to 0.15.1 (#43839) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 4046538d4e754..d6f628a2948a2 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.15.0" %} -{% set sha256 = "6f81bc682820139d859db26c2e4020284b6cae35422798774cf67bc263426a83" %} +{% set version = "0.15.1" %} +{% set sha256 = "07677b5af888207e3fd008be0ab606d0e83d4fd83ab3b72fbc10424ec74fe22d" %} package: name: mehari From 0c703351c52da2977560afd2c826be1b663303db Mon Sep 17 00:00:00 2001 From: Jonas Fuchs <78491186+jonas-fuchs@users.noreply.github.com> Date: Tue, 24 Oct 2023 11:41:44 +0200 Subject: [PATCH 0390/2173] Add virheat (#43841) * added licence and meta.yaml * finalized yaml * updated to version 0.5.3 --- recipes/virheat/LICENSE | 674 ++++++++++++++++++++++++++++++++++++++ recipes/virheat/meta.yaml | 48 +++ 2 files changed, 722 insertions(+) create mode 100644 recipes/virheat/LICENSE create mode 100644 recipes/virheat/meta.yaml diff --git a/recipes/virheat/LICENSE b/recipes/virheat/LICENSE new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/virheat/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/virheat/meta.yaml b/recipes/virheat/meta.yaml new file mode 100644 index 0000000000000..f522666804059 --- /dev/null +++ b/recipes/virheat/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "virheat" %} +{% set version = "0.5.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/virheat-{{ version }}.tar.gz + sha256: cd4a8f49e49a1f28fcb4e0c6ff574d15bd0f4f86066076a888723fa49c1f148e + +build: + entry_points: + - virheat = virheat.command:main + noarch: python + script: {{ PYTHON }} -m pip install . --no-deps -vvv + number: 0 + run_exports: + - {{ pin_subpackage('virheat', max_pin="x.x") }} + +requirements: + host: + - python >=3.9 + - pip + run: + - python >=3.9 + - matplotlib-base >=3.5.1,<=3.8.0 + - pandas >=1.4.4 + - numpy >=1.23.3 + +test: + imports: + - virheat + commands: + - pip check + - virheat --help + requires: + - pip + +about: + home: https://github.com/jonas-fuchs/virHEAT + summary: Visualize microbial evolution at the SNP level by creating a heatmap from vcf files. + license: GPL-3.0-or-later + license_file: LICENSE + +extra: + recipe-maintainers: + - jonas-fuchs From ac9b5e3b770f63a6c40aa99cffbbabf39815051a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 03:42:06 -0600 Subject: [PATCH 0391/2173] Update galaxy-files to 23.1.1 (#43829) --- recipes/galaxy-files/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml index ae647f8852cfb..047f835c6c4da 100644 --- a/recipes/galaxy-files/meta.yaml +++ b/recipes/galaxy-files/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.0.6" %} -{% set sha256 = "0636fb9e8acad5826a4538500d97b80b591a1ce322459023332072956679db0a" %} +{% set version = "23.1.1" %} +{% set sha256 = "830937bc1bf201da5c1c4e68981adf265ecbfad2cb1b8924349debe3523d5eab" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From cc7d4e02813f1a2157aa3c1c8d41815d07d54c28 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 04:23:08 -0600 Subject: [PATCH 0392/2173] Update galaxy-objectstore to 23.1.1 (#43830) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update galaxy-objectstore to 23.1.1 * remove six * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/galaxy-objectstore/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml index 4c0885af14ee7..2cf198441566b 100644 --- a/recipes/galaxy-objectstore/meta.yaml +++ b/recipes/galaxy-objectstore/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.0.6" %} -{% set sha256 = "8c749ac6d52297e3116949c5195071969b5d962cac14f4b84e7bd051ad8e2347" %} +{% set version = "23.1.1" %} +{% set sha256 = "1a4c5132944462b665b51af2539a07ec7e36bca9ea178de247204dece3d2c43a" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: @@ -25,8 +25,8 @@ requirements: run: - galaxy-util >={{ galaxy_version }} - pyyaml + - pydantic - python >=3.7 - - six >=1.9.0 test: imports: From 94ebd2900afb9e0e3428f80b4ab238851c70588d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matilda=20=C3=85slin?= Date: Tue, 24 Oct 2023 14:42:29 +0200 Subject: [PATCH 0393/2173] Update checkqc recipe (#43787) * Update requirements in checkqc recipe * checkqc: Bump build number * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/checkqc/meta.yaml | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/recipes/checkqc/meta.yaml b/recipes/checkqc/meta.yaml index fc9fb550cbfc4..4192646a5e34c 100644 --- a/recipes/checkqc/meta.yaml +++ b/recipes/checkqc/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 3aeb234d64aede3377f33b7573eb4719d7c665d68985e8713b16159a1be87988 build: - number: 0 + number: 1 noarch: python entry_points: - checkqc = checkQC.app:start @@ -22,16 +22,14 @@ build: requirements: host: - pip - - python >=3.6 + - python >=3.6,<3.11 run: - - click - - illumina-interop >=1.2.3 - - python >=3.6 - - pyyaml >=3.12 + - click >=8.1.1 + - PyYAML >=6.0 + - illumina-interop >=1.2.4 + - xmltodict >=0.13.0 + - tornado >=6.3.2 - sample-sheet >=0.13.0 - - tornado - - xmltodict - test: imports: - checkQC From 871f7a08b9d7d3f71afe60e0f80c3875b85c7094 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 06:43:43 -0600 Subject: [PATCH 0394/2173] Update pxblat to 0.3.10 (#43843) --- recipes/pxblat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index fb077b8cf6926..df5119dc2415a 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "0.3.6" %} -{% set sha256 = "d83a1dc414789f7da59d1bf490d20f6544c7ddaa41df5da6d751cc8189c94b2f" %} +{% set version = "0.3.10" %} +{% set sha256 = "a3ff4c8684ef47a2d642a1c72f853b8722d601cc5f50bf38ce583b042a550a28" %} package: name: {{ name|lower }} From 59cf31540164e0ac70f94134946d4758bb9749c3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 06:47:39 -0600 Subject: [PATCH 0395/2173] Update syngap to 1.0.1 (#43844) --- recipes/syngap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/syngap/meta.yaml b/recipes/syngap/meta.yaml index e1144f23bfe1b..d42fdd65b596e 100644 --- a/recipes/syngap/meta.yaml +++ b/recipes/syngap/meta.yaml @@ -1,5 +1,5 @@ {% set name = "syngap" %} -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/yanyew/SynGAP/releases/download/v{{ version }}/{{ name }}_v{{ version }}.tar.gz - sha256: a2848c925d8df49872ba23f4e0afbc176ff1688b60b04ee3c5f318d41dcc6c69 + sha256: f76d8155989a7ae47270d73a085f219fad17816dc146fb65f2f00d5d79e5f76d build: number: 0 From 7b2e15e8f34562a56c63cb8ace04dca9fdee12d8 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Tue, 24 Oct 2023 12:48:01 +0000 Subject: [PATCH 0396/2173] added recipe for isospecpy (#43846) * added recipe for isospecpy * added cxx compiler to deps --- recipes/isospecpy/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/isospecpy/meta.yaml diff --git a/recipes/isospecpy/meta.yaml b/recipes/isospecpy/meta.yaml new file mode 100644 index 0000000000000..a40f7264077e9 --- /dev/null +++ b/recipes/isospecpy/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "isospecpy" %} +{% set version = "2.2.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/IsoSpecPy-{{ version }}.tar.gz + sha256: 5426cd5ff70835b9d6b54de60b8d7b850eb63758c7443378bcb6d84601a69075 + +build: + script: {{ PYTHON }} -m pip install . -vv + number: 0 + run_exports: + - {{ pin_subpackage('isospecpy', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - python + - cffi + - pip + run: + - python + - cffi + +test: + imports: + - IsoSpecPy + commands: + - pip check + requires: + - pip + +about: + home: http://matteolacki.github.io/IsoSpec/ + summary: Python interface to IsoSpec++ isotopic envelope calculator library + license: BSD-3-Clause + license_file: debian/copyright + +extra: + recipe-maintainers: + - hechth From 8ba0c6e57d208a4a06318201ad2969ae4d5bc6c4 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Tue, 24 Oct 2023 14:48:15 +0200 Subject: [PATCH 0397/2173] Update pyopenms 3.1.0 (#43799) * Update pyopenms 3.1.0 * Update meta.yaml * Update meta.yaml * increase number of modules * Update build.sh * Update recipes/pyopenms/meta.yaml --- recipes/pyopenms/build.sh | 1 + recipes/pyopenms/meta.yaml | 10 ++++++---- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/pyopenms/build.sh b/recipes/pyopenms/build.sh index eb9c7eabe6927..870b51159778a 100644 --- a/recipes/pyopenms/build.sh +++ b/recipes/pyopenms/build.sh @@ -37,6 +37,7 @@ cmake ../src/pyOpenMS \ -DCMAKE_BUILD_WITH_INSTALL_NAME_DIR=ON \ -DPython_EXECUTABLE=$PYTHON \ -DPython_FIND_STRATEGY="LOCATION" \ + -DPY_NUM_MODULES=20 \ -DNO_DEPENDENCIES=ON \ -DNO_SHARE=ON diff --git a/recipes/pyopenms/meta.yaml b/recipes/pyopenms/meta.yaml index e05cc5c183bab..a3376b5a32f13 100644 --- a/recipes/pyopenms/meta.yaml +++ b/recipes/pyopenms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyopenms" %} -{% set version = "3.0.0" %} +{% set version = "3.1.0" %} # if ends with 'dev' it is considered a development release and pulled from GitHub package: name: {{ name|lower }} version: {{ version }} @@ -11,13 +11,15 @@ source: git_depth: 1 # (Defaults to -1/not shallow) {% else %} source: - url: https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/{{ version }}/OpenMS-{{ version }}-src.tar.gz - md5: 2b7ee0f4d8f42eb3c17384347df2dba4 + url: https://github.com/OpenMS/OpenMS/releases/download/Release{{ version }}/OpenMS-{{ version }}-src.tar.gz + md5: 6a60ef1a95c7ce915cc3a02e5bccd593 {% endif %} build: - skip: True # [py2k] + skip: True # [py2k or osx] number: 0 + run_exports: + - {{ pin_subpackage("pyopenms", max_pin="x.x") }} requirements: build: From 8d884b285800c856c63dc6e44c957a2ae1b48fbc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 06:54:57 -0600 Subject: [PATCH 0398/2173] Update annonars to 0.24.4 (#43818) * Update annonars to 0.24.3 * Update annonars to 0.24.4 --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index bf93462d3c7a3..e96c168424543 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.24.2" %} +{% set version = "0.24.4" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: c6bd5a0d1a49a337c24c0185390c081040fa136690fe16f7d9c7c30dbbcdf8f5 + sha256: 274c145712d467655ec29a377cd8514d6f2254a38c797baa9e2cc820a267db7d requirements: build: From 6efc2a15b028dae9a3ea6d0aab413028ea64facf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 08:45:10 -0600 Subject: [PATCH 0399/2173] Update ena-webin-cli to 6.7.0 (#43847) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index f0e3c950f8f47..087acc08ec287 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.6.0" %} -{% set sha256 = "4ea1aa1b5a79052cff9628004b85689caf59556cb70a814e12f217972e13058d" %} +{% set version = "6.7.0" %} +{% set sha256 = "dd8f3c7de02b5bebd392a4370d54eceeb5893dfa9beb4363a30c2fbd605aaba8" %} package: name: ena-webin-cli From 099ae00b5a2e283726c30f3389899806affdbf58 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 24 Oct 2023 18:35:45 +0200 Subject: [PATCH 0400/2173] add gawk as run-time dep to MAFFT (#43850) MAFFT uses awk to parse some command line options and performs complex enough operations that this matters. --- recipes/mafft/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/mafft/meta.yaml b/recipes/mafft/meta.yaml index 4464adcdccfad..132c40b37520a 100644 --- a/recipes/mafft/meta.yaml +++ b/recipes/mafft/meta.yaml @@ -11,14 +11,17 @@ source: sha256: "986042f7eb9d5aba237b7b9701974e20b6952cb7d585c66fd979137ed4a34c9b" build: - number: 2 -# skip: True # [osx] + number: 3 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: - make - {{ compiler('c') }} - {{ compiler('go-cgo') }} + run: + - gawk test: commands: From 9581038e91d3edb687b6ec9323219fa6490563ce Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 10:52:39 -0600 Subject: [PATCH 0401/2173] Update snakemake-interface-executor-plugins to 7.0.2 (#43848) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index 661b0777ce7e4..a850b2bae0c1d 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "7.0.1" %} +{% set version = "7.0.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: 40bbf9e562e20fc3eaa241ac1927e613fc52c22d9453c922a165c7ab2092cbd8 + sha256: bdd3c6ed98deeeef25f4abdc3fd68abd2a80edc276cc4c5dc3291890c1428030 build: noarch: python From fa737b1953c80d2123e6fe8f3cacfef212d9e80b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 11:06:40 -0600 Subject: [PATCH 0402/2173] Update piranha-polio to 1.1.1 (#43855) * Update piranha-polio to 1.1.1 * add entry_points --------- Co-authored-by: joshuazhuang7 --- recipes/piranha-polio/meta.yaml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/piranha-polio/meta.yaml b/recipes/piranha-polio/meta.yaml index 94c7f80c937ed..5e922acbfc0d1 100644 --- a/recipes/piranha-polio/meta.yaml +++ b/recipes/piranha-polio/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1" %} +{% set version = "1.1.1" %} package: name: piranha-polio @@ -6,14 +6,16 @@ package: source: url: https://github.com/polio-nanopore/piranha/archive/refs/tags/{{ version }}.tar.gz - sha256: 9fb5c04786c9f05bcb362e9d7073e95d51b3e00d0c49558a7b9fa7d52cf55622 + sha256: 239436a13de359e04bb4aecaa54d0e8b2cb957873f75efe61201c4f3ab648e0e build: number: 0 noarch: python - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv + entry_points: + - piranha = piranha.command:main run_exports: - - {{ pin_subpackage("piranha-polio", max_pin="x.x") }} + - {{ pin_subpackage("piranha-polio", max_pin="x") }} requirements: host: @@ -27,6 +29,7 @@ requirements: - mako >=1.2 - medaka >=1.7.1 - minimap2 >=2.17 + - numpy <=1.23.5 - pandas - pysam - python <3.10 @@ -43,5 +46,6 @@ test: about: home: https://github.com/polio-nanopore/piranha license: GPL-3.0-only + license_family: GPL3 license_file: LICENSE summary: Poliovirus Investigation Resource Automating Nanopore Haplotype Analysis From 926e1d921b85fb1afbd577972745d516d23678c7 Mon Sep 17 00:00:00 2001 From: Florian De Temmerman <69114541+fbdtemme@users.noreply.github.com> Date: Tue, 24 Oct 2023 19:10:19 +0200 Subject: [PATCH 0403/2173] update pixelator to 0.15.2 (#43851) --- recipes/pixelator/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pixelator/meta.yaml b/recipes/pixelator/meta.yaml index 1c5af2c8c9cc6..d92a24e509c76 100644 --- a/recipes/pixelator/meta.yaml +++ b/recipes/pixelator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pixelator" %} -{% set version = "0.15.0" %} +{% set version = "0.15.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/pixelgentechnologies/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 78ffabc98868679773b3a17f4dee7da9413f76353c253973108dbc72dafb4203 + sha256: 2b41e14fba232691513e4f16eb215deca8e21694ebb9ad676968d320645212d4 build: noarch: python From 7a94f9bbf7f9518510c65536dcec534f7d0de78c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 11:13:42 -0600 Subject: [PATCH 0404/2173] Update medaka to 1.11.1 (#43852) * Update medaka to 1.11.1 * Update meta.yaml * add wurlitzer --------- Co-authored-by: Chris Wright Co-authored-by: joshuazhuang7 --- recipes/medaka/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index d572bdf270026..96f01ac731ff9 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -1,6 +1,6 @@ {% set name = "Medaka" %} -{% set version = "1.11.0" %} -{% set sha256 = "a763d3eb35a3fcee97012ac92357f7ff9cefe3bf7511020152bd2bb1faeb4b1d" %} +{% set version = "1.11.1" %} +{% set sha256 = "4440762a17ddd66806ddbd7c3218140caa234b96a8c919ed54d7243d3e4a5dd1" %} # Bot PRs - Always review requirements.txt for new release package: @@ -62,6 +62,7 @@ requirements: - htslib >=1.14 - libcurl - openssl + - wurlitzer test: imports: @@ -81,8 +82,6 @@ about: dev_url: https://github.com/nanoporetech/medaka extra: - recipe-maintainers: - - cjw85 identifiers: - usegalaxy-eu:medaka_consensus - biotools:medaka From ad1e50e5a0a413b1e2169cbf81d10ab49c5d4381 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Tue, 24 Oct 2023 10:21:30 -0700 Subject: [PATCH 0405/2173] Add pyrodigal-gv (#43121) * Add pyrodigal-gv * Make recipe noarch * Remove the recipe-maintainers section * Use import test * retrigger ci * debugging * Modify build script * Update meta.yaml with a workaround hack fix * Update meta.yaml revert * Update pyrodigal-gv test * Fix test command * Add import test again * Update meta.yaml to v0.2.0 Fingers crossed * Bump `pyrodigal` requirement to v3.1 * use SPDX license identifier --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Robert A. Petit III Co-authored-by: George Bouras <84495559+gbouras13@users.noreply.github.com> Co-authored-by: Mateus Bernabe Fiamenghi <35854519+Matt-BF@users.noreply.github.com> --- recipes/pyrodigal-gv/meta.yaml | 43 ++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 recipes/pyrodigal-gv/meta.yaml diff --git a/recipes/pyrodigal-gv/meta.yaml b/recipes/pyrodigal-gv/meta.yaml new file mode 100644 index 0000000000000..2423c6bb8e5b3 --- /dev/null +++ b/recipes/pyrodigal-gv/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "pyrodigal-gv" %} +{% set version = "0.2.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pyrodigal_gv-{{ version }}.tar.gz + sha256: 8dc78704ba2021534e4a3f880063760450f12f2f4393835587d3fe4b0982851d + +build: + script: {{ PYTHON }} -m pip install . --ignore-installed --use-pep517 --no-deps -vvv + noarch: python + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + host: + - python + - setuptools >=46.4 + - wheel >=0.23 + - packaging >=19.1 + - pycparser + - pip + run: + - python + - pyrodigal >=3.1,<4 + - importlib-resources # [py<39] + +test: + imports: + - pyrodigal_gv + commands: + - python -m unittest -vv pyrodigal_gv.tests + +about: + home: https://github.com/althonos/pyrodigal-gv + summary: A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code. + license: GPL-3.0-or-later + license_family: GPL3 + license_file: COPYING From 69559d9db51c802ad8ccfcaaf6945e0156333cc3 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 24 Oct 2023 13:24:25 -0500 Subject: [PATCH 0406/2173] Update table2asn to 2023-10-05 (#43854) --- recipes/table2asn/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/table2asn/meta.yaml b/recipes/table2asn/meta.yaml index 35fb2ad798c9e..309a04dc74f0f 100644 --- a/recipes/table2asn/meta.yaml +++ b/recipes/table2asn/meta.yaml @@ -1,7 +1,7 @@ {% set name = "table2asn" %} -{% set version = "1.0.883" %} -{% set sha256 = "56f47a5cf69d93955b7ee32e6e3de82aa34d35c84644a0fc2d160c743d084417" %} -{% set release_date = "2023-07-13" %} +{% set version = "1.28.943" %} +{% set sha256 = "91632c6442986d5af455421ed8121647f9bd90e64560ba27ae0b2ab0a1289ae6" %} +{% set release_date = "2023-10-05" %} package: name: {{ name }} @@ -10,12 +10,14 @@ package: source: - url: https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/{{ release_date }}/by_program/{{ name }}/mac.{{ name }}.gz # [osx] - sha256: daad04b14e088af7c69df606e2de859e83e4d3f35689642270e869c98da062cc # [osx] + sha256: 3ecc9fc29beb69640d47cd49a43b342ee6d7627f25c7b2d78dd44fce00cd2c6d # [osx] - url: https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/{{ release_date }}/by_program/{{ name }}/linux64.{{ name }}.gz # [linux] sha256: {{ sha256 }} # [linux] build: number: 0 + run_exports: + - {{ pin_subpackage('table2asn', max_pin="x.x") }} requirements: host: From bc17362595b6623aa416198c86f1f68d41be5878 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 12:30:45 -0600 Subject: [PATCH 0407/2173] Update synapseclient to 3.1.0 (#43857) --- recipes/synapseclient/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/synapseclient/meta.yaml b/recipes/synapseclient/meta.yaml index 79ac91335d42f..fae9585940309 100644 --- a/recipes/synapseclient/meta.yaml +++ b/recipes/synapseclient/meta.yaml @@ -1,5 +1,5 @@ {% set name = "synapseclient" %} -{% set version="3.0.0" %} +{% set version="3.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/synapseclient-{{ version }}.tar.gz - sha256: 788289dc42a51a974efda747b75c634b6a6b38c089a4263affb8ca4ed75a0d04 + sha256: ec05a8792a5e5e332211426fb12a2929d6c14179746304b4f37acbb19f89bff3 build: noarch: python From 838a0a2db09e44a23b011213bedec49eb02768d5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 12:31:10 -0600 Subject: [PATCH 0408/2173] Update taxmyphage to 0.1.5 (#43853) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index d2acad12c11ae..0ac68fbb119ef 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.1.4" %} +{% set version = "0.1.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: 09dc32220e190a3404df5e5dda0082df3641479a510094bbed3b5c935b1f2b6a + sha256: 48b85651ab0692eb935ed82fa546358e54eddbd30a97b15850eb5af87b041373 build: entry_points: From c2fa9685c3a5ada3d1ad25cf7dbdd418238d358a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 12:43:44 -0600 Subject: [PATCH 0409/2173] Update pharokka to 1.5.0 (#43183) * Update pharokka to 1.5.0 * Update meta.yaml update pyrodigal and dnaapler to support pyrodigal v3 * Update meta.yaml * pip arguments for `pyrodigal-gv` * Update meta.yaml to get `pyrodigal-gv` to work x2 * Update meta.yaml * Update meta.yaml with `prodigal_gv` manually in build script * Update meta.yaml spell `pyrodigal-gv` properly * edit dependencies --------- Co-authored-by: George Bouras <84495559+gbouras13@users.noreply.github.com> Co-authored-by: joshuazhuang7 --- recipes/pharokka/meta.yaml | 51 ++++++++++++++++++++++---------------- 1 file changed, 30 insertions(+), 21 deletions(-) diff --git a/recipes/pharokka/meta.yaml b/recipes/pharokka/meta.yaml index 5249f49815287..f6e34449cfafe 100644 --- a/recipes/pharokka/meta.yaml +++ b/recipes/pharokka/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.5.0" %} {% set name = "pharokka" %} -{% set sha256 = "6184c11ddf83f38388d3aff6c39ac3a2bc8e8385bb9da41d04392f049319a20a" %} +{% set sha256 = "afb5d8ac68f1d1d48b0280096018c3c31eb6c4ed07d0a5ee78e7ff19c651a5da" %} {% set user = "gbouras13" %} package: @@ -10,7 +10,7 @@ package: build: number: 0 noarch: python - script: python -m pip install --no-deps --ignore-installed . + script: "{{ PYTHON }} -m pip install . --no-build-isolation --use-pep517 --no-deps -vvv" run_exports: - {{ pin_subpackage('pharokka', max_pin='x') }} @@ -19,24 +19,32 @@ source: sha256: {{ sha256 }} requirements: - host: - - python - - pip - run: - - bcbio-gff >=0.7.0 - - biopython >=1.78 - - phanotate >=1.5.0 - - mmseqs2 ==13.45111 - - trnascan-se >=2.0.9 - - minced >=0.4.2 - - aragorn >=1.2.41 - - mash >=2.2 - - dnaapler >=0.3.0 - - pyrodigal >=2.0.1 - - pycirclize >=0.3.1 - - alive-progress >=3.0.1 - - requests >=2.25.1 - - pyhmmer >=0.10.0 + host: + - python >=3.5 + - pip + run: + - python >=3.5 + - bcbio-gff >=0.7.0 + - biopython >=1.78 + - phanotate >=1.5.0 + - mmseqs2 ==13.45111 + - trnascan-se >=2.0.9 + - minced >=0.4.2 + - aragorn >=1.2.41 + - mash >=2.2 + - dnaapler >=0.3.2 + - pyrodigal >=3.0.0 + - pyrodigal-gv >=0.2.0 + - pycirclize >=0.3.1 + - alive-progress >=3.0.1 + - requests >=2.25.1 + - pyhmmer >=0.10.0 + - loguru >=0.5.4 + - pyyaml >=6.0 + - black >=22.3.0 + - isort >=5.10.1 + - pytest >=6.2.5 + - pytest-cov >=3.0.0 test: commands: @@ -47,6 +55,7 @@ test: about: home: https://github.com/gbouras13/pharokka license: MIT + license_family: MIT license_file: LICENSE summary: "Fast Phage Annotation Program" dev_url: https://github.com/gbouras13/pharokka From 1639a5c492428feadddbfadaed09436f9bd2cd78 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 13:04:41 -0600 Subject: [PATCH 0410/2173] Update pybiolib to 1.1.1437 (#43858) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index e38bdd87898b0..b0dd9b3a57269 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1423" %} +{% set version = "1.1.1437" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 1701e2974cd742fb8c40ee604c6312bc46767489c4cab3644d2853bf1872d6ac + sha256: 2a8ccace6636cd1a5e800e64e0943ee74cf634cda4cb288d4ea0c538efa01dac build: noarch: python From 041e09e91443ee70f325c219c5fa044632c9919f Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 24 Oct 2023 21:32:49 +0200 Subject: [PATCH 0411/2173] Update tower-cli to 0.9.0 (#43849) * Update tower-cli to 0.9.0 * add run_exports --------- Co-authored-by: Thanh Lee --- recipes/tower-cli/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/tower-cli/meta.yaml b/recipes/tower-cli/meta.yaml index c71734e7ab615..ac215c84eab25 100644 --- a/recipes/tower-cli/meta.yaml +++ b/recipes/tower-cli/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.0" %} +{% set version = "0.9.0" %} package: name: tower-cli @@ -6,13 +6,15 @@ package: build: number: 0 - + run_exports: + - {{ pin_subpackage("tower-cli", max_pin="x.x") }} + source: - url: https://github.com/seqeralabs/tower-cli/releases/download/v{{ version }}/tw-linux-x86_64 # [linux] - sha256: c0d08bbf3059296e4819d33c6ff9282cfdd4d97087213c2d9aa0b5943ced60f4 # [linux] + sha256: 55217d07e4615e12a46bb3d86057975113636c26f3f9ee57f5d79290d3c1606d # [linux] fn: tw # [linux] - url: https://github.com/seqeralabs/tower-cli/releases/download/v{{ version }}/tw-osx-x86_64 # [osx] - sha256: c32f9ad48a1a49f1aa62a496b253f24423ae361c1309740f22c429de7e9cc75a # [osx] + sha256: f809859e3de7e384ed42874d331e3a2c518292e4d6e2554054ec3c72649c808e # [osx] fn: tw # [osx] - url: https://github.com/seqeralabs/tower-cli/releases/download/{{ version }}/tw-windows-x86_64.exe # [win] sha256: 97c6aed555e1450bb5e32e0e031fe7416caec271925a64f48a4a14b420b3e457 # [win] @@ -30,4 +32,4 @@ about: extra: skip-lints: - should_be_noarch_generic - - should_not_use_fn \ No newline at end of file + - should_not_use_fn From 30e433a043427533ff95073428868b1ddde84ec4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 14:04:21 -0600 Subject: [PATCH 0412/2173] Update mashtree to 1.4.6 (#43859) --- recipes/mashtree/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mashtree/meta.yaml b/recipes/mashtree/meta.yaml index 14c878f1244e3..9352dab3ebbcd 100644 --- a/recipes/mashtree/meta.yaml +++ b/recipes/mashtree/meta.yaml @@ -1,6 +1,6 @@ {% set name = "mashtree" %} -{% set version = "1.4.5" %} -{% set hash = "37c76d11caabf80de2c478088741a1da30bf39a0658495e03fac629e7656dacd" %} +{% set version = "1.4.6" %} +{% set hash = "1bd427aba025886d9df99c95f685e06dc2226bca080a64a9cb9d341b5a3d6dac" %} package: name: {{ name|lower }} From 4b12b1ce80315c74b65c46d7b1016a99285aa95d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 16:27:28 -0600 Subject: [PATCH 0413/2173] Update callingcardstools to 1.1.0 (#43862) * Update callingcardstools to 1.1.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/callingcardstools/meta.yaml | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/recipes/callingcardstools/meta.yaml b/recipes/callingcardstools/meta.yaml index 5efa9d40f727b..d8fa5121c9729 100644 --- a/recipes/callingcardstools/meta.yaml +++ b/recipes/callingcardstools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "callingcardstools" %} -{% set version = "1.0.0" %} +{% set version = "1.1.0" %} package: name: "{{ name|lower }}" @@ -7,33 +7,29 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 74a20d1eb22f7bdf3373e70e57737caefe4ea63f115e975dba6c04be814288fd + sha256: 57df18119165ac1b38d90a318a2950aeb9b549069b93af13b7942f3800459569 build: noarch: python - number: 1 + number: 0 entry_points: - callingcardstools = callingcardstools:__main__.main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('callingcardstools', max_pin="x") }} requirements: host: - - biopython - - edlib >=1.3.9 - - numpy - - pandas - pip - - pysam - - poetry - - python >=3.9 + - poetry-core + - python >=3.8 run: - biopython - - edlib >=1.3.9 + - python-edlib >=1.3.9 - numpy - pandas - pysam - - poetry - - python >=3.9 + - python >=3.8 test: imports: From 057d4d17eeda75bc654724fd149851696860b27a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 24 Oct 2023 20:52:09 -0600 Subject: [PATCH 0414/2173] Update simpleaf to 0.15.0 (#43869) * Update simpleaf to 0.15.0 * Update meta.yaml add required run_exports * Update meta.yaml * Update build.sh Require we use the Cargo.lock file * Update build.sh --------- Co-authored-by: Rob Patro --- recipes/simpleaf/build.sh | 2 +- recipes/simpleaf/meta.yaml | 10 ++++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/simpleaf/build.sh b/recipes/simpleaf/build.sh index be24ecc64d3c6..05c57b630a9d8 100644 --- a/recipes/simpleaf/build.sh +++ b/recipes/simpleaf/build.sh @@ -7,4 +7,4 @@ export CXXFLAGS="${CFLAGS} -fcommon" export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" # build statically linked binary with Rust -RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . +RUST_BACKTRACE=1 cargo install --locked --verbose --root $PREFIX --path . diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index c9348e6543f68..5cb64d040e725 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.14.1" %} +{% set version = "0.15.0" %} package: name: simpleaf @@ -6,15 +6,17 @@ package: build: number: 0 + run_exports: + - {{ pin_subpackage("simpleaf", max_pin="x.x") }} # script: cargo install --path . --root ${PREFIX} source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: 82b8c6210ffc668bd97abefa316705416ae0e511fba2fdd103fafc74a0e32f16 + sha256: 10273eb0512983226eba9fdf8ead4aacf26bd1c46b1a69abc265a821cd9b100d requirements: build: - - rust >=1.66 + - rust >=1.73 - autoconf - make - {{ compiler('cxx') }} @@ -22,7 +24,7 @@ requirements: host: run: - alevin-fry >=0.8.1 - - salmon >=1.10.0 + - salmon >=1.10.1 test: commands: From 6ab48991d34f04e5dbf1c243ba79bfe2b067922c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 03:30:16 -0600 Subject: [PATCH 0415/2173] Update taxmyphage to 0.1.9 (#43874) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index 0ac68fbb119ef..2806cd8a3c398 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.1.5" %} +{% set version = "0.1.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: 48b85651ab0692eb935ed82fa546358e54eddbd30a97b15850eb5af87b041373 + sha256: 631a1557cd4ca134668d05bca689dc8ab2eb893e2a04d38f94b30813dede2c93 build: entry_points: From 5b412588c5076402bd2bbc4f1a0f9eba95174660 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 03:33:34 -0600 Subject: [PATCH 0416/2173] Update dnaapler to 0.4.0 (#43873) --- recipes/dnaapler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnaapler/meta.yaml b/recipes/dnaapler/meta.yaml index cb8e2c610f86a..029be166a23d9 100644 --- a/recipes/dnaapler/meta.yaml +++ b/recipes/dnaapler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dnaapler" %} -{% set version = "0.3.2" %} +{% set version = "0.4.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: cd4f5f6c83bed6f59dc4b54c8291f2c877ba6de1457e16dda1316d8ede9ccee1 + sha256: d6940a0fda068d67ee8c45353761188544b5504b6a7642d87775476d51918d9b build: number: 0 From 316197ff9d212bf13ed1a48f79c2214d2a7e2f8d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 03:53:10 -0600 Subject: [PATCH 0417/2173] Update pybiolib to 1.1.1467 (#43863) * Update pybiolib to 1.1.1445 * Update pybiolib to 1.1.1453 * Update pybiolib to 1.1.1455 * Update pybiolib to 1.1.1467 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index b0dd9b3a57269..27f009f1a4df6 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1437" %} +{% set version = "1.1.1467" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 2a8ccace6636cd1a5e800e64e0943ee74cf634cda4cb288d4ea0c538efa01dac + sha256: 508f10731db8a44e8458c0e64397badff8a068e2b73b518a722bafdbc8ee871f build: noarch: python From 4e7f34a4a58d40044ecf173c359ad732d13f7b81 Mon Sep 17 00:00:00 2001 From: Boas van der Putten <32385917+boasvdp@users.noreply.github.com> Date: Wed, 25 Oct 2023 14:09:24 +0200 Subject: [PATCH 0418/2173] Update auriclass recipe (#43875) * add build script * bump build number * move build/script from meta.yaml to build.sh * use curl instead of wget --- recipes/auriclass/build.sh | 12 ++++++++++++ recipes/auriclass/meta.yaml | 3 +-- 2 files changed, 13 insertions(+), 2 deletions(-) create mode 100644 recipes/auriclass/build.sh diff --git a/recipes/auriclass/build.sh b/recipes/auriclass/build.sh new file mode 100644 index 0000000000000..a2b39c5996f61 --- /dev/null +++ b/recipes/auriclass/build.sh @@ -0,0 +1,12 @@ +#!/bin/sh +set -eu + +$PYTHON -m pip install . --no-deps -vv + +curl --output "v${PKG_VERSION}.tar.gz" -L "https://github.com/RIVM-bioinformatics/auriclass/archive/v${PKG_VERSION}.tar.gz" + +tar zxvf "v${PKG_VERSION}.tar.gz" + +cp -r "auriclass-${PKG_VERSION}/data" "${PREFIX}/data" + +rm -rf "v${PKG_VERSION}.tar.gz" "auriclass-${PKG_VERSION}" diff --git a/recipes/auriclass/meta.yaml b/recipes/auriclass/meta.yaml index f095e4e7d4b8e..1bb590559688d 100644 --- a/recipes/auriclass/meta.yaml +++ b/recipes/auriclass/meta.yaml @@ -13,8 +13,7 @@ build: noarch: python entry_points: - auriclass = auriclass.main:main - script: {{ PYTHON }} -m pip install . --no-deps -vv - number: 0 + number: 1 run_exports: - {{ pin_subpackage('auriclass', max_pin='x.x') }} From 9cc362f8fa3ee761559b0829b5aed5b495333f66 Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Wed, 25 Oct 2023 08:11:46 -0400 Subject: [PATCH 0419/2173] profile_dists release 1.0.0 (#43866) * profile_dists release 1.0.0 * profile_dists release 1.0.0 with build req python3.8 * profile_dists release 1.0.0 with build req python3.8 * Update meta.yaml * profile_dists release 1.0.0 * profile_dists release 1.0.0 with correct numpy * profile_dists release 1.0.0 with correct numpy * profile_dists release 1.0.0 with correct numpy * profile_dists release 1.0.0 with correct numpy --------- Co-authored-by: Thanh Lee --- recipes/profile_dists/meta.yaml | 52 +++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/profile_dists/meta.yaml diff --git a/recipes/profile_dists/meta.yaml b/recipes/profile_dists/meta.yaml new file mode 100644 index 0000000000000..c3ad6afafffa7 --- /dev/null +++ b/recipes/profile_dists/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "profile_dists" %} +{% set version = "1.0.0" %} +{% set sha256 = "e0ebef9c8ee13eba957320209113a6e85ecae7ba59113d186a543b4ca0463d60" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/profile_dists-{{ version }}.tar.gz + sha256: {{ sha256 }} + + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage("profile_dists", max_pin="x.x") }} + script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vvv + entry_points: + - profile_dists=profile_dists.main:main + +requirements: + host: + - python + - pip + - pytest-runner + run: + - python >=3.8,<4 + - {{ pin_compatible('numpy') }} + - pyarrow >=12.0.0 + - fastparquet >=2023.4.0 + - numba + - pytables >=3.8.0 + - six >=1.16.0 + - pandas >=2.0.2 + - psutil + +test: + imports: + - profile_dists + commands: + - profile_dists -h + +about: + home: 'https://pypi.org/project/profile-dists' + summary: 'Profile Dists: Rapid calcualtion of allele profile distances and distance base querying' + license: Apache-2.0 + license_file: LICENSE + dev_url: 'https://github.com/phac-nml/profile_dists/' + + From f9daa2e50dbb63e9fec7d0a9e5a6b085e33389ec Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 08:52:27 -0600 Subject: [PATCH 0420/2173] Update assembly_finder to 0.3.3 (#43882) --- recipes/assembly_finder/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index 1e56d64487862..4b47a06f8097b 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "assembly_finder" %} -{% set version = "0.3.2" %} +{% set version = "0.3.3" %} package: name: "{{ name|lower }}" @@ -7,9 +7,9 @@ package: source: - url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9c6a59842c3e5bf19284dee0cec65e65cd61c897d6bf6127e2929088b051fbbc + sha256: 9aeec6ed2a58b7f701f1596ff7aa670ccd526d406da9273fb64a949b7b1ab866 build: - number: 1 + number: 0 entry_points: - assembly_finder = assembly_finder.assembly_finder:cli noarch: python From 943d8d6bcdd7cf028380179b54fb9de14c6bde64 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 08:53:15 -0600 Subject: [PATCH 0421/2173] Update r-goalie to 0.7.4 (#43881) --- recipes/r-goalie/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-goalie/meta.yaml b/recipes/r-goalie/meta.yaml index 178c2c800f2b4..9c8d72e1a74e8 100644 --- a/recipes/r-goalie/meta.yaml +++ b/recipes/r-goalie/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.3" %} +{% set version = "0.7.4" %} {% set github = "https://github.com/acidgenomics/r-goalie" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 5b3080a674c88a470a55e68b66916f1e0212493a4ceb2ff9125eeb45d4b7241d + sha256: e4a11a642893f8f4515720556e11d16ee35f2a95f83cb4fc95390a0e75e6bf0f build: number: 0 From 484cc3070a67f30b0e604f996a65cc58e16f141a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 08:53:53 -0600 Subject: [PATCH 0422/2173] Update auriclass to 0.5.3 (#43877) --- recipes/auriclass/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/auriclass/meta.yaml b/recipes/auriclass/meta.yaml index 1bb590559688d..6efebc43dc286 100644 --- a/recipes/auriclass/meta.yaml +++ b/recipes/auriclass/meta.yaml @@ -1,5 +1,5 @@ {% set name = "AuriClass" %} -{% set version = "0.5.2" %} +{% set version = "0.5.3" %} package: name: {{ name|lower }} @@ -7,13 +7,13 @@ package: source: url: https://github.com/RIVM-bioinformatics/auriclass/archive/v{{ version }}.tar.gz - sha256: 448569c7896aa27dd60628682db7c14aad29575cb0e92ae758f01c175865634b + sha256: 335395d64f8a4f40e47bb08bc114eb809c333f5680f9f14b46d75036f59a5ca3 build: noarch: python entry_points: - auriclass = auriclass.main:main - number: 1 + number: 0 run_exports: - {{ pin_subpackage('auriclass', max_pin='x.x') }} From e6bdc1dcfab38b4036eaba2fdff58812a43cd610 Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Wed, 25 Oct 2023 11:22:01 -0400 Subject: [PATCH 0423/2173] gas release v0.1.1 (#43876) * gas release v0.1.1 * gas release v0.1.1 --- recipes/genomic_address_service/meta.yaml | 51 +++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 recipes/genomic_address_service/meta.yaml diff --git a/recipes/genomic_address_service/meta.yaml b/recipes/genomic_address_service/meta.yaml new file mode 100644 index 0000000000000..75892e92cc52f --- /dev/null +++ b/recipes/genomic_address_service/meta.yaml @@ -0,0 +1,51 @@ +{% set name = "genomic_address_service" %} +{% set version = "0.1.1" %} +{% set sha256 = "5aa088e063190561f09c8d5f66f54af5a2c7561e2ad24eaf41055e56331b2954" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/genomic_address_service-{{ version }}.tar.gz + sha256: {{ sha256 }} + + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage("genomic_address_service", max_pin="x.x") }} + script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vvv + entry_points: + - gas=genomic_address_service.main:main + +requirements: + host: + - python + - pip + - pytest-runner + run: + - python >=3.8,<4 + - {{ pin_compatible('numpy') }} + - pyarrow >=12.0.0 + - fastparquet >=2023.4.0 + - numba + - pytables >=3.8.0 + - six >=1.16.0 + - pandas >=2.0.2 + +test: + imports: + - genomic_address_service + commands: + - gas -h + +about: + home: 'https://pypi.org/project/genomic-address-service' + summary: 'Genomic Address Service: De novo clustering and cluster address assignment' + license: Apache-2.0 + license_file: LICENSE + dev_url: 'https://github.com/phac-nml/genomic_address_service' + + From 6a0e352d2bb58ba5eef5fe46108d16d16379ebf8 Mon Sep 17 00:00:00 2001 From: Yangyang Li Date: Wed, 25 Oct 2023 13:11:48 -0500 Subject: [PATCH 0424/2173] Update License info for pxblat (#43856) * Update License info meta.yaml * Update meta.yaml --- recipes/pxblat/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index df5119dc2415a..8f486a9275c11 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [py < 39] script: {{ PYTHON }} -m pip install . --no-deps --use-pep517 -vvv run_exports: @@ -50,8 +50,7 @@ test: about: home: 'https://github.com/ylab-hi/pxblat' - license: MIT - license_family: MIT + license: OTHER license_file: LICENSE summary: "PxBLAT: An Efficient and Ergonomics Python Binding Library for BLAT." dev_url: 'https://pypi.org/project/pxblat/' From 2e5233c4c65f17deb118e33dceaf8e022c21b422 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 12:12:00 -0600 Subject: [PATCH 0425/2173] Update gndiff to 0.3.0 (#43864) --- recipes/gndiff/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gndiff/meta.yaml b/recipes/gndiff/meta.yaml index 26db301e0f13a..a87b5907e1781 100644 --- a/recipes/gndiff/meta.yaml +++ b/recipes/gndiff/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.1" %} -{% set sha256 = "c8b22048424584a633a4ebb1416ba4086b925b83eef994a92ac583d34bebb196" %} +{% set version = "0.3.0" %} +{% set sha256 = "a91176a7799f674ecbddfb8e7204b9ed81d1e599f11d5b45a8d6c269da04d1a8" %} package: name: "gndiff" From 5fc5b78858d94620eef5845329ba2f82e49d6270 Mon Sep 17 00:00:00 2001 From: Akihiro Kuno Date: Thu, 26 Oct 2023 03:12:22 +0900 Subject: [PATCH 0426/2173] Update DAJIN2 (#43865) --- recipes/dajin2/meta.yaml | 31 +++++++++++++++---------------- 1 file changed, 15 insertions(+), 16 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index 2ac840c7af6b9..8d5e06cf489f9 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,28 +1,27 @@ {% set name = "DAJIN2" %} -{% set version = "0.3.1" %} +{% set version = "0.3.2" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.tar.gz - sha256: e7f72e3039c7d8c217534b388e7e0967832983fe8eebca006e4e014372cf0805 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip + sha256: 712a5d35244943ff1ddcb3ffb06bb41b1cd4ba4c0753ad12a7f79eaac244f088 build: entry_points: - DAJIN2=DAJIN2.main:execute noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 run_exports: - - {{ pin_subpackage('dajin2', max_pin="x") }} + - {{ pin_subpackage('dajin2', max_pin="x.x") }} requirements: host: - python - pip - - setuptools run: - python ############################# @@ -35,21 +34,21 @@ requirements: - xz <5.3.0a0 - zlib <1.3.0a0 ############################# - - cstag ==0.4.1 - - flask >=2.2.0 - - jinja2 >=3.1.0 - - python-kaleido >=0.2.0 - - mappy >=2.24 - - midsv >=0.10.1 - numpy >=1.20.0 - - openpyxl >=3.0.0 + - scipy >=1.6.0 - pandas >=1.0.0 - - plotly >=5.0.0 + - openpyxl >=3.0.0 - rapidfuzz >=3.0.0 - - scikit-learn >=1.0.0 - - scipy >=1.6.0 - statsmodels >=0.13.5 + - scikit-learn >=1.0.0 + - mappy >=2.24 + - flask >=2.2.0 - waitress >=2.1.0 + - jinja2 >=3.1.0 + - plotly >=5.0.0 + - python-kaleido >=0.2.0 + - cstag >=0.4.1 + - midsv >=0.10.1 - wslpath >=0.3.0 test: From d937479a8d41f1f072aac87581184fef283d03c7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 14:14:15 -0600 Subject: [PATCH 0427/2173] Update npstructures to 0.2.13 (#43878) * Update npstructures to 0.2.13 * Update meta.yaml to pass lint * fix meta.yaml: variable `name` was missing --------- Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com> --- recipes/npstructures/meta.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/npstructures/meta.yaml b/recipes/npstructures/meta.yaml index 1fb0444528d9a..591ff746590ae 100644 --- a/recipes/npstructures/meta.yaml +++ b/recipes/npstructures/meta.yaml @@ -1,19 +1,20 @@ -{% set version = "0.2.12" %} - +{% set version = "0.2.13" %} +{% set name = "npstructures" %} package: - name: npstructures + name: {{ name }} version: {{ version }} source: - url: https://github.com/bionumpy/npstructures/archive/refs/tags/v{{ version }}.tar.gz - sha256: 7b61229a13a50a62465b68238cc5f1c5a87c20155c8a112e346de59f4946eb5d + url: https://github.com/bionumpy/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 3ae458ff31cc9afe1e845a8d15c36f1beca4f7c5de524aa845c99192425d7954 build: noarch: python number: 0 script: {{ PYTHON }} -m pip install . --no-deps -vv - + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: From 4ecc8473b63d819de0dca09ea89ce8b1db3d8361 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 14:45:09 -0600 Subject: [PATCH 0428/2173] Update psm-utils to 0.7.0 (#43886) * Update psm-utils to 0.6.1 * Update psm-utils to 0.7.0 --- recipes/psm-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index 052c9e1582c18..4d3452e76f701 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.6.0" %} -{% set sha256 = "2e4d43033b04ee3502d8f54417893d6b2f3b0967ff80bbc1c0f301ae2f8cac65" %} +{% set version = "0.7.0" %} +{% set sha256 = "c6d86813cc9c698a31fd7f458e73b1e2cb0e007a426603c8a82ea94c6f003080" %} package: name: {{ name|lower }} From edaa931a7e2c1adfb7e7ebe803e2ba45966c3103 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 14:45:30 -0600 Subject: [PATCH 0429/2173] Update fasten to 0.7.0 (#43887) --- recipes/fasten/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fasten/meta.yaml b/recipes/fasten/meta.yaml index 09c047247e57b..1d86a66586c1c 100644 --- a/recipes/fasten/meta.yaml +++ b/recipes/fasten/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6" %} -{% set sha256 = "677af7d67dba83695a3c11b096514d69439ed322c50d6315321885871c09bead" %} +{% set version = "0.7.0" %} +{% set sha256 = "017af4ff307a9b251a4a4248659b57f2f30dd9a08a89aab29fd0581aa4a47e7a" %} package: name: fasten From 644675ea19ba67128c96e5f31a6d889e27e78198 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 14:45:57 -0600 Subject: [PATCH 0430/2173] Update bionumpy to 0.2.27 (#43884) * Update bionumpy to 0.2.27 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/bionumpy/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index d88a923f79ee4..94b753eae7e19 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.26" %} +{% set version = "0.2.27" %} package: name: bionumpy @@ -6,13 +6,14 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: 8b3e332b86d301a0bc0d5228fab234147ff06c4709fcfb28d125bf010eb8d4ea + sha256: e5f981e3c0bdcef8306c3333e77249054e53f4108653142c6cf76d4a12a4c48e build: noarch: python number: 0 script: {{ PYTHON }} -m pip install . --no-deps -vv - + run_exports: + - {{ pin_subpackage("bionumpy", max_pin="x.x") }} requirements: host: From dc4b295c83e4e965e14062d5a3b7b4d173bb9689 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 14:46:24 -0600 Subject: [PATCH 0431/2173] Update physiofit to 3.3.0 (#43885) --- recipes/physiofit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/physiofit/meta.yaml b/recipes/physiofit/meta.yaml index 7e680d53051f0..319d30146fd90 100644 --- a/recipes/physiofit/meta.yaml +++ b/recipes/physiofit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "physiofit" %} -{% set version = "3.2.0" %} +{% set version = "3.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/physiofit-{{ version }}.tar.gz - sha256: 3b6257586da62c80ba33a5f302833da200f1d3a09c576139cc97a581c1b38132 + sha256: bf35004ab1d13b5a0f7ef8fca19c103271e79bb5ef5d54c81834895a7c411dbc build: entry_points: From 2b712a7128ddc56adbf0696bad65cffff89b0b6e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 14:49:53 -0600 Subject: [PATCH 0432/2173] Update microhapdb to 0.11 (#43888) --- recipes/microhapdb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/microhapdb/meta.yaml b/recipes/microhapdb/meta.yaml index b9cae1ccef513..166276f7667bc 100644 --- a/recipes/microhapdb/meta.yaml +++ b/recipes/microhapdb/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.10.1" %} -{% set sha256 = "cccc04ba440bc38dd8258c5c054ce60da80f6a37abce2cbe5247e47227743dba" %} +{% set version = "0.11" %} +{% set sha256 = "5cf7c52adb49682e62ac82fb65884203488f5ac4f82db730c29e378f8c7ec93c" %} package: name: microhapdb From a49fd0ea0298fd903c5196fde78ad8fa89626b66 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 17:01:46 -0600 Subject: [PATCH 0433/2173] Update callingcardstools to 1.2.0 (#43890) --- recipes/callingcardstools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/callingcardstools/meta.yaml b/recipes/callingcardstools/meta.yaml index d8fa5121c9729..cda0d39800ab3 100644 --- a/recipes/callingcardstools/meta.yaml +++ b/recipes/callingcardstools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "callingcardstools" %} -{% set version = "1.1.0" %} +{% set version = "1.2.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 57df18119165ac1b38d90a318a2950aeb9b549069b93af13b7942f3800459569 + sha256: 5a6b70800c91ed52c61edfd87b2fd773a660b77c01a81a554de1718146bfe7be build: noarch: python From 3a1a95a16e4c985c7d5be96337c3beef37254751 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 17:02:44 -0600 Subject: [PATCH 0434/2173] Update pxblat to 1.0.0 (#43891) --- recipes/pxblat/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index 8f486a9275c11..acc062e35af8c 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "0.3.10" %} -{% set sha256 = "a3ff4c8684ef47a2d642a1c72f853b8722d601cc5f50bf38ce583b042a550a28" %} +{% set version = "1.0.0" %} +{% set sha256 = "3a136da878464bfe68ab097731953ff13bae70db6eca2e5bd11a8c176bcff361" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 skip: True # [py < 39] script: {{ PYTHON }} -m pip install . --no-deps --use-pep517 -vvv run_exports: From 791aecce62c70fa0a88398596473fc1c67d06891 Mon Sep 17 00:00:00 2001 From: Julien Seiler Date: Thu, 26 Oct 2023 05:47:59 +0200 Subject: [PATCH 0435/2173] Update bismark 0.24.2 (#43880) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * update to bismark 0.24.2 * add missing run_exports statement * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/bismark/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/bismark/meta.yaml b/recipes/bismark/meta.yaml index 2a3a64310a32a..12da593691bcc 100644 --- a/recipes/bismark/meta.yaml +++ b/recipes/bismark/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.24.1" %} -{% set sha256 = "c5409f5fa470ea5ac07327ced28c60b793f5ef88c5a7bc75b71dde0f52f39894" %} +{% set version = "0.24.2" %} +{% set sha256 = "e86a5228f9bb63457e2aa713f67b462c63230517bed56df511fd372032acbe86" %} package: name: bismark @@ -8,13 +8,14 @@ package: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage("bismark", max_pin="x.x") }} source: - url: https://github.com/FelixKrueger/Bismark/archive/{{ version }}.tar.gz + url: https://github.com/FelixKrueger/Bismark/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: - build: run: - coreutils - perl From e0628590ded2e4d3e202536eae6683bbcf0ff445 Mon Sep 17 00:00:00 2001 From: farchaab <116543129+farchaab@users.noreply.github.com> Date: Thu, 26 Oct 2023 05:48:10 +0200 Subject: [PATCH 0436/2173] Update aspera-cli recipe (#43879) * Update meta.yaml removed dso whitelist and ignore run export * removed compiler * improved gem path install --- recipes/aspera-cli/build.sh | 19 ++++++++++--------- recipes/aspera-cli/meta.yaml | 18 ++++-------------- 2 files changed, 14 insertions(+), 23 deletions(-) diff --git a/recipes/aspera-cli/build.sh b/recipes/aspera-cli/build.sh index ce217e42e8955..37603d593282b 100644 --- a/recipes/aspera-cli/build.sh +++ b/recipes/aspera-cli/build.sh @@ -1,13 +1,14 @@ #!/usr/bin/env bash -gem_path=$PREFIX/${PKG_NAME}-${PKG_VERSION} -mkdir -p $gem_path -cp -r $SRC_DIR/* $gem_path -rm $gem_path/{conda_build,build_env_setup}.sh +set -o xtrace -o nounset -o pipefail -o errexit +export GEM_HOME=$PREFIX/share/rubygems +mkdir -p $GEM_HOME gem build aspera-cli.gemspec -gem install ${PKG_NAME}-${PKG_VERSION}.gem - +gem install --install-dir $GEM_HOME --bindir $GEM_HOME/bin ${PKG_NAME}-${PKG_VERSION}.gem +gem_path=$GEM_HOME/gems/${PKG_NAME}-${PKG_VERSION} +cp -r $SRC_DIR/* $gem_path +rm $gem_path/{conda_build,build_env_setup}.sh tail -n+3 bin/ascli > $gem_path/bin/ascli tail -n+3 bin/asession > $gem_path/bin/asession @@ -23,10 +24,10 @@ EOF echo "$(cat header.txt $gem_path/bin/ascli)" > $gem_path/bin/ascli echo "$(cat header.txt $gem_path/bin/asession)" > $gem_path/bin/asession -mv $gem_path $PREFIX/share/rubygems/gems -ln -s $PREFIX/share/rubygems/gems/${PKG_NAME}-${PKG_VERSION}/bin/* $PREFIX/bin + +ln -s $gem_path/bin/* $PREFIX/bin export ASCLI_HOME="$PREFIX/etc/aspera" ascli conf ascp install && ascli config ascp info cp $ASCLI_HOME/aspera-license . -ln -s $ASCLI_HOME/{ascp,aspera-license} $PREFIX/bin +ln -s $ASCLI_HOME/{ascp,aspera-license} $PREFIX/bin \ No newline at end of file diff --git a/recipes/aspera-cli/meta.yaml b/recipes/aspera-cli/meta.yaml index 2a69e661b65d4..1004a29c34209 100644 --- a/recipes/aspera-cli/meta.yaml +++ b/recipes/aspera-cli/meta.yaml @@ -11,26 +11,16 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('aspera-cli', max_pin="x") }} - missing_dso_whitelist: - - /lib64/ld-linux-x86-64.so.2 - - /lib64/libutil.so.1 - - /lib64/libpthread.so.0 - - /lib64/libc.so.6 - - /lib64/libdl.so.2 - - /lib64/librt.so.1 - - /lib64/libm.so.6 - ignore_run_exports: - - ruby requirements: build: - - ruby >=3 + - ruby >=3 + host: + - ruby >=3 run: - - libgcc-ng - - libstdcxx-ng - ruby >=3 test: From 67f2e43d6d9aec595cdbd74971993d3472759a74 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Thu, 26 Oct 2023 06:15:35 +0200 Subject: [PATCH 0437/2173] openms: remove pepnovo requirement (#43883) PepNovoAdapter has been deprecated in 3.1 --- recipes/openms-meta/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/openms-meta/meta.yaml b/recipes/openms-meta/meta.yaml index 98834890ba05b..b9142df48e67a 100644 --- a/recipes/openms-meta/meta.yaml +++ b/recipes/openms-meta/meta.yaml @@ -16,7 +16,7 @@ source: {% endif %} build: - number: 1 + number: 2 skip: True # [osx] # Try this when building with GUI @@ -146,7 +146,6 @@ outputs: - comet-ms ==2023010 - luciphor2 ==2020_04_03 - msgf_plus ==2023.01.1202 - - pepnovo ==20101117 - percolator ==3.5 - conda-forge::sirius-ms ==5.8.2 - thermorawfileparser ==1.4.3 From c5dd45caeea93197b5fb2f4c4f8f94b75aa83b5f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 22:27:35 -0600 Subject: [PATCH 0438/2173] Update solvebio to 2.25.0 (#43892) * Update solvebio to 2.25.0 * add entry_points --------- Co-authored-by: joshuazhuang7 --- recipes/solvebio/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/solvebio/meta.yaml b/recipes/solvebio/meta.yaml index 28b6cf19fd69e..5db0bbc3a8ebd 100644 --- a/recipes/solvebio/meta.yaml +++ b/recipes/solvebio/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.24.2" %} -{% set sha256 = "f3ba52bbb45c3cfc38bf186c9699c6ce1cbe3a5f56fc270794ffc854effc81f4" %} +{% set version = "2.25.0" %} +{% set sha256 = "0cbbdf281e1415385f91b8b2416681207945949ce709cd591505c29fb384fda7" %} package: name: solvebio @@ -14,7 +14,8 @@ build: number: 0 entry_points: - solvebio = solvebio.cli.main:main - script: python -m pip install --no-deps --ignore-installed --no-cache-dir . + - solvebio-recipes = recipes.sync_recipes:sync_recipes + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv run_exports: - {{ pin_subpackage("solvebio", max_pin="x.x") }} @@ -54,3 +55,4 @@ about: license_family: MIT license_file: LICENSE summary: The SolveBio Python client + doc_url: https://docs.solvebio.com/ From 3c24f4c4f3441da291ec601b601e1cf84e17b3d1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 25 Oct 2023 22:27:46 -0600 Subject: [PATCH 0439/2173] Update snakesv to 0.7 (#43889) * Update snakesv to 0.7 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/snakesv/build.sh | 2 +- recipes/snakesv/meta.yaml | 11 +++++++---- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/snakesv/build.sh b/recipes/snakesv/build.sh index 6dc9d68ab7c3f..4a480c4fc1177 100644 --- a/recipes/snakesv/build.sh +++ b/recipes/snakesv/build.sh @@ -4,7 +4,7 @@ mkdir -p $PREFIX/bin mkdir -p $PREFIX/opt/snakeSV/ # Full path to the Snakefile -sed -i "s|workflow/Snakefile|$PREFIX/opt/snakeSV/workflow/Snakefile|g" snakeSV +sed -i.bak "s|workflow/Snakefile|$PREFIX/opt/snakeSV/workflow/Snakefile|g" snakeSV cp -r * $PREFIX/opt/snakeSV/ ln -s $PREFIX/opt/snakeSV/snakeSV $PREFIX/bin/ diff --git a/recipes/snakesv/meta.yaml b/recipes/snakesv/meta.yaml index 47668a7ed7c9d..c44815b75d145 100644 --- a/recipes/snakesv/meta.yaml +++ b/recipes/snakesv/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakeSV" %} -{% set version = "0.6" %} +{% set version = "0.7" %} package: name: "{{ name|lower }}" @@ -7,15 +7,17 @@ package: source: url: https://github.com/RajLabMSSM/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 833c52a5acb4a167bd14a9f3e377b95f75e306583736b479d3a82b7a93849ebe + sha256: a9312b1992bb1eea9b824175f59b8d9bb3f9e773028ad98f31839d8a25b527a6 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('snakesv', max_pin="x.x") }} requirements: run: - - snakemake >=7.0.1 + - snakemake-minimal >=7.0.1 - mamba >=0.22.0 - pandas >=1.4.1 - bcftools >=1.15.1 @@ -26,6 +28,7 @@ test: about: home: https://github.com/RajLabMSSM/snakeSV/ - license: "The MIT License (MIT)" + license: MIT + license_family: MIT summary: "snakeSV: Flexible framework for large-scale SV discovery" From e2cd235e560fadacb2b3e4d51149d60277017307 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 02:06:41 -0600 Subject: [PATCH 0440/2173] Update sage-proteomics to 0.14.4 (#43893) --- recipes/sage-proteomics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sage-proteomics/meta.yaml b/recipes/sage-proteomics/meta.yaml index 12f6a50cdd1ef..a06ea0fb9ea15 100644 --- a/recipes/sage-proteomics/meta.yaml +++ b/recipes/sage-proteomics/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sage-proteomics" %} -{% set version = "0.14.3" %} -{% set sha256 = "1d4f7f8aceb558ae4b37a6b09296f7406d4b28f2d7b70fc6d89401d9a9c3aed7" %} +{% set version = "0.14.4" %} +{% set sha256 = "a527dce4892cf5b2fb85b56c54b5213e4b25d1ca8864f270eed47f5f223b4e6f" %} package: name: {{ name }} From 7149de38dd794fc57007f3cba430725cb6881d9c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 02:06:57 -0600 Subject: [PATCH 0441/2173] Update pharokka to 1.5.1 (#43895) --- recipes/pharokka/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/pharokka/meta.yaml b/recipes/pharokka/meta.yaml index f6e34449cfafe..329ca37487d77 100644 --- a/recipes/pharokka/meta.yaml +++ b/recipes/pharokka/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.5.0" %} +{% set version = "1.5.1" %} {% set name = "pharokka" %} -{% set sha256 = "afb5d8ac68f1d1d48b0280096018c3c31eb6c4ed07d0a5ee78e7ff19c651a5da" %} +{% set sha256 = "b862e2d44021e6a767dec317d78a12afcf2cd918bab2c0cb629413398923fb28" %} {% set user = "gbouras13" %} package: @@ -32,8 +32,8 @@ requirements: - minced >=0.4.2 - aragorn >=1.2.41 - mash >=2.2 - - dnaapler >=0.3.2 - - pyrodigal >=3.0.0 + - dnaapler >=0.4.0 + - pyrodigal >=3.1.0 - pyrodigal-gv >=0.2.0 - pycirclize >=0.3.1 - alive-progress >=3.0.1 From a9dba68527b2370b1c30e9c98378b09b6b2e7df8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 06:27:38 -0600 Subject: [PATCH 0442/2173] Update exomiser-rest-prioritiser to 13.3.0 (#43898) --- recipes/exomiser-rest-prioritiser/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/exomiser-rest-prioritiser/meta.yaml b/recipes/exomiser-rest-prioritiser/meta.yaml index 8a143ccf943d9..03395c15f4f0a 100644 --- a/recipes/exomiser-rest-prioritiser/meta.yaml +++ b/recipes/exomiser-rest-prioritiser/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "13.2.1" %} -{% set sha256 = "6acdb0ecb7b113fc7503de0989ae57f2523094fd1bbec1b5f8eb39abd48a25b2" %} +{% set version = "13.3.0" %} +{% set sha256 = "bff2399f63d26f11169e4b2de5e397bcd3c61f74022703a5d8eff20b2ac4926c" %} package: name: exomiser-rest-prioritiser From 21773fe2d3a8b1a72d59f458d6f794b8e3ceba1c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 06:28:02 -0600 Subject: [PATCH 0443/2173] Update snakemake-interface-executor-plugins to 7.0.3 (#43897) --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index a850b2bae0c1d..1e3188eee8369 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "7.0.2" %} +{% set version = "7.0.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: bdd3c6ed98deeeef25f4abdc3fd68abd2a80edc276cc4c5dc3291890c1428030 + sha256: ace3c8c9fdc80ce8f612af3d372a6e2e40bf10b031b2539660d5a37075dc257d build: noarch: python From 47c45b37cb344e703a337623e6f483597b2f9212 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 06:28:23 -0600 Subject: [PATCH 0444/2173] Update snakemake-interface-common to 1.14.1 (#43896) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 59989304ebb89..8aa85fc282a0c 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.14.0" %} +{% set version = "1.14.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 45835174fda3d3528b522637721ceb58c00c30dbd48e9c0791365cb0ec494afd + sha256: 4ade1fe41c514d929ccd0ca7aa3ec73a62ceccfe4fd08885be296accaec9cac6 build: noarch: python From 31d4bb5856a71239f77ac67853035a6a203784eb Mon Sep 17 00:00:00 2001 From: Alex Petty Date: Thu, 26 Oct 2023 07:29:36 -0500 Subject: [PATCH 0445/2173] Update r-phewas to latest release 0.99.6-1 (#43872) * Update recipe r-phewas to latest release 0.99.6-1 * Add run_exports statement. This is v0.99, so should pin x.x * This is the 2nd build of v0.99.6 so we'll just call it 0.99.6 --- recipes/r-phewas/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/r-phewas/meta.yaml b/recipes/r-phewas/meta.yaml index d34d3187ba2e8..20299cbc1494c 100644 --- a/recipes/r-phewas/meta.yaml +++ b/recipes/r-phewas/meta.yaml @@ -1,18 +1,20 @@ -{% set version = '0.12.1' %} +{% set version = '0.99.6' %} {% set name = 'PHeWAS' %} -{% set hash = '7063af0c3759e37e44f4ee2b92e22e579d9c58e15f0a529de593540489878544' %} +{% set hash = 'd462db49cd32dcbacc8e1f0e4611f1e1de21a7e9e227f0d53a63de16272533c7' %} package: name: 'r-{{ name|lower }}' version: '{{ version }}' source: - url: 'https://github.com/{{ name }}/{{ name }}/archive/v0.12.tar.gz' + url: 'https://github.com/{{ name }}/{{ name }}/archive/v{{ version }}-1.tar.gz' sha256: '{{ hash }}' build: - number: 8 + number: 0 skip: true # [win32] + run_exports: + - {{ pin_subpackage("r-phewas", max_pin="x.x") }} rpaths: - lib/R/lib/ From 103a01c2301ea04171ba6a1e4ae293d229c3cdb0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 09:00:54 -0600 Subject: [PATCH 0446/2173] Update monsda to 1.1.1 (#43901) --- recipes/monsda/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/monsda/meta.yaml b/recipes/monsda/meta.yaml index 56f318f439251..ef47e02a73861 100644 --- a/recipes/monsda/meta.yaml +++ b/recipes/monsda/meta.yaml @@ -1,6 +1,6 @@ {% set name = "MONSDA" %} -{% set version = "1.1.0" %} -{% set sha256 = "deca629eb1c67b2e36dcf243aad3dab7e688660b4701887b5f1f4db699923cbc" %} +{% set version = "1.1.1" %} +{% set sha256 = "6f4d389c848aa89722b267104344a3a82317e763166cade88511f3b79d3c099e" %} package: name: "{{ name|lower }}" @@ -11,7 +11,7 @@ source: sha256: "{{ sha256 }}" build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --use-pep517 --no-deps --ignore-installed -vvv" entry_points: - monsda = MONSDA.RunMONSDA:main From 64cb790944851ae77ffd9f820ac20b037a18ede1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 11:00:23 -0600 Subject: [PATCH 0447/2173] Update hmftools-orange to 3.0.0 (#43906) --- recipes/hmftools-orange/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-orange/meta.yaml b/recipes/hmftools-orange/meta.yaml index 186fbdf7b2da9..afd2ba038d8f9 100644 --- a/recipes/hmftools-orange/meta.yaml +++ b/recipes/hmftools-orange/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.7.1" %} -{% set sha256 = "596eb3bde589f51a6820b6a4b51bb58fdd249f5374076e923aa7d7dc8faa0a00" %} +{% set version = "3.0.0" %} +{% set sha256 = "ba3887c741501bd0d0815e701b68fe7a51dace01560ebd6e0f0647ff8c385e98" %} package: name: hmftools-orange From ebd83c784c6a98930a912892160627e9f34bc492 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 11:18:07 -0600 Subject: [PATCH 0448/2173] Update pyega3 to 5.1.0 (#43903) * Update pyega3 to 5.1.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/pyega3/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/pyega3/meta.yaml b/recipes/pyega3/meta.yaml index 76e3b71ca8c72..b2560c1d2c903 100644 --- a/recipes/pyega3/meta.yaml +++ b/recipes/pyega3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyega3" %} -{% set version = "5.0.2" %} +{% set version = "5.1.0" %} package: name: "{{ name|lower }}" @@ -7,25 +7,28 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 677f49564ff3178291ce14a7dcd4032a10bf8505d3f5c07ded13565302a89336 + sha256: f8ffa8558da52ad17b83bda2c94a289cd51f24e86e3230b8eff3aaba3f7db3ce build: number: 0 entry_points: - pyega3 = pyega3.pyega3:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" noarch: python + run_exports: + - {{ pin_subpackage('pyega3', max_pin="x") }} requirements: host: - pip - - python >3 + - python >=3.6 run: - - python >3 + - python >=3.6 - python-htsget - requests - - tqdm >=4.26.0 + - tqdm >=4.26.0 - psutil + - urllib3 test: imports: From 46d64247a031d9e0bd19570abf975ae2e11663a1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 11:35:50 -0600 Subject: [PATCH 0449/2173] Update vsearch to 2.24.0 (#43907) * Update vsearch to 2.24.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/vsearch/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index 19b601ca2618a..43c39d7f1c2a9 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.23.0" %} -{% set sha256 = "4686e35e1d8488ffedb4c6dd4de9b6eccc94f337d7b86e1759d932bce59c9b64" %} +{% set version = "2.24.0" %} +{% set sha256 = "036c3a5c7827958446e56155d750d22d03d460a53237c37fa6541208dc0bdca1" %} package: name: vsearch @@ -11,6 +11,8 @@ source: build: number: 0 + run_exports: + - {{ pin_subpackage('vsearch', max_pin="x") }} requirements: build: @@ -36,9 +38,9 @@ test: about: home: https://github.com/torognes/vsearch license: GPL-3.0-or-later OR BSD-2-Clause - license_family: GPL + license_family: GPL3 license_file: LICENSE.txt - summary: a versatile open source tool for metagenomics (USEARCH alternative) + summary: A versatile open source tool for metagenomics (USEARCH alternative) extra: identifiers: From 0ce54d5583c7dfb1ba5ba2bc98d2dd747ebe264e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 13:25:29 -0600 Subject: [PATCH 0450/2173] Update pybiolib to 1.1.1474 (#43899) * Update pybiolib to 1.1.1472 * Update pybiolib to 1.1.1474 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 27f009f1a4df6..e49d91d305f23 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1467" %} +{% set version = "1.1.1474" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 508f10731db8a44e8458c0e64397badff8a068e2b73b518a722bafdbc8ee871f + sha256: b789cabc62b4b784417f4880490b018c36a69bddd2ebf2d67a24b9508cdc86cc build: noarch: python From 7a418e014dc663058b4fbd3e0d539dbb9e7cedd5 Mon Sep 17 00:00:00 2001 From: Alex Ostrovsky <40246333+astrovsky01@users.noreply.github.com> Date: Thu, 26 Oct 2023 13:52:54 -0700 Subject: [PATCH 0451/2173] Merqury fk (#43666) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * add merquryfk * fix license * Fix build * fix gcc * add patch for gcc fix c/cxx patch patch patch * remove flags from build file * Update build.sh * cpath and headerpad to build file * remove osx --------- Co-authored-by: Alexander OSTROVSKY Co-authored-by: Björn Grüning --- recipes/merquryfk/build.sh | 15 ++++++++++++ recipes/merquryfk/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++ recipes/merquryfk/patch | 41 +++++++++++++++++++++++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 recipes/merquryfk/build.sh create mode 100644 recipes/merquryfk/meta.yaml create mode 100644 recipes/merquryfk/patch diff --git a/recipes/merquryfk/build.sh b/recipes/merquryfk/build.sh new file mode 100644 index 0000000000000..9f9bb40388aae --- /dev/null +++ b/recipes/merquryfk/build.sh @@ -0,0 +1,15 @@ +#!/bin/bash +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" +export CPATH=${PREFIX}/include + +make +mkdir -p $PREFIX/bin + +cp HAPmaker $PREFIX/bin +cp ASMplot $PREFIX/bin +cp CNplot $PREFIX/bin +cp HAPplot $PREFIX/bin +cp MerquryFK $PREFIX/bin +cp KatComp $PREFIX/bin +cp KatGC $PREFIX/bin +cp PloidyPlot $PREFIX/bin diff --git a/recipes/merquryfk/meta.yaml b/recipes/merquryfk/meta.yaml new file mode 100644 index 0000000000000..ba6212b78d301 --- /dev/null +++ b/recipes/merquryfk/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "MERQURYFK" %} +{% set version = "1.0.0" %} +{% set sha256 = "dac0c8426b491eaf38888ea9bb8abfdbb47702df3fc6b18692eaf55aa02a425f" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/thegenemyers/MERQURY.FK/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + patches: + - patch + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage("merquryfk", max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + - {{ compiler('c') }} + host: + - bzip2 + - zlib + - libcurl + +test: + commands: + - 'HAPmaker 2>&1 >/dev/null | grep "Usage: HAPmaker"' + - 'ASMplot 2>&1 >/dev/null | grep "Usage: ASMpLot"' + - 'CNplot 2>&1 >/dev/null | grep "Usage: CNpLot"' + - 'HAPplot 2>&1 >/dev/null | grep "Usage: HAPpLot"' + - 'MerquryFK 2>&1 >/dev/null | grep "Usage: MerquryFK"' + - 'KatComp 2>&1 >/dev/null | grep "Usage: KatComp"' + - 'KatGC 2>&1 >/dev/null | grep "Usage: KatGC"' + - 'PloidyPlot 2>&1 >/dev/null | grep "Usage: PloidyPlot"' + + +about: + license: https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE + summary: MerquryFK replaces meryl with the FastK k-mer counter suite to considerably speed up analyses. + home: https://github.com/thegenemyers/MERQURY.FK diff --git a/recipes/merquryfk/patch b/recipes/merquryfk/patch new file mode 100644 index 0000000000000..2aa82747db104 --- /dev/null +++ b/recipes/merquryfk/patch @@ -0,0 +1,41 @@ +diff --git a/Makefile b/Makefile +index 9e53dcb..94e1e75 100644 +--- a/Makefile ++++ b/Makefile +@@ -14,28 +14,28 @@ asm_plotter.c : cn_plot.R.h asm_plotter.h + hap_plotter.c : hap_plot.R.h hap_plotter.h + + HAPmaker: HAPmaker.c libfastk.c +- gcc $(CFLAGS) -o HAPmaker HAPmaker.c libfastk.c -lpthread -lm ++ $(CC) $(CFLAGS) -o HAPmaker HAPmaker.c libfastk.c -lpthread -lm + + CNplot: CNplot.c cn_plotter.c libfastk.c +- gcc $(CFLAGS) -o CNplot CNplot.c cn_plotter.c libfastk.c -lpthread -lm ++ $(CC) $(CFLAGS) -o CNplot CNplot.c cn_plotter.c libfastk.c -lpthread -lm + + ASMplot: ASMplot.c asm_plotter.c libfastk.c +- gcc $(CFLAGS) -o ASMplot ASMplot.c asm_plotter.c libfastk.c -lpthread -lm ++ $(CC) $(CFLAGS) -o ASMplot ASMplot.c asm_plotter.c libfastk.c -lpthread -lm + + HAPplot: HAPplot.c hap_plotter.c libfastk.c +- gcc $(CFLAGS) -o HAPplot HAPplot.c hap_plotter.c libfastk.c -lpthread -lm ++ $(CC) $(CFLAGS) -o HAPplot HAPplot.c hap_plotter.c libfastk.c -lpthread -lm + + MerquryFK: MerquryFK.c cn_plotter.c asm_plotter.c hap_plotter.c blk_plot.R.h libfastk.c +- gcc $(CFLAGS) -o MerquryFK MerquryFK.c cn_plotter.c asm_plotter.c hap_plotter.c libfastk.c -lpthread -lm ++ $(CC) $(CFLAGS) -o MerquryFK MerquryFK.c cn_plotter.c asm_plotter.c hap_plotter.c libfastk.c -lpthread -lm + + KatComp: KatComp.c libfastk.c kx_plot.R.h +- gcc $(CFLAGS) -o KatComp KatComp.c libfastk.c -lpthread -lm ++ $(CC) $(CFLAGS) -o KatComp KatComp.c libfastk.c -lpthread -lm + + KatGC: KatGC.c libfastk.c kgc_plot.R.h +- gcc $(CFLAGS) -o KatGC KatGC.c libfastk.c -lpthread -lm ++ $(CC) $(CFLAGS) -o KatGC KatGC.c libfastk.c -lpthread -lm + + PloidyPlot: PloidyPlot.c smu_plot.R.h libfastk.c libfastk.h matrix.c matrix.h +- gcc $(CFLAGS) -o PloidyPlot PloidyPlot.c libfastk.c matrix.c -lpthread -lm ++ $(CC) $(CFLAGS) -o PloidyPlot PloidyPlot.c libfastk.c matrix.c -lpthread -lm + + clean: + rm -f $(ALL) From f1ce4225f56446ab2148f684562ee902f6c00147 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 15:01:37 -0600 Subject: [PATCH 0452/2173] Update genomad to 1.7.1 (#43913) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update genomad to 1.7.1 * Replace `prodigal-gv` with `pyrodigal-gv` --------- Co-authored-by: Antônio Camargo --- recipes/genomad/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/genomad/meta.yaml b/recipes/genomad/meta.yaml index 01cf006ec28b4..cf128b29475fb 100644 --- a/recipes/genomad/meta.yaml +++ b/recipes/genomad/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genomad" %} -{% set version = "1.7.0" %} +{% set version = "1.7.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f0d8e81c9d4d7d7976cd0dbb5c6d491e3dfacab2ba6becf5c70aac23ab0765b7 + sha256: d435b72c401d7dc1755a5fc120601bca756db475232c0ebf32ea673b43da83f7 build: number: 0 @@ -25,7 +25,7 @@ requirements: - flit-core >=3.2,<4 run: - python >=3.8 - - prodigal-gv >=2.7.0 + - pyrodigal-gv - mmseqs2 =14.7e284 - aragorn - keras >=2.7 From 266c3e628f348cc656f689e50eb39562809d1871 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 15:08:12 -0600 Subject: [PATCH 0453/2173] Update virheat to 0.5.4 (#43914) --- recipes/virheat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/virheat/meta.yaml b/recipes/virheat/meta.yaml index f522666804059..9b41c34d5d907 100644 --- a/recipes/virheat/meta.yaml +++ b/recipes/virheat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "virheat" %} -{% set version = "0.5.3" %} +{% set version = "0.5.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/virheat-{{ version }}.tar.gz - sha256: cd4a8f49e49a1f28fcb4e0c6ff574d15bd0f4f86066076a888723fa49c1f148e + sha256: 7e1264b2652ba044c7b52a9da5a58771ee82e0cc18d1e278a335dec16cc4e877 build: entry_points: From 921e67b848bbbaaf52962cced53c92afc194e413 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 26 Oct 2023 20:04:11 -0600 Subject: [PATCH 0454/2173] Update zol to 1.3.11 (#43916) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index 931dcd8b5d621..756440cacb87d 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.10" %} +{% set version = "1.3.11" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 990fe4e49c6ca3f3a008ca93dd0e2ecbf97151d45ad550190b908c3343d8668c + sha256: ad0871f5922f74a4a5c9c8c73b6c0b3f8d0f59b4cbe752eb751ae9c96a11cfe1 build: number: 0 From 97ed7b6c16d6bbfa5c4c8c689f606970fd6107eb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 02:47:00 -0600 Subject: [PATCH 0455/2173] Update pmultiqc to 0.0.23 (#43925) --- recipes/pmultiqc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pmultiqc/meta.yaml b/recipes/pmultiqc/meta.yaml index 64a287454aa5d..bf170ac08f041 100644 --- a/recipes/pmultiqc/meta.yaml +++ b/recipes/pmultiqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pmultiqc" %} -{% set version = "0.0.22" %} +{% set version = "0.0.23" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e774aeb68818c0ec650cb192799dd0d47356dfffca1a34704033a2bd18b9eeaf + sha256: fc66361d1a9da0e2812ef2ca4bf328ed95ecf9ba925d25afa0d045765d9446ab build: number: 0 From cc61f248376034fee421552cc204bd01e012557f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 02:56:46 -0600 Subject: [PATCH 0456/2173] Update hybracter to 0.2.0 (#43920) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index 49ec79deaab36..997def4ef97a0 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.1.2" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 38bf79da71f8d4ae609ab4b9521443e5ad5d19e2ce5e969b44ada2e91ae8aebe + sha256: 46d9c4422cb97bb553d579f4c9d87abfbdcfc3e770d2e280db8ab2e7d5d229af build: number: 0 From e71e05f2da740d5e0f2abd0992be0e59d9216e85 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 04:14:49 -0600 Subject: [PATCH 0457/2173] Update pybiolib to 1.1.1476 (#43924) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index e49d91d305f23..48c3ad2f8e154 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1474" %} +{% set version = "1.1.1476" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: b789cabc62b4b784417f4880490b018c36a69bddd2ebf2d67a24b9508cdc86cc + sha256: 424af1c0872ed329419a0302d25102104ad6dce87ef11cc0197c73c67b23a538 build: noarch: python From 4e27efc1a5c6102c2e3436974e7f5e3613805272 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 04:46:03 -0600 Subject: [PATCH 0458/2173] Update lorax to 0.3.8 (#43926) * Update lorax to 0.3.8 * run_exports --------- Co-authored-by: Tobias Rausch --- recipes/lorax/meta.yaml | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/recipes/lorax/meta.yaml b/recipes/lorax/meta.yaml index a07470d8a3370..b774f1994a4ef 100644 --- a/recipes/lorax/meta.yaml +++ b/recipes/lorax/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.7" %} -{% set sha256 = "c4a69e876542d2d4f02ca9e0e724344376ed12577458ff4f696572119b5a0bd0" %} +{% set version = "0.3.8" %} +{% set sha256 = "a12755ed0007f8aa7aea4ae8f84bdb839d46c34ad535d83acc62dac33444d70d" %} package: name: lorax @@ -10,7 +10,9 @@ source: sha256: '{{ sha256 }}' build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage("lorax", max_pin="x.x") }} requirements: build: @@ -37,3 +39,7 @@ about: license_family: BSD license_file: LICENSE summary: A long-read analysis toolbox for cancer genomics + +extra: + identifiers: + - doi:10.1016/j.xgen.2023.100281 From b8ed50e556b30efc22af91ac86754818e9871726 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Fri, 27 Oct 2023 14:58:38 +0200 Subject: [PATCH 0459/2173] Update bioconductor-rhdf5lib: include `libcurl` dep and revert to default `configure` script (#43930) * bioconductor-rhdf5lib bump build number * move build section up * include libcurl as a dependency * introduce full_name to include `bioconductor-` prefix * add run_exports with extensive comment with linkouts * revert to default `configure` script by deleting recipes/bioconductor-rhdf5lib/configure * also delete recipes/bioconductor-rhdf5lib/configure.patch * also delete recipes/bioconductor-rhdf5lib/configure.patched --- recipes/bioconductor-rhdf5lib/configure | 4070 ----------------- recipes/bioconductor-rhdf5lib/configure.patch | 15 - .../bioconductor-rhdf5lib/configure.patched | 4070 ----------------- recipes/bioconductor-rhdf5lib/meta.yaml | 28 +- 4 files changed, 19 insertions(+), 8164 deletions(-) delete mode 100644 recipes/bioconductor-rhdf5lib/configure delete mode 100644 recipes/bioconductor-rhdf5lib/configure.patch delete mode 100644 recipes/bioconductor-rhdf5lib/configure.patched diff --git a/recipes/bioconductor-rhdf5lib/configure b/recipes/bioconductor-rhdf5lib/configure deleted file mode 100644 index 7c33b91f02917..0000000000000 --- a/recipes/bioconductor-rhdf5lib/configure +++ /dev/null @@ -1,4070 +0,0 @@ -#! /bin/sh -# Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.69 for Rhdf5lib 0.99.13. -# -# Report bugs to . -# -# -# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc. -# -# -# This configure script is free software; the Free Software Foundation -# gives unlimited permission to copy, distribute and modify it. -## -------------------- ## -## M4sh Initialization. ## -## -------------------- ## - 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"write failure creating $CONFIG_STATUS" "$LINENO" 5 - - -# configure is writing to config.log, and then calls config.status. -# config.status does its own redirection, appending to config.log. -# Unfortunately, on DOS this fails, as config.log is still kept open -# by configure, so config.status won't be able to write to it; its -# output is simply discarded. So we exec the FD to /dev/null, -# effectively closing config.log, so it can be properly (re)opened and -# appended to by config.status. When coming back to configure, we -# need to make the FD available again. -if test "$no_create" != yes; then - ac_cs_success=: - ac_config_status_args= - test "$silent" = yes && - ac_config_status_args="$ac_config_status_args --quiet" - exec 5>/dev/null - $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false - exec 5>>config.log - # Use ||, not &&, to avoid exiting from the if with $? = 1, which - # would make configure fail if this is the last instruction. - $ac_cs_success || as_fn_exit 1 -fi -if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 -$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} -fi - diff --git a/recipes/bioconductor-rhdf5lib/meta.yaml b/recipes/bioconductor-rhdf5lib/meta.yaml index 067b1a04cf8e3..16d7c44733a9d 100644 --- a/recipes/bioconductor-rhdf5lib/meta.yaml +++ b/recipes/bioconductor-rhdf5lib/meta.yaml @@ -1,35 +1,45 @@ {% set version = "1.22.0" %} {% set name = "Rhdf5lib" %} +{% set full_name = "bioconductor-" ~ name|lower %} {% set bioc = "3.17" %} package: - name: 'bioconductor-{{ name|lower }}' + name: '{{ full_name }}' version: '{{ version }}' source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ full_name }}/{{ full_name }}_{{ version }}_src_all.tar.gz' md5: 27c19bd24858ba26ff4762d41f3b2a16 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: + # This pinning is preliminary. It should be changed if either: + # * a general policy for pinning bioconductor packages is decided and differs: + # https://github.com/bioconda/bioconda-recipes/issues/43905 + # * the author of this package assures us that he adheres to semantic + # versioning, in which case we can unpin the minor version, see: + # https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782567153 + - {{ pin_subpackage(full_name, max_pin="x.x") }} # Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - r-base - libblas - liblapack + - libcurl run: - r-base - build: - - {{ compiler('c') }} - - automake - - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -40,7 +50,7 @@ about: description: 'Provides C and C++ hdf5 libraries.' extra: parent_recipe: - name: bioconductor-rhdf5lib - path: recipes/bioconductor-rhdf5lib + name: '{{ full_name }}' + path: 'recipes/{{ full_name }}' version: 1.2.1 From 8d161ddd899984e8e5989ac4f7da6478a08e3015 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 07:14:19 -0600 Subject: [PATCH 0460/2173] Update pangolin-data to 1.23.1 (#43917) --- recipes/pangolin-data/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangolin-data/meta.yaml b/recipes/pangolin-data/meta.yaml index 63aa7e7f4c2dd..99468f431af4a 100644 --- a/recipes/pangolin-data/meta.yaml +++ b/recipes/pangolin-data/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.23" %} +{% set version = "1.23.1" %} package: name: pangolin-data @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pangolin-data/archive/refs/tags/v{{ version }}.tar.gz - sha256: b739d9275a6164e6acd7127a323e55463345cea652d9ad0c1f5ed31dcd256d9b + sha256: 3a845838cf31131d8bc7e0c19cb3e78e2c99a5894ac44452bfa5f86a91dca056 build: number: 0 From a3c9abf9d85df32e492c5675471e8746319575ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gr=C3=A9goire=20Denay?= Date: Fri, 27 Oct 2023 16:07:23 +0200 Subject: [PATCH 0461/2173] Update skesa (#38473) * Update recipe to last relesae and expand to other tools included * Update skesa, remove from blacklist * Only skesa * Update * Update * update boost value, remove run dependencies * include all binaries built by skesa * reset build * add tests for additional binaries * add run_exports * fix missing file on sed * add depends to run for OSX * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Robert A. Petit III --- build-fail-blacklist | 1 - recipes/skesa/build.sh | 18 +++++++++++++----- recipes/skesa/meta.yaml | 29 ++++++++++++++++++++--------- 3 files changed, 33 insertions(+), 15 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 906027be843e0..10e5edb091f81 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -251,7 +251,6 @@ recipes/prosampler recipes/methylextract recipes/blasr recipes/asn2gb -recipes/skesa recipes/orfm recipes/maaslin recipes/seqmap diff --git a/recipes/skesa/build.sh b/recipes/skesa/build.sh index 7eef6c2a8b0f7..788ad7a98c066 100644 --- a/recipes/skesa/build.sh +++ b/recipes/skesa/build.sh @@ -1,18 +1,26 @@ #!/bin/bash export LIBRARY_PATH=${PREFIX}/lib +export LD_LIBRARY_PATH=${PREFIX}/lib export CPP_INCLUDE_PATH=${PREFIX}/include export CPLUS_INCLUDE_PATH=${PREFIX}/include export CXX_INCLUDE_PATH=${PREFIX}/include -makefile="Makefile.nongs" - if [ "$(uname)" == "Darwin" ]; then - sed -i.bak 's/-Wl,-Bstatic//' $makefile - sed -i.bak 's/-Wl,-Bdynamic -lrt//' $makefile + sed -i.bak 's/-Wl,-Bstatic//' Makefile.nongs + sed -i.bak 's/-Wl,-Bdynamic -lrt//' Makefile.nongs fi -make -f $makefile BOOST_PATH=${PREFIX} CC="$CXX $CXXFLAGS" +LDFLAGS=-L${PREFIX}/lib + +make -f Makefile.nongs \ + BOOST_PATH=${PREFIX} \ + CC="$CXX $CXXFLAGS" \ + LDFLAGS=$LDFLAGS mkdir -p ${PREFIX}/bin mv skesa ${PREFIX}/bin/ +mv saute ${PREFIX}/bin/ +mv saute_prot ${PREFIX}/bin/ +mv gfa_connector ${PREFIX}/bin/ +mv kmercounter ${PREFIX}/bin/ diff --git a/recipes/skesa/meta.yaml b/recipes/skesa/meta.yaml index 7c11768fe3e0e..b525d025cfcec 100644 --- a/recipes/skesa/meta.yaml +++ b/recipes/skesa/meta.yaml @@ -1,34 +1,45 @@ {% set name="skesa" %} -{% set version="2.4.0" %} +{% set release_tag="skesa.2.4.0_saute.1.3.0_2" %} +{% set version="2.5.1" %} +# version number does not always match release tag. Please review the source +# file at: https://github.com/ncbi/SKESA/blob/master/skesa.cpp package: name: {{ name }} version: {{ version }} source: - url: https://github.com/ncbi/SKESA/archive/v{{ version }}.tar.gz - sha256: 5bd8fa7e6efcb717c7a69156d783a298011028f7756b82d917314e11db6adb36 + url: https://github.com/ncbi/SKESA/archive/refs/tags/{{ release_tag }}.tar.gz + sha256: dc5ad60f963afb09d3f2a3bab8917e657bd93364f0deca6e6844ede44968e979 build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} requirements: build: - make - {{ compiler('cxx') }} host: + # Last version of conda-forge::boost that included static files (.a) + - boost 1.71 - zlib - - boost run: - - zlib - - boost + - libstdcxx-ng # [linux] + - boost 1.71 # [osx] + - zlib # [osx] test: commands: - skesa --version + - saute --version + - saute_prot --version + - gfa_connector --version + - kmercounter --version about: - home: https://ftp.ncbi.nlm.nih.gov/pub/agarwala/skesa + home: https://github.com/ncbi/SKESA license: Public Domain license_file: LICENSE - summary: 'Strategic Kmer Extension for Scrupulous Assemblies' + summary: 'Strategic Kmer Extension for Scrupulous Assemblies & Sequence Assembly Using Target Enrichment' From b5b9b530fe70496148ed1941eb0647425e55c93f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 09:54:27 -0600 Subject: [PATCH 0462/2173] Update r-acidsinglecell to 0.4.1 (#43934) --- recipes/r-acidsinglecell/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidsinglecell/meta.yaml b/recipes/r-acidsinglecell/meta.yaml index 36ad195dda0da..ad35a25f806b7 100644 --- a/recipes/r-acidsinglecell/meta.yaml +++ b/recipes/r-acidsinglecell/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.0" %} +{% set version = "0.4.1" %} {% set github = "https://github.com/acidgenomics/r-acidsinglecell" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 5cbcbfe093902e7a7f6b316130241b6f07f5ceb465a58b6e6801608b50b1334b + sha256: 69b81a103280720ac91f05056b81c8a485e5a70cc5802cfb39a23db7ebdc2487 build: number: 0 From bb45131bb6ae314f38cdfaec9fca32ea2aab4b9d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 10:01:13 -0600 Subject: [PATCH 0463/2173] Update psims to 1.2.9 (#43915) --- recipes/psims/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psims/meta.yaml b/recipes/psims/meta.yaml index d53e581dd81ee..d2c1445027deb 100644 --- a/recipes/psims/meta.yaml +++ b/recipes/psims/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.2.8" %} -{% set sha256 = "74d1905fc9b0cb506e3ccb33937c4f7609f97379ad41bf107603f1d4494fd6af" %} +{% set version = "1.2.9" %} +{% set sha256 = "35cc03660a86b41c94928f367bee091609af34cd092b46d31c4e8f91884b0813" %} package: name: "psims" From 8dca5aea86defec8c0123c3cebbe89c4f34b3714 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 10:01:31 -0600 Subject: [PATCH 0464/2173] Update plassembler to 1.4.0 (#43921) --- recipes/plassembler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/plassembler/meta.yaml b/recipes/plassembler/meta.yaml index 242a3302891e2..58e5f1b06aab3 100644 --- a/recipes/plassembler/meta.yaml +++ b/recipes/plassembler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "plassembler" %} -{% set version = "1.3.0" %} +{% set version = "1.4.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: ec6b0e4056e170b71dfc281f70f331ff4538a8f4c61c09a10b1e77b4733d9499 + sha256: 90b7a25b742e871f02d9e9015173d162bf3bb0f0e6f7eaaca93854b194095ef0 build: number: 0 From e9795096c9a232237dd6c25f283bf3f3792c2aa4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 11:18:07 -0600 Subject: [PATCH 0465/2173] Update harpy to 0.4.0 (#43936) --- recipes/harpy/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index f74ea4b5862be..616da31c08dfc 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.0" %} -{% set sha256 = "c8767dd26b51776286917436dfde31430b5912435b5c4fda125a559dd3642c20" %} +{% set version = "0.4.0" %} +{% set sha256 = "6062ece4701b6de964d1f25fc6e9e0d6b6525f3b04f9ca22d8b90191c7767928" %} package: name: harpy @@ -11,7 +11,7 @@ source: build: skip: True # [osx] - number: 3 + number: 0 run_exports: - {{ pin_subpackage('harpy', max_pin="x.x") }} @@ -72,4 +72,4 @@ extra: recipe-maintainers: - pdimens skip-lints: - - should_be_noarch_generic \ No newline at end of file + - should_be_noarch_generic From 3548fbe41e0f46a923c72f756ffb4ea0bf1471c0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 11:21:12 -0600 Subject: [PATCH 0466/2173] Update r-acidexperiment to 0.5.3 (#43935) --- recipes/r-acidexperiment/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidexperiment/meta.yaml b/recipes/r-acidexperiment/meta.yaml index 5c004ca3d3d0c..91b75662280e9 100644 --- a/recipes/r-acidexperiment/meta.yaml +++ b/recipes/r-acidexperiment/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.2" %} +{% set version = "0.5.3" %} {% set github = "https://github.com/acidgenomics/r-acidexperiment" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: da4d283bef0cc580abe09828f102091b2dc628298e3efdcf59d0c667943211d2 + sha256: 9124f900518566cd1555ec439411b7b3f4c59736f92ed0a3d784583697f661b1 build: number: 0 From 8baaa4c65dabbdd88e9a7b676370e1f06cdd6e31 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 11:22:20 -0600 Subject: [PATCH 0467/2173] Update auriclass to 0.5.4 (#43928) --- recipes/auriclass/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/auriclass/meta.yaml b/recipes/auriclass/meta.yaml index 6efebc43dc286..ca42bc5f1cd6e 100644 --- a/recipes/auriclass/meta.yaml +++ b/recipes/auriclass/meta.yaml @@ -1,5 +1,5 @@ {% set name = "AuriClass" %} -{% set version = "0.5.3" %} +{% set version = "0.5.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/RIVM-bioinformatics/auriclass/archive/v{{ version }}.tar.gz - sha256: 335395d64f8a4f40e47bb08bc114eb809c333f5680f9f14b46d75036f59a5ca3 + sha256: 10ff5421fc968097ff64812be5b248bf14e6c5b9a086ef0156e3de1cc4c2902b build: noarch: python From 784128acbdd1af9e19af816dc4f07b5309282ea6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 11:31:45 -0600 Subject: [PATCH 0468/2173] Update bactopia-assembler to 1.0.3 (#42973) * Update bactopia-assembler to 1.0.3 * Update meta.yaml * pin medaka version * Update meta.yaml * test with conda build config * Update meta.yaml * Pin tensorflow * Debugging vs local build * Use pinnings working locally * Update meta.yaml * Update meta.yaml * Update meta.yaml * try dropping config build * Update meta.yaml * pin shovill build * try pinning skesa to match local build * debugging * debugging * debugging shovill * more debugging * debug * debugging skesa * Update meta.yaml * Create conda_build_config.yaml * bump skesa pinning --------- Co-authored-by: Robert A. Petit III --- recipes/bactopia-assembler/meta.yaml | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/recipes/bactopia-assembler/meta.yaml b/recipes/bactopia-assembler/meta.yaml index 4cea042c5b5aa..d44aba6c79699 100644 --- a/recipes/bactopia-assembler/meta.yaml +++ b/recipes/bactopia-assembler/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.2" %} +{% set version = "1.0.3" %} package: name: bactopia-assembler @@ -7,23 +7,22 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('bactopia-assembler', max_pin='x') }} source: url: https://github.com/bactopia/bactopia-assembler/archive/v{{version}}.tar.gz - sha256: 4d2bd49f9cdec7484e7b37028e77d0e772eb041d6420d59dc478936378cb761a + sha256: d4f318b7ba97a5c54823f7405bb79f03e0244bc7ccc52313acb4dcffbc1b7347 requirements: run: - - assembly-scan >=1.0.0 - coreutils - - dragonflye >=1.1.1 + - dragonflye >=1.1.2 - importlib-metadata <5 - - nanoq >=0.9.0 - - python >3.6,<3.11 - - pigz - sed - - shovill-se >=1.1.0se - - unicycler + - shovill-se + - skesa >=2.5.1 + - unicycler >=0.5.0 - wget test: From 229942d901fa33226e9dad9b06955ba4d343886c Mon Sep 17 00:00:00 2001 From: Lucas van Dijk Date: Fri, 27 Oct 2023 14:09:37 -0400 Subject: [PATCH 0469/2173] Update StrainGE recipe, new version, add run_exports, and fix scipy dependency version (#43334) * Fix StrainGE scipy dependency version * Update version and pin build versions * fix: Put run_exports in the correct place * fix: Reset StrainGE build number --- recipes/strainge/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/strainge/meta.yaml b/recipes/strainge/meta.yaml index fa4a3096a8882..3857b0e6df44a 100644 --- a/recipes/strainge/meta.yaml +++ b/recipes/strainge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "strainge" %} -{% set version = "1.3.7" %} +{% set version = "1.3.8" %} package: name: "{{ name|lower }}" @@ -7,16 +7,18 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f73bbd9f5e1e4775ee070fc681eadeaba6bd6ab4300bda68144d9e669502c9b5 + sha256: d93f1d5fea0f13519cdf19e6b0914c8ef5ce07778d653b74db267e92643e4bd1 build: - number: 1 + number: 0 skip: true # [py<38] entry_points: - strainge=strainge.cli.main:strainge_cli - straingst=strainge.cli.main:straingst_cli - straingr=strainge.cli.main:straingr_cli script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + run_exports: + - {{ pin_subpackage("strainge", max_pin="x") }} requirements: build: @@ -34,10 +36,10 @@ requirements: - h5py - intervaltree - matplotlib-base - - scikit-bio >=0.5 + - scikit-bio >=0.5.8 - scikit-learn >=0.24 - pysam >=0.10 - - scipy <1.9 + - scipy test: imports: From 205baba8f98ca887ee5a91f9189a2dc1e477c59f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 14:36:45 -0600 Subject: [PATCH 0470/2173] Update bayescode to 1.3.2 (#43929) --- recipes/bayescode/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bayescode/meta.yaml b/recipes/bayescode/meta.yaml index 85a836c0a1394..92815ce859119 100644 --- a/recipes/bayescode/meta.yaml +++ b/recipes/bayescode/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.3.1" %} -{% set sha256 = "d96b0d193eba18b5264851c5e64648bd4a4c57ffd44f14d66ef74d15408d7e8b" %} +{% set version = "1.3.2" %} +{% set sha256 = "53febe5e4495bfb029da04b209c5722ee0de0c13db53ec98de277d571469d26f" %} package: name: bayescode From 0727598622a90ae870b22a0dacb12b69475ded8b Mon Sep 17 00:00:00 2001 From: Celio Santos-Jr Date: Fri, 27 Oct 2023 17:37:10 -0300 Subject: [PATCH 0471/2173] Fix Python version to macrel execution (#43912) * Fix Python version to macrel execution Python after 3.11 only accepts newer version of sklearn that does not unpickle the tree estimator properly inducing a error. * Fix Run_exports and "build number" * remove spaces * Update meta.yaml * Update meta.yaml * Update meta.yaml * Fix pin exports * fix run_exports using variables * fix comments * fix run_exports * change pin value --------- Co-authored-by: Thanh Lee --- recipes/macrel/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/macrel/meta.yaml b/recipes/macrel/meta.yaml index 5056d2d5e2a71..af7a36f07f3a7 100644 --- a/recipes/macrel/meta.yaml +++ b/recipes/macrel/meta.yaml @@ -12,26 +12,29 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - macrel= macrel.main:main script: python -m pip install --disable-pip-version-check --no-cache-dir --ignore-installed --no-deps -vv . + run_exports: + - {{ pin_subpackage("macrel", max_pin="x.x") }} requirements: host: - - python + - python <3.11 - pip run: - - python + - python <3.11 - atomicwrites - ngless - megahit - paladin - pandas - - scikit-learn + - scikit-learn <1.3.0 + - joblib <1.3.0 - tzlocal - - pyrodigal - + - pyrodigal >=0.7.3,<3.0.0 + test: imports: - macrel From a38fd85dd754321b164a5a120d3eed3584bd774d Mon Sep 17 00:00:00 2001 From: Arafat Rahman Date: Fri, 27 Oct 2023 13:37:21 -0700 Subject: [PATCH 0472/2173] Release beav v0.5.5 (#43911) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/beav/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/beav/meta.yaml b/recipes/beav/meta.yaml index e82a265f199d3..7d75bcf8331a9 100644 --- a/recipes/beav/meta.yaml +++ b/recipes/beav/meta.yaml @@ -1,12 +1,12 @@ {% set name = "beav" %} -{% set version = "0.5.2" %} -{% set sha256 = "28b1f541725d59b28543c76a40be0f74cd0e9b763e59c2cb58a3c5658e777e09" %} +{% set version = "0.5.5" %} +{% set sha256 = "2ae8d96e2ada0686af9279e7a84abe6094acbd07c8ea3049f3a1974e78be2014" %} {% set dbscan_git = "condabeav0.5" %} {% set dbscan_sha256 = "2fe08873026fe63a9992bfb997e59fecce7facb903778983dc6917c962573463" %} {% set gapmind_git = "Beav0.5.1conda" %} {% set gapmind_sha256 = "a5d0c4855d65355fa4675172a65b97cb03d4ec2e5098a08bece84f677e48a244" %} -{% set pycirclize_git = "v0.5.1-beav0.5.1" %} -{% set pycirclize_sha256 = "969990f486ebdb51b73cef7d8f6cea9ae34b97fe8e2de376e5599aff339aa78f" %} +{% set pycirclize_git = "v0.5.2-beav0.5.3" %} +{% set pycirclize_sha256 = "5ed895e82be37e651a897344d9a9b7dddf36bbf04b00526209f834db13734274" %} package: name: {{ name }} @@ -37,7 +37,7 @@ requirements: - perl >=5.22.0 - hmmer >=3.3.2 - bakta >=1.6 - - integron_finder =2.0rc6 + - integron_finder =2.0.2 - macsyfinder - defense-finder - fastani From 74630c7c4300ad60ad18093cecdb445e1795b6ac Mon Sep 17 00:00:00 2001 From: farchaab <116543129+farchaab@users.noreply.github.com> Date: Fri, 27 Oct 2023 22:37:37 +0200 Subject: [PATCH 0473/2173] updated maintainers list (#43894) --- recipes/assembly_finder/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index 4b47a06f8097b..b05ec69e03bcb 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -9,7 +9,7 @@ source: - url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz sha256: 9aeec6ed2a58b7f701f1596ff7aa670ccd526d406da9273fb64a949b7b1ab866 build: - number: 0 + number: 1 entry_points: - assembly_finder = assembly_finder.assembly_finder:cli noarch: python @@ -44,6 +44,5 @@ extra: container: extended-base: true recipe-maintainers: - - idfarbanecha + - farchaab - tpillone - From f7652cef4afd3b846a9e80bb7bb6a86a23eb0b13 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 14:38:17 -0600 Subject: [PATCH 0474/2173] Update gdmicro to 1.0.9 (#43904) * Update gdmicro to 1.0.7 * fix spacing * Update gdmicro to 1.0.9 --------- Co-authored-by: joshuazhuang7 --- recipes/gdmicro/meta.yaml | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/recipes/gdmicro/meta.yaml b/recipes/gdmicro/meta.yaml index f4c29f068e691..620f554f827de 100644 --- a/recipes/gdmicro/meta.yaml +++ b/recipes/gdmicro/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gdmicro" %} -{% set version = "1.0.6" %} +{% set version = "1.0.9" %} package: name: "{{ name|lower }}" @@ -7,21 +7,23 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8b890f8e609c854726ed294044fe2daaf56c69d5b25f01c2f4440fffa46903a7 + sha256: d63985f69f411e98a3d745b5b4cfde5cf3333c232cbce2d1e2426695c5f08859 build: - number: 1 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" run_exports: - {{ pin_subpackage('gdmicro', max_pin="x") }} + entry_points: + - gdmicro = GDmicro.GDmicro:main noarch: python requirements: host: - pip - - python ==3.7.3 + - python ==3.7.3 run: - - python ==3.7.3 + - python ==3.7.3 - numpy - pandas - scipy @@ -35,7 +37,6 @@ requirements: - r-yaml ==2.2.1 - r-tidyverse ==1.2.1 - test: imports: - GDmicro @@ -45,6 +46,7 @@ test: about: home: https://github.com/liaoherui/GDmicro license: MIT + license_family: MIT summary: GDmicro - Use GCN and Deep adaptation network to classify host disease status based on human gut microbiome data extra: From 7ee4a2acc2a2f7ad8bd700e8afc8458213919c73 Mon Sep 17 00:00:00 2001 From: kokul-atx <99668099+kokul-atx@users.noreply.github.com> Date: Fri, 27 Oct 2023 16:40:07 -0400 Subject: [PATCH 0475/2173] Fixing the perl paths for all relevant gmap scripts (#43919) * fixing the perl paths for all relevant gmap scripts * adding the updated meta yml file --- recipes/gmap/build.sh | 19 +++++++++++++++++++ recipes/gmap/meta.yaml | 2 +- 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/recipes/gmap/build.sh b/recipes/gmap/build.sh index 24882e8d773e2..ed5ed8319b2d8 100644 --- a/recipes/gmap/build.sh +++ b/recipes/gmap/build.sh @@ -30,4 +30,23 @@ make install make clean # Fix perl shebang +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/dbsnp_iit +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/ensembl_genes +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/fa_coords +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/gff3_genes +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/gff3_introns +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/gff3_splicesites sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/gmap_build +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/gmap_cat +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/gmap_process +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/gtf_genes +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/gtf_introns +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/gtf_splicesites +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/gtf_transcript_splicesites +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/gvf_iit +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/md_coords +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/psl_genes +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/psl_introns +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/psl_splicesites +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/vcf_iit + diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index 74c8b1a25c564..13f1ad8b29cb3 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -13,7 +13,7 @@ source: - single_quote_paths.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('gmap', max_pin=None) }} From b52c712a32dfca44b252891b95968090d98296a3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 14:53:46 -0600 Subject: [PATCH 0476/2173] Update pxblat to 1.1.1 (#43918) * Update pxblat to 1.0.3 * Update pxblat to 1.1.0 * Update pxblat to 1.1.1 --- recipes/pxblat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index acc062e35af8c..e94e092e49f68 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "1.0.0" %} -{% set sha256 = "3a136da878464bfe68ab097731953ff13bae70db6eca2e5bd11a8c176bcff361" %} +{% set version = "1.1.1" %} +{% set sha256 = "df8d366c01fc79fa6a5a6200f6e76df5c18666219368404cfd456b49e109c9e0" %} package: name: {{ name|lower }} From b331b6aa3d1532597ceae0ee3e18a9137d122adb Mon Sep 17 00:00:00 2001 From: "Ricardo A. Vialle" Date: Fri, 27 Oct 2023 15:56:27 -0500 Subject: [PATCH 0477/2173] Update snakeSV recipe (#43909) * Update snakeSV build recipe * Update snakeSV build recipe * Update snakeSV build recipe * Update meta.yaml --- recipes/snakesv/build.sh | 2 +- recipes/snakesv/meta.yaml | 9 ++++----- 2 files changed, 5 insertions(+), 6 deletions(-) mode change 100644 => 100755 recipes/snakesv/build.sh mode change 100644 => 100755 recipes/snakesv/meta.yaml diff --git a/recipes/snakesv/build.sh b/recipes/snakesv/build.sh old mode 100644 new mode 100755 index 4a480c4fc1177..d9a21d8370899 --- a/recipes/snakesv/build.sh +++ b/recipes/snakesv/build.sh @@ -4,7 +4,7 @@ mkdir -p $PREFIX/bin mkdir -p $PREFIX/opt/snakeSV/ # Full path to the Snakefile -sed -i.bak "s|workflow/Snakefile|$PREFIX/opt/snakeSV/workflow/Snakefile|g" snakeSV +#sed -i "s|workflow/Snakefile|$PREFIX/opt/snakeSV/workflow/Snakefile|g" snakeSV cp -r * $PREFIX/opt/snakeSV/ ln -s $PREFIX/opt/snakeSV/snakeSV $PREFIX/bin/ diff --git a/recipes/snakesv/meta.yaml b/recipes/snakesv/meta.yaml old mode 100644 new mode 100755 index c44815b75d145..b73185dd4151c --- a/recipes/snakesv/meta.yaml +++ b/recipes/snakesv/meta.yaml @@ -10,17 +10,16 @@ source: sha256: a9312b1992bb1eea9b824175f59b8d9bb3f9e773028ad98f31839d8a25b527a6 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('snakesv', max_pin="x.x") }} requirements: run: - - snakemake-minimal >=7.0.1 - - mamba >=0.22.0 - - pandas >=1.4.1 - - bcftools >=1.15.1 + - snakemake =7.0.1 + - mamba + - bcftools =1.15.1 test: commands: From 5a504133ed6b3ef2f466ea47b0351eaada69f965 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 15:54:41 -0600 Subject: [PATCH 0478/2173] Update fastmlst to 0.0.16 (#43938) * Update fastmlst to 0.0.16 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fastmlst/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/fastmlst/meta.yaml b/recipes/fastmlst/meta.yaml index 22c34e311471d..e2d2bc9e5699b 100644 --- a/recipes/fastmlst/meta.yaml +++ b/recipes/fastmlst/meta.yaml @@ -1,7 +1,7 @@ {% set name = "FastMLST" %} -{% set version = "0.0.15" %} +{% set version = "0.0.16" %} {% set user = "EnzoAndree" %} -{% set sha256 = "5501a2785852c2551c3ba1835b83350eb5f7de10cd4e56bfb411bbdb6a23fc33" %} +{% set sha256 = "3a2f45079f085481f381047c2b56e40fd47f2ae3a80a7add0642fa41dd068b61" %} package: name: "{{ name|lower }}" @@ -10,7 +10,9 @@ package: build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('fastmlst', max_pin="x") }} source: url: https://github.com/{{ user }}/{{ name }}/archive/v{{ version }}.tar.gz From 062eec1a032a86b735ffc9c97e86861904de5a52 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 17:32:06 -0600 Subject: [PATCH 0479/2173] Update ncbi-datasets-pylib to 15.25.0 (#43940) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index d972bddd85175..f8358051d1c30 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.24.0" %} -{% set sha256 = "7d48d95d078128736d4d2ef98408d68cfa422ae4db9897e924983224a8070b0e" %} +{% set version = "15.25.0" %} +{% set sha256 = "573a95edace0b3d7de00a64ddf9ff0f5b1ae170432c83d8bd71cfcd4c35bcca7" %} package: name: {{ name|lower }} From 14b556659efaac8df51f92aecdaf103d2f060f5d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 17:32:27 -0600 Subject: [PATCH 0480/2173] Update jbrowse2 to 2.7.2 (#43939) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index dc27517914864..4a107ead1f045 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.7.1" %} +{% set version = "2.7.2" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 478dacd55070f37a28ea3788d4aeec66a809512613a02481efc29f1591b10ea8 + sha256: 8b43ea96d071a4dfa28458be20cc10b0e116fb7d5926565494f0e515cf09ba3a url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From 22b2a74e823d2c6247a07ba0a73667e6e9aaff8d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 17:32:59 -0600 Subject: [PATCH 0481/2173] Update fastv to 0.10.0 (#43922) * Update fastv to 0.10.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fastv/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/fastv/meta.yaml b/recipes/fastv/meta.yaml index bc5bcffdd2b75..b7e927e3e3c51 100644 --- a/recipes/fastv/meta.yaml +++ b/recipes/fastv/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.1" %} -{% set sha256 = "210d098c6169393fc44c3fe13db34221cdcb2f3f5d71685fc0f88eb96ee1b406" %} +{% set version = "0.10.0" %} +{% set sha256 = "06acd1b57f1d3df0dbd344f7b47506b7a0b667481a36263a6ebbe3710f3d361f" %} package: name: fastv @@ -10,7 +10,9 @@ source: sha256: '{{ sha256 }}' build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage('fastv', max_pin="x") }} requirements: build: @@ -28,4 +30,4 @@ about: license: MIT license_family: MIT license_file: LICENSE - summary: An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. + summary: An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. From 7f1fc7aaad5c445d293ab6492f80f5cd815ccdc5 Mon Sep 17 00:00:00 2001 From: ziyewang Date: Sat, 28 Oct 2023 07:35:08 +0800 Subject: [PATCH 0482/2173] Add COMEBin (#43910) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * add COMEBin * add Comebin * add COMEBin * add COMEBin * add COMEBin * add COMEBin * add COMEBin * add COMEBin * add COMEBin * add COMEBin * add COMEBin * add COMEBin * add COMEBin * add COMEBin * Update build.sh chmod a+x auxiliary/* * Update meta.yaml * Update meta.yaml --------- Co-authored-by: 王子叶 <2630494503@qq.com> --- recipes/comebin/build.sh | 9 ++++++ recipes/comebin/meta.yaml | 58 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 recipes/comebin/build.sh create mode 100644 recipes/comebin/meta.yaml diff --git a/recipes/comebin/build.sh b/recipes/comebin/build.sh new file mode 100644 index 0000000000000..26fb91279a8cf --- /dev/null +++ b/recipes/comebin/build.sh @@ -0,0 +1,9 @@ +#!/usr/bin/env bash + +mkdir -p $PREFIX/bin/ +cp -r COMEBin $PREFIX/bin/ +chmod a+x auxiliary/* +cp -r auxiliary $PREFIX/bin/ +chmod a+x bin/run_comebin.sh +cp bin/run_comebin.sh $PREFIX/bin/ + diff --git a/recipes/comebin/meta.yaml b/recipes/comebin/meta.yaml new file mode 100644 index 0000000000000..d2ae3fbdb6298 --- /dev/null +++ b/recipes/comebin/meta.yaml @@ -0,0 +1,58 @@ +package: + name: comebin + version: "1.0.2" + +source: + url: https://github.com/ziyewang/COMEBin/archive/refs/tags/1.0.2.tar.gz + sha256: 8e1bfe609f723743f7e1703dfd89483a8a4def19b9e9a3283839c7eb7c93d1ab + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('comebin', max_pin="x.x") }} + +requirements: + run: + - atomicwrites 1.4.0 + - bedtools 2.30.0 + - biolib 0.1.6 + - biopython 1.76 + - bwa 0.7.17 + - checkm-genome 1.1.3 + - fraggenescan 1.31 + - hmmer 3.1b2 + - matplotlib-base 3.5.1 + - matplotlib-inline 0.1.3 + - numpy 1.19.0 + - pplacer 1.1.alpha19 + - prodigal 2.6.3 + - python 3.7 + - python-dateutil 2.8.2 + - python-fastjsonschema 2.15.3 + - pytorch 1.10.2 + - pip 22.0.4 + - samtools 1.15.1 + - scipy 1.7.3 + - setuptools 59.5.0 + - tensorboard 1.15.0 + - click 8.0.4 + - hnswlib 0.6.2 + - igraph 0.9.9 + - joblib 1.1.0 + - leidenalg 0.8.10 + - networkx 2.6.3 + - pandas 1.3.5 + - scanpy 1.9.1 + - scikit-learn 0.22.1 + - seaborn 0.12.1 + - pyyaml 6.0 + +test: + commands: + - which run_comebin.sh + +about: + home: "https://github.com/ziyewang/COMEBin" + license: BSD + summary: "COMEBin allows effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning" From 03f1b2f86108fcfdcbde06d68b5203f87464e1bf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 27 Oct 2023 17:35:24 -0600 Subject: [PATCH 0483/2173] Update taxmyphage to 0.2.0 (#43942) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index 2806cd8a3c398..5b3089c798c3b 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.1.9" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: 631a1557cd4ca134668d05bca689dc8ab2eb893e2a04d38f94b30813dede2c93 + sha256: 63ba54760961c92f525385db8df214eba0c3af2bcb8de869ced23ade1c7c9bca build: entry_points: From e1c34d03fefb3a1bcd9bd595712e600dbb40e8a4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 28 Oct 2023 04:53:46 -0600 Subject: [PATCH 0484/2173] Update r-syntactic to 0.7.1 (#43937) --- recipes/r-syntactic/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-syntactic/meta.yaml b/recipes/r-syntactic/meta.yaml index 171f4103eea44..26f0dde275c31 100644 --- a/recipes/r-syntactic/meta.yaml +++ b/recipes/r-syntactic/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} {% set github = "https://github.com/acidgenomics/r-syntactic" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: d59f4019a6b0667e8e5200864f8608bc132919d153e7ab6ff2b8d3e5721c0629 + sha256: d2409c5fa7a57748f8f7f548ea2d083ef0a1765ef13f95daa2a9ebe40777cca1 build: noarch: generic From c95afd1acd7c9c970dca9172f31850fb2c20442b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 28 Oct 2023 06:24:27 -0600 Subject: [PATCH 0485/2173] Update fasten to 0.7.2 (#43946) --- recipes/fasten/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fasten/meta.yaml b/recipes/fasten/meta.yaml index 1d86a66586c1c..dc2a8ac7831b5 100644 --- a/recipes/fasten/meta.yaml +++ b/recipes/fasten/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.0" %} -{% set sha256 = "017af4ff307a9b251a4a4248659b57f2f30dd9a08a89aab29fd0581aa4a47e7a" %} +{% set version = "0.7.2" %} +{% set sha256 = "95e6c224c9afe30b857f002c425929f10ef022180915c0e26199cf01ca18dcab" %} package: name: fasten From 0f7b22b184822c0b9e0788654f4216e43d6681c4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 28 Oct 2023 06:24:54 -0600 Subject: [PATCH 0486/2173] Update pygenomeviz to 0.4.4 (#43948) --- recipes/pygenomeviz/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pygenomeviz/meta.yaml b/recipes/pygenomeviz/meta.yaml index d5b45a7e27cc8..ca5040a1cf463 100644 --- a/recipes/pygenomeviz/meta.yaml +++ b/recipes/pygenomeviz/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pygenomeviz" %} -{% set version = "0.4.3" %} +{% set version = "0.4.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pygenomeviz-{{ version }}.tar.gz - sha256: 357469bc0afe4bf2e8ead5c4e79d47a003858e8b81e093e8a98b6d20114283ca + sha256: 0e3566fba142f522efa363ace1d95cb1af4701e42fdb1e51fbf35840a5347c86 build: entry_points: From 200b6a827b2a8803613d1506c63c157308fee478 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 28 Oct 2023 06:28:56 -0600 Subject: [PATCH 0487/2173] Update gdmicro to 1.0.10 (#43947) --- recipes/gdmicro/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gdmicro/meta.yaml b/recipes/gdmicro/meta.yaml index 620f554f827de..27718cb32aaea 100644 --- a/recipes/gdmicro/meta.yaml +++ b/recipes/gdmicro/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gdmicro" %} -{% set version = "1.0.9" %} +{% set version = "1.0.10" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: d63985f69f411e98a3d745b5b4cfde5cf3333c232cbce2d1e2426695c5f08859 + sha256: d71dd9b5fdaf1e88b97374d16462b00381242fd2830b5a0b7b5d62bfaca9e4f6 build: number: 0 From 1172e6a656864f9e5062088df6551ae877e42e55 Mon Sep 17 00:00:00 2001 From: Xi Chen <38089207+xinehc@users.noreply.github.com> Date: Sun, 29 Oct 2023 00:51:49 +0800 Subject: [PATCH 0488/2173] update recipe for args_oap (#43949) --- recipes/args_oap/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/args_oap/meta.yaml b/recipes/args_oap/meta.yaml index 3b590862f73d1..b1ba2e9244fda 100644 --- a/recipes/args_oap/meta.yaml +++ b/recipes/args_oap/meta.yaml @@ -1,5 +1,5 @@ {% set name = "args_oap" %} -{% set version = "3.2.3" %} +{% set version = "3.2.4" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: https://github.com/xinehc/args_oap/archive/refs/tags/v{{ version }}.tar.gz - sha256: cadde1bda8d4a9c16fb36cc0d7a1202a6aa15ac94cd4caf496bea2bbb5bc6477 + sha256: de53ff4a1a69b2c225389586284ca977814420692f12aba6d3692228d808c5aa build: noarch: python number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('args_oap', max_pin='x.x') }} requirements: host: @@ -41,4 +43,4 @@ about: extra: recipe-maintainers: - xiaole99 - - xinehc + - xinehc \ No newline at end of file From e5f7e4aad4f8aa19d6650efcb129eb92c6179091 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 28 Oct 2023 13:49:45 -0600 Subject: [PATCH 0489/2173] Update mehari to 0.15.2 (#43951) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index d6f628a2948a2..e3f56c7d2cc4e 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.15.1" %} -{% set sha256 = "07677b5af888207e3fd008be0ab606d0e83d4fd83ab3b72fbc10424ec74fe22d" %} +{% set version = "0.15.2" %} +{% set sha256 = "50e2c0fab299b94c5ca92ecf0ff726d56bcf69b4379a1dc2fdc58aa74a80d9b6" %} package: name: mehari From f0b85b6efc123ca3c27e336b1bd895d6edb6e2ba Mon Sep 17 00:00:00 2001 From: Arafat Rahman Date: Sat, 28 Oct 2023 13:01:27 -0700 Subject: [PATCH 0490/2173] Update beav v0.5.5 (#43944) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml --- recipes/beav/build.sh | 2 ++ recipes/beav/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/beav/build.sh b/recipes/beav/build.sh index 21c585b4bf8ff..c42a98bd2634d 100755 --- a/recipes/beav/build.sh +++ b/recipes/beav/build.sh @@ -21,6 +21,8 @@ mv PyCirclize $BEAV_DIR/software/ mv PaperBLAST $BEAV_DIR/software/ mkdir $BEAV_DIR/software/PaperBLAST/bin/blast +chmod +x $BEAV_DIR/scripts/* + #TIGER #TIGER must be downloaded in the build script because the official release contains linux binaries and a broken softlink. #Downloading in the meta.yaml script breaks the build and so it must be downloaded here with the exclude parameters. diff --git a/recipes/beav/meta.yaml b/recipes/beav/meta.yaml index 7d75bcf8331a9..0e0cce08fc38d 100644 --- a/recipes/beav/meta.yaml +++ b/recipes/beav/meta.yaml @@ -27,9 +27,9 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - - {{ pin_subpackage(name, max_pin='x') }} + - {{ pin_subpackage("beav", max_pin='x.x') }} requirements: run: From ea9a30d79695b91047c27de6b4c4f1ce82e4be4e Mon Sep 17 00:00:00 2001 From: "Ricardo A. Vialle" Date: Sat, 28 Oct 2023 15:02:43 -0500 Subject: [PATCH 0491/2173] Update snakesv build (#43943) * Update snakeSV build recipe * Update snakeSV build recipe * Update snakeSV build recipe * Update meta.yaml * Update snakeSV build recipe --- recipes/snakesv/build.sh | 2 +- recipes/snakesv/meta.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakesv/build.sh b/recipes/snakesv/build.sh index d9a21d8370899..82ea9ab4075c0 100755 --- a/recipes/snakesv/build.sh +++ b/recipes/snakesv/build.sh @@ -4,7 +4,7 @@ mkdir -p $PREFIX/bin mkdir -p $PREFIX/opt/snakeSV/ # Full path to the Snakefile -#sed -i "s|workflow/Snakefile|$PREFIX/opt/snakeSV/workflow/Snakefile|g" snakeSV +sed -i "s|\$(dirname \$(which snakeSV))/workflow/Snakefile|$PREFIX/opt/snakeSV/workflow/Snakefile|g" snakeSV cp -r * $PREFIX/opt/snakeSV/ ln -s $PREFIX/opt/snakeSV/snakeSV $PREFIX/bin/ diff --git a/recipes/snakesv/meta.yaml b/recipes/snakesv/meta.yaml index b73185dd4151c..90a1453f584aa 100755 --- a/recipes/snakesv/meta.yaml +++ b/recipes/snakesv/meta.yaml @@ -10,7 +10,7 @@ source: sha256: a9312b1992bb1eea9b824175f59b8d9bb3f9e773028ad98f31839d8a25b527a6 build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_subpackage('snakesv', max_pin="x.x") }} From 2f1fe179c6c5e1d372c86f8748cfabf758daaabf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 28 Oct 2023 14:03:01 -0600 Subject: [PATCH 0492/2173] Update taxmyphage to 0.2.1 (#43952) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index 5b3089c798c3b..8974d4c1f6713 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: 63ba54760961c92f525385db8df214eba0c3af2bcb8de869ced23ade1c7c9bca + sha256: ccec70d7e0fbe0db8b205772a595e8673e6b2304ba4cfc74049bafe8640ba683 build: entry_points: From 94ac4cd802a4e41b34bacb95f16ed8d848bd46b3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 28 Oct 2023 21:38:29 -0600 Subject: [PATCH 0493/2173] Update simpleaf to 0.15.1 (#43955) --- recipes/simpleaf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index 5cb64d040e725..689fa08030ddc 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.15.0" %} +{% set version = "0.15.1" %} package: name: simpleaf @@ -12,7 +12,7 @@ build: source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: 10273eb0512983226eba9fdf8ead4aacf26bd1c46b1a69abc265a821cd9b100d + sha256: 888ebb199a27ef4f009fa890fce221da3ed8b08420269faee3169e48d754932a requirements: build: From be7eaae5fbc23767f09eb1d432944e41d12caea5 Mon Sep 17 00:00:00 2001 From: Kathryn Kananen Date: Sun, 29 Oct 2023 06:06:19 -0400 Subject: [PATCH 0494/2173] Add Phylogenize (#43941) --- recipes/phylogenize/build.sh | 2 ++ recipes/phylogenize/meta.yaml | 58 +++++++++++++++++++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 recipes/phylogenize/build.sh create mode 100644 recipes/phylogenize/meta.yaml diff --git a/recipes/phylogenize/build.sh b/recipes/phylogenize/build.sh new file mode 100644 index 0000000000000..9ae63aae5d8e2 --- /dev/null +++ b/recipes/phylogenize/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +R -e "devtools::install_bitbucket('pbradz/phylogenize/package/phylogenize')" diff --git a/recipes/phylogenize/meta.yaml b/recipes/phylogenize/meta.yaml new file mode 100644 index 0000000000000..cd42efff092fe --- /dev/null +++ b/recipes/phylogenize/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "0.91" %} +{% set sha256 = "3d428440f7a8aed3be18bbe094d3afe94f2d5357daa715d13e963c665384f2ab" %} +{% set name = "phylogenize" %} + +package: + name: phylogenize + version: "{{ version }}" + +source: + url: https://github.com/pbradleylab/phylogenize/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - perl =5.32.1 + - r-base =4.3.1 + - r-devtools <=2.4.5 + - vsearch =2.24.0 + - r-ragg <=1.2.6 + - r-phylolm =2.6.2 + - r-phangorn =2.11.1 + - 'bioconductor-ggtree <=3.8.0,>1.16.0' + - 'bioconductor-biomformat =1.28.0' + run: + - perl =5.32.1 + - r-base =4.3.1 + - r-devtools <=2.4.5 + - vsearch =2.24.0 + - r-ragg <=1.2.6 + - r-phylolm =2.6.2 + - r-phangorn =2.11.1 + - 'bioconductor-ggtree <=3.8.0,>1.16.0' + - 'bioconductor-biomformat =1.28.0' + +test: + commands: + - '$R -e "library(devtools)"' + - $R -e "devtools::install_github('pbradleylab/phylogenize/package/phylogenize')" + - '$R -e "?phylogenize"' + +about: + home: https://github.com/pbradleylab/phylogenize + license: MIT + summary: "Phylogenize is a tool that allows users to link microbial genes to environments, accounting for phylogeny." +extra: + recipe-maintainers: + - kekananen + indentifiers: + - doi: "https://doi.org/10.1093/bioinformatics/btz722" From d4ec16d4a3c46448915d08cee14d19e433ec7f90 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 29 Oct 2023 06:17:31 -0600 Subject: [PATCH 0495/2173] Update planemo to 0.75.15 (#43958) --- recipes/planemo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index a799baa098e11..017d0addc62e9 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "planemo" %} -{% set version = "0.75.14" %} -{% set sha256 = "d317157d1a68ef9ea6a6dfce101de7861a414bb8abe719c0c23188d503fdb984" %} +{% set version = "0.75.15" %} +{% set sha256 = "40ab64beb13f3d953761e70244aa55a88595627abcacba09f3286f7908464885" %} package: name: {{ name|lower }} From 7165ea8c05349591e1b9d9c19e1dc7dea9761226 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 29 Oct 2023 06:20:11 -0600 Subject: [PATCH 0496/2173] Update comebin to 1.0.3 (#43957) --- recipes/comebin/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/comebin/meta.yaml b/recipes/comebin/meta.yaml index d2ae3fbdb6298..655515c4b5f9f 100644 --- a/recipes/comebin/meta.yaml +++ b/recipes/comebin/meta.yaml @@ -1,10 +1,10 @@ package: name: comebin - version: "1.0.2" + version: "1.0.3" source: - url: https://github.com/ziyewang/COMEBin/archive/refs/tags/1.0.2.tar.gz - sha256: 8e1bfe609f723743f7e1703dfd89483a8a4def19b9e9a3283839c7eb7c93d1ab + url: https://github.com/ziyewang/COMEBin/archive/refs/tags/1.0.3.tar.gz + sha256: 27001cff1029ddf492da18ba8f4db18c055f48e062237bb9e17ad65ed7602930 build: number: 0 From f2f8c96c14242f5d2ecc9e92a8073d066f2d92ef Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 29 Oct 2023 06:20:48 -0600 Subject: [PATCH 0497/2173] Update taxmyphage to 0.2.3 (#43959) * Update taxmyphage to 0.2.2 * Update taxmyphage to 0.2.3 --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index 8974d4c1f6713..ec427135f67eb 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.2.1" %} +{% set version = "0.2.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: ccec70d7e0fbe0db8b205772a595e8673e6b2304ba4cfc74049bafe8640ba683 + sha256: 3eb12912217fd1020230756cf4d266922f98af7fbb2485ad69c7dc333f3bf6f0 build: entry_points: From 1ccecee24999ce8be41a95a4ba019da163431898 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 29 Oct 2023 06:24:15 -0600 Subject: [PATCH 0498/2173] Update pybiolib to 1.1.1478 (#43954) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 48c3ad2f8e154..68d39bc0f1c0f 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1476" %} +{% set version = "1.1.1478" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 424af1c0872ed329419a0302d25102104ad6dce87ef11cc0197c73c67b23a538 + sha256: ad9506793224ef0478eff3ab42200e8c77994e3c5705ba8f7f348f487c8267b3 build: noarch: python From d78b0d8c5a451c4b5d5d43bf7243ffef7fe7265b Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Sun, 29 Oct 2023 14:45:20 +0100 Subject: [PATCH 0499/2173] Update bioconductor-rhdf5filters: include run_exports and rebuild after bioconductor-rhdf5lib update (#43931) * include run_exports * set the used full_name variable * move build section to start of requirements * bump build number --- recipes/bioconductor-rhdf5filters/meta.yaml | 25 ++++++++++++++------- 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/recipes/bioconductor-rhdf5filters/meta.yaml b/recipes/bioconductor-rhdf5filters/meta.yaml index 35e8c317dedbf..5b9f894ca93e7 100644 --- a/recipes/bioconductor-rhdf5filters/meta.yaml +++ b/recipes/bioconductor-rhdf5filters/meta.yaml @@ -1,25 +1,39 @@ {% set version = "1.12.1" %} {% set name = "rhdf5filters" %} +{% set full_name = "bioconductor-" ~ name|lower %} {% set bioc = "3.17" %} package: - name: 'bioconductor-{{ name|lower }}' + name: '{{ full_name }}' version: '{{ version }}' source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ full_name }}/{{ full_name }}_{{ version }}_src_all.tar.gz' md5: 8cef74eea9c788b536c4561603f265b4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: + # This pinning is preliminary. It should be changed if either: + # * a general policy for pinning bioconductor packages is decided and differs: + # https://github.com/bioconda/bioconda-recipes/issues/43905 + # * the author of this package assures us that he adheres to semantic + # versioning, in which case we can unpin the minor version, see: + # https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782567153 + - {{ pin_subpackage(full_name, max_pin="x.x") }} # Suggests: BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.34.0) # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - r-base @@ -28,11 +42,6 @@ requirements: run: - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make test: commands: - '$R -e "library(''{{ name }}'')"' From e4038a7a27be9614d8a939dbce31cf3b71bd6d68 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Sun, 29 Oct 2023 18:33:31 +0100 Subject: [PATCH 0500/2173] Add missing pyopenms dependency (#43961) --- recipes/psm-utils/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index 4d3452e76f701..f3efb17639518 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 entry_points: - psm-utils=psm-utils.__main__:main script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" @@ -27,6 +27,7 @@ requirements: run: - python >=3.7 - pyteomics >=4 + - pyopenms - lxml - psims - pandas From b8ea8cf93b0b812877fd36912baa6790322db4ed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 29 Oct 2023 11:33:50 -0600 Subject: [PATCH 0501/2173] Update pyhmmer to 0.10.4 (#43962) --- recipes/pyhmmer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index f77198d955447..65622ccd0e60d 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.3" %} +{% set version = "0.10.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 761eaa5b4ea2054f926f5638c5bee4cf595841bed7ee3b14d548c27951602bad + sha256: 08bc02aadf0f113df2b2912478bb02be9daf5d322df9c72bcd07fa01fe53a87b build: number: 0 From 1a3584aa07ef381d1dbe6d641750dc594fc71325 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 29 Oct 2023 12:36:10 -0600 Subject: [PATCH 0502/2173] Update r-grain to 1.4.0 (#43956) * Update r-grain to 1.4.0 * run_exports * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/r-grain/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/r-grain/meta.yaml b/recipes/r-grain/meta.yaml index cd19680d1c453..56a8bae3d728e 100644 --- a/recipes/r-grain/meta.yaml +++ b/recipes/r-grain/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.3.14' %} +{% set version = '1.4.0' %} package: name: r-grain @@ -8,14 +8,15 @@ source: url: - {{ cran_mirror }}/src/contrib/gRain_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/gRain/gRain_{{ version }}.tar.gz - sha256: 28824922aa82e00af32917c38da69b813f935eb6a3ec7ea4020ccc68f0aacef0 + sha256: c0ccd33448fff881aea6b09927da99af37be63f4795abe4c65591fbbcbb09690 build: number: 0 rpaths: - lib/R/lib/ - lib/ - + run_exports: + - {{ pin_subpackage("r-grain", max_pin="x.x") }} requirements: build: - {{ compiler('c') }} From 37507e05747a1f0a18ae160166de17d0b10c97e3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 29 Oct 2023 13:23:01 -0600 Subject: [PATCH 0503/2173] Update nanoplot to 1.42.0 (#43960) * Update nanoplot to 1.42.0 * run_exports * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/nanoplot/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/nanoplot/meta.yaml b/recipes/nanoplot/meta.yaml index ca2e5abb6cf6d..b40260be1a127 100644 --- a/recipes/nanoplot/meta.yaml +++ b/recipes/nanoplot/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.41.6" %} +{% set version = "1.42.0" %} package: name: nanoplot @@ -6,14 +6,15 @@ package: source: url: https://pypi.io/packages/source/n/nanoplot/NanoPlot-{{ version }}.tar.gz - sha256: 94157f2d96c4849f5753fc7cc1a7c51e7cc74c20016e46bdd2f7b36d519291b7 + sha256: 0f8fd2cffd33a346b3306716058c6cb4091c931e8ab502f10b17a28749e8b6d9 build: entry_points: - NanoPlot=nanoplot.NanoPlot:main number: 0 noarch: python - + run_exports: + - {{ pin_subpackage("nanoplot", max_pin="x.x") }} requirements: host: - python >=3 From 12a16e8a8894bf5172e3510379150fe878ff3dbe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 29 Oct 2023 14:00:00 -0600 Subject: [PATCH 0504/2173] Update itolparser to 0.2.1 (#43964) * Update itolparser to 0.2.1 * add run_exports * edit tests --------- Co-authored-by: joshuazhuang7 --- recipes/itolparser/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/itolparser/meta.yaml b/recipes/itolparser/meta.yaml index f0e662973d928..5a97dfed5a9c4 100644 --- a/recipes/itolparser/meta.yaml +++ b/recipes/itolparser/meta.yaml @@ -1,5 +1,5 @@ {% set name = "itolparser" %} -{% set version = "0.1.6" %} +{% set version = "0.2.1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: ecb810be727d5984d7b7098927f3841e034a25ad6c09f1716ce1956c3ad435e0 + sha256: 8699adea2caf5ea1c645c5bc1abf4be8aa232a7c6c51f8a1f229c465408b6570 build: number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('itolparser', max_pin="x") }} requirements: host: @@ -27,14 +29,12 @@ requirements: test: commands: - itolparser -h - imports: - - itolparser_functions about: home: "https://github.com/boasvdp/itolparser" license: MIT license_family: MIT - license_file: LICENSE + license_file: LICENSE summary: "Small script to produce iTOL colorstrip metadata files from a table" extra: From e6fbca6f8a1207586b71dac3b979b80e90537dcc Mon Sep 17 00:00:00 2001 From: Mikhail Kolmogorov Date: Sun, 29 Oct 2023 14:05:57 -0700 Subject: [PATCH 0505/2173] Add severus (#43963) * add severus --- recipes/severus/build.sh | 3 +++ recipes/severus/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 recipes/severus/build.sh create mode 100644 recipes/severus/meta.yaml diff --git a/recipes/severus/build.sh b/recipes/severus/build.sh new file mode 100644 index 0000000000000..5227f51eca79f --- /dev/null +++ b/recipes/severus/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record record.txt diff --git a/recipes/severus/meta.yaml b/recipes/severus/meta.yaml new file mode 100644 index 0000000000000..51de9dbeecbb8 --- /dev/null +++ b/recipes/severus/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.1.1" %} + +package: + name: severus + version: {{ version }} + +source: + url: https://github.com/KolmogorovLab/Severus/archive/refs/tags/{{ version }}.tar.gz + sha256: aa9cf7bfc78234b770e5b67a38e6ee98ee94c1e45e11d61429d8e02df8793570 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('severus', max_pin='x.x') }} + +requirements: + host: + - python >=3.8 + - setuptools + - pip + run: + - python >=3.8 + - setuptools + - pip + - samtools >=1.14 + - networkx >=2.6 + - pygraphviz + - pydot + - matplotlib-base + - biopython + - numpy + - pysam + +extra: + skip-lints: + - uses_setuptools #uses pkg_resources + +test: + commands: + - severus -h | grep breakpoint + +about: + home: https://github.com/KolmogorovLab/Severus + license: BSD-3-Clause + summary: A tool for somatic structural variant calling using long reads From b42b78fce31507360f0f5a08e9388817851a24b0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 29 Oct 2023 16:29:14 -0600 Subject: [PATCH 0506/2173] Update micom to 0.33.0 (#43965) * Update micom to 0.33.0 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/micom/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/micom/meta.yaml b/recipes/micom/meta.yaml index d2cee25a7021d..2e740c6af928e 100644 --- a/recipes/micom/meta.yaml +++ b/recipes/micom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "micom" %} -{% set version = "0.32.5" %} +{% set version = "0.33.0" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b3e7024f266c8b6a2070475e7f8d30d1e5b9f35ff1a725331b90bc7e9dd35f0b + sha256: 489d15dd2b7aa14db6c2c2887069f3ef5588df95c06a2b397bd81bb8b8970604 build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: From f04d63db397a5484981a09fb4c9eca83f7aeccd9 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Mon, 30 Oct 2023 09:39:31 +0100 Subject: [PATCH 0507/2173] update bioconductor-rhdf5: rebuild after including libcurl dependency downstream in bioconductor-rhdf5lib, include pin_subpackage syntax (#43900) * fix: [bioconductor-rhdf5] explicitly include libcurl dependency I think that this will fix an issue with `libcrypto.so` not being found that I reported over at `rhdf5`: https://github.com/grimbough/rhdf5/issues/131 * bump version number * Update bioconductor-rhdf5: include `run_exports` with `pin_subpackage` * introduce full_name variable to include `bioconductor-` prefix * remove libcurl again, as this is handled downstream in bioconductor-rhd5flib This is the PR that handles this: https://github.com/bioconda/bioconda-recipes/pull/43930 And here's the discussion that pinpoints where the libcurl dependency belongs: https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782502851 * clean up full_name usage * include comment about pinning not necessarily being decided, yet * move the build section to the start of requirements * fix typo --- recipes/bioconductor-rhdf5/meta.yaml | 29 ++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 77ff1c59b2fd9..22e76300066cf 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -1,25 +1,39 @@ {% set version = "2.44.0" %} {% set name = "rhdf5" %} +{% set full_name = "bioconductor-" ~ name|lower %} {% set bioc = "3.17" %} package: - name: 'bioconductor-{{ name|lower }}' + name: '{{ full_name }}' version: '{{ version }}' source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ full_name }}/{{ full_name }}_{{ version }}_src_all.tar.gz' md5: 19c8340a70f1ce28043ba56bb9da1238 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: + # This pinning is preliminary. It should be changed if either: + # * a general policy for pinning bioconductor packages is decided and differs: + # https://github.com/bioconda/bioconda-recipes/issues/43905 + # * the author of this package assures us that he adheres to semantic + # versioning, in which case we can unpin the minor version, see: + # https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782567153 + - {{ pin_subpackage(full_name, max_pin="x.x") }} # Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' @@ -30,11 +44,6 @@ requirements: - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -47,7 +56,7 @@ extra: identifiers: - biotools:rhdf5 parent_recipe: - name: bioconductor-rhdf5 - path: recipes/bioconductor-rhdf5 + name: '{{ full_name }}' + path: 'recipes/{{ full_name }}' version: 2.24.0 From cc9faf17be6d854c63dc13ca680f1a1a4d765c97 Mon Sep 17 00:00:00 2001 From: Daniel Doerr Date: Mon, 30 Oct 2023 17:46:30 +0100 Subject: [PATCH 0508/2173] Update GFAffix (#43756) * Update meta.yaml * Add run_exports directory * Disable pinning * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml Here comes nothing! Really, I mean it. It's literally nothing and aimed only at triggering bioconda's merge checks. * Update meta.yaml Let's try the original version again * Update meta.yaml set allow_no_other_outputs=True --- recipes/gfaffix/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/gfaffix/meta.yaml b/recipes/gfaffix/meta.yaml index d9ed82ae1cf45..9bab54cd82305 100644 --- a/recipes/gfaffix/meta.yaml +++ b/recipes/gfaffix/meta.yaml @@ -1,5 +1,7 @@ {% set name = "GFAffix" %} -{% set version = "0.1.5" %} +{% set version = "0.1.5b" %} +{% set sha256 = "7a49a588c374670316f52f30d209766c93c99391e03d68262a0e40e75898e43c " %} + package: name: {{ name|lower }} @@ -7,10 +9,12 @@ package: source: url: https://github.com/marschall-lab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: cce2b5015b17065e90b6d3303d9dff6034ab89471f18a71e726b4dfffbe0dfe5 + sha256: {{ sha256 }} build: number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x.x", allow_no_other_outputs=True) }} requirements: build: From bc527b55a665f66bd4d84c87bc1755a97a85e350 Mon Sep 17 00:00:00 2001 From: Anders Jemt Date: Mon, 30 Oct 2023 17:47:16 +0100 Subject: [PATCH 0509/2173] build bump (#43923) --- recipes/vcf2cytosure/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/vcf2cytosure/meta.yaml b/recipes/vcf2cytosure/meta.yaml index b12cd42dbb2bb..72983aa7275bf 100644 --- a/recipes/vcf2cytosure/meta.yaml +++ b/recipes/vcf2cytosure/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - vcf2cytosure=vcf2cytosure.vcf2cytosure:main script: "{{ PYTHON }} -m pip install . -vv" From 49a3c23b399131304fe3d02d0d5d61b3910b0d53 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 14:54:29 -0600 Subject: [PATCH 0510/2173] Update mercat2 to 1.1 (#43967) --- recipes/mercat2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mercat2/meta.yaml b/recipes/mercat2/meta.yaml index b987d6a8d7705..bd0df0780487e 100644 --- a/recipes/mercat2/meta.yaml +++ b/recipes/mercat2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mercat2" %} -{% set version = "1.0" %} +{% set version = "1.1" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 30dd54de28e8648c83c6ed0a773934655d8b62ffc3a0541864848d9e618e4bf0 + sha256: 4e08b025e80f390980afdefd875bd24bcc6a72ae000be6733929975d56843062 build: - number: 1 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install . -vv" run_exports: From 32436080588f66d8d596cf80c0a194d0acd416b5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 14:54:42 -0600 Subject: [PATCH 0511/2173] Update plassembler to 1.4.1 (#43968) --- recipes/plassembler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/plassembler/meta.yaml b/recipes/plassembler/meta.yaml index 58e5f1b06aab3..e10aca1a997f6 100644 --- a/recipes/plassembler/meta.yaml +++ b/recipes/plassembler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "plassembler" %} -{% set version = "1.4.0" %} +{% set version = "1.4.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 90b7a25b742e871f02d9e9015173d162bf3bb0f0e6f7eaaca93854b194095ef0 + sha256: 86167accca01b6e33ae4bff780c6ccbd8f208af41f605cbedc6c78272959f88a build: number: 0 From 9c55d972ab7c3429986628b15cc1588fa7135b7e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 14:55:21 -0600 Subject: [PATCH 0512/2173] Update captus to 0.9.98 (#43972) --- recipes/captus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/captus/meta.yaml b/recipes/captus/meta.yaml index 2b734bfee4370..df3ba80239977 100644 --- a/recipes/captus/meta.yaml +++ b/recipes/captus/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.9.97" %} -{% set sha256 = "f01b262ab429849e0b7404caae01bb2ddec7fe81eec64b4f74accbc5e6fe6aa2" %} +{% set version = "0.9.98" %} +{% set sha256 = "b35d31d6c9c9ed2c2753f5e83346945f64357a00d3859236cda83f774320aeb9" %} package: name: captus From fdbf603cbd30d34ff56b98e7b204eba811400364 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 14:56:12 -0600 Subject: [PATCH 0513/2173] Update pybiolib to 1.1.1495 (#43970) * Update pybiolib to 1.1.1480 * Update pybiolib to 1.1.1483 * Update pybiolib to 1.1.1495 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 68d39bc0f1c0f..98e26822cf159 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1478" %} +{% set version = "1.1.1495" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: ad9506793224ef0478eff3ab42200e8c77994e3c5705ba8f7f348f487c8267b3 + sha256: 0390d2220960f1041b4bb68be93dca0fc6b36a6202bc6591c3ab3df6b69097b3 build: noarch: python From 7093aa3c5d32067f1686c5c5e387a213066a33f3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 15:03:23 -0600 Subject: [PATCH 0514/2173] Update spoa to 4.1.3 (#43975) --- recipes/spoa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/spoa/meta.yaml b/recipes/spoa/meta.yaml index 685666e09f6cf..ec3856161cf56 100644 --- a/recipes/spoa/meta.yaml +++ b/recipes/spoa/meta.yaml @@ -1,6 +1,6 @@ {% set name = "spoa" %} -{% set version = "4.1.2" %} -{% set sha256 = "5619c7f1a9ebb9a04550771d1834ff61c4aa377bea44fbd99912e4137b1ac1f7" %} +{% set version = "4.1.3" %} +{% set sha256 = "3f6c8de40a6163e68cf797d4040348db5f2b9ea067193c7ab78ce2582c10aa21" %} package: name: {{ name }} From ecc27308aff5af94193ae1b7b69b85ebb6d47c57 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 15:03:39 -0600 Subject: [PATCH 0515/2173] Update dxpy to 0.362.0 (#43974) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 2aa768cf2e5fe..8ff182ec2ab9a 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.361.0" %} +{% set version = "0.362.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 455c2a63764e7a1158cdb48abcf987e80d186fb92c23c539d8e6f2e4cc0368c7 + sha256: 18a397a9b2496f89751dd0ae4a6f38ea9143108af28b5d78ef2e74bd628cf90d build: number: 0 From cece2584fb644038ff97a428222115e404e61f85 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 15:40:57 -0600 Subject: [PATCH 0516/2173] Update snakedeploy to 0.9.1 (#43979) * Update snakedeploy to 0.9.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/snakedeploy/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/snakedeploy/meta.yaml b/recipes/snakedeploy/meta.yaml index 254146ce7a431..4a3d9f0e594f6 100644 --- a/recipes/snakedeploy/meta.yaml +++ b/recipes/snakedeploy/meta.yaml @@ -1,5 +1,4 @@ -{% set version = "0.8.6" %} - +{% set version = "0.9.1" %} package: name: snakedeploy @@ -7,14 +6,16 @@ package: source: url: https://pypi.io/packages/source/s/snakedeploy/snakedeploy-{{ version }}.tar.gz - sha256: 5f19eb36478ec26b5964ed260ac75292d42743c0a85b8077fc28fd399e5e7fc8 + sha256: 3ce399ae67f991647f62ff67a73649cbf786842d888c17a93b1f98b34bfb98e5 build: number: 0 noarch: python entry_points: - snakedeploy=snakedeploy.client:main - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv + run_exports: + - {{ pin_subpackage('snakedeploy', max_pin="x.x") }} requirements: host: From eab20844240f41e712447ccce75c33edca640ae5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 15:42:31 -0600 Subject: [PATCH 0517/2173] Update hiphase to 1.0.0 (#43981) --- recipes/hiphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index aca9785f60d1f..448e441c918b4 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "0.10.2" %} -{% set hiphase_sha256 = "2a20fc437ab5c0f2437246e8a36e7590c68f5ae5caa0cecb8e85a371f5357c6c" %} +{% set version = "1.0.0" %} +{% set hiphase_sha256 = "7aee796e83263a8158b0f5b3ed21ca701cf8fc3e7db275fec05f974a859c2510" %} package: name: {{ name }} From 8d91765becc5879707f450bc0f827d84efd8381d Mon Sep 17 00:00:00 2001 From: Jacob Morrison Date: Mon, 30 Oct 2023 17:45:49 -0400 Subject: [PATCH 0518/2173] Update biscuit to v1.3.0 (#43932) * update biscuit to v1.3.0 * add run_exports to biscuit * change dupsifter to biscuit * change pin to x.x --- recipes/biscuit/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/biscuit/meta.yaml b/recipes/biscuit/meta.yaml index ebf3a5127fee1..380b874c46af9 100644 --- a/recipes/biscuit/meta.yaml +++ b/recipes/biscuit/meta.yaml @@ -1,19 +1,21 @@ -{% set version = "1.2.1.20230601" %} +{% set version = "1.3.0.20231027" %} package: name: biscuit version: {{ version }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('biscuit', max_pin='x.x') }} source: - url: https://github.com/huishenlab/biscuit/releases/download/v{{ version }}/release-source.zip - sha256: 8462887bd0fd6bc1fdc04a390414710423d77d35cbd7f6800612735c63bd16a5 + sha256: 027d4343a49fde7c497f4a0292a2cb5bb475b4bcacedb17f251680dbf4f56995 patches: - patch - url: https://github.com/huishenlab/biscuit/releases/download/v{{ version }}/QC.sh - sha256: 8b3fe494c59691184b7584d5b7abee9506ce507518fe564f9a2be8a417f706bd + sha256: f2b9237f1166681a5f4e2cb0b297b2c2a086ea4975948a292b4871e391244b13 - url: https://github.com/huishenlab/biscuit/releases/download/v{{ version }}/build_biscuit_QC_assets.pl sha256: 7967240b63c8f816e7da79c3c0eb890933ec47df1114f6893b9e9736c8e564a8 From ed3b79f8870169ece5f90eb24a7d8a10fdeb613c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 15:46:44 -0600 Subject: [PATCH 0519/2173] Update atlas-fastq-provider to 0.4.7 (#43978) * Update atlas-fastq-provider to 0.4.7 * fix atlas-fastq-provider * "x.x" as version starts with a 0 --------- Co-authored-by: Jonathan Manning Co-authored-by: Pedro Madrigal <8195212+pmb59@users.noreply.github.com> --- recipes/atlas-fastq-provider/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/atlas-fastq-provider/meta.yaml b/recipes/atlas-fastq-provider/meta.yaml index ea7af33e445c4..ff46a16c2692f 100644 --- a/recipes/atlas-fastq-provider/meta.yaml +++ b/recipes/atlas-fastq-provider/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.6" %} +{% set version = "0.4.7" %} package: name: atlas-fastq-provider @@ -6,11 +6,13 @@ package: source: url: https://github.com/ebi-gene-expression-group/atlas-fastq-provider/archive/v{{ version }}.tar.gz - sha256: e3c9c7dbbf9447576167ba5d24911b6e794184fd16ec1c80ecc38f8e0bb766a6 + sha256: 578d1b69a7582fa47073ba4ad7b3bf98df4aceea6fe96a25bb38674a1d362f33 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage("atlas-fastq-provider", max_pin="x.x") }} requirements: build: From 45e41a8f6d98efa4e63e3cb4479b8779bf121aa2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 16:38:07 -0600 Subject: [PATCH 0520/2173] Update mzmine to 3.9.0 (#42030) * Update mzmine to 3.7.0 * Update mzmine to 3.7.2 * Update mzmine to 3.8.0 * Update mzmine to 3.9.0 * Update meta.yaml * Update meta.yaml * update patch --------- Co-authored-by: Devon Ryan Co-authored-by: M Bernt --- recipes/mzmine/build.patch | 18 +++++++++--------- recipes/mzmine/meta.yaml | 6 ++++-- 2 files changed, 13 insertions(+), 11 deletions(-) diff --git a/recipes/mzmine/build.patch b/recipes/mzmine/build.patch index dcfd2832aa3ff..81685331a8262 100644 --- a/recipes/mzmine/build.patch +++ b/recipes/mzmine/build.patch @@ -1,9 +1,9 @@ # - without installerType set jpackage tries to create rpm and deb # we don't need any of them, but I did not find a way to disable # both. so we leave rpm which is available in conda (spkg isn't) -diff -ruN mzmine3-3.6.0-org/build.gradle mzmine3-3.6.0/build.gradle ---- mzmine3-3.6.0-org/build.gradle 2023-06-21 14:39:23.000000000 +0200 -+++ mzmine3-3.6.0/build.gradle 2023-06-22 17:53:22.239977816 +0200 +diff -ruN mzmine3-3.9.0-org/build.gradle mzmine3-3.9.0/build.gradle +--- mzmine3-3.9.0-org/build.gradle 2023-06-21 14:39:23.000000000 +0200 ++++ mzmine3-3.9.0/build.gradle 2023-06-22 17:53:22.239977816 +0200 @@ -392,7 +392,7 @@ if (OperatingSystem.current().isLinux()) { // leave installer type empty to generate all that match @@ -14,15 +14,15 @@ diff -ruN mzmine3-3.6.0-org/build.gradle mzmine3-3.6.0/build.gradle imageOptions = ["--icon", "src/main/resources/MZmineIcon.png"] installerOptions = ["--linux-shortcut", # version is set wrong https://github.com/mzmine/mzmine3/issues/1405 -diff -ruN mzmine3-3.6.0-org/src/main/resources/mzmineversion.properties mzmine3-3.6.0/src/main/resources/mzmineversion.properties ---- mzmine3-3.6.0-org/src/main/resources/mzmineversion.properties 2023-06-21 14:39:23.000000000 +0200 -+++ mzmine3-3.6.0/src/main/resources/mzmineversion.properties 2023-06-22 19:14:12.455764423 +0200 +diff -ruN mzmine3-3.9.0-org/src/main/resources/mzmineversion.properties mzmine3-3.9.0/src/main/resources/mzmineversion.properties +--- mzmine3-3.9.0-org/src/main/resources/mzmineversion.properties 2023-06-21 14:39:23.000000000 +0200 ++++ mzmine3-3.9.0/src/main/resources/mzmineversion.properties 2023-06-22 19:14:12.455764423 +0200 @@ -3,6 +3,6 @@ version.buildmeta= version.major=3 - version.minor=6 + version.minor=9 -version.patch=1 +version.patch=0 version.prerelease= --version.semver=3.6.1 -+version.semver=3.6.0 +-version.semver=3.9.1 ++version.semver=3.9.0 diff --git a/recipes/mzmine/meta.yaml b/recipes/mzmine/meta.yaml index 74db59cb8c9e1..84b0ebd88566b 100644 --- a/recipes/mzmine/meta.yaml +++ b/recipes/mzmine/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.6.0" %} +{% set version = "3.9.0" %} package: name: mzmine @@ -7,10 +7,12 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('mzmine', max_pin='x') }} source: - url: https://github.com/mzmine/mzmine3/archive/refs/tags/v{{ version }}.tar.gz - sha256: 0446c3e9c0fa777904fcb1354a57aaf611ef5718042930fd8c243c9245157ef2 + sha256: ca0c206f63201e82d6e7e337c373449e69b4510dbd51adec8f13bed519e07257 patches: - "build.patch" From 63f4fe5d967edb9c1de25a317f9a5c75bc445d33 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 16:56:07 -0600 Subject: [PATCH 0521/2173] Update pxblat to 1.1.8 (#43969) * Update pxblat to 1.1.2 * Update pxblat to 1.1.5 * Update pxblat to 1.1.7 * Update pxblat to 1.1.8 * edit dependencies --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pxblat/meta.yaml | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index e94e092e49f68..53d2ffda50e87 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "1.1.1" %} -{% set sha256 = "df8d366c01fc79fa6a5a6200f6e76df5c18666219368404cfd456b49e109c9e0" %} +{% set version = "1.1.8" %} +{% set sha256 = "3c5609e8be17c77c3740ffa016d1ca7e5072d2a34581fe4327ca7f10ac3bb629" %} package: name: {{ name|lower }} @@ -12,8 +12,10 @@ source: build: number: 0 - skip: True # [py < 39] - script: {{ PYTHON }} -m pip install . --no-deps --use-pep517 -vvv + skip: True # [py < 38] + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + entry_points: + - pxblat = pxblat.cli.cli:app run_exports: - {{ pin_subpackage('pxblat', max_pin="x") }} @@ -26,20 +28,16 @@ requirements: - poetry-core >=1.2.0 - pybind11 >=2.9.1 - setuptools >=46.4 - - htslib - - openssl - - zlib run: - python - loguru + - pybind11 >=2.10.4 - rich - pysimdjson - biopython - typer - deprecated - mashumaro - - numpy >=1.24.3 - - gevent - urllib3 test: From 20683e39f676ee584741311af3ef250fd4d7fd2c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 17:13:37 -0600 Subject: [PATCH 0522/2173] Update ontime to 0.2.2 (#43973) * Update ontime to 0.2.1 * add run_exports * Update ontime to 0.2.2 --------- Co-authored-by: joshuazhuang7 --- recipes/ontime/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/ontime/meta.yaml b/recipes/ontime/meta.yaml index 379b445a83dde..f6a2639c0f31a 100644 --- a/recipes/ontime/meta.yaml +++ b/recipes/ontime/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.3" %} +{% set version = "0.2.2" %} {% set name = "ontime" %} package: @@ -7,10 +7,12 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz - sha256: ce1b03582969694f06e62dd7c2445fb17ba240b8539220cad0b79317b42d360f + sha256: f24f3b617fa56230a4a3b32a32a19bba4f2684a0abc7538902a2dee63a87521c build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('ontime', max_pin="x.x") }} requirements: build: @@ -24,6 +26,7 @@ test: about: home: https://github.com/mbhall88/ontime license: MIT + license_family: MIT summary: Extract subsets of ONT (Nanopore) reads based on time license_file: LICENSE From 89313fc57b94c8d717f27928c7566e7de457577c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 18:17:17 -0600 Subject: [PATCH 0523/2173] Update psm-utils to 0.7.1 (#43983) * Update psm-utils to 0.7.1 * edit run_exports as versioning is 0.x.x --------- Co-authored-by: joshuazhuang7 --- recipes/psm-utils/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index f3efb17639518..1f6d413af873c 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.7.0" %} -{% set sha256 = "c6d86813cc9c698a31fd7f458e73b1e2cb0e007a426603c8a82ea94c6f003080" %} +{% set version = "0.7.1" %} +{% set sha256 = "b4d1a6da74cb0fe7601b5f9c106826a3dfb8d85011e23bcc18ce022bafa4fc16" %} package: name: {{ name|lower }} @@ -11,13 +11,13 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 entry_points: - psm-utils=psm-utils.__main__:main script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python run_exports: - - {{ pin_subpackage('psm-utils', max_pin="x") }} + - {{ pin_subpackage('psm-utils', max_pin="x.x") }} requirements: host: From 41a000d36ccae9b080aebce041b170aa62ac67a2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 20:43:18 -0600 Subject: [PATCH 0524/2173] Update ontime to 0.2.3 (#43985) --- recipes/ontime/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ontime/meta.yaml b/recipes/ontime/meta.yaml index f6a2639c0f31a..84e0131fe612f 100644 --- a/recipes/ontime/meta.yaml +++ b/recipes/ontime/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.2" %} +{% set version = "0.2.3" %} {% set name = "ontime" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz - sha256: f24f3b617fa56230a4a3b32a32a19bba4f2684a0abc7538902a2dee63a87521c + sha256: 6ac4f5e76cb01c16e306661d865a11918604873b5d057afa1a8a37dc4829e682 build: number: 0 From fad5de0a7ef168e974a5b57942ed114dd8f44d9b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 30 Oct 2023 23:47:25 -0600 Subject: [PATCH 0525/2173] Update semibin to 2.0.2 (#43989) --- recipes/semibin/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/semibin/meta.yaml b/recipes/semibin/meta.yaml index c56e56d7083b8..bdc98bc800525 100644 --- a/recipes/semibin/meta.yaml +++ b/recipes/semibin/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SemiBin" %} -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 835743d810012b2edf33274d335adfced5b861a6bb61d945572a88af469f3506 + sha256: b428a68fa9a16e6c713001f8f5afb0b19ae1997a10b66c54076a72d75b1ad8d8 build: noarch: python From a3ab7ab6ecbc3f0f793c271991a3252cd364dbaf Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Tue, 31 Oct 2023 03:04:56 -0700 Subject: [PATCH 0526/2173] Update auspice to 2.50.0 (#43984) --- recipes/auspice/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/auspice/meta.yaml b/recipes/auspice/meta.yaml index b49647d77b8c5..32592ef4fcbe1 100644 --- a/recipes/auspice/meta.yaml +++ b/recipes/auspice/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.49.0" %} +{% set version = "2.50.0" %} package: name: auspice @@ -6,7 +6,7 @@ package: source: url: https://registry.npmjs.org/auspice/-/auspice-{{ version }}.tgz - sha256: b2da7108dabc7edee7545edb00763ab35280688b70ecef482c7f063bb1994a9a + sha256: 60642de3c9cbbce388a81668f1d116ca8c28520abe5770298dd51aebd94660b0 build: number: 0 From 656e87dc5a3a2bc9133f85fb351776d31db8f7d6 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Tue, 31 Oct 2023 11:15:28 +0100 Subject: [PATCH 0527/2173] Update OpenMS thirdparty dependency (#43971) --- recipes/openms-meta/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/openms-meta/meta.yaml b/recipes/openms-meta/meta.yaml index b9142df48e67a..e23a028516e73 100644 --- a/recipes/openms-meta/meta.yaml +++ b/recipes/openms-meta/meta.yaml @@ -16,7 +16,7 @@ source: {% endif %} build: - number: 2 + number: 3 skip: True # [osx] # Try this when building with GUI @@ -150,7 +150,7 @@ outputs: - conda-forge::sirius-ms ==5.8.2 - thermorawfileparser ==1.4.3 - xtandem ==15.12.15.2 - - sage-proteomics ==0.14.3 + - sage-proteomics ==0.14.4 - gnuplot - r-gplots test: From f13ae6ca9933f515cf706cf378d0469d0b4cd1a0 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 31 Oct 2023 12:09:07 +0100 Subject: [PATCH 0528/2173] Update: gtfparse: fix dependency (#43977) * gtfparse: add polars<0.17 as >=0.17 is incompatible * increase build number * add build run export * remove redundant build run export * pin x to x.x --------- Co-authored-by: Thanh Lee Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> --- recipes/gtfparse/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gtfparse/meta.yaml b/recipes/gtfparse/meta.yaml index 1323ff3fa7935..a5ac6588aa3d5 100644 --- a/recipes/gtfparse/meta.yaml +++ b/recipes/gtfparse/meta.yaml @@ -11,11 +11,11 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . --no-deps -vvv run_exports: - - {{ pin_subpackage('gtfparse', max_pin="x") }} + - {{ pin_subpackage('gtfparse', max_pin="x.x") }} requirements: host: @@ -23,7 +23,7 @@ requirements: - pip run: - python - - polars + - polars <0.17 - numpy >=1.7 - pandas >=0.15 From 05c99f8db0ebe6a8e10680ef08ec41f7dbe6192d Mon Sep 17 00:00:00 2001 From: Joe Wirth <71667025+dr-joe-wirth@users.noreply.github.com> Date: Tue, 31 Oct 2023 09:56:57 -0400 Subject: [PATCH 0529/2173] Add phantasm-xenogi (#43736) * added recipe for phantasm-xenogi * added sha256 * add run_exports and test * got test passing * updated the sha256 to the current release * updated xenoGI version, sha256, and python3 version * add spdx --------- Co-authored-by: Robert A. Petit III --- recipes/phantasm-xenogi/meta.yaml | 43 +++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 recipes/phantasm-xenogi/meta.yaml diff --git a/recipes/phantasm-xenogi/meta.yaml b/recipes/phantasm-xenogi/meta.yaml new file mode 100644 index 0000000000000..5a4b7c0e9f895 --- /dev/null +++ b/recipes/phantasm-xenogi/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "xenoGI" %} +{% set version = "3.1.2" %} + +package: + name: "phantasm-{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: ef4254f1dfef45888480aaa2db908d6afff648d446eff29a4f6c2df93e1209f0 + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('phantasm-xenogi', max_pin="x") }} + +requirements: + host: + - python >=3.9 + - pip + run: + - biopython + - blast + - fasttree + - generax + - muscle >=5 + - numpy + - parasail-python + - python >=3.9 + - scipy + +test: + commands: + - touch $PREFIX/tmp.py && xenoGI $PREFIX/tmp.py version + +about: + home: https://github.com/dr-joe-wirth/{{ name }} + license: GPL-3.0 + license_family: GPL3 + license_file: LICENSE + summary: "xenoGI for PHANTASM" From 3c1c7621850c20f57c028b55c7898cc0df66b42d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 31 Oct 2023 11:32:50 -0600 Subject: [PATCH 0530/2173] Update cramino to 0.13.1 (#43999) --- recipes/cramino/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cramino/meta.yaml b/recipes/cramino/meta.yaml index dc7c845506e1b..0d07842df6aad 100644 --- a/recipes/cramino/meta.yaml +++ b/recipes/cramino/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.13.0" %} +{% set version = "0.13.1" %} package: name: cramino @@ -12,7 +12,7 @@ build: source: url: https://github.com/wdecoster/cramino/archive/v{{ version }}.tar.gz - sha256: ed88f207f0fbcac4f19d56c05cef715069b6f00518ccb9df267cfb46afaf9e37 + sha256: 92e60915b2fccacb21f2c5b71253b667615e1a99f964f232569122458cf64c40 requirements: build: From 9f8a1d35c729754ea56d9fce96e9cf756476a1cb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 31 Oct 2023 14:16:39 -0600 Subject: [PATCH 0531/2173] Update earlgrey to 3.2 (#43997) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index 394a1630e30cb..187a257bbae45 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "3.1" %} -{% set sha256 = "ae448b2f7edcb484a6cfd5b41be95e589c74e8c18eada391a3a87c81f19ed06b" %} +{% set version = "3.2" %} +{% set sha256 = "2a6423bcc267fc6c4287d7b8e29484ba216a305d6c3aa9d994d474962a64abca" %} package: name: {{ name|lower }} From 6d9708e4dfb60ed0eef1cbe2f5fe03485fc40675 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 31 Oct 2023 14:16:59 -0600 Subject: [PATCH 0532/2173] Update oakvar to 2.9.54 (#43986) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 929115cd483f2..59cfac10fec0f 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.53" %} -{% set sha256 = "d2cc4f1762fd90afc3b7a0721b5be04a5bae6530cf8849fbf1fd7831daa63acf" %} +{% set version = "2.9.54" %} +{% set sha256 = "1b497437aac7a779fd22452b39228ac0af034ac55f0acd7c858e7a9970215a50" %} package: name: {{ name|lower }} From 1df786aca27baad1e0212b41490b3e027b587dfd Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Wed, 1 Nov 2023 05:18:30 +0900 Subject: [PATCH 0533/2173] Update MMseqs2 to Release 15 (#43991) * MMseqs2 build for ARM64 * Add run_exports * Update MMseqs2 to Release 15 --- recipes/mmseqs2/build.sh | 13 ++++++++++++- recipes/mmseqs2/meta.yaml | 10 +++++++--- 2 files changed, 19 insertions(+), 4 deletions(-) diff --git a/recipes/mmseqs2/build.sh b/recipes/mmseqs2/build.sh index dccd8da45922c..b06956020200b 100644 --- a/recipes/mmseqs2/build.sh +++ b/recipes/mmseqs2/build.sh @@ -1,7 +1,18 @@ #!/bin/bash +ARCH_BUILD="" +case $(uname -m) in + x86_64) ARCH_BUILD="-DHAVE_SSE4_1=1" ;; + arm64|aarch64) ARCH_BUILD="-DHAVE_ARM8=1" ;; +esac + +if [ -z "${ARCH_BUILD}" ]; then + echo "Invalid architecture" + exit 1 +fi + mkdir build cd build -cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 -DHAVE_SSE4_1=1 -DVERSION_OVERRIDE="${PKG_VERSION}" .. +cmake -DCMAKE_INSTALL_PREFIX="${PREFIX}" -DHAVE_TESTS=0 -DHAVE_MPI=0 ${ARCH_BUILD} -DVERSION_OVERRIDE="${PKG_VERSION}" .. make -j${CPU_COUNT} ${VERBOSE_CM} make install diff --git a/recipes/mmseqs2/meta.yaml b/recipes/mmseqs2/meta.yaml index 670a0ce949518..e7ecac44899cc 100644 --- a/recipes/mmseqs2/meta.yaml +++ b/recipes/mmseqs2/meta.yaml @@ -1,12 +1,14 @@ -{% set version = "14-7e284" %} -{% set sha256 = "a15fd59b121073fdcc8b259fc703e5ce4c671d2c56eb5c027749f4bd4c28dfe1" %} +{% set version = "15-6f452" %} +{% set sha256 = "7115ac5a7e2a49229466806aaa760d00204bb08c870e3c231b00e525c77531dc" %} package: name: mmseqs2 version: {{ version|replace("-", ".") }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('mmseqs2', max_pin=None) }} source: url: https://github.com/soedinglab/mmseqs2/archive/{{ version }}.tar.gz @@ -50,3 +52,5 @@ extra: - doi:10.1101/2020.11.27.401018 - biotools:mmseqs2 - biotools:linclust + additional-platforms: + - linux-aarch64 From a320863212a3a40e3d3f45bc416a1799d1300b68 Mon Sep 17 00:00:00 2001 From: kowallus Date: Tue, 31 Oct 2023 21:19:08 +0100 Subject: [PATCH 0534/2173] Update mbgc recipe (#44002) * updated mbgc recipe to v2.0 * updated build section in meta.yaml --- recipes/mbgc/build.sh | 1 - recipes/mbgc/meta.yaml | 11 ++++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/mbgc/build.sh b/recipes/mbgc/build.sh index 2e01843378622..241cc53ea2f60 100644 --- a/recipes/mbgc/build.sh +++ b/recipes/mbgc/build.sh @@ -8,7 +8,6 @@ export CXXPATH=${BUILD_PREFIX}/include export CFLAGS="$CFLAGS -I$BUILD_PREFIX/include" export CXXFLAGS="$CFLAGS -I$BUILD_PREFIX/include" export LDFLAGS="$LDFLAGS -L$BUILD_PREFIX/lib" -cp $BUILD_PREFIX/lib/libdeflate.h $BUILD_PREFIX/include/ cmake .. make mbgc cp mbgc $PREFIX/bin diff --git a/recipes/mbgc/meta.yaml b/recipes/mbgc/meta.yaml index 9176ad183af56..cc8deff5207e3 100644 --- a/recipes/mbgc/meta.yaml +++ b/recipes/mbgc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.1" %} +{% set version = "2.0" %} package: name: mbgc @@ -6,18 +6,19 @@ package: build: skip: True # [osx] - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage('mbgc', max_pin="x") }} source: url: https://github.com/kowallus/mbgc/archive/refs/tags/v{{ version }}.tar.gz - sha256: 7c1e01caa8128fe2467132b6ee53b1c2a1375f3127866f1bf81ed2d129bf206a + sha256: 58620079cd813cd7bc8c5362af514fb92bf166a71f7f5f978923e36dd5bd655d requirements: build: - {{ compiler('cxx') }} - - cmake >=3.4 + - cmake >=3.5 - make - - libdeflate =1.2 test: commands: From eb5354b6f6cd9857c7edb00a6c2dce4e3c5daa22 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 31 Oct 2023 16:53:16 -0600 Subject: [PATCH 0535/2173] Update pybiolib to 1.1.1499 (#44003) * Update pybiolib to 1.1.1497 * Update pybiolib to 1.1.1499 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 98e26822cf159..9018ff953bcb6 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1495" %} +{% set version = "1.1.1499" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 0390d2220960f1041b4bb68be93dca0fc6b36a6202bc6591c3ab3df6b69097b3 + sha256: 8628c079d230e56beee5767584ab783e03625cf7689d4209355e6e5bdcb7d96c build: noarch: python From 4dd9bafa10f311bc236fca3509b9f9472df5efa6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 31 Oct 2023 23:24:08 -0600 Subject: [PATCH 0536/2173] Update perl-math-bigint to 2.000000 (#44005) --- recipes/perl-math-bigint/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-math-bigint/meta.yaml b/recipes/perl-math-bigint/meta.yaml index ecb66eceeb05a..215290cbdcac4 100644 --- a/recipes/perl-math-bigint/meta.yaml +++ b/recipes/perl-math-bigint/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-math-bigint" %} -{% set version = "1.999842" %} -{% set sha256 = "54601c50c6993e7ee13d8c3ac3346cf15a4d8063149cdbbe86eb01e5610e4675" %} +{% set version = "2.000000" %} +{% set sha256 = "7d111a47431294db99cd130ff8586e88f0e9b64b4e7fb3bb3e15dec5fd14f1c7" %} package: name: {{ name }} From 3a45d822627862bbbd6395feec9ec6a032dd3a1c Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Wed, 1 Nov 2023 15:29:39 +0900 Subject: [PATCH 0537/2173] ColabFold 1.5.3 (#43715) --- recipes/colabfold/meta.yaml | 73 +++++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 recipes/colabfold/meta.yaml diff --git a/recipes/colabfold/meta.yaml b/recipes/colabfold/meta.yaml new file mode 100644 index 0000000000000..f5962e107e4bd --- /dev/null +++ b/recipes/colabfold/meta.yaml @@ -0,0 +1,73 @@ +{% set cf_version = "1.5.3" %} +{% set cf_hash = "1b2776f285981796559effbc3691ebbcfcde68514cc05559583ebab76c4c25e8" %} +{% set af_version = "2.3.5" %} +{% set af_hash = "6244c2143987dd4a6a87c1174c7a801c220034fbeb8d13f901b0f950b69d8543" %} + +package: + name: colabfold + version: {{ cf_version }} + +build: + noarch: python + script: | + python -m pip install --no-deps --ignore-installed colabfold/ + python -m pip install --no-deps --ignore-installed alphafold/ + run_exports: + - {{ pin_subpackage('colabfold', max_pin="x") }} + number: 0 + +source: + - url: https://github.com/sokrypton/ColabFold/archive/refs/tags/v{{ cf_version }}.tar.gz + sha256: {{ cf_hash }} + folder: colabfold + - url: https://github.com/steineggerlab/alphafold/archive/refs/tags/v{{ af_version }}.tar.gz + sha256: {{ af_hash }} + folder: alphafold + +requirements: + host: + - pip + - python + - poetry + run: + - python + - absl-py + - matplotlib-base + - numpy + - scipy + - requests + - tqdm + - pandas + - appdirs + - py3Dmol + - dm-haiku + - dm-tree + - ml-collections + - immutabledict + - importlib-metadata + - biopython + - jax ==0.4.14 + - jaxlib ==0.4.14 + - chex ==0.1.8 + - tensorflow ==2.12.1=cpu* + - mmseqs2 >=15.6f452 + - kalign2 >=2.04 + - hhsuite >=3.3.0 + - openmm ==7.7.0 + - pdbfixer + +test: + commands: + - which colabfold_batch + +about: + home: https://github.com/sokrypton/ColabFold + summary: "ColabFold: making protein folding accessible to all" + license: MIT + +extra: + identifiers: + - doi:10.1038/s41592-022-01488-1 + - biotools:colabfold + recipe-maintainers: + - milot-mirdita From ef98340151159d82996db1ce52170e710f2c1f56 Mon Sep 17 00:00:00 2001 From: Adrian Altenhoff Date: Wed, 1 Nov 2023 09:23:38 +0100 Subject: [PATCH 0538/2173] Adds Rmath4 library (#44001) --- recipes/rmath4/meta.yaml | 46 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/rmath4/meta.yaml diff --git a/recipes/rmath4/meta.yaml b/recipes/rmath4/meta.yaml new file mode 100644 index 0000000000000..4a32e38ee15a5 --- /dev/null +++ b/recipes/rmath4/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "rmath4" %} +{% set version = "4.3.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/Rmath4-{{ version }}.tar.gz + sha256: c39a75e1c883fd6f5d6b6677213b4e0704ce014f060d0d00b89f5ff608b72300 + +build: + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - python + - setuptools + - wheel + - pip + run: + - python + +test: + imports: + - Rmath4 + commands: + - pip check + - python -c "import Rmath4; assert 0<=Rmath4.unif_rand()<1" + requires: + - pip + +about: + home: https://github.com/alex-wave/Rmath-python + summary: standalone Rmath library from R + license: GPL-2.0 + license_file: COPYING + +extra: + recipe-maintainers: + - alpae From 77949dcc104c3f60f3351fc4392532ea6fea7012 Mon Sep 17 00:00:00 2001 From: mjohnpayne Date: Wed, 1 Nov 2023 21:36:06 +1100 Subject: [PATCH 0539/2173] Update stecfinder to 1.1.1 (#44016) * Update stecfinder to 1.1.1 * Update stecfinder to 1.1.1 * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/stecfinder/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/stecfinder/meta.yaml b/recipes/stecfinder/meta.yaml index bc0c594097248..93560d5d7a168 100644 --- a/recipes/stecfinder/meta.yaml +++ b/recipes/stecfinder/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.0" %} +{% set version = "1.1.1" %} {% set name = "stecfinder" %} package: @@ -7,12 +7,14 @@ package: source: url: https://github.com/LanLab/{{ name }}/archive/v{{ version }}.tar.gz - sha256: a22dfd6a68ae5146dc7a4c101727dbf039fab0673d4091cf92c46b4b6d4e8839 + sha256: 270a80b78f7ab9d69f35b67128da967e23a08538a608dc919865158236ca5de5 build: noarch: python number: 0 script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_subpackage('stecfinder', max_pin="x.x") }} requirements: host: From aa60015a2ebf92da7e1e2e9089ec5a2e67148579 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 07:23:18 -0600 Subject: [PATCH 0540/2173] Update sdm to 2.14 (#44019) --- recipes/sdm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sdm/meta.yaml b/recipes/sdm/meta.yaml index a6d9470841bc6..5045bdd0bd67c 100644 --- a/recipes/sdm/meta.yaml +++ b/recipes/sdm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sdm" %} -{% set version = "2.13" %} +{% set version = "2.14" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/hildebra/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 9942b7190825353eeff89d0af1a269e91d71a28671bc4ec2746f2b4922781140 + sha256: 08bbfecf0cff39511198405774fe845c339b6e684df5ff2e50e4aa76ce7d4399 patches: - sdm_1.83.patch From a23dfe22f61a09b87a3ebfd2c53ac2b5a3ce551b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 09:02:30 -0600 Subject: [PATCH 0541/2173] Update hybracter to 0.2.1 (#44015) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index 997def4ef97a0..14f18c8cdb326 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 46d9c4422cb97bb553d579f4c9d87abfbdcfc3e770d2e280db8ab2e7d5d229af + sha256: 2d696acaeb4999234ee5c7190ec9e63ee2c9c4bdea3e47e4d8363d44e458b7a0 build: number: 0 From ede857f149b965fd85b8bb1e4d97bdbd10ab89ba Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 10:17:00 -0600 Subject: [PATCH 0542/2173] Update cptac to 1.5.7 (#43980) * Update cptac to 1.5.6 * Update cptac to 1.5.7 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cptac/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cptac/meta.yaml b/recipes/cptac/meta.yaml index 877c6c133951f..715c3afce8b96 100644 --- a/recipes/cptac/meta.yaml +++ b/recipes/cptac/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cptac" %} -{% set version = "1.5.5" %} +{% set version = "1.5.7" %} package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8f68c964443bf9774905e909930207ea0f203e6efa48433a92cafc9b3a39f19f + sha256: 824e255f63b003479cda300c141b60f482c0b0e6dbd0dbd2489b64c1e470d070 build: number: 0 From 057b61cee32e49d9138ad765cd617a6bc7eee6f3 Mon Sep 17 00:00:00 2001 From: Adrian Altenhoff Date: Wed, 1 Nov 2023 17:30:45 +0100 Subject: [PATCH 0543/2173] Add pysais library (#44000) * Add pysais library * fix linting error * fix linting error * runtime does not need full dependencies, e.g. cython not required --- recipes/pysais/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/pysais/meta.yaml diff --git a/recipes/pysais/meta.yaml b/recipes/pysais/meta.yaml new file mode 100644 index 0000000000000..b6fe70a385acb --- /dev/null +++ b/recipes/pysais/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "pysais" %} +{% set version = "1.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/PySAIS-{{ version }}.tar.gz + sha256: 6547748a32ab876c1a50553b63d486d585f12a40352387a932eab8b908a13f20 + +build: + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - python + - setuptools + - wheel + - numpy + - cython >=3.0.0 + - pip + run: + - python + - pytables + - {{ pin_compatible('numpy') }} + +test: + imports: + - PySAIS + commands: + - python3 -c "import PySAIS, numpy; arr=numpy.fromiter('ADARINA','S1'); assert(arr[PySAIS.sais(arr.tobytes())].tobytes() == b'AAADINR')" + +about: + home: https://bitbucket.org/alex-warwickvesztrocy/pysais + summary: Suffix array computation with induced sorting algorithm. + license: MIT + license_file: PySAIS/COPYING + +extra: + recipe-maintainers: + - alpae From a41508bffdc2e2d945e4e8fb9f394b7ead2899c2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 10:31:33 -0600 Subject: [PATCH 0544/2173] Update paraphase to 3.0.0 (#44009) * Update paraphase to 3.0.0 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/paraphase/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/paraphase/meta.yaml b/recipes/paraphase/meta.yaml index cb1be59e43301..df5ccd7268957 100644 --- a/recipes/paraphase/meta.yaml +++ b/recipes/paraphase/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.2.3" %} -{% set sha256 = "02f9117efbe9587faafc2fdf82bba8716c37c43429293dafe0542b7963e8cc54" %} +{% set version = "3.0.0" %} +{% set sha256 = "d26599b567e7e57003daedc5645cf19fc92789f1a4e88baff2e092723fbc3085" %} package: name: paraphase @@ -15,6 +15,8 @@ build: entry_points: - paraphase = paraphase.__main__:main script: python -m pip install --no-deps -vv . + run_exports: + - {{ pin_subpackage("paraphase", max_pin="x.x") }} requirements: host: From 2c481d76829bac1d59057a097b1a0a4976af4985 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 10:41:04 -0600 Subject: [PATCH 0545/2173] Update trust4 to 1.0.13 (#44006) * Update trust4 to 1.0.13 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/trust4/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/trust4/meta.yaml b/recipes/trust4/meta.yaml index 2398a7982137e..5dcd3365b3e4f 100644 --- a/recipes/trust4/meta.yaml +++ b/recipes/trust4/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.12" %} +{% set version = "1.0.13" %} package: name: trust4 @@ -6,10 +6,12 @@ package: build: number: 0 + run_exports: + - {{ pin_subpackage('trust4', max_pin="x") }} source: url: https://github.com/liulab-dfci/TRUST4/archive/v{{ version }}.tar.gz - sha256: 215715de74454e540b7326875b0b76fbf9cbd116bcc0fc71bf0f46ed0e2a7d1d + sha256: 64069e2cad65960471f32daaf8568c05214b1d8b6b32b7fd138e56b90d634bb8 requirements: build: @@ -37,7 +39,8 @@ test: - which run-trust4 about: - home: https://github.com/liulab-dfci/TRUST4 + home: https://github.com/liulab-dfci/TRUST4 summary: TCR and BCR assembly from bulk or single-cell RNA-seq data license: GPL-3.0-only + license_family: GPL3 license_file: LICENSE.txt From f1b8a1f85986ec6a5109f8a9453f72bf8944f68a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 10:41:39 -0600 Subject: [PATCH 0546/2173] Update catch to 1.5.2 (#44013) * Update catch to 1.5.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/catch/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/catch/meta.yaml b/recipes/catch/meta.yaml index ad6f7f7ad1756..2b2f3d2315b08 100644 --- a/recipes/catch/meta.yaml +++ b/recipes/catch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.5.1" %} -{% set sha256 = "9b3f266e5ac77749f35a98bf37aed859836c9e7b1955e1af31df1f9c66266df0" %} +{% set version = "1.5.2" %} +{% set sha256 = "7b2312d55f8a13f5c459a3b3f0f192affff7cb796ab296dd3a5e18992f40cd5e" %} package: name: catch @@ -12,7 +12,9 @@ source: build: noarch: python number: 0 - script: '{{ PYTHON }} -m pip install --no-deps --ignore-installed --no-cache-dir -vvv .' + script: '{{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir -vvv .' + run_exports: + - {{ pin_subpackage('catch', max_pin="x") }} requirements: host: From 700ff819fe3494d3741380c5d50d3adb452d587a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 10:53:47 -0600 Subject: [PATCH 0547/2173] Update planemo to 0.75.17 (#44024) --- recipes/planemo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 017d0addc62e9..743c623d6ba16 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "planemo" %} -{% set version = "0.75.15" %} -{% set sha256 = "40ab64beb13f3d953761e70244aa55a88595627abcacba09f3286f7908464885" %} +{% set version = "0.75.17" %} +{% set sha256 = "451da7eb82c8e1f6ab5ea854a765b6b4551327e5b374e7e991d33323f0c46aea" %} package: name: {{ name|lower }} From 20ccaed7610ca934b45e7611702dc90aa210a3dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 10:54:19 -0600 Subject: [PATCH 0548/2173] Update celltypist to 1.6.2 (#44017) --- recipes/celltypist/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/celltypist/meta.yaml b/recipes/celltypist/meta.yaml index c8b1ffadcaa15..71d9216a1a3c3 100644 --- a/recipes/celltypist/meta.yaml +++ b/recipes/celltypist/meta.yaml @@ -1,5 +1,5 @@ {% set name = "celltypist" %} -{% set version = "1.6.1" %} +{% set version = "1.6.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 36a27b45fa47c3abe95377330ca6905c9ec085b90ccec73827265f6e2a79b973 + sha256: a22309230c578c3738f72643492387167053f35a610625c75d66b056cf520361 build: number: 0 From 60a6e6dba576ec63b9e5662761db01af212596d2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 10:54:34 -0600 Subject: [PATCH 0549/2173] Update dna_features_viewer to 3.1.3 (#44014) * Update dna_features_viewer to 3.1.3 * add run_exports * edit run_exports * edit run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/dna_features_viewer/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/dna_features_viewer/meta.yaml b/recipes/dna_features_viewer/meta.yaml index 06ea643d219e5..515615420e7d3 100644 --- a/recipes/dna_features_viewer/meta.yaml +++ b/recipes/dna_features_viewer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dna_features_viewer" %} -{% set version = "3.1.2" %} +{% set version = "3.1.3" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b8b2b7657e2a9f165edd6f68fb679abfa0c2fdeb887cbd04c22b514997f52d12 + sha256: 7af179ab1b3c0dedd09e9e667cbd0fb804721ecbfc0cb4d0dda8a165437b3919 build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('dna_features_viewer', max_pin="x") }} requirements: host: From 82a137c65bf6a2a9126d01eca82117f0ada51c83 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 11:11:17 -0600 Subject: [PATCH 0550/2173] Update chronumental to 0.0.63 (#44023) --- recipes/chronumental/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/chronumental/meta.yaml b/recipes/chronumental/meta.yaml index 4b74164daea1c..72c19011e38a4 100644 --- a/recipes/chronumental/meta.yaml +++ b/recipes/chronumental/meta.yaml @@ -1,5 +1,5 @@ {% set name = "chronumental" %} -{% set version = "0.0.61" %} +{% set version = "0.0.63" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/chronumental-{{ version }}.tar.gz - sha256: 3be20131b1185c01bf1b32009c11bb11accb8ecd5c8cd470fb8e2fa7f6d35d38 + sha256: f008bae186592447609cdd51ad940e0474b61a6c0ce9db1b44ed317d3b02f35f build: noarch: python From bad15269f890df7dc33ef979a6bedd2db9402e6a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 11:11:50 -0600 Subject: [PATCH 0551/2173] Update pxblat to 1.1.10 (#44007) * Update pxblat to 1.1.9 * Update pxblat to 1.1.10 * edit python dependency --------- Co-authored-by: joshuazhuang7 --- recipes/pxblat/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index 53d2ffda50e87..2a0c29693aa1f 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "1.1.8" %} -{% set sha256 = "3c5609e8be17c77c3740ffa016d1ca7e5072d2a34581fe4327ca7f10ac3bb629" %} +{% set version = "1.1.10" %} +{% set sha256 = "d20b48ac4c761ad26c680cd1a10e7fb22f581212d5221cbfc2bc7f522a6b81d2" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ source: build: number: 0 - skip: True # [py < 38] + skip: True # [py < 39] script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - pxblat = pxblat.cli.cli:app @@ -26,7 +26,7 @@ requirements: - python - pip - poetry-core >=1.2.0 - - pybind11 >=2.9.1 + - pybind11 >2.9.1 - setuptools >=46.4 run: - python From 22d1e2e1b91cfa7043decaede94270444b357e04 Mon Sep 17 00:00:00 2001 From: ningOTI Date: Thu, 2 Nov 2023 01:13:31 +0800 Subject: [PATCH 0552/2173] Add ucsc-chainscore (#44011) --- recipes/ucsc-chainscore/build.sh | 13 +++++++ recipes/ucsc-chainscore/include.patch | 40 ++++++++++++++++++++++ recipes/ucsc-chainscore/meta.yaml | 49 +++++++++++++++++++++++++++ recipes/ucsc-chainscore/run_test.sh | 2 ++ 4 files changed, 104 insertions(+) create mode 100644 recipes/ucsc-chainscore/build.sh create mode 100644 recipes/ucsc-chainscore/include.patch create mode 100644 recipes/ucsc-chainscore/meta.yaml create mode 100644 recipes/ucsc-chainscore/run_test.sh diff --git a/recipes/ucsc-chainscore/build.sh b/recipes/ucsc-chainscore/build.sh new file mode 100644 index 0000000000000..0136af36bb813 --- /dev/null +++ b/recipes/ucsc-chainscore/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash +mkdir -p "$PREFIX/bin" +export MACHTYPE=x86_64 +export BINDIR=$(pwd)/bin +export L="${LDFLAGS}" +mkdir -p "$BINDIR" +(cd kent/src/lib && make) +(cd kent/src/htslib && make) +(cd kent/src/jkOwnLib && make) +(cd kent/src/hg/lib && make) +(cd kent/src/hg/mouseStuff/chainScore && make) +cp bin/chainScore "$PREFIX/bin" +chmod +x "$PREFIX/bin/chainScore" diff --git a/recipes/ucsc-chainscore/include.patch b/recipes/ucsc-chainscore/include.patch new file mode 100644 index 0000000000000..e4831ef2dea13 --- /dev/null +++ b/recipes/ucsc-chainscore/include.patch @@ -0,0 +1,40 @@ +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +@@ -17,7 +17,7 @@ + endif + + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} +-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include + + # to check for Mac OSX Darwin specifics: + UNAME_S := $(shell uname -s) +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + # expMatrixToBarchartBed + """ + Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. +--- kent/src/hg/lib/straw/makefile ++++ kent/src/hg/lib/straw/makefile +@@ -3,8 +3,8 @@ + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o + straw.o: straw.cpp straw.h +- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o ++ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include + cStraw.o: cStraw.cpp straw.h +- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o ++ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include + clean: + rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainscore/meta.yaml b/recipes/ucsc-chainscore/meta.yaml new file mode 100644 index 0000000000000..1902cceb93c8d --- /dev/null +++ b/recipes/ucsc-chainscore/meta.yaml @@ -0,0 +1,49 @@ +{% set package = "ucsc-chainscore" %} +{% set program = "chainScore" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} + +package: + name: "{{ package }}" + version: "{{ version }}" + +source: + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" + patches: + - "include.patch" + +build: + skip: True # [osx] + number: 0 + run_exports: + - {{ pin_subpackage("ucsc-chainscore", max_pin=None) }} + +requirements: + build: + - make + - {{ compiler('c') }} + - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info + - {{ compiler('cxx') }} + host: + - libpng + - libuuid + - mysql-connector-c + - openssl + - zlib + run: + - libpng + - libuuid + - mysql-connector-c + - openssl + - zlib + +test: + commands: + # just check for existence, because the individual packages have no unified behavior + - which {{ program }} + +about: + home: "http://hgdownload.cse.ucsc.edu/admin/exe/" + license: "varies; see http://genome.ucsc.edu/license" + summary: "Remove chain-breaking alignments from chains that break nested chains." diff --git a/recipes/ucsc-chainscore/run_test.sh b/recipes/ucsc-chainscore/run_test.sh new file mode 100644 index 0000000000000..8bbf608067e64 --- /dev/null +++ b/recipes/ucsc-chainscore/run_test.sh @@ -0,0 +1,2 @@ +#!/bin/bash +chainScore 2> /dev/null || [[ "$?" == 255 ]] From d1e419ef7136446f6235e61d6651c7f6083c4768 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 11:13:51 -0600 Subject: [PATCH 0553/2173] Update pybiolib to 1.1.1508 (#44018) * Update pybiolib to 1.1.1502 * Update pybiolib to 1.1.1508 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 9018ff953bcb6..cb78bb2f06835 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1499" %} +{% set version = "1.1.1508" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 8628c079d230e56beee5767584ab783e03625cf7689d4209355e6e5bdcb7d96c + sha256: 6bf3b639faf12079ee699f12ee846871b82ade1fac5192e15fe6be129c2c37c3 build: noarch: python From 1f156636e06a5ffe042a6586b1c28d92f82baf2e Mon Sep 17 00:00:00 2001 From: ningOTI Date: Thu, 2 Nov 2023 01:14:17 +0800 Subject: [PATCH 0554/2173] Add ucsc-pslsortacc (#44012) * Add ucsc-pslsortacc * Fix wrong directory for pslSortAcc compilation --- recipes/ucsc-pslsortacc/build.sh | 13 +++++++ recipes/ucsc-pslsortacc/include.patch | 40 ++++++++++++++++++++++ recipes/ucsc-pslsortacc/meta.yaml | 49 +++++++++++++++++++++++++++ recipes/ucsc-pslsortacc/run_test.sh | 2 ++ 4 files changed, 104 insertions(+) create mode 100644 recipes/ucsc-pslsortacc/build.sh create mode 100644 recipes/ucsc-pslsortacc/include.patch create mode 100644 recipes/ucsc-pslsortacc/meta.yaml create mode 100644 recipes/ucsc-pslsortacc/run_test.sh diff --git a/recipes/ucsc-pslsortacc/build.sh b/recipes/ucsc-pslsortacc/build.sh new file mode 100644 index 0000000000000..63d55501cca2e --- /dev/null +++ b/recipes/ucsc-pslsortacc/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash +mkdir -p "$PREFIX/bin" +export MACHTYPE=x86_64 +export BINDIR=$(pwd)/bin +export L="${LDFLAGS}" +mkdir -p "$BINDIR" +(cd kent/src/lib && make) +(cd kent/src/htslib && make) +(cd kent/src/jkOwnLib && make) +(cd kent/src/hg/lib && make) +(cd kent/src/hg/pslSortAcc && make) +cp bin/pslSortAcc "$PREFIX/bin" +chmod +x "$PREFIX/bin/pslSortAcc" diff --git a/recipes/ucsc-pslsortacc/include.patch b/recipes/ucsc-pslsortacc/include.patch new file mode 100644 index 0000000000000..e4831ef2dea13 --- /dev/null +++ b/recipes/ucsc-pslsortacc/include.patch @@ -0,0 +1,40 @@ +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +@@ -17,7 +17,7 @@ + endif + + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} +-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include + + # to check for Mac OSX Darwin specifics: + UNAME_S := $(shell uname -s) +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + # expMatrixToBarchartBed + """ + Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. +--- kent/src/hg/lib/straw/makefile ++++ kent/src/hg/lib/straw/makefile +@@ -3,8 +3,8 @@ + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o + straw.o: straw.cpp straw.h +- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o ++ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include + cStraw.o: cStraw.cpp straw.h +- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o ++ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include + clean: + rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-pslsortacc/meta.yaml b/recipes/ucsc-pslsortacc/meta.yaml new file mode 100644 index 0000000000000..0041b30f4489a --- /dev/null +++ b/recipes/ucsc-pslsortacc/meta.yaml @@ -0,0 +1,49 @@ +{% set package = "ucsc-pslsortacc" %} +{% set program = "pslSortAcc" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} + +package: + name: "{{ package }}" + version: "{{ version }}" + +source: + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" + patches: + - "include.patch" + +build: + skip: True # [osx] + number: 0 + run_exports: + - {{ pin_subpackage("ucsc-pslsortacc", max_pin=None) }} + +requirements: + build: + - make + - {{ compiler('c') }} + - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info + - {{ compiler('cxx') }} + host: + - libpng + - libuuid + - mysql-connector-c + - openssl + - zlib + run: + - libpng + - libuuid + - mysql-connector-c + - openssl + - zlib + +test: + commands: + # just check for existence, because the individual packages have no unified behavior + - which {{ program }} + +about: + home: "http://hgdownload.cse.ucsc.edu/admin/exe/" + license: "varies; see http://genome.ucsc.edu/license" + summary: "Remove chain-breaking alignments from chains that break nested chains." diff --git a/recipes/ucsc-pslsortacc/run_test.sh b/recipes/ucsc-pslsortacc/run_test.sh new file mode 100644 index 0000000000000..8453138f6168a --- /dev/null +++ b/recipes/ucsc-pslsortacc/run_test.sh @@ -0,0 +1,2 @@ +#!/bin/bash +pslSortAcc 2> /dev/null || [[ "$?" == 255 ]] From c4f48b356dbb3fded2ae042d1b5d8d4bddef2bf8 Mon Sep 17 00:00:00 2001 From: ningOTI Date: Thu, 2 Nov 2023 01:14:37 +0800 Subject: [PATCH 0555/2173] Add ucsc-chaincleaner (#43993) * Add ucsc-chaincleaner * Fix local install errors * Format for lint check: space btwn package and vers * Fix wrong build number 1 -> 0 * Add run_exports * Fix bad version pin string --------- Co-authored-by: ning --- recipes/ucsc-chaincleaner/build.sh | 13 +++++++ recipes/ucsc-chaincleaner/include.patch | 40 ++++++++++++++++++++ recipes/ucsc-chaincleaner/meta.yaml | 49 +++++++++++++++++++++++++ recipes/ucsc-chaincleaner/run_test.sh | 2 + 4 files changed, 104 insertions(+) create mode 100644 recipes/ucsc-chaincleaner/build.sh create mode 100644 recipes/ucsc-chaincleaner/include.patch create mode 100644 recipes/ucsc-chaincleaner/meta.yaml create mode 100644 recipes/ucsc-chaincleaner/run_test.sh diff --git a/recipes/ucsc-chaincleaner/build.sh b/recipes/ucsc-chaincleaner/build.sh new file mode 100644 index 0000000000000..0885639b0aa13 --- /dev/null +++ b/recipes/ucsc-chaincleaner/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash +mkdir -p "$PREFIX/bin" +export MACHTYPE=x86_64 +export BINDIR=$(pwd)/bin +export L="${LDFLAGS}" +mkdir -p "$BINDIR" +(cd kent/src/lib && make) +(cd kent/src/htslib && make) +(cd kent/src/jkOwnLib && make) +(cd kent/src/hg/lib && make) +(cd kent/src/hg/mouseStuff/chainCleaner && make) +cp bin/chainCleaner "$PREFIX/bin" +chmod +x "$PREFIX/bin/chainCleaner" diff --git a/recipes/ucsc-chaincleaner/include.patch b/recipes/ucsc-chaincleaner/include.patch new file mode 100644 index 0000000000000..e4831ef2dea13 --- /dev/null +++ b/recipes/ucsc-chaincleaner/include.patch @@ -0,0 +1,40 @@ +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +@@ -17,7 +17,7 @@ + endif + + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} +-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include + + # to check for Mac OSX Darwin specifics: + UNAME_S := $(shell uname -s) +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + # expMatrixToBarchartBed + """ + Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. +--- kent/src/hg/lib/straw/makefile ++++ kent/src/hg/lib/straw/makefile +@@ -3,8 +3,8 @@ + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o + straw.o: straw.cpp straw.h +- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o ++ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include + cStraw.o: cStraw.cpp straw.h +- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o ++ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include + clean: + rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chaincleaner/meta.yaml b/recipes/ucsc-chaincleaner/meta.yaml new file mode 100644 index 0000000000000..4417d84ba8197 --- /dev/null +++ b/recipes/ucsc-chaincleaner/meta.yaml @@ -0,0 +1,49 @@ +{% set package = "ucsc-chaincleaner" %} +{% set program = "chainCleaner" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} + +package: + name: "{{ package }}" + version: "{{ version }}" + +source: + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" + patches: + - "include.patch" + +build: + skip: True # [osx] + number: 0 + run_exports: + - {{ pin_subpackage("ucsc-chaincleaner", max_pin=None) }} + +requirements: + build: + - make + - {{ compiler('c') }} + - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info + - {{ compiler('cxx') }} + host: + - libpng + - libuuid + - mysql-connector-c + - openssl + - zlib + run: + - libpng + - libuuid + - mysql-connector-c + - openssl + - zlib + +test: + commands: + # just check for existence, because the individual packages have no unified behavior + - which {{ program }} + +about: + home: "http://hgdownload.cse.ucsc.edu/admin/exe/" + license: "varies; see http://genome.ucsc.edu/license" + summary: "Remove chain-breaking alignments from chains that break nested chains." diff --git a/recipes/ucsc-chaincleaner/run_test.sh b/recipes/ucsc-chaincleaner/run_test.sh new file mode 100644 index 0000000000000..e2ce68c8a3c0e --- /dev/null +++ b/recipes/ucsc-chaincleaner/run_test.sh @@ -0,0 +1,2 @@ +#!/bin/bash +chainCleaner 2> /dev/null || [[ "$?" == 255 ]] From f1941720e7943a75c7aef925bde5405016450262 Mon Sep 17 00:00:00 2001 From: Ilya Shlyakhter Date: Wed, 1 Nov 2023 13:14:50 -0400 Subject: [PATCH 0556/2173] Update dwgsim to 1.1.14 (#43815) Co-authored-by: Thanh Lee --- recipes/dwgsim/meta.yaml | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/recipes/dwgsim/meta.yaml b/recipes/dwgsim/meta.yaml index ddd3ac58bbc9f..5f0f3b94548a8 100644 --- a/recipes/dwgsim/meta.yaml +++ b/recipes/dwgsim/meta.yaml @@ -1,16 +1,21 @@ +{% set name = "dwgsim" %} +{% set version = "1.1.14" %} + package: - name: dwgsim - version: '1.1.13' + name: {{ name }} + version: {{ version }} source: - - url: https://github.com/nh13/DWGSIM/archive/dwgsim.0.1.13.tar.gz - sha256: 445be90283203d9603386c4359e29d6beb1705e418791fbfb5a5d1ee1e3baeb0 + - url: https://github.com/nh13/DWGSIM/archive/{{ name }}.0.1.14.tar.gz + sha256: a974a253bf6bcd5a2162f9ebc6c78c56a29c541850f375a45ddb2b649574ce1b - url: http://github.com/samtools/samtools/archive/28391e5898804ce6b805016.tar.gz sha256: b17bc6564eef101aeefc2d572347f7141bdb8eb5cdaa81725fdd768cf80d1a2b folder: samtools build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: @@ -30,5 +35,11 @@ test: about: home: https://github.com/nh13/DWGSIM license: GNU General Public License v2 (GPLv2) + license_file: LICENSE license_family: GPL summary: 'Whole Genome Simulator for Next-Generation Sequencing' + +extra: + recipe-maintainers: + - notestaff + - nh13 From d6d6d0559d91e570e6a065319199878cb3fba32e Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Wed, 1 Nov 2023 13:15:24 -0400 Subject: [PATCH 0557/2173] Genomic Address Service v0.1.1 build #1 due to missed scipy dependency (#44025) * gas release v0.1.1 * gas release v0.1.1 * scipy dependency added * scipy and psutil dependency added --- recipes/genomic_address_service/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/genomic_address_service/meta.yaml b/recipes/genomic_address_service/meta.yaml index 75892e92cc52f..6eea935428e20 100644 --- a/recipes/genomic_address_service/meta.yaml +++ b/recipes/genomic_address_service/meta.yaml @@ -12,7 +12,7 @@ source: build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage("genomic_address_service", max_pin="x.x") }} @@ -34,6 +34,8 @@ requirements: - pytables >=3.8.0 - six >=1.16.0 - pandas >=2.0.2 + - scipy + - psutil test: imports: From 0db189c449f5b3385a4546d1975ab7ef231bc390 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 11:15:41 -0600 Subject: [PATCH 0558/2173] Update oakvar to 2.9.55 (#44010) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 59cfac10fec0f..692811a1b81e6 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.54" %} -{% set sha256 = "1b497437aac7a779fd22452b39228ac0af034ac55f0acd7c858e7a9970215a50" %} +{% set version = "2.9.55" %} +{% set sha256 = "7c16f5bd221a132d1066891c77957815fb69163316a91e1440913564b8c4deba" %} package: name: {{ name|lower }} From 69121123f7127f6a7f9c37f3028c8a4dc6a15d03 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Wed, 1 Nov 2023 17:16:47 +0000 Subject: [PATCH 0559/2173] Add pspecterlib (#43820) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * added meta.yaml file for pspecterlib * added missing deps * added rawrr * added run_esports * added license * reset build number * fix subpackage pinning * fixed package name * updated SHA * changed to bsd2-clause license * Update recipes/r-pspecterlib/meta.yaml Co-authored-by: Björn Grüning * Update meta.yaml --------- Co-authored-by: Björn Grüning Co-authored-by: Thanh Lee --- recipes/r-pspecterlib/meta.yaml | 88 +++++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 recipes/r-pspecterlib/meta.yaml diff --git a/recipes/r-pspecterlib/meta.yaml b/recipes/r-pspecterlib/meta.yaml new file mode 100644 index 0000000000000..12969788a83f7 --- /dev/null +++ b/recipes/r-pspecterlib/meta.yaml @@ -0,0 +1,88 @@ +{% set name = "pspecterlib" %} +{% set version = "1.1.0" %} +{% set github = "https://github.com/EMSL-Computing/pspecterlib" %} + +package: + name: "r-{{ name|lower }}" + version: "{{ version }}" + +source: + url: "{{ github }}/archive/refs/tags/{{ version }}.tar.gz" + sha256: 8ca6c456365f815bb1c80feecca5bbb8d32e785fab2a1a7be06574c1e29bbcd2 + +build: + number: 0 + noarch: generic + rpaths: + - lib/R/lib/ + - lib/ + script: R CMD INSTALL --build . + run_exports: + - {{ pin_subpackage("r-pspecterlib", max_pin="x.x") }} + +requirements: + host: + - r-base >=4.2 + - bioconductor-rhdf5 + - bioconductor-mzr + - bioconductor-msnbase + - r-lsa + - r-seqinr + - r-dplyr + - r-reshape2 + - r-gtools + - r-readxl + - r-data.table + - r-plotly + - r-ggplot2 + - r-magrittr + - r-purrr + - r-tidyr + - r-htmltools + - r-rcolorbrewer + - r-isopat + - r-chnosz + - r-cairo + - r-rmarkdown + - r-knitr + - bioconductor-rawrr + run: + - r-base >=4.2 + - bioconductor-rhdf5 + - bioconductor-mzr + - bioconductor-msnbase + - r-lsa + - r-seqinr + - r-dplyr + - r-reshape2 + - r-gtools + - r-readxl + - r-data.table + - r-plotly + - r-ggplot2 + - r-magrittr + - r-purrr + - r-tidyr + - r-htmltools + - r-rcolorbrewer + - r-isopat + - r-chnosz + - r-cairo + - r-rmarkdown + - r-knitr + - bioconductor-rawrr + +test: + commands: + - $R -e "library('pspecterlib')" + +about: + home: "{{ github }}" + license_file: license.txt + license: BSD-2-Clause + summary: Proteomics R package for matching peaks in digested and intact proteomics + +extra: + recipe-maintainers: + - hechth + From b93778f893efeb59b7e29b38954b58ab32a8f006 Mon Sep 17 00:00:00 2001 From: Ben Fulton Date: Wed, 1 Nov 2023 13:17:00 -0400 Subject: [PATCH 0560/2173] Update CAFE to 5.1 (#43791) * Update cafe to 5.1 * Add run_exports section * Reset numbering to 0 * Change max_pin from x to x.x * Fix link to download --- recipes/cafe/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/cafe/meta.yaml b/recipes/cafe/meta.yaml index b3e946cc15d5d..09aead5b1a062 100644 --- a/recipes/cafe/meta.yaml +++ b/recipes/cafe/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "5.0.0" %} -{% set sha256 = "9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118" %} +{% set version = "5.1.0" %} +{% set sha256 = "71871bdc74c2ffc7c1c0f4500f4742f2ff46a15cfaba78dc179d21bb1ba67ba8" %} package: name: cafe version: {{ version }} source: - url: https://github.com/hahnlab/CAFE5/releases/download/v5.0/CAFE5-{{ version }}.tar.gz + url: https://github.com/hahnlab/CAFE5/releases/download/v5.1/CAFE5-{{ version }}.tar.gz sha256: {{ sha256 }} build: - number: 3 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('cafe', max_pin="x.x") }} requirements: build: From c93927d94dd717de1027c5a9fc1ac3f73c1ffaff Mon Sep 17 00:00:00 2001 From: Jim Shaw Date: Wed, 1 Nov 2023 10:17:26 -0700 Subject: [PATCH 0561/2173] added flopp recipe (#44022) --- recipes/flopp/build.sh | 8 ++++++++ recipes/flopp/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 recipes/flopp/build.sh create mode 100644 recipes/flopp/meta.yaml diff --git a/recipes/flopp/build.sh b/recipes/flopp/build.sh new file mode 100644 index 0000000000000..3662f6efb60db --- /dev/null +++ b/recipes/flopp/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --verbose --path . --root $PREFIX diff --git a/recipes/flopp/meta.yaml b/recipes/flopp/meta.yaml new file mode 100644 index 0000000000000..83083d68a75bd --- /dev/null +++ b/recipes/flopp/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "0.2.0" %} + +package: + name: flopp + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('flopp', max_pin="x") }} + +source: + url: https://github.com/bluenote-1577/flopp/archive/v{{ version }}.tar.gz + sha256: 28398c18fff183c5552689569f96c85488ff77a8f838e4834f98a8f4aa2116ae + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.39 + - make + - cmake >=3.12 + +test: + commands: + - flopp --help + +about: + home: https://github.com/bluenote-1577/flopp + license: MIT + summary: flopp is a software package for single individual haplotype phasing of polyploid organisms from long read sequencing. + + +extra: + recipe-maintainers: + - bluenote-1577 + From 00c42e0ae39b1a752bf4e49df13b949b2a0eab85 Mon Sep 17 00:00:00 2001 From: yanyew <90335707+yanyew@users.noreply.github.com> Date: Thu, 2 Nov 2023 01:18:34 +0800 Subject: [PATCH 0562/2173] update syngap recipes (#44004) --- recipes/syngap/build.sh | 2 ++ recipes/syngap/meta.yaml | 16 ++++++++++++++-- 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/recipes/syngap/build.sh b/recipes/syngap/build.sh index bc4aec66a541f..cdfdffb832323 100644 --- a/recipes/syngap/build.sh +++ b/recipes/syngap/build.sh @@ -2,6 +2,8 @@ mkdir -p $PREFIX/bin cp -rf $SRC_DIR/bin $PREFIX/bin cp -rf $SRC_DIR/scripts $PREFIX/bin cp $SRC_DIR/SynGAP.py $PREFIX/bin +cp $SRC_DIR/initdb.py $PREFIX/bin +cp $SRC_DIR/master.py $PREFIX/bin cp $SRC_DIR/dual.py $PREFIX/bin cp $SRC_DIR/triple.py $PREFIX/bin cp $SRC_DIR/custom.py $PREFIX/bin diff --git a/recipes/syngap/meta.yaml b/recipes/syngap/meta.yaml index d42fdd65b596e..62014cd0a04d1 100644 --- a/recipes/syngap/meta.yaml +++ b/recipes/syngap/meta.yaml @@ -1,5 +1,5 @@ {% set name = "syngap" %} -{% set version = "1.0.1" %} +{% set version = "1.1.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/yanyew/SynGAP/releases/download/v{{ version }}/{{ name }}_v{{ version }}.tar.gz - sha256: f76d8155989a7ae47270d73a085f219fad17816dc146fb65f2f00d5d79e5f76d + sha256: a6b58dcf7c650e0be290352c4cec5889fb79fd610a666d7754f670e8ea8b14b3 build: number: 0 @@ -63,6 +63,8 @@ test: source_files: - run_test.sh - SynGAP.py + - initdb.py + - master.py - dual.py - triple.py - custom.py @@ -73,8 +75,18 @@ test: - scripts/* imports: - SynGAP + - initdb + - master + - dual + - triple + - custom + - genepair + - evi + - eviplot commands: - syngap -h + - syngap initdb -h + - syngap master -h - syngap dual -h - syngap triple -h - syngap custom -h From 86362b31e9f5a549c08f8408551ce36463641ed1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 11:20:20 -0600 Subject: [PATCH 0563/2173] Update r-biomartr to 1.0.6 (#43462) * Update r-biomartr to 1.0.5 * add run_exports * try double quotes * Update r-biomartr to 1.0.6 * edit run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/r-biomartr/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/r-biomartr/meta.yaml b/recipes/r-biomartr/meta.yaml index 2da9ca48024d0..8f656c787839f 100644 --- a/recipes/r-biomartr/meta.yaml +++ b/recipes/r-biomartr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.0.4' %} +{% set version = '1.0.6' %} package: name: r-biomartr @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/biomartr_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/biomartr/biomartr_{{ version }}.tar.gz - sha256: 2008c202575344da527854b18748656744a137f4d5fd238f82a8d8cabcf96443 + sha256: 35fe0d6090a71c68df989932cb98cffd321f0f73e880966e47856bcd84468d1b build: noarch: generic - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-biomartr', max_pin="x") }} requirements: host: From 2b33b4be5dc8f0d39f38179bd2e5589c2c6aeb2f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 11:42:40 -0600 Subject: [PATCH 0564/2173] Update bustools to 0.43.1 (#44021) * Update bustools to 0.43.1 * add run_exports --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: joshuazhuang7 --- recipes/bustools/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/bustools/meta.yaml b/recipes/bustools/meta.yaml index 9842c2c986e53..331adae0b3b1a 100644 --- a/recipes/bustools/meta.yaml +++ b/recipes/bustools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.43.0" %} +{% set version = "0.43.1" %} package: name: bustools @@ -6,10 +6,12 @@ package: source: url: https://github.com/BUStools/bustools/archive/v{{ version }}.tar.gz - sha256: a881fd273e4242a422a60e69b2d47210880fba855346a13efbc5480e7a2f9721 + sha256: ac94a33ca459de81c5756825a7a7f8daeae357fc6bf0ef88d4900e77b70f2b90 build: number: 0 + run_exports: + - {{ pin_subpackage('bustools', max_pin="x.x") }} requirements: build: @@ -22,11 +24,12 @@ requirements: test: commands: - - bustools sort + - bustools sort about: home: https://github.com/BUStools/bustools - license: BSD 2-Clause "Simplified" License + license: BSD-2-Clause "Simplified" License + license_family: BSD license_file: LICENSE summary: | - bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. + bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. From 0461a8d72f8777bc0cc3affc2a045814b2b8ecff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 14:40:24 -0600 Subject: [PATCH 0565/2173] Update kallisto to 0.50.1 (#44020) * Update kallisto to 0.50.1 * add run_exports --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/kallisto/meta.yaml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/recipes/kallisto/meta.yaml b/recipes/kallisto/meta.yaml index c312886ba195e..88a82fc9c9e7f 100644 --- a/recipes/kallisto/meta.yaml +++ b/recipes/kallisto/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.50.0" %} +{% set version = "0.50.1" %} package: name: kallisto @@ -6,10 +6,12 @@ package: source: url: https://github.com/pachterlab/kallisto/archive/v{{ version }}.tar.gz - sha256: f9cc0058d08206cb6dde4a4dcaf8a778df5a939a6e021508eea9b00b0d6d5368 + sha256: 030752bab3b0e33cd3f23f6d8feddd74194e5513532ffbf23519e84db2a86d34 build: number: 0 + run_exports: + - {{ pin_subpackage('kallisto', max_pin="x.x") }} requirements: build: @@ -35,8 +37,11 @@ test: about: home: "http://pachterlab.github.io/kallisto" - license: BSD_2_Clause + license: BSD-2-Clause + license_family: BSD summary: Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. + dev_url: https://github.com/pachterlab/kallisto + doc_url: "https://pachterlab.github.io/kallisto/manual.html" extra: identifiers: From 99698e6526c7e3cd14124914e447fbf992747a0f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 14:41:30 -0600 Subject: [PATCH 0566/2173] Update usher to 0.6.3 (#44030) * Update usher to 0.6.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/usher/meta.yaml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/recipes/usher/meta.yaml b/recipes/usher/meta.yaml index de9d93fe8116c..63b3f108e082f 100644 --- a/recipes/usher/meta.yaml +++ b/recipes/usher/meta.yaml @@ -1,4 +1,4 @@ -{% set version="0.6.2" %} +{% set version="0.6.3" %} package: name: usher @@ -6,10 +6,12 @@ package: source: - url: https://github.com/yatisht/usher/archive/v{{ version }}.tar.gz - sha256: 2549b9329301abb1d2f5b20dbf17f436c5dc148f3400652c700f762b94d16b22 + sha256: 95aba8f748599915f21f7bdf883c2e532f2d821138f06cb2e4e58d7323019946 build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('usher', max_pin="x.x") }} requirements: build: @@ -46,3 +48,8 @@ about: license_family: MIT license_file: LICENSE summary: Ultrafast Sample Placement on Existing Trees (UShER) + doc_url: https://usher-wiki.readthedocs.io/en/latest/ + +extra: + identifiers: + - doi:10.1038/s41588-021-00862-7 From c38477e43410f0ed6d7360cbfd0fb31b7fae1843 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 15:41:03 -0600 Subject: [PATCH 0567/2173] Update genomedata to 1.7.2 (#44032) * Update genomedata to 1.7.2 * edit dependencies --------- Co-authored-by: joshuazhuang7 --- recipes/genomedata/build.sh | 2 +- recipes/genomedata/meta.yaml | 29 +++++++++++++++++++++++------ 2 files changed, 24 insertions(+), 7 deletions(-) diff --git a/recipes/genomedata/build.sh b/recipes/genomedata/build.sh index b53be74eadecd..29ed708237cbf 100644 --- a/recipes/genomedata/build.sh +++ b/recipes/genomedata/build.sh @@ -6,7 +6,7 @@ export HDF5_DIR=$PREFIX export CPPFLAGS='-D_FORTIFY_SOURCE=2 -O2' export LD_LIBRARY_PATH=$PREFIX/lib -$PYTHON -m pip install -vv --disable-pip-version-check --no-deps --no-cache-dir --ignore-installed . +$PYTHON -m pip install -vvv --disable-pip-version-check --no-deps --no-cache-dir --no-build-isolation . # Work around for no 'source_files' support in test section of meta.yaml cp test/run_tests.py $PREFIX/bin/run_genomedata_tests.py cp test/test_genomedata.py $PREFIX/bin diff --git a/recipes/genomedata/meta.yaml b/recipes/genomedata/meta.yaml index 31c9aba2b6b00..c79e56a3185bc 100644 --- a/recipes/genomedata/meta.yaml +++ b/recipes/genomedata/meta.yaml @@ -1,6 +1,6 @@ {% set name = "genomedata" %} -{% set version = "1.7.1" %} -{% set sha256 = "d70fff2fc59fa3e85833698fc5c0566912d935b71e4c21a187f756cd0198a90c" %} +{% set version = "1.7.2" %} +{% set sha256 = "588efabd6a163af059e945aa6c638b9e9129ab46f27c4a35baafdbfb5f7edbbd" %} package: name: {{ name|lower }} @@ -9,10 +9,23 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz sha256: {{ sha256 }} - + build: - skip: True # [osx or py < 37] + skip: True # [osx or py < 39] number: 0 + entry_points: + - genomedata-close-data = genomedata._close_data:main + - genomedata-erase-data = genomedata._erase_data:main + - genomedata-hardmask = genomedata._hardmask:main + - genomedata-histogram = genomedata._histogram:main + - genomedata-info = genomedata._info:main + - genomedata-load = genomedata.load_genomedata:main + - genomedata-load-assembly = genomedata._load_seq:main + - genomedata-load-data = genomedata._load_data:main + - genomedata-load-seq = genomedata._load_seq:main + - genomedata-open-data = genomedata._open_data:main + - genomedata-query = genomedata._query:main + - genomedata-report = genomedata._report:main run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -62,8 +75,12 @@ test: about: home: http://genomedata.hoffmanlab.org/ - license: GPL2 - summary: 'tools for accessing large amounts of genomic data' + license: GPL-2.0 + license_family: GPL2 + license_file: LICENSE + summary: 'Tools for accessing large amounts of genomic data' + doc_url: https://genomedata.readthedocs.io/en/latest/ + dev_url: https://github.com/hoffmangroup/genomedata extra: identifiers: From 38616479b09c4c5aa3a2cdb04be29f7e37607f4e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 15:41:17 -0600 Subject: [PATCH 0568/2173] Update lotus2 to 2.28.1 (#44029) --- recipes/lotus2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/lotus2/meta.yaml b/recipes/lotus2/meta.yaml index be61b41c8a0bc..243fc6cb3b5e7 100644 --- a/recipes/lotus2/meta.yaml +++ b/recipes/lotus2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "lotus2" %} -{% set version = "2.28" %} -{% set sha256 = "ce4787c906255b40c18863f0655e20cbd1bf8bcfa57d8760624227c51c6ca16a" %} +{% set version = "2.28.1" %} +{% set sha256 = "0e7ed1f816db8d8e6946a101bc22924323e772484e0dc4bde319a36451d22186" %} package: name: {{ name }} From 6d7fb315d86ad10aef618dd0a404990ec9cccae6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 15:41:28 -0600 Subject: [PATCH 0569/2173] Update synapseclient to 3.1.1 (#44031) --- recipes/synapseclient/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/synapseclient/meta.yaml b/recipes/synapseclient/meta.yaml index fae9585940309..5d5376fe5e1dc 100644 --- a/recipes/synapseclient/meta.yaml +++ b/recipes/synapseclient/meta.yaml @@ -1,5 +1,5 @@ {% set name = "synapseclient" %} -{% set version="3.1.0" %} +{% set version="3.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/synapseclient-{{ version }}.tar.gz - sha256: ec05a8792a5e5e332211426fb12a2929d6c14179746304b4f37acbb19f89bff3 + sha256: ab78a1202725d22c21f92798191c1862e779b2b31c01ff06f59789bb05fa1174 build: noarch: python From 42bd00977e54c97a673ee157dcde27cd73d70f14 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 1 Nov 2023 15:41:41 -0600 Subject: [PATCH 0570/2173] Update ncbi-datasets-pylib to 15.26.0 (#44033) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index f8358051d1c30..19e134e9231ef 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.25.0" %} -{% set sha256 = "573a95edace0b3d7de00a64ddf9ff0f5b1ae170432c83d8bd71cfcd4c35bcca7" %} +{% set version = "15.26.0" %} +{% set sha256 = "29d5a6f9a982e77eaf4a153ad1fc25ed06a679beaee13bd626f593597ba02dc9" %} package: name: {{ name|lower }} From 26c8cb8c36c25d30819f494f10b4ec3e622634be Mon Sep 17 00:00:00 2001 From: Michael Uhl Date: Wed, 1 Nov 2023 22:57:14 +0100 Subject: [PATCH 0571/2173] Update to Rbpbench v02 (#44036) * add rbpbench meta yaml * add run exports * update recipe to rbpbench v02 --- recipes/rbpbench/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/rbpbench/meta.yaml b/recipes/rbpbench/meta.yaml index e31256fec927c..523b5b1c8312a 100644 --- a/recipes/rbpbench/meta.yaml +++ b/recipes/rbpbench/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RBPBench" %} -{% set version = "0.1" %} -{% set sha256 = "ab8bd57b28ab8d349788450072cc2efe5385483d288efd0eec0634da52c161d3" %} +{% set version = "0.2" %} +{% set sha256 = "d037994f935a3e41b9bc597dc6a895adc1392e007e349fef04ff1aa6e207818b" %} package: name: {{ name|lower }} @@ -32,6 +32,7 @@ requirements: - matplotlib-venn - infernal - bedtools + - upsetplot test: commands: From ed6a87e755b6e0cc846d0f576df6df339cbf1c38 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 1 Nov 2023 17:08:26 -0500 Subject: [PATCH 0572/2173] Add recipe for orthofisher v1.1.0 (#43966) * Add recipe for orthofisher v1.1.0 * edit run_exports --- recipes/orthofisher/meta.yaml | 47 +++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/orthofisher/meta.yaml diff --git a/recipes/orthofisher/meta.yaml b/recipes/orthofisher/meta.yaml new file mode 100644 index 0000000000000..5c44d64e8a351 --- /dev/null +++ b/recipes/orthofisher/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "orthofisher" %} +{% set version = "1.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/orthofisher-{{ version }}.tar.gz + sha256: e8600178d630f1978cf8c6657a6ff128c309dc6bc3bb6f6549ffc04ed4e02e29 + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + entry_points: + - orthofisher = orthofisher.orthofisher:main + run_exports: + - {{ pin_subpackage('orthofisher', max_pin="x.x") }} + +requirements: + host: + - python >=3.9 + - pip + run: + - python >=3.9 + - biopython >=1.81 + - numpy >=1.24.0 + - tqdm >=4.66.1 + +test: + imports: + - orthofisher + commands: + - orthofisher --help + +about: + home: https://github.com/JLSteenwyk/orthofisher.git + summary: Orthofisher is a broadly applicable tool for automated gene identification and retrieval. + license: MIT + license_family: MIT + license_file: LICENSE.md + doc_url: https://jlsteenwyk.com/orthofisher/ + +extra: + identifiers: + - doi:10.1093/g3journal/jkab250 From 99339d377248bb632f832a09a91b530a9d7adfba Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 1 Nov 2023 21:24:38 -0500 Subject: [PATCH 0573/2173] Add recipe for gfftk v23.9.6 (#43982) * Add recipe for gfftk v23.9.6 * add table2asn --- recipes/gfftk/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/gfftk/meta.yaml diff --git a/recipes/gfftk/meta.yaml b/recipes/gfftk/meta.yaml new file mode 100644 index 0000000000000..6951a1651e927 --- /dev/null +++ b/recipes/gfftk/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "gfftk" %} +{% set version = "23.9.6" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/gfftk-{{ version }}.tar.gz + sha256: ee6b9aeef9923bea566bf3cb60fc4de0fec1c73dd157990d50cb26ecd8b6c495 + +build: + number: 0 + noarch: python + entry_points: + - gfftk = gfftk.__main__:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('gfftk', max_pin="x") }} + +requirements: + host: + - python >=3.6 + - pip + run: + - python >=3.6 + - natsort + - numpy + - table2asn + +test: + imports: + - gfftk + commands: + - gfftk --help + +about: + home: https://github.com/nextgenusfs/gfftk + summary: 'GFFtk: genome annotation GFF3 tool kit' + license: BSD-2-Clause + license_family: BSD + license_file: LICENSE.md + +extra: + recipe-maintainers: + - nextgenusfs From 313c9b01e01ee3f11fa9987c65efcfd565d0b96c Mon Sep 17 00:00:00 2001 From: Ian Fiddes Date: Thu, 2 Nov 2023 00:00:40 -0700 Subject: [PATCH 0574/2173] Add pytrf (#44008) --- recipes/pytrf/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 recipes/pytrf/meta.yaml diff --git a/recipes/pytrf/meta.yaml b/recipes/pytrf/meta.yaml new file mode 100644 index 0000000000000..92846f4d81cd6 --- /dev/null +++ b/recipes/pytrf/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "pytrf" %} +{% set version = "1.2.1" %} +{% set sha256 = "47d201d0cb2dad705f9a4e6030d374878c4b6e30762eefd08f159c28db7402df" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://github.com/lmdu/{{ name }}/archive/refs/tags/{{ version }}.tar.gz" + sha256: "{{ sha256 }}" + +build: + number: 0 + script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + run_exports: + - {{ pin_subpackage("pytrf", max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - pip + - python >=3.6,<3.12 + run: + - python >=3.6,<3.12 + +test: + imports: + - pytrf + +about: + home: "https://github.com/lmdu/pytrf" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "a fast Python package for finding tandem repeat sequences" From a79325071e89ab1b581fa0c2a5ce94afed8524fd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 2 Nov 2023 05:26:18 -0600 Subject: [PATCH 0575/2173] Update piranha-polio to 1.1.2 (#44044) --- recipes/piranha-polio/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/piranha-polio/meta.yaml b/recipes/piranha-polio/meta.yaml index 5e922acbfc0d1..77f178381c48f 100644 --- a/recipes/piranha-polio/meta.yaml +++ b/recipes/piranha-polio/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.1" %} +{% set version = "1.1.2" %} package: name: piranha-polio @@ -6,7 +6,7 @@ package: source: url: https://github.com/polio-nanopore/piranha/archive/refs/tags/{{ version }}.tar.gz - sha256: 239436a13de359e04bb4aecaa54d0e8b2cb957873f75efe61201c4f3ab648e0e + sha256: ca64487dc513ebd13f7ca6d9d3770c27b84ad1bbf3f408cbbb1da928910ac3b8 build: number: 0 From fd0a39d8b8ee946880766c1ac452962ecb11cf78 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 2 Nov 2023 05:27:05 -0600 Subject: [PATCH 0576/2173] Update pyteomics to 4.6.3 (#44037) --- recipes/pyteomics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyteomics/meta.yaml b/recipes/pyteomics/meta.yaml index 5357401964726..1f42dfe14a83d 100644 --- a/recipes/pyteomics/meta.yaml +++ b/recipes/pyteomics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.6.2" %} +{% set version = "4.6.3" %} package: name: pyteomics @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/p/pyteomics/pyteomics-{{ version }}.tar.gz - sha256: 8c0608b7fbcfc65409e455c4bc8edb91aa9beed65744f37eacac9119ca7335d5 + sha256: e3bb11e57da3e52ca768d94fed12c9f66d7300fd58bccbc6736dfc0707fd9546 build: noarch: python From e228f579bddd2dc57b8fe4061c04df85eb49acf0 Mon Sep 17 00:00:00 2001 From: ningOTI Date: Thu, 2 Nov 2023 19:45:19 +0800 Subject: [PATCH 0577/2173] Update ucsc-twobittofa from 447 to 455 (#44039) * Update ucsc-twobittofa from 447 to 455 --- recipes/ucsc-twobittofa/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/ucsc-twobittofa/meta.yaml b/recipes/ucsc-twobittofa/meta.yaml index e1a9af495a86d..60da0e0bea610 100644 --- a/recipes/ucsc-twobittofa/meta.yaml +++ b/recipes/ucsc-twobittofa/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-twobittofa" %} {% set program = "twoBitToFa" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: {{ package }} @@ -14,11 +14,13 @@ source: - include.patch build: - number: 0 skip: True # [osx] + number: 0 ignore_run_exports: - libpng - libuuid + run_exports: + - {{ pin_subpackage("ucsc-twobittofa", max_pin=None) }} requirements: build: From 984c6f51503e566b2148f3c007b017d68de850aa Mon Sep 17 00:00:00 2001 From: ningOTI Date: Thu, 2 Nov 2023 19:45:50 +0800 Subject: [PATCH 0578/2173] Update ucsc-fatotwobit from 447 to 455 (#44040) * Update ucsc-fatotwobit from 447 to 455 --- recipes/ucsc-fatotwobit/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ucsc-fatotwobit/meta.yaml b/recipes/ucsc-fatotwobit/meta.yaml index eaaf15bc647e4..9809766e8251f 100644 --- a/recipes/ucsc-fatotwobit/meta.yaml +++ b/recipes/ucsc-fatotwobit/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fatotwobit" %} {% set program = "faToTwoBit" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -19,6 +19,8 @@ build: ignore_run_exports: - libpng - libuuid + run_exports: + - {{ pin_subpackage("ucsc-fatotwobit", max_pin=None) }} requirements: build: From f1a1098d7d911120c5569b60e6c4af3963751d20 Mon Sep 17 00:00:00 2001 From: ningOTI Date: Thu, 2 Nov 2023 19:46:40 +0800 Subject: [PATCH 0579/2173] Update ucsc-chainsort from 377 to 455 (#44041) * Update ucsc-chainsort from 377 to 455 * Remove this package from blacklist --- build-fail-blacklist | 1 - recipes/ucsc-chainsort/include.patch | 26 +++++++++++++++++--------- recipes/ucsc-chainsort/meta.yaml | 12 ++++++++---- 3 files changed, 25 insertions(+), 14 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 10e5edb091f81..54ac98663262b 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -845,7 +845,6 @@ recipes/ucsc-chainfilter recipes/ucsc-chainmergesort recipes/ucsc-chainnet recipes/ucsc-chainprenet -recipes/ucsc-chainsort recipes/ucsc-chainsplit recipes/ucsc-chainstitchid recipes/ucsc-chainswap diff --git a/recipes/ucsc-chainsort/include.patch b/recipes/ucsc-chainsort/include.patch index eb32b88d8f358..e9c8621194325 100644 --- a/recipes/ucsc-chainsort/include.patch +++ b/recipes/ucsc-chainsort/include.patch @@ -1,22 +1,30 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a +--- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 ++++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 @@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +-KENT_INC=-I../../../inc ++KENT_INC=-I../../../inc -I${PREFIX}/include + + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-chainsort/meta.yaml b/recipes/ucsc-chainsort/meta.yaml index 812585c2231ec..3864af0708530 100644 --- a/recipes/ucsc-chainsort/meta.yaml +++ b/recipes/ucsc-chainsort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainsort" %} {% set program = "chainSort" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -15,19 +15,23 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage("ucsc-chainsort", max_pin=None) }} requirements: build: - make - {{ compiler('c') }} + - {{ compiler('cxx') }} + - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - openssl + - libopenssl-static - zlib - run: - libpng - libuuid From 9f2f997a404efd18d8def73909abe8eeadcfe8a7 Mon Sep 17 00:00:00 2001 From: Leon Rauschning <99650940+lrauschning@users.noreply.github.com> Date: Thu, 2 Nov 2023 13:20:20 +0100 Subject: [PATCH 0580/2173] add mTM-align (#43730) * add mtmalign --- recipes/mtm-align/build.sh | 16 ++++++++++++++++ recipes/mtm-align/meta.yaml | 29 +++++++++++++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 recipes/mtm-align/build.sh create mode 100644 recipes/mtm-align/meta.yaml diff --git a/recipes/mtm-align/build.sh b/recipes/mtm-align/build.sh new file mode 100644 index 0000000000000..f0a634f2e9b81 --- /dev/null +++ b/recipes/mtm-align/build.sh @@ -0,0 +1,16 @@ +#!/bin/bash +set -ex + +cd src/ + +## This doesn't seem to work reliably +# the makefile directly calls g++, and doesn't use env variables +# use an alias to redirect to the correct compiler without changing the makefile +#alias "g++"=$CXX +#make # builds the package + +## instead just build with a manual call to the compiler +$CXX -O3 -ffast-math -lm -o mTM-align main.cpp TMM.cpp UPGMA.cpp + +mkdir -p $PREFIX/bin +mv mTM-align $PREFIX/bin/mtm-align diff --git a/recipes/mtm-align/meta.yaml b/recipes/mtm-align/meta.yaml new file mode 100644 index 0000000000000..4e78d94b7ce57 --- /dev/null +++ b/recipes/mtm-align/meta.yaml @@ -0,0 +1,29 @@ +{% set version = "20220104" %} +{% set sha256 = "f7ed827ff2fb4ffdd85c4fa6a8e43f0eae776b4b4715896172f5fe52c4853d2e" %} +package: + name: mtm-align + version: '{{version}}' + +source: + - url: http://yanglab.nankai.edu.cn/mTM-align/version/mTM-align.tar.bz2 + sha256: '{{sha256}}' + +build: + skip: True # [osx] + number: 0 + run_exports: + - {{ pin_subpackage('mtm-align', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + +test: + commands: + - mtm-align -h + +about: + home: http://yanglab.nankai.edu.cn/mTM-align/help/ + license: Unknown + summary: Align multiple protein structures From 60618bd71f87a192912a94093668edef97d8a910 Mon Sep 17 00:00:00 2001 From: Sudaraka Mallawaarachchi Date: Fri, 3 Nov 2023 05:44:37 +1100 Subject: [PATCH 0581/2173] r-ldweaver add missing pin (#44042) * add_openjdk_pin * add_openjdk_pin * bump_v1.3.1 --- recipes/r-ldweaver/meta.yaml | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/recipes/r-ldweaver/meta.yaml b/recipes/r-ldweaver/meta.yaml index 0eaa2453f417b..f5c10cbc6684e 100644 --- a/recipes/r-ldweaver/meta.yaml +++ b/recipes/r-ldweaver/meta.yaml @@ -1,6 +1,6 @@ {% set name = "r-ldweaver" %} -{% set version = "1.2" %} -{% set sha256 = "66a51a318be2029ae163f2cd70ae0f66a925bc2313aea070d34d25b72efdc528" %} +{% set version = "1.3.1" %} +{% set sha256 = "a926d946b4fea6abdc2e7fdcc3ac8a55865da0403d45180eeb60cda0b92d3de0" %} package: name: {{ name }} @@ -12,6 +12,7 @@ source: build: number: 0 + # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ - lib/ @@ -22,6 +23,7 @@ requirements: build: - {{ compiler('c') }} # [not win] - {{ compiler('cxx') }} # [not win] + host: - r-base 4.* - bioconductor-genomicranges @@ -46,6 +48,8 @@ requirements: - r-phytools - r-plyr - r-stringi + - openjdk + run: - r-base 4.* - bioconductor-genomicranges @@ -70,9 +74,11 @@ requirements: - r-phytools - r-plyr - r-stringi + - openjdk test: commands: + # You can put additional test commands to be run here. - $R -e "library('LDWeaver')" # [not win] about: From d084dec9aca6b9369391a2c8a74651ef7394bacc Mon Sep 17 00:00:00 2001 From: Michael Uhl Date: Thu, 2 Nov 2023 19:45:37 +0100 Subject: [PATCH 0582/2173] Update to Rbpbench v03 (#44050) * add rbpbench meta yaml * add run exports * update recipe to rbpbench v03 --- recipes/rbpbench/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rbpbench/meta.yaml b/recipes/rbpbench/meta.yaml index 523b5b1c8312a..986258197fc9b 100644 --- a/recipes/rbpbench/meta.yaml +++ b/recipes/rbpbench/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RBPBench" %} -{% set version = "0.2" %} -{% set sha256 = "d037994f935a3e41b9bc597dc6a895adc1392e007e349fef04ff1aa6e207818b" %} +{% set version = "0.3" %} +{% set sha256 = "b119b8cfd8a81d4db8af4c66c60b7b482bb7476bafd3a4206bf8b01f280e3f10" %} package: name: {{ name|lower }} From e59da515371cb103b359c1f8bf3d9274db6c0a10 Mon Sep 17 00:00:00 2001 From: Gleb Ebert <5892266+gl-eb@users.noreply.github.com> Date: Thu, 2 Nov 2023 19:52:53 +0100 Subject: [PATCH 0583/2173] Update HTSeq to 2.0.4 (#44048) * update htseq to 2.0.4 * reset recipe build number to 0 * add run_export statement --- recipes/htseq/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/htseq/meta.yaml b/recipes/htseq/meta.yaml index 7cf49211da43e..a68cff9aff26b 100644 --- a/recipes/htseq/meta.yaml +++ b/recipes/htseq/meta.yaml @@ -1,17 +1,19 @@ -{% set version = '2.0.3' %} +{% set version = '2.0.4' %} package: name: htseq version: {{ version }} source: - url: https://files.pythonhosted.org/packages/83/61/05ce20ed21cedf9c31a0bc20cdffb66012e6ac202609ea1207322895c301/HTSeq-{{ version }}.tar.gz - sha256: c7e7eb29bdc44e80d2d68e3599fa8a8f1d9d6475624dcf1b9644285a8a9c0fac + url: https://files.pythonhosted.org/packages/ed/ca/6f1e2f556cb2aad34ea8481f41a5a16dc52bef2e4fa55e7107b0b8e6bfe5/HTSeq-{{ version }}.tar.gz + sha256: 5510d855617d61efff2287af4cdc60a73e94bd735e44c15b57f189ea0634e6e0 build: - number: 1 + number: 0 skip: True # [py2k or py == 36] script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + run_exports: + - {{ pin_subpackage('htseq', max_pin="x") }} requirements: build: From 006f54d2b21d0cfc8b733c052f187931d0782ea3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 2 Nov 2023 13:31:15 -0600 Subject: [PATCH 0584/2173] Update isocor to 2.2.2 (#44052) * Update isocor to 2.2.2 * add run_exports * tidy meta.yaml format --------- Co-authored-by: joshuazhuang7 --- recipes/isocor/meta.yaml | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/recipes/isocor/meta.yaml b/recipes/isocor/meta.yaml index 5c03e2d2696ee..5155ad414905e 100644 --- a/recipes/isocor/meta.yaml +++ b/recipes/isocor/meta.yaml @@ -1,10 +1,13 @@ +{% set name = "isocor" %} +{% set version = "2.2.2" %} + package: - name: "isocor" - version: "2.2.1" + name: {{ name|lower }} + version: {{ version }} source: - url: https://files.pythonhosted.org/packages/e7/13/00a3753450d1ec9b478da3329ae83f334b8a9b8601aa3e2600a0562ff0c1/IsoCor-2.2.1.tar.gz - sha256: 528714817b5672fddd489771baeae1d8372d2529974568aaddfd7e197e8baf8e + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/IsoCor-{{ version }}.tar.gz + sha256: eb4c91d2ed5b626adc6208454fd82b3e2ddd9a3ad0ccd964c8f16f9a310673e7 build: number: 0 @@ -12,15 +15,17 @@ build: entry_points: - isocorcli = isocor.ui.isocorcli:start_cli - isocor = isocor.ui.isocorgui:start_gui - script: python -m pip install . --no-deps --ignore-installed + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('isocor', max_pin="x") }} requirements: host: - pip - - python >=3.6 + - python >=3.7 run: - pandas >=0.17.1 - - python >=3.6 + - python >=3.7 - scipy >=0.12.1 - numpy >=1.15 @@ -34,7 +39,7 @@ test: about: home: https://github.com/MetaSys-LISBP/IsoCor/ - license: GNU General Public v3 or later (GPLv3+) + license: GPL-3.0-or-later license_family: GPL3 license_file: LICENSE.md summary: A Isotope Correction for mass spectrometry labeling experiments From 47577b99fe665f0fd234821acc35237afa372acb Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Thu, 2 Nov 2023 20:31:40 +0100 Subject: [PATCH 0585/2173] add pyopenms as dependency (#44047) --- recipes/ms2rescore/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index 34525e62a3608..abcb896b63201 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d3fa5112038d2e92a916f57b47f634fec5235836260fe0949fd8cc4549cc7410 build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -31,6 +31,7 @@ requirements: - pandas >=1.0 - rich >=12 - pyteomics >=4.1.0 + - pyopenms - lxml >=4.5 - ms2pip >=4.0.0-dev4 - click >=7 From 0affed971a2afe174b2b75ab7bb060e1658e9cf3 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 2 Nov 2023 15:15:43 -0500 Subject: [PATCH 0586/2173] Add recipe for gapmm2 v0.2.0 (#44055) --- recipes/gapmm2/meta.yaml | 46 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/gapmm2/meta.yaml diff --git a/recipes/gapmm2/meta.yaml b/recipes/gapmm2/meta.yaml new file mode 100644 index 0000000000000..85b65281456ef --- /dev/null +++ b/recipes/gapmm2/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "gapmm2" %} +{% set version = "0.2.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/gapmm2-{{ version }}.tar.gz + sha256: 185faa005babf32d5c1a0eab2032af8d7d370aa297643362b9673075c67cd2d6 + +build: + number: 0 + noarch: python + entry_points: + - gapmm2 = gapmm2.__main__:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('gapmm2', max_pin="x.x") }} + +requirements: + host: + - python >=3.6 + - pip + run: + - python >=3.6 + - mappy + - python-edlib + - natsort + +test: + imports: + - gapmm2 + commands: + - gapmm2 --help + +about: + home: https://github.com/nextgenusfs/gapmm2 + summary: 'gapmm2: gapped alignment using minimap2' + license: BSD-2-Clause + license_family: BSD + license_file: LICENSE.md + +extra: + recipe-maintainers: + - nextgenusfs From 5953e61603f37eca147697bcb63d84152d9839df Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 2 Nov 2023 14:47:42 -0600 Subject: [PATCH 0587/2173] Update liftover to 1.1.17 (#44054) * Update liftover to 1.1.17 * add run_exports --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/liftover/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/liftover/meta.yaml b/recipes/liftover/meta.yaml index 4e19245919b8b..8c82c1069fba5 100644 --- a/recipes/liftover/meta.yaml +++ b/recipes/liftover/meta.yaml @@ -1,6 +1,6 @@ {% set name = "liftover" %} -{% set version = "1.1.16" %} -{% set sha256 = "fc1c92ef3279b61a2ccfd8c3cdb9cb4829b11a0f9356d15097c611fc0064fd0f" %} +{% set version = "1.1.17" %} +{% set sha256 = "cb06a3843b570ec554fbc0dd871c0b87d3645200e2c65f6cc97cd4b6146efaf9" %} package: name: {{ name|lower }} @@ -12,8 +12,10 @@ source: build: number: 0 - skip: True # [py < 37] - script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vv + skip: True # [py < 38] + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('liftover', max_pin="x") }} requirements: build: @@ -22,7 +24,6 @@ requirements: - python - cython - pip - - setuptools - wheel - zlib run: @@ -37,6 +38,7 @@ about: home: 'https://github.com/jeremymcrae/liftover' summary: 'A Python package for converting point coordinates between genome assemblies, inspired by pyliftover.' license: MIT + license_family: MIT license_file: LICENSE.txt dev_url: 'https://pypi.org/project/liftover/' From f7200de051253df0e731a6655e70b8019138fff4 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 2 Nov 2023 16:05:02 -0500 Subject: [PATCH 0588/2173] Add recipe for buscolite v23.10.26 (#44056) * Add recipe for buscolite v23.10.26 * pin augustus >=3.5.0 older augustus versions have a whole bunch of build problems for the ppx module (protein profile) that is used here, so lets pin to at least that version --------- Co-authored-by: Jon Palmer --- recipes/buscolite/meta.yaml | 48 +++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 recipes/buscolite/meta.yaml diff --git a/recipes/buscolite/meta.yaml b/recipes/buscolite/meta.yaml new file mode 100644 index 0000000000000..7f4e086d17901 --- /dev/null +++ b/recipes/buscolite/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "buscolite" %} +{% set version = "23.10.26" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/buscolite-{{ version }}.tar.gz + sha256: c641dc6c702fa198fd6fa661b756aedde4468ea591c8c64f8b8bd9c8a865b72d + +build: + number: 0 + noarch: python + entry_points: + - buscolite = buscolite.__main__:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('buscolite', max_pin="x") }} + +requirements: + host: + - python >=3.6 + - pip + run: + - python >=3.6 + - augustus >=3.5.0 + - miniprot + - natsort + - pyhmmer + - pyfastx + +test: + imports: + - buscolite + commands: + - buscolite --help + +about: + home: https://github.com/nextgenusfs/buscolite + summary: 'buscolite: busco analysis for gene predictions' + license: BSD-2-Clause + license_family: BSD + license_file: LICENSE.md + +extra: + recipe-maintainers: + - nextgenusfs From c668fa690572ddec9d5760e745776f320d3c7d60 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 2 Nov 2023 15:25:49 -0600 Subject: [PATCH 0589/2173] Update viralmsa to 1.1.38 (#44053) --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index 948d8ae71d3f2..d134a5f1ceb9e 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.36" %} +{% set version = "1.1.38" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: d34ee3a12cd0cba0404519772330450f9f54de1da1f8473395f204e84cf66aea + sha256: 1100b08575ad6335d9aff3423315419f05a08ffeab82d42cb3333aa9298f533b requirements: run: From ea0c8fb136e45b74a80e35704ed930ac09a49622 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 2 Nov 2023 15:26:55 -0600 Subject: [PATCH 0590/2173] Update snakemake-interface-common to 1.14.2 (#44046) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 8aa85fc282a0c..6b89e7aa82e39 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.14.1" %} +{% set version = "1.14.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 4ade1fe41c514d929ccd0ca7aa3ec73a62ceccfe4fd08885be296accaec9cac6 + sha256: 377aa7760220f92deade72473cd9409b8715eaa2cd6f76b1965e035a5556ffe2 build: noarch: python From e31d7ca0622e7d57654e71e16b34f3d052996df9 Mon Sep 17 00:00:00 2001 From: ANGSD Date: Fri, 3 Nov 2023 02:21:52 +0100 Subject: [PATCH 0591/2173] update recipe for newest v0.4 version (#44026) * Updated recipe for newest v0.4 version * change version value --------- Co-authored-by: fvr124 Co-authored-by: Thanh Lee --- recipes/metadmg/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/metadmg/meta.yaml b/recipes/metadmg/meta.yaml index 4df3f4b966692..599061d0629ce 100644 --- a/recipes/metadmg/meta.yaml +++ b/recipes/metadmg/meta.yaml @@ -1,17 +1,17 @@ {% set name = "metadmg" %} -{% set version = "0.3" %} -{% set sha256 = "e0b71911de01e56bd67b5f9faa5039a875dab3d40c087fa041fecb219a85e50c" %} +{% set version = "0.4" %} +{% set sha256 = "072486bf4103c256bbc907d265d24993b3f5a90eca7dd3fced63f5a8f5840b64" %} package: name: {{ name }} version: {{ version }} source: - url: https://github.com/metaDMG-dev/metaDMG-cpp/archive/refs/tags/{{ version }}.tar.gz + url: https://github.com/metaDMG-dev/metaDMG-cpp/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} build: - number: 1 + number: 0 skip: false run_exports: - {{ pin_subpackage(name, max_pin="x") }} From 1f6f9882aa3b7a0eac04b3229a9b61d43119dd3e Mon Sep 17 00:00:00 2001 From: Adrian Altenhoff Date: Fri, 3 Nov 2023 02:23:04 +0100 Subject: [PATCH 0592/2173] Add omamer (#44034) * Add omamer * don't run pip check in test --- recipes/omamer/meta.yaml | 60 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 recipes/omamer/meta.yaml diff --git a/recipes/omamer/meta.yaml b/recipes/omamer/meta.yaml new file mode 100644 index 0000000000000..ff8007093ef01 --- /dev/null +++ b/recipes/omamer/meta.yaml @@ -0,0 +1,60 @@ +{% set name = "omamer" %} +{% set version = "2.0.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/omamer-{{ version }}.tar.gz + sha256: 749ccd0f3f1dad48b00651c7298f8e83c08e1bceef288ff53068dd8abda705f5 + +build: + entry_points: + - omamer = omamer.main:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - alive-progress + - biopython + - ete3 + - numba + - numpy + - pandas >2.0.0 + - property-manager + - rmath4 + - scipy + - pytables + - tqdm # +# Extra: build + - pysais + +test: + imports: + - omamer + commands: + - omamer --help + +about: + home: https://github.com/DessimozLab/omamer + summary: OMAmer - tree-driven and alignment-free protein assignment to sub-families + license: LGPL-3.0 + license_file: + - LICENSE + - COPYING.LESSER + - COPYING + +extra: + recipe-maintainers: + - alpae + identifiers: + - doi:10.1093/bioinformatics/btab219 From e37363fed382cf9127697ff024e8fc07c6db05f9 Mon Sep 17 00:00:00 2001 From: ningOTI Date: Fri, 3 Nov 2023 14:34:45 +0800 Subject: [PATCH 0593/2173] Update ucsc-axtchain from 377 to 455 (#44059) * Update ucsc-axtchain from 377 to 455 * Remove this package (ucsc-axtchain) from blacklist * Fix unincremented version (should be 455, not 377) * Fix missing build dependencies * Fix malformed jinja expression --- build-fail-blacklist | 1 - recipes/ucsc-axtchain/include.patch | 31 ++++++++++++++++++++--------- recipes/ucsc-axtchain/meta.yaml | 11 ++++++---- 3 files changed, 29 insertions(+), 14 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 54ac98663262b..d82bf5d900c11 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -802,7 +802,6 @@ recipes/ucsc-autodtd recipes/ucsc-autosql recipes/ucsc-autoxml recipes/ucsc-avecols -recipes/ucsc-axtchain recipes/ucsc-axtsort recipes/ucsc-axtswap recipes/ucsc-axttomaf diff --git a/recipes/ucsc-axtchain/include.patch b/recipes/ucsc-axtchain/include.patch index eb32b88d8f358..e4831ef2dea13 100644 --- a/recipes/ucsc-axtchain/include.patch +++ b/recipes/ucsc-axtchain/include.patch @@ -1,5 +1,5 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,14 +9,14 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -@@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,3 +25,16 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. +--- kent/src/hg/lib/straw/makefile ++++ kent/src/hg/lib/straw/makefile +@@ -3,8 +3,8 @@ + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o + straw.o: straw.cpp straw.h +- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o ++ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include + cStraw.o: cStraw.cpp straw.h +- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o ++ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include + clean: + rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-axtchain/meta.yaml b/recipes/ucsc-axtchain/meta.yaml index 0298a36b08794..72064fd875b92 100644 --- a/recipes/ucsc-axtchain/meta.yaml +++ b/recipes/ucsc-axtchain/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axtchain" %} {% set program = "axtChain" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -15,19 +15,22 @@ source: build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} + - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info + - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - openssl - zlib - run: - libpng - libuuid From 2c35d1e1b8498b67e9924815cadf815ca70340da Mon Sep 17 00:00:00 2001 From: Adrian Altenhoff Date: Fri, 3 Nov 2023 09:57:03 +0100 Subject: [PATCH 0594/2173] Add omark (#44067) * Add omark * fix lint errors --- recipes/omark/meta.yaml | 50 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 recipes/omark/meta.yaml diff --git a/recipes/omark/meta.yaml b/recipes/omark/meta.yaml new file mode 100644 index 0000000000000..8ae9f2fd269ec --- /dev/null +++ b/recipes/omark/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "omark" %} +{% set version = "0.3.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/omark-{{ version }}.tar.gz + sha256: fa35e4ba3a8697aa06c3242394909e794a6ea574cfd1eaf90827ab9f98fc3f3b + +build: + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + noarch: python + +requirements: + host: + - python + - pip + run: + - python + - biopython + - ete3 + - omamer >=2.0.0 + - matplotlib-base + - jinja2 + +test: + imports: + - omark + commands: + - omark -h + +about: + home: https://github.com/DessimozLab/omark + summary: OMArk - Proteome quality assesment based on OMAmer placements + license: LGPL-3.0 + license_file: + - LICENSE + - COPYING.LESSER + - COPYING + +extra: + recipe-maintainers: + - alpae + identifiers: + - doi:10.1101/2022.11.25.517970 From 8d2c11870c5eb8880082e5e0d7dcd28cb75ccb85 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 03:07:29 -0600 Subject: [PATCH 0595/2173] Update ont-modkit to 0.2.2 (#44066) --- recipes/ont-modkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml index e265a6e9485fb..b9c9b8d249964 100644 --- a/recipes/ont-modkit/meta.yaml +++ b/recipes/ont-modkit/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.1" %} -{% set sha256 = "5602a3dbf3c2cfc962b45743da229dbf440d91b2e0d4e50d98413e371c8c0b51" %} +{% set version = "0.2.2" %} +{% set sha256 = "3271c54a34d2b9a413169079ed357ead056b60c54a3ade1dcac71350899555ac" %} package: name: ont-modkit From a91b5dbd1a97d622d2170726900da813dbbb6875 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 03:08:19 -0600 Subject: [PATCH 0596/2173] Update mercat2 to 1.2 (#44057) --- recipes/mercat2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mercat2/meta.yaml b/recipes/mercat2/meta.yaml index bd0df0780487e..3f4f4ce59329c 100644 --- a/recipes/mercat2/meta.yaml +++ b/recipes/mercat2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mercat2" %} -{% set version = "1.1" %} +{% set version = "1.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 4e08b025e80f390980afdefd875bd24bcc6a72ae000be6733929975d56843062 + sha256: 45c90499dae461ba52e8993359ed04c65c60ed2fa693d417fac9ec274aad3775 build: number: 0 From 78af60a9bc7b55beaea76f78fbf66a6d0f60bc16 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 05:19:03 -0600 Subject: [PATCH 0597/2173] Update npstructures to 0.2.14 (#44070) --- recipes/npstructures/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/npstructures/meta.yaml b/recipes/npstructures/meta.yaml index 591ff746590ae..c83ef94138932 100644 --- a/recipes/npstructures/meta.yaml +++ b/recipes/npstructures/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.13" %} +{% set version = "0.2.14" %} {% set name = "npstructures" %} package: name: {{ name }} @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3ae458ff31cc9afe1e845a8d15c36f1beca4f7c5de524aa845c99192425d7954 + sha256: 2b9b8aab8b9209f3a96e783b2c773dd98be70ef171865b53cc0fbb283b11fee6 build: From 46c0bdcd8d0c86321a4b125abfb268a05ae2d323 Mon Sep 17 00:00:00 2001 From: "Ricardo A. Vialle" Date: Fri, 3 Nov 2023 08:10:35 -0500 Subject: [PATCH 0598/2173] Update snakeSV build recipe (#44069) --- recipes/snakesv/build.sh | 2 +- recipes/snakesv/meta.yaml | 7 +++---- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/snakesv/build.sh b/recipes/snakesv/build.sh index 82ea9ab4075c0..369a431cd5030 100755 --- a/recipes/snakesv/build.sh +++ b/recipes/snakesv/build.sh @@ -4,7 +4,7 @@ mkdir -p $PREFIX/bin mkdir -p $PREFIX/opt/snakeSV/ # Full path to the Snakefile -sed -i "s|\$(dirname \$(which snakeSV))/workflow/Snakefile|$PREFIX/opt/snakeSV/workflow/Snakefile|g" snakeSV +sed -i "s|\$(dirname \$(which snakeSV))|$PREFIX/opt/snakeSV|g" snakeSV cp -r * $PREFIX/opt/snakeSV/ ln -s $PREFIX/opt/snakeSV/snakeSV $PREFIX/bin/ diff --git a/recipes/snakesv/meta.yaml b/recipes/snakesv/meta.yaml index 90a1453f584aa..5fc97c81faf42 100755 --- a/recipes/snakesv/meta.yaml +++ b/recipes/snakesv/meta.yaml @@ -10,16 +10,15 @@ source: sha256: a9312b1992bb1eea9b824175f59b8d9bb3f9e773028ad98f31839d8a25b527a6 build: - number: 2 + number: 3 noarch: generic run_exports: - {{ pin_subpackage('snakesv', max_pin="x.x") }} requirements: run: - - snakemake =7.0.1 - - mamba - - bcftools =1.15.1 + - snakemake =7.32.4 + - bcftools =1.9 test: commands: From f706780349a5e55bba53cccc8a52a754f96c9bff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 08:04:14 -0600 Subject: [PATCH 0599/2173] Update flight-genome to 1.6.0 (#44071) * Update flight-genome to 1.6.0 * run_exports * add spaces --------- Co-authored-by: Thanh Lee --- recipes/flight-genome/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/flight-genome/meta.yaml b/recipes/flight-genome/meta.yaml index 142b74d3d2722..2990b52651e74 100644 --- a/recipes/flight-genome/meta.yaml +++ b/recipes/flight-genome/meta.yaml @@ -1,5 +1,5 @@ {% set name = "flight-genome" %} -{% set version = "1.5.0" %} +{% set version = "1.6.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 5af30d98fe44de7d60a993f05577316817c91a5ed1561d2051f42df117d31450 + sha256: c91a42b8164f46678bbc3a3d812de290c42898f1b38a544257afd5a829b60698 build: number: 0 @@ -15,13 +15,15 @@ build: entry_points: - flight = flight.flight:main script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: - pip - python run: - - python>=3.8 + - python >=3.8 - biopython From f56972af2a23902b1d55c66287c8c21850275096 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 08:04:36 -0600 Subject: [PATCH 0600/2173] Update bionumpy to 0.2.29 (#44072) * Update bionumpy to 0.2.28 * Update bionumpy to 0.2.29 --- recipes/bionumpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index 94b753eae7e19..ed28b0321744e 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.27" %} +{% set version = "0.2.29" %} package: name: bionumpy @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: e5f981e3c0bdcef8306c3333e77249054e53f4108653142c6cf76d4a12a4c48e + sha256: 63064c721294d083b7d5725265f2d75a3f47a08d81b1886ea24395d947a71aca build: noarch: python From 6dae5518b6c305507718c95c4413a9fe3e6d29d7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 08:07:03 -0600 Subject: [PATCH 0601/2173] Update ncbi-datasets-pylib to 15.27.0 (#44058) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 19e134e9231ef..eddc286517934 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.26.0" %} -{% set sha256 = "29d5a6f9a982e77eaf4a153ad1fc25ed06a679beaee13bd626f593597ba02dc9" %} +{% set version = "15.27.0" %} +{% set sha256 = "25554af9fd4447e5471c79c06091ec890d31a218928032608fe67ee9d3aecac2" %} package: name: {{ name|lower }} From 328b7172a35c0a6e4344b3b21e6a15ea4409c2fd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 10:07:07 -0600 Subject: [PATCH 0602/2173] Update annotsv to 3.3.7 (#44073) * Update annotsv to 3.3.7 * add run_exports * add back noarch:generic --------- Co-authored-by: joshuazhuang7 --- recipes/annotsv/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/annotsv/meta.yaml b/recipes/annotsv/meta.yaml index 61a93cc9581cb..bf1cfc713ab97 100644 --- a/recipes/annotsv/meta.yaml +++ b/recipes/annotsv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "annotsv" %} -{% set version = "3.3.6" %} -{% set sha256 = "d19b3280faa78acde595db3341f34761926732304af20bfc866d54ab0510a2a1" %} +{% set version = "3.3.7" %} +{% set sha256 = "abf2a0a1604275d8ded66aba7a7084659430d43242eb28fa2a59467487efe7bf" %} package: name: {{ name }} @@ -9,6 +9,8 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('annotsv', max_pin="x") }} source: url: https://github.com/lgmgeo/AnnotSV/archive/refs/tags/v{{ version }}.tar.gz @@ -42,6 +44,7 @@ test: about: home: https://github.com/lgmgeo/AnnotSV - license: GPL-3.0 + license: GPL-3.0-only + license_family: GPL3 license_file: License.txt - summary: Annotation and Ranking of Structural Variation + summary: Annotation and Ranking of Structural Variation From 228b652e9ea92393881921a339859337f7a9f3a1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 10:52:11 -0600 Subject: [PATCH 0603/2173] Update fiji-simple_omero_client to 5.16.0 (#44079) --- recipes/fiji-simple_omero_client/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fiji-simple_omero_client/meta.yaml b/recipes/fiji-simple_omero_client/meta.yaml index a661de59a926b..1a71aba5be3a5 100644 --- a/recipes/fiji-simple_omero_client/meta.yaml +++ b/recipes/fiji-simple_omero_client/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fiji-simple_omero_client" %} -{% set version = "5.15.0" %} +{% set version = "5.16.0" %} package: name: {{ name | lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/GReD-Clermont/simple-omero-client/releases/download/{{ version }}/simple-omero-client-{{ version }}.jar - sha256: 14a6ee2a9f15c5e97dd37967f95ba41f45b5c29ed702ac3d2783f810d55e6298 + sha256: 577a1edcea00a4f3ad50360e8e53c0f25474b44ae21ffc20afbc757cc6c6c9d3 build: number: 0 From 03e5f873dfc5824170c201123ba97907b7021037 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 11:48:32 -0600 Subject: [PATCH 0604/2173] Update blockclust to 1.1.1 (#44076) * Update blockclust to 1.1.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/blockclust/meta.yaml | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/recipes/blockclust/meta.yaml b/recipes/blockclust/meta.yaml index 57083469dcca1..14c611f30d91b 100644 --- a/recipes/blockclust/meta.yaml +++ b/recipes/blockclust/meta.yaml @@ -1,14 +1,19 @@ +{% set name = "blockclust" %} +{% set version = "1.1.1" %} + package: - name: blockclust - version: 1.1.0 + name: {{ name|lower }} + version: {{ version }} source: - url: https://github.com/pavanvidem/blockclust/archive/v1.1.0.tar.gz - sha256: 2376c567f17537da4ac6eba1f75dd1f56079ea406e7e801c5de1ac9e82c08219 + url: https://github.com/pavanvidem/blockclust/archive/refs/tags/v{{ version }}.tar.gz + sha256: 80ee2b32085b93966254083574b2bf3988771ffe28d73775be96a16cfda5579b build: - number: 9 + number: 0 skip: True # [osx or py2k] + run_exports: + - {{ pin_subpackage('blockclust', max_pin="x") }} requirements: build: @@ -34,7 +39,8 @@ test: about: home: https://github.com/pavanvidem/blockclust - license: GPL + license: GPL-2.0-or-later + license_family: GPL2 license_file: LICENSE summary: Efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. From 57e8493b8e74342ca8932434b076a50a5721b7e2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 11:49:35 -0600 Subject: [PATCH 0605/2173] Update bioconda-utils to 2.8.0 (#43423) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update bioconda-utils to 2.5.0 * debug by excluding python 3.12 * Update bioconda-utils to 2.5.0 * Update bioconda-utils to 2.6.0 * Update bioconda-utils to 2.7.0 * whitespace * undo whitespace change * Update bioconda-utils to 2.7.0 * Update bioconda-utils to 2.8.0 * use mamba for test install * remove python constraint * Update meta.yaml --------- Co-authored-by: Robert A. Petit III Co-authored-by: aliciaaevans Co-authored-by: Björn Grüning --- recipes/bioconda-utils/meta.yaml | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index 3febcfdf6ffb3..ce46ad1994248 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.4.0" %} -{% set sha256 = "a4744a1b4d89deb628c604889cc2b3922861a54181fedf649a63c1e4b5a2020c" %} +{% set version = "2.8.0" %} +{% set sha256 = "5a555f97ca64423b5dbfd695214caab0eee66168b6bf24d4e86fc93bdd27e1da" %} package: name: bioconda-utils @@ -20,10 +20,10 @@ build: requirements: host: - - python >=3.7 + - python - pip run: - - python >=3.7 + - python - conda 23.3.* - boa 0.15.* - conda-build 3.24.* @@ -75,8 +75,10 @@ requirements: - tabulate 0.9.* test: - imports: - - bioconda_utils + #imports: + # - bioconda_utils + # [Nov 2 22:37:22] SERR bash: -c: line 1: syntax error near unexpected token `&&' + # [Nov 2 22:37:22] SERR bash: -c: line 1: ` && python -c "import bioconda_utils"' commands: - bioconda-utils --help - bioconda-utils lint --help @@ -84,10 +86,10 @@ test: - > CONDA_AGGRESSIVE_UPDATE_PACKAGES= CONDA_AUTO_UPDATE_CONDA=0 - "${PREFIX}/bin/conda" install --prefix="${PREFIX}" --dry-run --satisfied-skip-solve + "${PREFIX}/bin/mamba" install --prefix="${PREFIX}" --dry-run --satisfied-skip-solve --file="$( python -c 'from os.path import dirname, join; import bioconda_utils; print(join(dirname(bioconda_utils.__file__), "bioconda_utils-requirements.txt"))' - )" 2>&1 | grep -qF 'All requested packages already installed.' + )" 2>&1 | grep -qF 'All requested packages already installed' about: home: http://bioconda.github.io/build-system.html From f6930d040a29f5a85a2485590096a352d907258d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 11:52:20 -0600 Subject: [PATCH 0606/2173] Update r-pipette to 0.14.2 (#44074) --- recipes/r-pipette/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-pipette/meta.yaml b/recipes/r-pipette/meta.yaml index 119f2f93c52ee..676e5fc893c6b 100644 --- a/recipes/r-pipette/meta.yaml +++ b/recipes/r-pipette/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.14.1" %} +{% set version = "0.14.2" %} {% set github = "https://github.com/acidgenomics/r-pipette" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 8574ee337b22eb709b19b4d661a231b04512e408e542fec985cffdeb8807722c + sha256: 14f41aaed6afa3c0332282ca1a256774602ef7e12986afa82a09dd056ba4e5aa build: number: 0 From da56b930ca34c539a519f222dcc9db06b00fd63e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 12:00:30 -0600 Subject: [PATCH 0607/2173] Update bamdash to 0.2.1 (#44075) --- recipes/bamdash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bamdash/meta.yaml b/recipes/bamdash/meta.yaml index 41d2eb08cdfca..76aee2edec5e6 100644 --- a/recipes/bamdash/meta.yaml +++ b/recipes/bamdash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bamdash" %} -{% set version = "0.2" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/bamdash-{{ version }}.tar.gz - sha256: 563b6fd7a0362dffd57a5affb57acccf672bc8a6153e9e84d79eb2b1ca593b13 + sha256: 2e3fbd2e4baddf09f64e12168fa77549d1f2fe6bf869883ea4c349180e690980 build: entry_points: From 797ee2f1a25d4d060b520e2da1948cd7f32e4442 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 12:00:55 -0600 Subject: [PATCH 0608/2173] Update chewbbaca to 3.3.1 (#44080) --- recipes/chewbbaca/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index 412df0e410395..c54514c5a1e82 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -1,5 +1,5 @@ {% set name = 'chewBBACA' %} -{% set version = '3.3.0' %} +{% set version = '3.3.1' %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 6ca1a4971ede86ecb5e1e3e6c484fbe16e4ba87d3aebb751594480d3a674be67 + sha256: e8abae869c60763670b2d53515188cd06ab4b48ef05e7387ba9849511c695f18 build: - number: 1 + number: 0 noarch: python entry_points: - chewBBACA.py = CHEWBBACA.chewBBACA:main From e38663d8f0e3d19e96405934327a3ff9a8b41318 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 12:30:29 -0600 Subject: [PATCH 0609/2173] Update toulligqc to 2.5 (#44077) * Update toulligqc to 2.5 * add run_exports * add tqdm * add pysam --------- Co-authored-by: joshuazhuang7 --- recipes/toulligqc/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/toulligqc/meta.yaml b/recipes/toulligqc/meta.yaml index 47373894f471d..2cdff47f0734c 100644 --- a/recipes/toulligqc/meta.yaml +++ b/recipes/toulligqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "toulligqc" %} -{% set version = "2.4" %} +{% set version = "2.5" %} package: name: "{{ name|lower }}" @@ -7,14 +7,16 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 6ce0d4db04e6296130853eddc4f9ee8b3c3954693b0310a2116ee8f0b8e4477f + sha256: 8c8f5406e8f8dbfaa260ef446b08875a337ef3201dbaad6c8a4e0fa5cbf42f85 build: number: 0 entry_points: - toulligqc=toulligqc.toulligqc:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" noarch: python + run_exports: + - {{ pin_subpackage('toulligqc', max_pin="x") }} requirements: host: @@ -27,9 +29,11 @@ requirements: - scipy >=1.3.3 - pandas >=0.25.3 - plotly >=4.5.0 + - pysam - python >=3.8 - seaborn >=0.10 - scikit-learn >=0.22 + - tqdm test: imports: From 3da09b9215f67be70658b686ea733aa591854e79 Mon Sep 17 00:00:00 2001 From: clreda <20943910+clreda@users.noreply.github.com> Date: Fri, 3 Nov 2023 19:34:54 +0100 Subject: [PATCH 0610/2173] Add NORDic recipe (#42756) * adding NORDic package * adding NORDic package (checking out guidelines) * add run_exports and python version * add channels * add versions * fix versioning issue * fix noarch issue * fix noarch issue 2 * add channels for packages * fix source file url * fix source file url * add building step (make maboss) * add building step (make maboss, remove noarch) * add building step (use conda-build idiomatic approach) * add building step (add sha256 for MaBoSS) * add building step (solve dir issue) * add building step (fix sha256) * separate builds for different python versions * edit pip install command according to recent grayskull releaser * modify install of maboss * fix package source * fix build.sh * identified root folder * fix flex error * fix bison error * fix cc1plus error * fix bonesis error * fix bonesis mpbn error * fix bonesis mpbn nordic error * add license --------- Co-authored-by: REDA Clemence Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/nordic/LICENSE | 21 +++++++++ recipes/nordic/build.sh | 23 ++++++++++ recipes/nordic/meta.yaml | 92 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 136 insertions(+) create mode 100644 recipes/nordic/LICENSE create mode 100644 recipes/nordic/build.sh create mode 100644 recipes/nordic/meta.yaml diff --git a/recipes/nordic/LICENSE b/recipes/nordic/LICENSE new file mode 100644 index 0000000000000..08f13e3f57263 --- /dev/null +++ b/recipes/nordic/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright © 2023 Clémence Réda + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. \ No newline at end of file diff --git a/recipes/nordic/build.sh b/recipes/nordic/build.sh new file mode 100644 index 0000000000000..887d0d743b9ae --- /dev/null +++ b/recipes/nordic/build.sh @@ -0,0 +1,23 @@ +#!/usr/bin/env bash + +cd ${SRC_DIR}"/MaBoSS-2.0/engine/src/" + +make install \ + CC="${CC}" \ + CXX="${CXX}" \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + prefix="${PREFIX}" + +cd ${SRC_DIR}"/mpbn-3.3/" + +"${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv + +cd ${SRC_DIR}"/bonesis-0.5.7/" + +"${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv + +cd ${SRC_DIR}"/NORDic-2.4.4/" + +"${PYTHON}" -m pip install --no-deps --no-build-isolation . -vvv \ No newline at end of file diff --git a/recipes/nordic/meta.yaml b/recipes/nordic/meta.yaml new file mode 100644 index 0000000000000..7fe723c149cf6 --- /dev/null +++ b/recipes/nordic/meta.yaml @@ -0,0 +1,92 @@ +{% set name = "nordic" %} +{% set ucname = "NORDic" %} +{% set version = "2.4.4" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + - url: "https://github.com/sysbio-curie/MaBoSS-env-2.0/archive/refs/heads/master.tar.gz" + sha256: 5952813f3c38e10bbc2f0d4bbb91936bc738c47bcf9941da298cea3bfb753d19 + folder: "MaBoSS-2.0" + - url: "https://files.pythonhosted.org/packages/f8/ff/4b5fd3c1968c99d59972da395c926be65e601d7306602ec6cc39c418e24f/mpbn-3.3.tar.gz" + sha256: 8831531216d94616e7303925c4571bfc40f5d750b33b69d0155edc8404223831 + folder: "mpbn-3.3" + - url: "https://files.pythonhosted.org/packages/fb/c9/8fa247a95e6d6b7c650f2d4f879e6027fbb9eeca2aaba8d97f999bfadcfd/bonesis-0.5.7.tar.gz" + sha256: 0ccef4daa089347f7fd4ac8355f7ab3a8eecf63757e6bf000cc66b7c54bfdb0a + folder: "bonesis-0.5.7" + - url: "https://files.pythonhosted.org/packages/f3/9b/817e2004a1e7f798b5f361dc04d28d7b99657cc469f26abde2d9095fd1e4/{{ ucname }}-{{ version }}.tar.gz" + sha256: 01a5d9fbc95c603e46e916a734dd6eecdc20dff914d36c91009337d62488d525 + folder: "{{ ucname }}-{{ version }}" + +build: + number: 0 + skip: True # [py < 38] + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - flex + - bison + - make + host: + - python + - pip + - clingo >=5.6.1 + - cmappy + - scikit-learn + - graphviz + - matplotlib-base + - numpy >=1.22.4 + - omnipath >=1.0.6 + - openpyxl >=3.0.10 + - pandas >=1.5.1 + - qnorm >=0.5.1 + - quadprog >=0.1.11 + - scipy >=1.6.2 + - seaborn >=0.12.1 + - tqdm >=4.62.3 + run: + - python + - clingo >=5.6.1 + - cmappy + - scikit-learn + - graphviz + - matplotlib-base + - numpy >=1.22.4 + - omnipath >=1.0.6 + - openpyxl >=3.0.10 + - pandas >=1.5.1 + - qnorm >=0.5.1 + - quadprog >=0.1.11 + - scipy >=1.6.2 + - seaborn >=0.12.1 + - tqdm >=4.62.3 + +test: + imports: + - NORDic + - NORDic.NORDic_DR + - NORDic.NORDic_DS + - NORDic.NORDic_NI + - NORDic.NORDic_PMR + - NORDic.UTILS + +about: + home: "https://github.com/clreda/NORDic" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "NORDic: a Network-Oriented package for the Repurposing of Drugs" + doc_url: "https://github.com/clreda/NORDic/blob/main/README.md" + dev_url: "https://github.com/clreda/NORDic" + +extra: + recipe-maintainers: + - clreda + identifiers: + - doi:10.5281/zenodo.7239047 From 91b41525a87aceaf6c085a735d08b3c18f429d50 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 12:48:01 -0600 Subject: [PATCH 0611/2173] Update r-goalie to 0.7.5 (#44084) --- recipes/r-goalie/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-goalie/meta.yaml b/recipes/r-goalie/meta.yaml index 9c8d72e1a74e8..adf24485490bf 100644 --- a/recipes/r-goalie/meta.yaml +++ b/recipes/r-goalie/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.4" %} +{% set version = "0.7.5" %} {% set github = "https://github.com/acidgenomics/r-goalie" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: e4a11a642893f8f4515720556e11d16ee35f2a95f83cb4fc95390a0e75e6bf0f + sha256: 8810a75efb99fa923d8fd5e08b1d6f7fb0926684578fbdf125a8228ab9002e14 build: number: 0 From 054d291aade77ff9757e248f19ae03437e4f17bd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 14:34:43 -0600 Subject: [PATCH 0612/2173] Update assembly_finder to 0.4.0 (#44081) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/assembly_finder/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index b05ec69e03bcb..bca873c722ec1 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "assembly_finder" %} -{% set version = "0.3.3" %} +{% set version = "0.4.0" %} package: name: "{{ name|lower }}" @@ -7,9 +7,9 @@ package: source: - url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9aeec6ed2a58b7f701f1596ff7aa670ccd526d406da9273fb64a949b7b1ab866 + sha256: ed8d3b8cfaeebfeb32769e93a9c6a6c91f5c6509c91aba174e7ba4aa8a9f93cf build: - number: 1 + number: 0 entry_points: - assembly_finder = assembly_finder.assembly_finder:cli noarch: python From f80b101a6344554e8aa2a58035af5f491b7f9cc2 Mon Sep 17 00:00:00 2001 From: ningOTI Date: Sat, 4 Nov 2023 04:42:14 +0800 Subject: [PATCH 0613/2173] Update ucsc-chainnet from 377 to 455 (#44064) * Update ucsc-chainnet from 377 to 455 * Fix malformed jinja expression --- build-fail-blacklist | 1 - recipes/ucsc-chainnet/include.patch | 35 ++++++++++++++++++++--------- recipes/ucsc-chainnet/meta.yaml | 11 +++++---- 3 files changed, 31 insertions(+), 16 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index d82bf5d900c11..7ab2bed1d8322 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -842,7 +842,6 @@ recipes/ucsc-chainantirepeat recipes/ucsc-chainbridge recipes/ucsc-chainfilter recipes/ucsc-chainmergesort -recipes/ucsc-chainnet recipes/ucsc-chainprenet recipes/ucsc-chainsplit recipes/ucsc-chainstitchid diff --git a/recipes/ucsc-chainnet/include.patch b/recipes/ucsc-chainnet/include.patch index eb32b88d8f358..5404b18b5467a 100644 --- a/recipes/ucsc-chainnet/include.patch +++ b/recipes/ucsc-chainnet/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib +HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -@@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,3 +25,16 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. +--- kent/src/hg/lib/straw/makefile ++++ kent/src/hg/lib/straw/makefile +@@ -3,8 +3,8 @@ + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o + straw.o: straw.cpp straw.h +- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o ++ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include + cStraw.o: cStraw.cpp straw.h +- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o ++ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include + clean: + rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainnet/meta.yaml b/recipes/ucsc-chainnet/meta.yaml index 05a902095b4c5..070f24c45a620 100644 --- a/recipes/ucsc-chainnet/meta.yaml +++ b/recipes/ucsc-chainnet/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainnet" %} {% set program = "chainNet" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -15,19 +15,22 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} + - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info + - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - openssl - zlib - run: - libpng - libuuid From 248f808fcda86f9b8e5c591f08b383316868259e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 3 Nov 2023 14:42:39 -0600 Subject: [PATCH 0614/2173] Update ncbi-datasets-pylib to 15.27.1 (#44085) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index eddc286517934..46955df4b6c6b 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.27.0" %} -{% set sha256 = "25554af9fd4447e5471c79c06091ec890d31a218928032608fe67ee9d3aecac2" %} +{% set version = "15.27.1" %} +{% set sha256 = "81417faef837b2276ffb40aa3ee078c9aec54d6ff6c51db13bb950cc6ac19d8c" %} package: name: {{ name|lower }} From a50ee28e6d635b833c4880db746ef3609bd09c49 Mon Sep 17 00:00:00 2001 From: ningOTI Date: Sat, 4 Nov 2023 04:46:21 +0800 Subject: [PATCH 0615/2173] Update ucsc-axttopsl from 377 to 455 (#44060) * Update ucsc-axttopsl from 377 to 455 * Remove this package (ucsc-axttopsl) from blacklist * Fix malformed jinja expression --- build-fail-blacklist | 1 - recipes/ucsc-axttopsl/include.patch | 35 ++++++++++++++++++++--------- recipes/ucsc-axttopsl/meta.yaml | 11 +++++---- 3 files changed, 31 insertions(+), 16 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 7ab2bed1d8322..8b2a2aa912a9c 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -805,7 +805,6 @@ recipes/ucsc-avecols recipes/ucsc-axtsort recipes/ucsc-axtswap recipes/ucsc-axttomaf -recipes/ucsc-axttopsl recipes/ucsc-bamtopsl recipes/ucsc-bedclip recipes/ucsc-bedcommonregions diff --git a/recipes/ucsc-axttopsl/include.patch b/recipes/ucsc-axttopsl/include.patch index eb32b88d8f358..5404b18b5467a 100644 --- a/recipes/ucsc-axttopsl/include.patch +++ b/recipes/ucsc-axttopsl/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib +HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -@@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,3 +25,16 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. +--- kent/src/hg/lib/straw/makefile ++++ kent/src/hg/lib/straw/makefile +@@ -3,8 +3,8 @@ + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o + straw.o: straw.cpp straw.h +- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o ++ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include + cStraw.o: cStraw.cpp straw.h +- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o ++ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include + clean: + rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-axttopsl/meta.yaml b/recipes/ucsc-axttopsl/meta.yaml index 8fd5324f934ef..d3c5108e5d1c7 100644 --- a/recipes/ucsc-axttopsl/meta.yaml +++ b/recipes/ucsc-axttopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axttopsl" %} {% set program = "axtToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -15,19 +15,22 @@ source: build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} + - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info + - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - openssl - zlib - run: - libpng - libuuid From 24b199e81de24d50637d2a35387a5eb35563da8b Mon Sep 17 00:00:00 2001 From: ningOTI Date: Sat, 4 Nov 2023 05:00:11 +0800 Subject: [PATCH 0616/2173] Update ucsc-chainantirepeat from 377 to 455 (#44061) * Update ucsc-chainantirepeat from 377 to 455 * Remove this (chainantirepeat) from blacklist * Fix malformed jinja expression --- build-fail-blacklist | 1 - recipes/ucsc-chainantirepeat/include.patch | 35 +++++++++++++++------- recipes/ucsc-chainantirepeat/meta.yaml | 10 +++++-- 3 files changed, 31 insertions(+), 15 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 8b2a2aa912a9c..dc1ff3128118a 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -837,7 +837,6 @@ recipes/ucsc-bigwigmerge recipes/ucsc-blasttopsl recipes/ucsc-catdir recipes/ucsc-catuncomment -recipes/ucsc-chainantirepeat recipes/ucsc-chainbridge recipes/ucsc-chainfilter recipes/ucsc-chainmergesort diff --git a/recipes/ucsc-chainantirepeat/include.patch b/recipes/ucsc-chainantirepeat/include.patch index eb32b88d8f358..5404b18b5467a 100644 --- a/recipes/ucsc-chainantirepeat/include.patch +++ b/recipes/ucsc-chainantirepeat/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib +HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -@@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,3 +25,16 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. +--- kent/src/hg/lib/straw/makefile ++++ kent/src/hg/lib/straw/makefile +@@ -3,8 +3,8 @@ + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o + straw.o: straw.cpp straw.h +- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o ++ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include + cStraw.o: cStraw.cpp straw.h +- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o ++ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include + clean: + rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainantirepeat/meta.yaml b/recipes/ucsc-chainantirepeat/meta.yaml index 8d2bec89f3e46..c08a1b271ba4a 100644 --- a/recipes/ucsc-chainantirepeat/meta.yaml +++ b/recipes/ucsc-chainantirepeat/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainantirepeat" %} {% set program = "chainAntiRepeat" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -15,12 +15,16 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} + - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info + - {{ compiler('cxx') }} host: - libpng - libuuid From f996dc36d2e975080a5ca7fb6056b146fce417b3 Mon Sep 17 00:00:00 2001 From: ningOTI Date: Sat, 4 Nov 2023 05:05:58 +0800 Subject: [PATCH 0617/2173] Update ucsc-chainfilter from 377 to 455 (#44062) * Update ucsc-chainfilter from 377 to 455 * Remove this package (chainfilter) from blacklist * Fix malformed jinja expression * Fix malformed jinja expression, again --- build-fail-blacklist | 1 - recipes/ucsc-chainfilter/include.patch | 35 ++++++++++++++++++-------- recipes/ucsc-chainfilter/meta.yaml | 10 +++++--- 3 files changed, 31 insertions(+), 15 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index dc1ff3128118a..df3102767e2d5 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -838,7 +838,6 @@ recipes/ucsc-blasttopsl recipes/ucsc-catdir recipes/ucsc-catuncomment recipes/ucsc-chainbridge -recipes/ucsc-chainfilter recipes/ucsc-chainmergesort recipes/ucsc-chainprenet recipes/ucsc-chainsplit diff --git a/recipes/ucsc-chainfilter/include.patch b/recipes/ucsc-chainfilter/include.patch index eb32b88d8f358..5404b18b5467a 100644 --- a/recipes/ucsc-chainfilter/include.patch +++ b/recipes/ucsc-chainfilter/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib +HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -@@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,3 +25,16 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. +--- kent/src/hg/lib/straw/makefile ++++ kent/src/hg/lib/straw/makefile +@@ -3,8 +3,8 @@ + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o + straw.o: straw.cpp straw.h +- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o ++ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include + cStraw.o: cStraw.cpp straw.h +- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o ++ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include + clean: + rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainfilter/meta.yaml b/recipes/ucsc-chainfilter/meta.yaml index 35fcbefe4e89e..eb41f55eb619f 100644 --- a/recipes/ucsc-chainfilter/meta.yaml +++ b/recipes/ucsc-chainfilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainfilter" %} {% set program = "chainFilter" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -15,12 +15,16 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} + - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info + - {{ compiler('cxx') }} host: - libpng - libuuid From 3b1b8f217bc6d5cfdb8fb54813290e23e8628a6b Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 3 Nov 2023 21:40:42 +0000 Subject: [PATCH 0618/2173] Fix sdm requirement pin in LotuS2 (#44086) * Fix sdm requirement pin LotuS2 2.28.1 requires sdm 2.14 * Add extra section to lotus2 recipe --- recipes/lotus2/meta.yaml | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/recipes/lotus2/meta.yaml b/recipes/lotus2/meta.yaml index 243fc6cb3b5e7..ec89fad4686f5 100644 --- a/recipes/lotus2/meta.yaml +++ b/recipes/lotus2/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -37,7 +37,7 @@ requirements: - r-dplyr - rdp_classifier - rtk - - sdm ==2.10 + - sdm ==2.14 - swarm - unzip - vsearch @@ -54,3 +54,10 @@ about: license: GPL-3.0-or-later license_file: COPYING summary: LotuS2 is a lightweight complete 16S/18S/ITS pipeline + +extra: + identifiers: + - doi:10.1186/s40168-022-01365-1 + - biotools:lotus2 + recipe-maintainers: + - nsoranzo From 17b583af8e7b7b73002fdbe8403707481d32faf0 Mon Sep 17 00:00:00 2001 From: Julia Haag Date: Fri, 3 Nov 2023 23:42:37 +0200 Subject: [PATCH 0619/2173] Update eigensoft: fix build for osx-arm64 (#44082) * fix build for osx-arm64 * fix duplicate extra key * add run_exports for linter --- recipes/eigensoft/0002-replace-finite.patch | 13 ++++++++++ .../eigensoft/0003-remove-wrong-cflag.patch | 10 ++++++++ recipes/eigensoft/build.sh | 3 +-- recipes/eigensoft/meta.yaml | 25 +++++++++++++------ 4 files changed, 42 insertions(+), 9 deletions(-) create mode 100644 recipes/eigensoft/0002-replace-finite.patch create mode 100644 recipes/eigensoft/0003-remove-wrong-cflag.patch diff --git a/recipes/eigensoft/0002-replace-finite.patch b/recipes/eigensoft/0002-replace-finite.patch new file mode 100644 index 0000000000000..3e0bc94b5c927 --- /dev/null +++ b/recipes/eigensoft/0002-replace-finite.patch @@ -0,0 +1,13 @@ +diff --git a/src/admutils.c b/src/admutils.c +index dae3657..35a4427 100644 +--- a/src/admutils.c ++++ b/src/admutils.c +@@ -537,7 +537,7 @@ testnan (double *a, int n) + int i; + + for (i = 0; i < n; i++) { +- if (!finite (a[i])) ++ if (!isfinite (a[i])) + fatalx ("(testnan) fails: index %d\n", i); + } + } diff --git a/recipes/eigensoft/0003-remove-wrong-cflag.patch b/recipes/eigensoft/0003-remove-wrong-cflag.patch new file mode 100644 index 0000000000000..392dc3822ad25 --- /dev/null +++ b/recipes/eigensoft/0003-remove-wrong-cflag.patch @@ -0,0 +1,10 @@ +diff --git a/src/nicksrc/Makefile b/src/nicksrc/Makefile +index 55d7733..2d1742d 100644 +--- a/src/nicksrc/Makefile ++++ b/src/nicksrc/Makefile +@@ -1,4 +1,4 @@ +-override CFLAGS += -c -O3 -g -p -Wimplicit -I../../include ++override CFLAGS += -c -O3 -g -Wimplicit -I../../include + + all: libnick.a + diff --git a/recipes/eigensoft/build.sh b/recipes/eigensoft/build.sh index b5b73e3e95a8d..e5d538abac1ba 100644 --- a/recipes/eigensoft/build.sh +++ b/recipes/eigensoft/build.sh @@ -1,6 +1,5 @@ +set -xeuo pipefail cd src -make clobber - make all # Install (makefile install has hard-coded destination, so have to do this manually) diff --git a/recipes/eigensoft/meta.yaml b/recipes/eigensoft/meta.yaml index 01ab3fe31a440..346ef87b9d9b4 100644 --- a/recipes/eigensoft/meta.yaml +++ b/recipes/eigensoft/meta.yaml @@ -1,15 +1,22 @@ -package: - name: eigensoft - version: "8.0.0" +{% set name = "eigensoft" %} +{% set version = "8.0.0" %} -build: - number: 3 +package: + name: {{ name|lower }} + version: {{ version }} source: - url: https://github.com/DReichLab/EIG/archive/refs/tags/v8.0.0.tar.gz + url: https://github.com/DReichLab/EIG/archive/v{{ version }}.tar.gz sha256: e3459e8ac0134da369910454854eae5c7b261e8816318ccbd2d371b4c6c35741 patches: - 0001-Add-gfortran-to-LDLIBS.patch + - 0002-replace-finite.patch + - 0003-remove-wrong-cflag.patch # [osx] + +build: + number: 4 + run_exports: + - {{ pin_subpackage('eigensoft', max_pin='x.x') }} requirements: build: @@ -25,11 +32,15 @@ requirements: test: commands: - - smartpca > /dev/null 2>&1 + - smartpca + # both tools crash without input, there is other way to check whether installation worked... + - which convertf + - which mergeit about: home: https://github.com/DReichLab/EIG license: Custom OSS + license_file: LICENSE.txt summary: The EIGENSOFT package implements methods for analzing population structure and performing stratification correction extra: From 10f547eb6705a37bbf7294900736d463a081cec5 Mon Sep 17 00:00:00 2001 From: Jeremy Volkening Date: Sat, 4 Nov 2023 04:46:33 -0500 Subject: [PATCH 0620/2173] Update abricate: add missing dep to fix database download issues (#44088) * add missing dep to fix database download issues * fix linting by adding run_exports --- recipes/abricate/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/abricate/meta.yaml b/recipes/abricate/meta.yaml index 99fefc82f95b7..f2370a576149a 100644 --- a/recipes/abricate/meta.yaml +++ b/recipes/abricate/meta.yaml @@ -8,8 +8,10 @@ package: version: {{ version }} build: - number: 1 + number: 2 noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} source: url: https://github.com/{{ user }}/{{ name }}/archive/v{{ version }}.tar.gz @@ -32,6 +34,7 @@ requirements: - perl-path-tiny - perl-list-moreutils - perl-json + - perl-lwp-protocol-https - perl-lwp-simple - blast >=2.7 - zlib From 71fb4792ec9e18fd2e9bdef520ca76e935a5613c Mon Sep 17 00:00:00 2001 From: ningOTI Date: Sat, 4 Nov 2023 17:47:15 +0800 Subject: [PATCH 0621/2173] Update ucsc-chainmergesort from 377 to 455 (#44063) * Update ucsc-chainmergesort from 377 to 455 * Fix malformed jinja expression --- build-fail-blacklist | 3 +- recipes/ucsc-chainmergesort/include.patch | 35 ++++++++++++++++------- recipes/ucsc-chainmergesort/meta.yaml | 10 +++++-- 3 files changed, 33 insertions(+), 15 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index df3102767e2d5..00d75314e3ff2 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -838,7 +838,8 @@ recipes/ucsc-blasttopsl recipes/ucsc-catdir recipes/ucsc-catuncomment recipes/ucsc-chainbridge -recipes/ucsc-chainmergesort +recipes/ucsc-chainfilter +recipes/ucsc-chainnet recipes/ucsc-chainprenet recipes/ucsc-chainsplit recipes/ucsc-chainstitchid diff --git a/recipes/ucsc-chainmergesort/include.patch b/recipes/ucsc-chainmergesort/include.patch index eb32b88d8f358..5404b18b5467a 100644 --- a/recipes/ucsc-chainmergesort/include.patch +++ b/recipes/ucsc-chainmergesort/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib +HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -@@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,3 +25,16 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. +--- kent/src/hg/lib/straw/makefile ++++ kent/src/hg/lib/straw/makefile +@@ -3,8 +3,8 @@ + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o + straw.o: straw.cpp straw.h +- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o ++ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include + cStraw.o: cStraw.cpp straw.h +- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o ++ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include + clean: + rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainmergesort/meta.yaml b/recipes/ucsc-chainmergesort/meta.yaml index 9cda28af06190..a8116c2079423 100644 --- a/recipes/ucsc-chainmergesort/meta.yaml +++ b/recipes/ucsc-chainmergesort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainmergesort" %} {% set program = "chainMergeSort" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -15,12 +15,16 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} + - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info + - {{ compiler('cxx') }} host: - libpng - libuuid From 09e074c723e41be3ca9084c7565aac8f90e1631b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 4 Nov 2023 03:48:32 -0600 Subject: [PATCH 0622/2173] Update gencove to 2.8.1 (#44087) --- recipes/gencove/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gencove/meta.yaml b/recipes/gencove/meta.yaml index 24f62927d4580..4f89bdef799e2 100644 --- a/recipes/gencove/meta.yaml +++ b/recipes/gencove/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.8.0" %} -{% set sha256 = "f738535c5366a3d17c61d1095968194ebd7a90f600a2bc7eddae47d7d53ff5eb" %} +{% set version = "2.8.1" %} +{% set sha256 = "bcda1ddbea0bf4b14e343c6e11e88755f41b8fd1df9225ac55993b438bb45c32" %} package: name: gencove From 9a6cc893db5530b1d50e9a7d11319e3e6019efeb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 4 Nov 2023 11:14:54 -0600 Subject: [PATCH 0623/2173] Update rosella to 0.5.0 (#44090) * Update rosella to 0.5.0 * Update rosella to 0.5.0 * Update meta.yaml Ref https://github.com/bioconda/bioconda-recipes/pull/44090#issuecomment-1793392686 * matplotlib-base * spaces --------- Co-authored-by: Thanh Lee --- recipes/rosella/meta.yaml | 39 +++++++++++++++++++++++++++++---------- 1 file changed, 29 insertions(+), 10 deletions(-) diff --git a/recipes/rosella/meta.yaml b/recipes/rosella/meta.yaml index d32d59af789c3..e112f18d75e8e 100644 --- a/recipes/rosella/meta.yaml +++ b/recipes/rosella/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.4.2" %} +{% set version = "0.5.0" %} {% set name = "rosella" %} -{% set hash = "1a3d62da637d7cca45c72d33a120edec31aca1626862e243d2b8076cda52fdfc" %} +{% set hash = "f89a41facff14d45220fe04cf412d42272913070ac702678446d70e33252aeb8" %} package: name: rosella @@ -11,12 +11,13 @@ source: sha256: {{ hash }} build: - number: 2 + number: 0 skip: True # [osx] - + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: - - rust >=1.40 + - rust >=1.70 - {{ compiler('c') }} - {{ compiler('cxx') }} - pkg-config @@ -30,11 +31,29 @@ requirements: - openssl - clangdev run: - - parallel - - samtools - - starcode - - bwa - - minimap2 + - coverm >=0.6.1 + - python >=3.8,<=3.10 + - numba >=0.53,<=0.57 + - numpy <=1.24 + - joblib >=1.1.0,<=1.3 + - scikit-bio >=0.5.7 + - umap-learn >=0.5.3 + - scipy <=1.11 + - pandas >=1.3 + - pynndescent >=0.5.7 + - hdbscan >=0.8.28 + - scikit-learn >=1.0.2,<=1.1 + - flight-genome >=1.6.0 + - coverm >=0.6.1 + - biopython >=1.81 + - seaborn >=0.12 + - imageio >=2.31 + - matplotlib-base >=3.8 + - tqdm >=4.66 + - tbb >=2021.10.0 + - joblib >=1.3.0 + - pebble >=5.0 + - threadpoolctl >=3.2.0 test: commands: From be4f109dcb191f6470274648774079a548f11cd1 Mon Sep 17 00:00:00 2001 From: xxmalcala <86986240+xxmalcala@users.noreply.github.com> Date: Sat, 4 Nov 2023 11:15:39 -0600 Subject: [PATCH 0624/2173] Add TIdeS package to BioConda (#44083) * Initial release of TIdeS * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/tides-ml/meta.yaml | 57 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 recipes/tides-ml/meta.yaml diff --git a/recipes/tides-ml/meta.yaml b/recipes/tides-ml/meta.yaml new file mode 100644 index 0000000000000..c3a3d4bc436e8 --- /dev/null +++ b/recipes/tides-ml/meta.yaml @@ -0,0 +1,57 @@ +{% set name = "tides-ml" %} +{% set version = "1.1.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/TIdeS-ML-{{ version }}.tar.gz + sha256: 17ad86b841d5e8fca4dbad58d114aa919d332a22190c7d002472ec6c1541609a + +build: + entry_points: + - tides = tides.tides:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - biopython >=1.79 + - ete3 >=3.1.2 + - optuna >=3.0 + - pandas >=2.0 + - seaborn >=0.12.2 + - scikit-learn >=1.3.0 + - diamond >=2.1.3 + - cd-hit >=4.8.1 + - barrnap >=0.9 + - kraken2 >=2.0.0 + +test: + imports: + - tides + commands: + - cd-hit --help | grep 'Usage' > /dev/null + - diamond --help 2>&1 > /dev/null + - (barrnap --help 2>&1; true) | grep -q Options + - tides --help + - kraken2 --version + + +about: + home: https://github.com/xxmalcala/TIdeS + summary: Tool for ORF-calling and ORF-classification using ML approaches + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - xxmalcala From b3664c3b9aac22e24027d96e67773940602fb3ef Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 4 Nov 2023 11:15:57 -0600 Subject: [PATCH 0625/2173] Update cat to 5.3 (#44091) * Update cat to 5.3 * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/cat/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/cat/meta.yaml b/recipes/cat/meta.yaml index f5fddea1afd14..81e3fc1cbdc4b 100644 --- a/recipes/cat/meta.yaml +++ b/recipes/cat/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "5.2.3" %} -{% set sha256 = "19a8eb28c0ebd3fc5a04b006d305a916dd1af00a32b70d2f30df35f32ca2929b" %} +{% set version = "5.3" %} +{% set sha256 = "2893ee18b0d5b24a291edd7d8ca1738d40ea189d18ba0fb7aad3e38973a787e7" %} package: name: cat @@ -10,9 +10,10 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: generic - + run_exports: + - {{ pin_subpackage("cat", max_pin="x") }} requirements: run: - python 3 From 5e3ad3754d789b60dfec9c7c94b9f0f39119fbbf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 4 Nov 2023 12:28:52 -0600 Subject: [PATCH 0626/2173] Update sirius-csifingerid to 5.8.4 (#44089) * Update sirius-csifingerid to 5.8.4 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/sirius-csifingerid/meta.yaml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/recipes/sirius-csifingerid/meta.yaml b/recipes/sirius-csifingerid/meta.yaml index 0d29f028b0cca..09dbd0553ab9b 100644 --- a/recipes/sirius-csifingerid/meta.yaml +++ b/recipes/sirius-csifingerid/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "5.8.3" %} +{% set version = "5.8.4" %} {% set siriusDistDir = "sirius_gui_dist" %} package: @@ -10,9 +10,13 @@ build: script_env: - siriusDistName={{ siriusDistDir }}-sirius - siriusDistDir={{ siriusDistDir }} + run_exports: + - {{ pin_subpackage('sirius-csifingerid', max_pin="x") }} + source: - url: https://github.com/boecker-lab/sirius/archive/refs/tags/v{{ version }}.zip - sha256: b93928c8a26fd70c67bf48d3751e2c8cf1a8bdb3513c252ab5d730d96b0f5c1f + sha256: 547abcafb297798b4fd4291889f1fbcf55b73f3fb97c95b2ec3a718eae0c5938 + requirements: build: - openjdk 17.* @@ -22,6 +26,7 @@ requirements: test: requires: - wget # [not win] + about: home: https://bio.informatik.uni-jena.de/software/sirius/ license: AGPL-3.0-only AND OTHER From 3819f2c78615515984f4c67215c9e3cbe1163b19 Mon Sep 17 00:00:00 2001 From: fgiacomoni Date: Sat, 4 Nov 2023 20:41:34 +0100 Subject: [PATCH 0627/2173] Update perl-metabolomics-fragment-annotation v0.6.9.0 (#41109) * Update package version, deps * update tar url + sha256 * replace tags by new values * add run_exports --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- .../meta.yaml | 33 ++++++++++++++++--- 1 file changed, 28 insertions(+), 5 deletions(-) diff --git a/recipes/perl-metabolomics-fragment-annotation/meta.yaml b/recipes/perl-metabolomics-fragment-annotation/meta.yaml index df8afb0df41a4..ec913d82183e5 100644 --- a/recipes/perl-metabolomics-fragment-annotation/meta.yaml +++ b/recipes/perl-metabolomics-fragment-annotation/meta.yaml @@ -1,33 +1,56 @@ +{% set name = "perl-metabolomics-fragment-annotation" %} +{% set version = "0.6.9" %} +{% set sha256 = "6abbb01d252df760004f0869d8a065c1402410bc4f8daaa4309c9ca74c710e0b" %} + + package: - name: perl-metabolomics-fragment-annotation - version: "0.6.3" + name: {{ name }} + version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/G/GI/GIACOMONI/Metabolomics-Fragment-Annotation-0.6.3.tar.gz - sha256: 9689922ed34f11e7286271ae8bf1472e848a5033271db6f0ef393cf5d0826916 + url: https://cpan.metacpan.org/authors/id/G/GI/GIACOMONI/Metabolomics-Fragment-Annotation-{{ version }}.tar.gz + sha256: {{ sha256 }} build: - number: 2 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('perl-metabolomics-fragment-annotation', max_pin="x.x") }} requirements: build: - make host: - perl + - perl-class-accessor + - perl-uri-query - perl-file-share - perl-text-csv - perl-text-csv_xs - perl-xml-twig - perl-file-sharedir-install + - perl-json + - perl-html-template + - perl-uri + - perl-log-any + - perl-datetime + - perl-lwp-protocol-https run: - perl + - perl-class-accessor + - perl-uri-query - perl-file-share - perl-text-csv - perl-text-csv_xs - perl-xml-twig - perl-file-sharedir-install + - perl-json + - perl-html-template + - perl-uri + - perl-log-any + - perl-datetime + - perl-lwp-protocol-https test: # Perl 'use' tests From 8db62ba5b61286abe3508f79527b316cb10dfc06 Mon Sep 17 00:00:00 2001 From: Alan Collins <38288262+Alan-Collins@users.noreply.github.com> Date: Sat, 4 Nov 2023 15:45:54 -0400 Subject: [PATCH 0628/2173] Add el_gato package to Bioconda (#44028) * add el_gato recipe * add build and run_export --- recipes/el_gato/build.sh | 6 ++++++ recipes/el_gato/meta.yaml | 42 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 recipes/el_gato/build.sh create mode 100644 recipes/el_gato/meta.yaml diff --git a/recipes/el_gato/build.sh b/recipes/el_gato/build.sh new file mode 100644 index 0000000000000..73991f59b0666 --- /dev/null +++ b/recipes/el_gato/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +$PYTHON -m pip install . -vv + +mkdir -p $PREFIX/bin/db +cp el_gato/db/* $PREFIX/bin/db/ diff --git a/recipes/el_gato/meta.yaml b/recipes/el_gato/meta.yaml new file mode 100644 index 0000000000000..c4ddd980219d7 --- /dev/null +++ b/recipes/el_gato/meta.yaml @@ -0,0 +1,42 @@ +{% set name = "el_gato" %} +{% set version = "1.14.4" %} +{% set hash = "120b294baa58d833d9973da2d203eb88090a4ecc9538a34b0c5d6c8382cac1a4" %} +{% set user = "appliedbinf" %} + +package: + name: el_gato + version: {{ version }} + +source: + url: https://github.com/{{ user }}/{{ name }}/archive/refs/tags/{{ version }}.tar.gz + sha256: {{ hash }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +requirements: + host: + - python >=3.8,<3.12 + - pip + - setuptools + run: + - python >=3.8,<3.12 + - minimap2 >=2.24 + - samtools >=1.15.1 + - blast >=2.13 + - ispcr >=33.0 + - nextflow + - fpdf2 + +test: + commands: + - el_gato.py --version + +about: + home: https://github.com/{{ user }}/{{ name }} + license: MIT + license_file: LICENSE + summary: Perform Legionella pneumophila Sequence Based Typing (SBT) from short reads or assemblies From 8fa8a643e9b890ee57218dc264d69a62616c5b99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sinan=20U=C4=9Fur=20Umu?= Date: Sat, 4 Nov 2023 20:46:22 +0100 Subject: [PATCH 0629/2173] Update meta.yaml to a new build due to a package update bug (#44092) * Update meta.yaml A recent update on r-dbplyr package causes a bug, explained here https://stackoverflow.com/questions/77370659/error-failed-to-collect-lazy-table-caused-by-error-in-db-collect-using Therefore I restricted the package version to an old version. Cheers, * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/cellsnake/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/cellsnake/meta.yaml b/recipes/cellsnake/meta.yaml index 819bb89b53190..bf926aaacca29 100644 --- a/recipes/cellsnake/meta.yaml +++ b/recipes/cellsnake/meta.yaml @@ -12,11 +12,12 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - cellsnake=cellsnake.command_line:main script: python -m pip install . -vv - + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: @@ -43,6 +44,7 @@ requirements: - r-igraph ==1.3.4 - r-ggraph ==2.1.0 - r-clustree ==0.5.0 + - r-dbplyr <=2.3.2 - r-ggthemes - r-viridis - r-librarian From 3c115834c3c12e4356201c2c9e9f47c9c9fe905c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 4 Nov 2023 14:59:57 -0600 Subject: [PATCH 0630/2173] Update tidk to 0.2.41 (#44095) * Update tidk to 0.2.41 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/tidk/meta.yaml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/recipes/tidk/meta.yaml b/recipes/tidk/meta.yaml index aa7f115b33c8e..6d4db203c6073 100644 --- a/recipes/tidk/meta.yaml +++ b/recipes/tidk/meta.yaml @@ -1,15 +1,17 @@ -{% set version = "0.2.31" %} +{% set version = "0.2.41" %} package: name: tidk version: {{ version }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('tidk', max_pin="x.x") }} source: url: https://github.com/tolkit/telomeric-identifier/archive/{{ version }}.tar.gz - sha256: a3cd376a312a3d93d57fc57394a6b17b19755c86624a92b9a6912a125e803d5b + sha256: 28cac3506d66ffc7ee37ff48a429663dde68aa23ba5d9b28ee0a6656aeea03d4 requirements: build: @@ -18,10 +20,7 @@ requirements: - cmake - make - rust >=1.52 - - pkg-config # [osx] - host: - run: - + - pkg-config # [osx] test: commands: @@ -31,5 +30,6 @@ test: about: home: https://github.com/tolkit/telomeric-identifier license: MIT + license_family: MIT summary: | Identify and find telomeres, or telomeric repeats in a genome. From 7f8e7fbd04e8746f315dd122ef6c80d7433d547d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 5 Nov 2023 03:50:51 -0700 Subject: [PATCH 0631/2173] Update versionix to 0.2.2 (#44100) --- recipes/versionix/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/versionix/meta.yaml b/recipes/versionix/meta.yaml index 1a9fc020c7240..c4521bdef86ad 100644 --- a/recipes/versionix/meta.yaml +++ b/recipes/versionix/meta.yaml @@ -1,5 +1,5 @@ {% set name = "versionix" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/versionix-{{ version }}.tar.gz - sha256: 43b21f5596774ef7bbe26357b97e511a2541c321426c79bd35d441fbd4e0e623 + sha256: a0c215b827b17213ab3bc8980c55ccd4b0f5a5bc42e61cda6338cdf6fd61b6b9 build: entry_points: From 9af213f9eb3dc43e3e95da0c0951967046172b6b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 5 Nov 2023 03:51:13 -0700 Subject: [PATCH 0632/2173] Update snakesv to 0.8 (#44101) --- recipes/snakesv/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakesv/meta.yaml b/recipes/snakesv/meta.yaml index 5fc97c81faf42..3896026f8d80f 100755 --- a/recipes/snakesv/meta.yaml +++ b/recipes/snakesv/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakeSV" %} -{% set version = "0.7" %} +{% set version = "0.8" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: https://github.com/RajLabMSSM/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: a9312b1992bb1eea9b824175f59b8d9bb3f9e773028ad98f31839d8a25b527a6 + sha256: ebddad04d499e3d0a3e65a0615bfeac2697505bbb3a02a74d91dc711e82df481 build: - number: 3 + number: 0 noarch: generic run_exports: - {{ pin_subpackage('snakesv', max_pin="x.x") }} From 68fcdacdf143e0ee015cec233190413e817016bb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 5 Nov 2023 03:51:27 -0700 Subject: [PATCH 0633/2173] Update psims to 1.3.0 (#44097) --- recipes/psims/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psims/meta.yaml b/recipes/psims/meta.yaml index d2c1445027deb..38c81b54605da 100644 --- a/recipes/psims/meta.yaml +++ b/recipes/psims/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.2.9" %} -{% set sha256 = "35cc03660a86b41c94928f367bee091609af34cd092b46d31c4e8f91884b0813" %} +{% set version = "1.3.0" %} +{% set sha256 = "0de9e1ae6b87177626f87639dc19555be7679bc6f5f29a7bdfff06e0b20f2b3e" %} package: name: "psims" From 0b51527ad422cf295dd47f4ca5cae67fb68d97d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 5 Nov 2023 03:51:39 -0700 Subject: [PATCH 0634/2173] Update oakvar to 2.9.56 (#44096) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 692811a1b81e6..a1396c221aa56 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.55" %} -{% set sha256 = "7c16f5bd221a132d1066891c77957815fb69163316a91e1440913564b8c4deba" %} +{% set version = "2.9.56" %} +{% set sha256 = "fc46074f7deacf6809ba979fc97a5f65445558a43907800e9d5c15601911f31d" %} package: name: {{ name|lower }} From d8f8892909d1fe3f153d3f6de248583c1863a1d9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 5 Nov 2023 03:52:21 -0700 Subject: [PATCH 0635/2173] Update capcruncher to 0.3.7 (#44103) --- recipes/capcruncher/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/capcruncher/meta.yaml b/recipes/capcruncher/meta.yaml index 6d285b8f2bce1..8bda4d9f2f501 100644 --- a/recipes/capcruncher/meta.yaml +++ b/recipes/capcruncher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "capcruncher" %} -{% set version = "0.3.6" %} +{% set version = "0.3.7" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/capcruncher-{{ version }}.tar.gz - sha256: 1f3c23b3c022b0c681f8d66d7a54463591c06632721cbe6684246df64e23015d + sha256: 70d5a4f70ba165681c605de66562020ae65de6c3546d4b4534edf7bc1ab8cb2c build: number: 0 From e9a5d4e20a2971177747ff08a26f62a58df9ce61 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 5 Nov 2023 17:48:44 -0700 Subject: [PATCH 0636/2173] Update pypolca to 0.2.0 (#44111) --- recipes/pypolca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pypolca/meta.yaml b/recipes/pypolca/meta.yaml index f2563aea92d94..40f4fefedf5c0 100644 --- a/recipes/pypolca/meta.yaml +++ b/recipes/pypolca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pypolca" %} -{% set version = "0.1.1" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 2e0ab4f28aa64eb1363afc7952728196d3dfbfbd5cbb2a5d61950de28164ab36 + sha256: 5534fb54316931a664a6e5eb0bb020d432b39687fd5d932b00cd1d5e6dea5ef8 build: number: 0 From 27afed5d5fa166cc10461c1291c31c4afd51b6b0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 03:11:15 -0700 Subject: [PATCH 0637/2173] Update pyrodigal to 3.1.1 (#44113) --- recipes/pyrodigal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyrodigal/meta.yaml b/recipes/pyrodigal/meta.yaml index 4a6a010947372..53c5b56be6855 100644 --- a/recipes/pyrodigal/meta.yaml +++ b/recipes/pyrodigal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrodigal" %} -{% set version = "3.1.0" %} +{% set version = "3.1.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: efc01ca72e798efd07a8e79209c92b518f9f403e98012d01eca37fe2416487df + sha256: 1ccb0304c4a4257cd87e862286870095d9e5fd8cd5d2662ff7ae5368d1221895 build: number: 0 From f7c80c6aed380c1ee899ab119176c3b078709dfd Mon Sep 17 00:00:00 2001 From: "Ricardo A. Vialle" Date: Mon, 6 Nov 2023 06:09:01 -0600 Subject: [PATCH 0638/2173] Update SnakeSV recipe (#44109) --- recipes/snakesv/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/snakesv/meta.yaml b/recipes/snakesv/meta.yaml index 3896026f8d80f..d838376d65d19 100755 --- a/recipes/snakesv/meta.yaml +++ b/recipes/snakesv/meta.yaml @@ -10,7 +10,7 @@ source: sha256: ebddad04d499e3d0a3e65a0615bfeac2697505bbb3a02a74d91dc711e82df481 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('snakesv', max_pin="x.x") }} @@ -19,6 +19,10 @@ requirements: run: - snakemake =7.32.4 - bcftools =1.9 + - python =3.11.6 + - mamba =1.4.2 + build: + - conda-build >=3.27 test: commands: From 28a0e67173ea80ab7d54f1d3521ef1fb0d621ade Mon Sep 17 00:00:00 2001 From: Adam Taranto Date: Tue, 7 Nov 2023 00:37:34 +1100 Subject: [PATCH 0639/2173] Update meta.yaml [teloclip] (#44118) * Update meta.yaml Bump to v0.0.4 * Update meta.yaml Add run_exports --- recipes/teloclip/meta.yaml | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/recipes/teloclip/meta.yaml b/recipes/teloclip/meta.yaml index 90ad81721cf80..288843e270285 100644 --- a/recipes/teloclip/meta.yaml +++ b/recipes/teloclip/meta.yaml @@ -1,5 +1,5 @@ {% set name = "teloclip" %} -{% set version = "0.0.3" %} +{% set version = "0.0.4" %} package: name: '{{ name|lower }}' @@ -7,20 +7,24 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 48b25ce0a3dce9f44bc2703ccbcb9738861c260568a9ce1f3687c4aca054b14d + sha256: 7f9919c1aa5d3d9f8e21c3a49bc3edccb7d9ef1c4ad0686761a9a9f623999ade build: + run_exports: + - {{ pin_subpackage('teloclip', max_pin="x.x") }} noarch: python - number: 1 + number: 0 entry_points: - - teloclip=teloclip.run_self:main - - teloclip-extract=teloclip.run_extract:main - script: python setup.py install --single-version-externally-managed --record=record.txt + - teloclip=teloclip.app:main + - teloclip-extract=teloclip.app_extract:main + script: "{{ PYTHON }} -m pip install . -vv" requirements: host: - python >=3 + - pip - setuptools + - setuptools-scm run: - python >=3 @@ -42,4 +46,5 @@ about: dev_url: '' extra: - recipe-maintainers: 'Adam Taranto' + recipe-maintainers: + - 'Adamtaranto' From 183bcd2cef1615b5a4c4129faf928d0014f2a99c Mon Sep 17 00:00:00 2001 From: Vlad Savelyev Date: Mon, 6 Nov 2023 17:09:14 +0100 Subject: [PATCH 0640/2173] MultiQC: add missing dependencies, pin to Python >=3.8 (#44121) * MultiQC: add missing deps, pin to Python >=3.8 * Clean up * Bump build * add constraints * Add importlib-metadata * Pin Python * Update recipes/multiqc/meta.yaml Co-authored-by: Phil Ewels * Don't pin <3.12 for `run` --------- Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com> Co-authored-by: Phil Ewels --- recipes/multiqc/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index f8d70ecd88c2a..9eeb34ce7ab11 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -9,7 +9,7 @@ source: sha256: f28268e50ef57dbc330ba40eb8dcbb2b86029bc4542dd420fe180c914c284d34 build: - number: 0 + number: 1 entry_points: - multiqc=multiqc.__main__:run_multiqc noarch: python @@ -19,20 +19,23 @@ build: requirements: host: - - python >=3.6 + - python >=3.8 - pip run: - - python >=3.6 + - python >=3.8 - setuptools - click - coloredlogs - future >0.14.0 + - humanize - jinja2 >=3.0.0 + - importlib-metadata - lzstring - markdown - matplotlib-base >=2.1.1 - networkx >=2.5.1 - numpy + - packaging - pyyaml >=4 - requests - rich >=10 From 941dbeb3a008a8f23023fbb0a4a445711f1e7a97 Mon Sep 17 00:00:00 2001 From: ningOTI Date: Tue, 7 Nov 2023 00:27:04 +0800 Subject: [PATCH 0641/2173] Update ucsc-fasomerecords from 377 to 455 (#44115) * Update ucsc-fasomerecords from 377 to 455 * Fix wrong run_exports --- build-fail-blacklist | 1 - recipes/ucsc-fasomerecords/include.patch | 31 +++++++++++++++++------- recipes/ucsc-fasomerecords/meta.yaml | 11 ++++++--- 3 files changed, 29 insertions(+), 14 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 00d75314e3ff2..0a289136ed3a2 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -876,7 +876,6 @@ recipes/ucsc-fapolyasizes recipes/ucsc-farandomize recipes/ucsc-farc recipes/ucsc-fasize -recipes/ucsc-fasomerecords recipes/ucsc-fasplit recipes/ucsc-fastqstatsandsubsample recipes/ucsc-fastqtofa diff --git a/recipes/ucsc-fasomerecords/include.patch b/recipes/ucsc-fasomerecords/include.patch index eb32b88d8f358..e4831ef2dea13 100644 --- a/recipes/ucsc-fasomerecords/include.patch +++ b/recipes/ucsc-fasomerecords/include.patch @@ -1,5 +1,5 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,14 +9,14 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -@@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,3 +25,16 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. +--- kent/src/hg/lib/straw/makefile ++++ kent/src/hg/lib/straw/makefile +@@ -3,8 +3,8 @@ + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o + straw.o: straw.cpp straw.h +- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o ++ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include + cStraw.o: cStraw.cpp straw.h +- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o ++ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include + clean: + rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-fasomerecords/meta.yaml b/recipes/ucsc-fasomerecords/meta.yaml index b3f3b568fae30..507bf2b0b7cd6 100644 --- a/recipes/ucsc-fasomerecords/meta.yaml +++ b/recipes/ucsc-fasomerecords/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fasomerecords" %} {% set program = "faSomeRecords" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -15,19 +15,22 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} + - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info + - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - openssl - zlib - run: - libpng - libuuid From f1cb719690289373c5960648586d2b6dc4540029 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 09:27:35 -0700 Subject: [PATCH 0642/2173] Update sylph to 0.4.0 (#44104) --- recipes/sylph/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sylph/meta.yaml b/recipes/sylph/meta.yaml index 4afd678e234b5..c3703e9973199 100644 --- a/recipes/sylph/meta.yaml +++ b/recipes/sylph/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.0" %} +{% set version = "0.4.0" %} package: name: sylph @@ -11,7 +11,7 @@ build: source: url: https://github.com/bluenote-1577/sylph/archive/v{{ version }}.tar.gz - sha256: b94c6f7363b8d6dcb0524a385c6b101c7285f8a24a7dbf0d0598f53afd2d33e2 + sha256: 66fae78c240ffc514fe784dce8783d63e8551a7de1486c95083367956ef33d8f requirements: build: From 3e5d863fd9cdce313dea2382dd00783b3a477767 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 09:28:37 -0700 Subject: [PATCH 0643/2173] Update pybiolib to 1.1.1514 (#44120) * Update pybiolib to 1.1.1512 * Update pybiolib to 1.1.1514 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index cb78bb2f06835..712aacd6db1e8 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1508" %} +{% set version = "1.1.1514" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 6bf3b639faf12079ee699f12ee846871b82ade1fac5192e15fe6be129c2c37c3 + sha256: fbef1e55c3ff2d0bf55f3fca1bb38033f1f2e5de5a85b552f69d00eb2ae45192 build: noarch: python From 87b6c2340ce0892a10e7580368b3a8b9a6a94744 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 09:42:05 -0700 Subject: [PATCH 0644/2173] Update hifiasm to 0.19.8 (#44116) --- recipes/hifiasm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hifiasm/meta.yaml b/recipes/hifiasm/meta.yaml index 13e47d1eabfc2..bccbad7ff9feb 100644 --- a/recipes/hifiasm/meta.yaml +++ b/recipes/hifiasm/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.19.7" %} +{% set version = "0.19.8" %} package: name: hifiasm @@ -6,7 +6,7 @@ package: source: url: https://github.com/chhylp123/hifiasm/archive/{{ version }}.tar.gz - sha256: 16d6127c7efb2d450630f25402a05e7d691b411465b304950d84d8afd53d5ee6 + sha256: 86cb2275be2a0ed73996f947c80eaef93da92b166bcc18cc57ef426c587cb2e3 build: number: 0 From 318c906b91fe35d3e3960a4b9f5bf9e294a3981e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 09:43:05 -0700 Subject: [PATCH 0645/2173] Update piranha-polio to 1.2.1 (#44110) * Update piranha-polio to 1.2 * Update piranha-polio to 1.2.1 --- recipes/piranha-polio/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/piranha-polio/meta.yaml b/recipes/piranha-polio/meta.yaml index 77f178381c48f..f02a40a7be400 100644 --- a/recipes/piranha-polio/meta.yaml +++ b/recipes/piranha-polio/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.2" %} +{% set version = "1.2.1" %} package: name: piranha-polio @@ -6,7 +6,7 @@ package: source: url: https://github.com/polio-nanopore/piranha/archive/refs/tags/{{ version }}.tar.gz - sha256: ca64487dc513ebd13f7ca6d9d3770c27b84ad1bbf3f408cbbb1da928910ac3b8 + sha256: a0c8e145868946664a9a1be07ae94cca514c63f06ce7e70e2a5dde660f2b228c build: number: 0 From 660e1d3b2488696901474995c8967654d9ef5c01 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 09:43:52 -0700 Subject: [PATCH 0646/2173] Update assembly_finder to 0.4.1 (#44119) --- recipes/assembly_finder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index bca873c722ec1..0da7d56f0b95d 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "assembly_finder" %} -{% set version = "0.4.0" %} +{% set version = "0.4.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: - url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: ed8d3b8cfaeebfeb32769e93a9c6a6c91f5c6509c91aba174e7ba4aa8a9f93cf + sha256: be7b470ad55c5ca304816b7414bf6d8f50db351b92ed9c6be6842ec0ed8cee8b build: number: 0 entry_points: From 0f9bdcd2b7493b598661d25b3b2bc0bc3f251922 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 12:56:35 -0700 Subject: [PATCH 0647/2173] Update bioconda-utils to 2.9.0 (#44124) --- recipes/bioconda-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index ce46ad1994248..22d380d54a236 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.8.0" %} -{% set sha256 = "5a555f97ca64423b5dbfd695214caab0eee66168b6bf24d4e86fc93bdd27e1da" %} +{% set version = "2.9.0" %} +{% set sha256 = "f11c5971ff2b618b61bea8f9e7ebd2b53e41739aa794c0d1c6af82e8c030e31c" %} package: name: bioconda-utils From 4277a481172a2cec2b3f8c25904f6beaec8e964b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 12:57:00 -0700 Subject: [PATCH 0648/2173] Update ena-webin-cli to 6.7.1 (#44125) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index 087acc08ec287..f11c051dd940b 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.7.0" %} -{% set sha256 = "dd8f3c7de02b5bebd392a4370d54eceeb5893dfa9beb4363a30c2fbd605aaba8" %} +{% set version = "6.7.1" %} +{% set sha256 = "f2c49ac1426ee804dec86cc062f071e695f4dfe7ad52234a20bc6495a4f387ec" %} package: name: ena-webin-cli From c2d8d3a13e3dd1b3dcc2131c7ff21c01876cd8dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 12:57:18 -0700 Subject: [PATCH 0649/2173] Update dxpy to 0.363.0 (#44128) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 8ff182ec2ab9a..1faed26dfbf60 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.362.0" %} +{% set version = "0.363.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 18a397a9b2496f89751dd0ae4a6f38ea9143108af28b5d78ef2e74bd628cf90d + sha256: 0da6f5c783f5614220d8962969eacc73767a991c0656a238c403a48f2b0dc3f1 build: number: 0 From 9ce2644d801233d258c04edadc383845f991ec2d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 14:08:24 -0700 Subject: [PATCH 0650/2173] Update bactopia-teton to 1.0.2 (#44130) * Update bactopia-teton to 1.0.2 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Robert A. Petit III --- recipes/bactopia-teton/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/bactopia-teton/meta.yaml b/recipes/bactopia-teton/meta.yaml index c11ed0e190790..52ec542ba5e0d 100644 --- a/recipes/bactopia-teton/meta.yaml +++ b/recipes/bactopia-teton/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: bactopia-teton @@ -7,10 +7,12 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('bactopia-teton', max_pin='x.x') }} source: url: https://github.com/bactopia/bactopia-teton/archive/v{{version}}.tar.gz - sha256: f89f6f93990807e7131c91ead41ce9bd605d27a5d376ae3f563e94165c9cf2bc + sha256: 3e1e78616b1b07747c6b54fe51e2bb300fbbd5171927388f4384dac3afb9b1dc requirements: run: @@ -18,6 +20,7 @@ requirements: - coreutils - fastq-scan >=1.0.1 - gsl 2.6 + - hostile >=0.1.0 - kraken2 >=2.1.3 - krakentools >=1.2 - krona >=2.8.1 @@ -25,6 +28,7 @@ requirements: - pigz - python >=3.6,<3.11 - sed + - sra-human-scrubber >=2.2 test: commands: From a679c5f2307e36279273ffaf0f7bf975d20d7ce3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 18:42:44 -0700 Subject: [PATCH 0651/2173] Update scmap-cli to 0.1.0 (#44102) * Update scmap-cli to 0.1.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/scmap-cli/meta.yaml | 38 ++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/recipes/scmap-cli/meta.yaml b/recipes/scmap-cli/meta.yaml index ecbba44befedb..6af9968474cf5 100644 --- a/recipes/scmap-cli/meta.yaml +++ b/recipes/scmap-cli/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.0.11" %} +{% set version = "0.1.0" %} package: name: scmap-cli @@ -6,29 +6,31 @@ package: source: url: https://github.com/ebi-gene-expression-group/scmap-cli/archive/{{ version }}.tar.gz - sha256: 7ea94d5e3cd20121bace848fffe01027c206c08825cc4a6b76d872afe5cec78b + sha256: 58444bf3e5a1f10261635b585aaeb1f259fd6e21561817899f5378a4b2811498 build: - number: 1 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('scmap-cli', max_pin="x.x") }} requirements: - run: - - bioconductor-biobase - - bioconductor-singlecellexperiment - - bioconductor-loomexperiment - - bioconductor-scmap >=1.6.0,<1.7 - - r-optparse - - r-workflowscriptscommon + run: + - bioconductor-biobase + - bioconductor-singlecellexperiment + - bioconductor-loomexperiment + - bioconductor-scmap >=1.6.0,<1.7 + - r-optparse + - r-workflowscriptscommon test: - commands: - - scmap-index-cell.R --help - - scmap-scmap-cluster.R --help - - scmap-index-cluster.R --help - - scmap-scmap-cell.R --help - - scmap-select-features.R --help - - which scmap-cli-post-install-tests.sh + commands: + - scmap-index-cell.R --help + - scmap-scmap-cluster.R --help + - scmap-index-cluster.R --help + - scmap-scmap-cell.R --help + - scmap-select-features.R --help + - which scmap-cli-post-install-tests.sh about: home: https://github.com/ebi-gene-expression-group/scmap-cli @@ -45,5 +47,3 @@ about: formats allowing composite workflows using a variety of software packages. license_family: GPL - - From b50dc592fedb752e88fe712d255c721c39a63ddc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 19:18:27 -0700 Subject: [PATCH 0652/2173] Update nmrml2isa to 0.3.3 (#44123) * Update nmrml2isa to 0.3.3 * add run_exports * limit python to <3.10 --------- Co-authored-by: joshuazhuang7 --- recipes/nmrml2isa/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/nmrml2isa/meta.yaml b/recipes/nmrml2isa/meta.yaml index 7cbf85da35d69..2dbd4c565d29e 100644 --- a/recipes/nmrml2isa/meta.yaml +++ b/recipes/nmrml2isa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nmrml2isa" %} -{% set version = "0.3.1" %} +{% set version = "0.3.3" %} package: name: "{{ name|lower }}" @@ -7,23 +7,25 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 5bae79e717eaed9a0147324adae7dcb54d435f80683e7a1b2cec032a2803f97c + sha256: 87269827b36b7df01f8909e4148c67ad585d8441432135fe41bf8abf4c41e99f build: number: 0 noarch: python entry_points: - nmrml2isa = nmrml2isa.parsing:run - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('nmrml2isa', max_pin="x") }} requirements: host: - pip - - python >=3 + - python <3.10 run: - openpyxl - pronto - - python >=3 + - python <3.10 - lxml - six @@ -35,5 +37,6 @@ test: about: home: http://github.com/ISA-tools/nmrml2isa - license: GNU General Public License v3 (GPLv3) + license: GPL-3.0-or-later + license_family: GPL3 summary: 'nmrml2isa - nmrML to ISA-Tab parsing tool' From 5eefb4c45b8c039b1ce4e53d5d14741b5113c448 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 19:48:31 -0700 Subject: [PATCH 0653/2173] Update blastbesties to 1.1.2 (#44132) * Update blastbesties to 1.1.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/blastbesties/build.sh | 2 -- recipes/blastbesties/meta.yaml | 30 ++++++++++++++++++------------ 2 files changed, 18 insertions(+), 14 deletions(-) delete mode 100644 recipes/blastbesties/build.sh diff --git a/recipes/blastbesties/build.sh b/recipes/blastbesties/build.sh deleted file mode 100644 index cace456c098dc..0000000000000 --- a/recipes/blastbesties/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$PYTHON setup.py install --single-version-externally-managed --record=record.txt \ No newline at end of file diff --git a/recipes/blastbesties/meta.yaml b/recipes/blastbesties/meta.yaml index d887737be5278..ea69200a2fbcb 100644 --- a/recipes/blastbesties/meta.yaml +++ b/recipes/blastbesties/meta.yaml @@ -1,34 +1,40 @@ +{% set name = "blastbesties" %} +{% set version = "1.1.2" %} + package: - name: blastbesties - version: "1.1.1" + name: {{ name|lower }} + version: {{ version }} source: - url: https://pypi.python.org/packages/86/61/b71bc19d93ac15bf69f2d883ec50ac36b351366d26b81761880ca2775587/blastbesties-1.1.1.tar.gz - md5: 42f74b3b5ba2c11ec3a2a39b1dee79ef + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/blastbesties-{{ version }}.tar.gz + sha256: 6dce21a9f92d8e47875a020c279e420ed5077d00ced3534844993a26e779e57d build: - number: 2 + number: 0 noarch: python entry_points: - - blastbesties=blastbesties.cmd_rbb:main + - blastbesties = blastbesties.app:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('blastbesties', max_pin="x") }} requirements: host: - - python - - setuptools - + - python >=3.7 + - pip + - setuptools-scm run: - - python + - python >=3.7 test: imports: - blastbesties - commands: - blastbesties --help about: home: https://github.com/Adamtaranto/blast-besties - license: MIT License + license: MIT summary: 'Rapid discovery of reciprocal best blast pairs from BLAST output files.' license_family: MIT + license_file: LICENSE From f52f402bbfc51cc44aaa767b834b5b55ef215296 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 6 Nov 2023 19:48:48 -0700 Subject: [PATCH 0654/2173] Update amptk to 1.6.0 (#44129) * Update amptk to 1.6.0 * add run_exports * edit tests --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/amptk/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/amptk/meta.yaml b/recipes/amptk/meta.yaml index 09e42d3681c10..69f4b96b9ca4f 100644 --- a/recipes/amptk/meta.yaml +++ b/recipes/amptk/meta.yaml @@ -1,5 +1,5 @@ {% set name = "amptk" %} -{% set version = "1.5.5" %} +{% set version = "1.6.0" %} package: name: "{{ name|lower }}" @@ -7,19 +7,23 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 0ac8e1c1a312e0cdc46de08b0506bbafd493da1b4c7ee419fe0025c22f3d44a6 + sha256: dbb6383ccfc26204a8d3147be8650a42ea6add8afcf73159c53bf2ecf3d47581 build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + entry_points: + - amptk=amptk.amptk:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('amptk', max_pin="x") }} requirements: host: - pip - - python + - python >=3 run: - - python + - python >=3 - biopython - psutil - python-edlib >=1.2.1 @@ -50,7 +54,7 @@ test: about: home: https://github.com/nextgenusfs/amptk - license: BSD-2 + license: BSD-2-Clause license_family: BSD license_file: LICENSE.md doc_url: http://amptk.readthedocs.io/ From 417721ef1f0a4bb6c6c283d3d05e530c3ba147f0 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Tue, 7 Nov 2023 11:50:01 +0900 Subject: [PATCH 0655/2173] Upldate LAST recipe (#43610) * New LAST upstream release * edit build number and run_exports * remove last from blacklist * edit tests * edit tests * edit tests --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: joshuazhuang7 --- build-fail-blacklist | 3 --- recipes/last/meta.yaml | 13 ++++++------- 2 files changed, 6 insertions(+), 10 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 0a289136ed3a2..67c1df1136542 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1056,9 +1056,6 @@ recipes/mapseq # permission error recipes/perl-gd -# source download not possible due to invalid https certificates -recipes/last - # sha mismatch when downloading source recipes/fmlrc2 diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index ec7e9a9425a2a..c8c8a65658219 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1454" %} +{% set version = "1512" %} package: name: {{ name|lower }} @@ -7,10 +7,12 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: 937f9f79ba0b585524b7872e04ea7e5e9be683fdf7703a123511511e2ef8873e + sha256: ed367c7eb8403a41ec43386e1c401d9dba9d7967427d24db3d95ed1919c6783e build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('last', max_pin=None) }} script: make install CXXFLAGS="$CXXFLAGS -msse4 -pthread" prefix=$PREFIX requirements: @@ -30,15 +32,12 @@ test: commands: - lastal -h - lastdb -h - - lastal5 -h - - lastdb5 -h - last-split -h - last-merge-batches -h - maf-convert -h - last-dotplot -h - last-map-probs -h - last-postmask -h - - last-split5 -h - last-train -h - last-pair-probs -h - fastq-interleave -h @@ -54,7 +53,7 @@ test: about: home: https://gitlab.com/mcfrith/last license: GPL-3.0-or-later - license_family: GPL + license_family: GPL3 license_file: COPYING.txt summary: "LAST finds & aligns related regions of sequences." description: "LAST finds & aligns related regions of sequences. It is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially good at: finding rearrangements and recombinations; finding DNA-versus-protein related regions; unusual data like AT-rich DNA; sensitive DNA-DNA search." From d2c1eaca0b1c78abf55db6c84400fee6524651e7 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 7 Nov 2023 08:10:01 +0100 Subject: [PATCH 0656/2173] bandage_ng: add a real test (#41091) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * add a real test for bandage currently fails with: ``` Bandage: error while loading shared libraries: libEGL.so.1: cannot open shared object file: No such file or directory ``` * try to fix test * try cdt * libglvnd * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update build.sh * Update build.sh * fix spdx --------- Co-authored-by: Björn Grüning Co-authored-by: Cameron Hyde <42562517+neoformit@users.noreply.github.com> --- recipes/bandage_ng/build.sh | 17 ++++++++++++++--- recipes/bandage_ng/meta.yaml | 32 ++++++++++++++++++++------------ 2 files changed, 34 insertions(+), 15 deletions(-) diff --git a/recipes/bandage_ng/build.sh b/recipes/bandage_ng/build.sh index bfdab287aefb2..511eeffad3281 100644 --- a/recipes/bandage_ng/build.sh +++ b/recipes/bandage_ng/build.sh @@ -1,13 +1,24 @@ #!/bin/bash set -ex -mkdir build && cd build +mkdir -p build && cd build + +if [[ $(uname) == "Linux" ]]; then + CMAKE_ARGS="${CMAKE_ARGS} -DFEATURE_egl=ON -DFEATURE_eglfs=ON" +fi + cmake \ -DCMAKE_PREFIX_PATH=${PREFIX} \ - -DCMAKE_CXX_FLAGS="${CXXFLAGS} -D__STDC_FORMAT_MACROS" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS} \ + -D__STDC_FORMAT_MACROS" \ + -DEGL_INCLUDE_DIR:PATH=${BUILD_PREFIX}/${HOST}/sysroot/usr/include \ + -DEGL_LIBRARY:FILEPATH=${BUILD_PREFIX}/${HOST}/sysroot/usr/lib/libEGL.so.1 \ + -DOPENGL_egl_LIBRARY:FILEPATH=${BUILD_PREFIX}/${HOST}/sysroot/usr/lib/libEGL.so.1 \ + -DEGL_opengl_LIBRARY:FILEPATH=${BUILD_PREFIX}/${HOST}/sysroot/usr/lib64/libGL.so \ + -DOPENGL_opengl_LIBRARY:FILEPATH=${BUILD_PREFIX}/${HOST}/sysroot/usr/lib64/libGL.so \ .. make # Install -mkdir $PREFIX/bin +mkdir -p $PREFIX/bin cp BandageNG $PREFIX/bin/Bandage diff --git a/recipes/bandage_ng/meta.yaml b/recipes/bandage_ng/meta.yaml index d0fe090443a5f..8068c2cda5f82 100644 --- a/recipes/bandage_ng/meta.yaml +++ b/recipes/bandage_ng/meta.yaml @@ -1,43 +1,51 @@ {% set name = "bandage_ng" %} {% set version = "2022.09" %} -{% set versionx = "2022_09" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - - url: https://github.com/asl/BandageNG/archive/refs/tags/v2022.09.tar.gz + - url: https://github.com/asl/BandageNG/archive/refs/tags/v{{ version }}.tar.gz sha256: 892c36350ee0eb8a58ec7187cf08b6b5b288915bd74f6d69e68c7aa2fdd704f0 build: - number: 2 + number: 3 skip: True # [osx] + run_exports: + - {{ pin_subpackage("bandage_ng", max_pin=None) }} requirements: build: - make - cmake - {{ compiler('cxx') }} - - {{ cdt('mesa-libgl-devel') }} - - {{ cdt('mesa-dri-drivers') }} - - {{ cdt('libselinux') }} - - {{ cdt('libxdamage') }} - - {{ cdt('libxxf86vm') }} - - {{ cdt('libxfixes') }} - - xorg-libxext + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-libegl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libdrm-devel') }} # [linux] + - {{ cdt('libglvnd-glx') }} # [linux and cdt_name != 'cos6'] + host: + - xorg-libx11 # [linux] + - xorg-libxext # [linux] + - xorg-libxdamage # [linux] + - xorg-libsm # [linux] + - xorg-libice # [linux] + - xorg-libxcomposite # [linux] + - xorg-libxxf86vm # [linux] + - xorg-xf86vidmodeproto # [linux] - qt6-main run: - qt6-main - fonts-conda-ecosystem - - xorg-libxrender test: commands: - which Bandage + - QT_QPA_PLATFORM='offscreen' Bandage --version about: home: https://github.com/asl/BandageNG - license: GNU General Public License, version 3 + license: GPL-3.0 license_family: GPL3 license_file: COPYING summary: Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily From 51925252fda5248f882dfded1b35a4c61fa64a27 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 Nov 2023 04:11:18 -0700 Subject: [PATCH 0657/2173] Update pbmm2 to 1.13.1 (#44133) --- recipes/pbmm2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbmm2/meta.yaml b/recipes/pbmm2/meta.yaml index 8a2c2f1bff336..1f60756da774d 100644 --- a/recipes/pbmm2/meta.yaml +++ b/recipes/pbmm2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbmm2" %} -{% set version = "1.13.0" %} -{% set sha256 = "616f42a6c95d6a1e873f168e681c7cdc5a03acefd28c2d855432fd06c3914df4" %} +{% set version = "1.13.1" %} +{% set sha256 = "4e764bbea99a4c712fb74e4d6c82c227562d431c47670628f1d004b2f0e8a8db" %} package: name: {{ name }} From 70298cf27485c5b574182d8c429f7b087428bb88 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 Nov 2023 13:31:06 -0700 Subject: [PATCH 0658/2173] Update keggcharter to 0.7.1 (#44143) --- recipes/keggcharter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/keggcharter/meta.yaml b/recipes/keggcharter/meta.yaml index 500d94f3f7feb..c93435f02d255 100644 --- a/recipes/keggcharter/meta.yaml +++ b/recipes/keggcharter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "keggcharter" %} -{% set version = "0.7.0" %} -{% set sha256 = "8e79e92eef943d0b7cfbd035b4d3d9ef5f6f51a6f4d43f8d58989fd849625696" %} +{% set version = "0.7.1" %} +{% set sha256 = "bbbe3cb4d371a631cfdca68787af4f4f2b183556de0d71f6350f256e3b11437e" %} package: name: {{ name|lower }} From e0c8b4d087f49f77e295141f51496efda8148eb6 Mon Sep 17 00:00:00 2001 From: Philippe Bordron Date: Tue, 7 Nov 2023 21:33:42 +0000 Subject: [PATCH 0659/2173] fix: dgenies flask version (#44136) --- recipes/dgenies/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/dgenies/meta.yaml b/recipes/dgenies/meta.yaml index 8030d3a292043..4bc4d0ebcf5b6 100644 --- a/recipes/dgenies/meta.yaml +++ b/recipes/dgenies/meta.yaml @@ -10,8 +10,10 @@ source: sha256: "74be9d66095a1e3e1dcc70f69c3a61a0d651b16594a85878d83216dfc6979aa5" build: - number: 0 + number: 1 noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: @@ -20,7 +22,7 @@ requirements: run: - python >=3.6 - biopython >=1.70 - - flask >=1.0 + - flask =2 - intervaltree =3 - jinja2 >=2.11.3 - markdown >=2.6 From 35f89c5bf2980ae9c991632775e3427247914b21 Mon Sep 17 00:00:00 2001 From: stuber Date: Tue, 7 Nov 2023 15:34:21 -0600 Subject: [PATCH 0660/2173] vsnp3 version 3.17 (#44135) * vsnp3 version 3.17 * vsnp3 version 3.17 --- recipes/vsnp3/meta.yaml | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/recipes/vsnp3/meta.yaml b/recipes/vsnp3/meta.yaml index 5d2f44ab76bf0..c7f1f13a0f903 100644 --- a/recipes/vsnp3/meta.yaml +++ b/recipes/vsnp3/meta.yaml @@ -1,7 +1,7 @@ {% set user = "USDA-VS" %} {% set name = "vsnp3" %} -{% set version = "3.16" %} -{% set sha256 = "dd6919ec2003f55a80c21a05afd127eb72107176c0af47c6f1257860bd61b949" %} +{% set version = "3.17" %} +{% set sha256 = "68f4dc521c57ba2418511d8649e9ed8698d93f096f2d9f76c50782ba66925625" %} package: name: {{ name|lower }} @@ -19,31 +19,31 @@ source: requirements: run: - - python >=3.8 + - python >=3.8,<3.10 - bcftools - - biopython + - biopython >=1.79 - bwa - - minimap2 - - cairosvg - - dask - - freebayes - - humanize + - minimap2 >=2.24 + - cairosvg >=2.5.2 + - dask >=2022.01.1 + - freebayes >=1.3.5 + - humanize >=3.14.0 - numpy - - openpyxl - - xlsxwriter + - openpyxl >=3.0.9 + - xlsxwriter >=3.0.2 - pandas - parallel - pigz - - regex - - samtools - - seqkit - - vcflib - - vcftools - - sourmash - - spades - - svgwrite + - regex >=2.5.110 + - samtools >=1.14 + - seqkit >=2.1.0 + - vcflib =1.0.9 + - vcftools =0.1.16 + - sourmash >=4.2.4 + - spades >=3.15.2 + - svgwrite >=1.4.1 - py-cpuinfo - - raxml + - raxml >=8.2.12 test: commands: From 69c373796fdf876d7984913b75add97c7658e1b0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 Nov 2023 18:27:48 -0700 Subject: [PATCH 0661/2173] Update augur to 23.1.1 (#44150) --- recipes/augur/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index e4f81276b1c0e..bc3674cd3735a 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "23.1.0" %} +{% set version = "23.1.1" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: 1f1b67ebf2a89984e37a9978b86b876bfb2f30eb4cebc90c33968e6c990ea934 + sha256: 1b6f8fb1f20c147d24806764761f8e977c8e100a58e04e06d3110bb72268518f build: number: 0 From 18c998fb8be8984818ce67632210dd2dec947326 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 Nov 2023 18:38:42 -0700 Subject: [PATCH 0662/2173] Update assemblycomparator2 to 2.5.9 (#44142) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index 8b7f3fe701c6d..4131a21c4050d 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.8" %} +{% set version = "2.5.9" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - md5: 42d29dc011d2e057992a0801e41fa4ac + sha256: 3967e1f245cd7a4a4524bc3ec7e78dfe018c767ae4f57d678d20003cdd98ee2a build: From 0024f589a0154c35bfc112ec7ee24c8bfafde5ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 Nov 2023 19:24:33 -0700 Subject: [PATCH 0663/2173] Update bedtools to 2.31.1 (#44154) --- recipes/bedtools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bedtools/meta.yaml b/recipes/bedtools/meta.yaml index d2303ca82f12d..2c96f9e40ecca 100644 --- a/recipes/bedtools/meta.yaml +++ b/recipes/bedtools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bedtools" %} -{% set version = "2.31.0" %} +{% set version = "2.31.1" %} package: name: {{ name }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/arq5x/bedtools2/releases/download/v{{ version }}/bedtools-{{ version }}.tar.gz - sha256: a93e6b6bfdd8d33db1e6decbefdd2b03771e0ac63ac69a4059b7b3464efe281d + sha256: fc7e660c2279b1e008b80aca0165a4a157daf4994d08a533ee925d73ce732b97 build: - number: 3 + number: 0 run_exports: - {{ pin_subpackage('bedtools', max_pin="x") }} From 127bd380abc610ebf6d891636ebb11fd686f602e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 02:50:11 -0700 Subject: [PATCH 0664/2173] Update annonars to 0.24.5 (#44159) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index e96c168424543..906b402fd2f00 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.24.4" %} +{% set version = "0.24.5" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 274c145712d467655ec29a377cd8514d6f2254a38c797baa9e2cc820a267db7d + sha256: 8e66712ff006206eeb55ef4c3342b38b1f30bfb414951bfeb9269d7c3ee7c5f4 requirements: build: From 328e096eb8520631c6d55f50aacafa7794b50553 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 06:14:29 -0700 Subject: [PATCH 0665/2173] Update bionumpy to 0.2.31 (#44162) * Update bionumpy to 0.2.30 * Update bionumpy to 0.2.31 --- recipes/bionumpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index ed28b0321744e..6e09348526ff0 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.29" %} +{% set version = "0.2.31" %} package: name: bionumpy @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: 63064c721294d083b7d5725265f2d75a3f47a08d81b1886ea24395d947a71aca + sha256: 5216b0bb72fedae87cfe35a06e189b803b39e5051bcdb347886762a4aaea956d build: noarch: python From 33721cfa78575aadb1bfd3e13451c945160a790c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 08:43:17 -0700 Subject: [PATCH 0666/2173] Update recognizer to 1.9.4 (#44168) --- recipes/recognizer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/recognizer/meta.yaml b/recipes/recognizer/meta.yaml index 1c31ed52badde..e894c66dab43d 100644 --- a/recipes/recognizer/meta.yaml +++ b/recipes/recognizer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "recognizer" %} -{% set version = "1.9.3" %} -{% set sha256 = "fdf8aa7f6c7731e4ffa91a4defadf6142d0878d7d14ba76f7e269c29c8997e8a" %} +{% set version = "1.9.4" %} +{% set sha256 = "36c3f08fff9c5eff6bf45491b3332eee44507d08f9839766b4fe81eeb8715630" %} package: name: {{ name|lower }} From c964a0bc4eb8530c68b93e392e02fc08a83f77cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 13:10:41 -0700 Subject: [PATCH 0667/2173] Update brooklyn_plot to 0.0.4 (#44152) * Update brooklyn_plot to 0.0.4 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/brooklyn_plot/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/brooklyn_plot/meta.yaml b/recipes/brooklyn_plot/meta.yaml index 2ea875c760e46..1e8515815024b 100644 --- a/recipes/brooklyn_plot/meta.yaml +++ b/recipes/brooklyn_plot/meta.yaml @@ -1,5 +1,5 @@ {% set name = "brooklyn_plot" %} -{% set version = "0.0.3" %} +{% set version = "0.0.4" %} package: name: "{{ name|lower }}" @@ -7,23 +7,25 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a3b4c7174515d61e7a1386e0ac0ae49087f1a9c9b12eb952196b6b0b0b6f1bee + sha256: 6e9821999aa52b10710e59c1cd4777d6b364fef806da949e61058e6d311b97fa build: number: 0 entry_points: - brooklyn_plot = brooklyn_plot.__main__:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('brooklyn_plot', max_pin="x.x") }} requirements: host: - pip - - python >=3.6 + - python >=3.7 run: - numpy <1.24 - pandas - - python >=3.6 + - python >=3.7 - scanpy - scipy From b0811919d19009ae12d3f06827cc91807eaa1c18 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 14:42:08 -0700 Subject: [PATCH 0668/2173] Update pypints to 1.1.10 (#44141) * Update pypints to 1.1.10 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/pypints/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/pypints/meta.yaml b/recipes/pypints/meta.yaml index a33a7e0a23d7c..b32637aeeaf6e 100644 --- a/recipes/pypints/meta.yaml +++ b/recipes/pypints/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyPINTS" %} -{% set version = "1.1.9" %} +{% set version = "1.1.10" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b153a9122fe0542dddfdb18b2822e2ab83de34f9a187bcd0d2917234538a0638 + sha256: 91e4e6e8a308ad4e4e829068b96282385a0285512a2351cedd9793c50e8a7f63 build: number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('pypints', max_pin="x") }} requirements: host: @@ -41,7 +43,7 @@ test: about: home: "https://pints.yulab.org" license: GPL-3.0-only - license_family: GPL + license_family: GPL3 license_file: LICENSE summary: "Peak Identifier for Nascent Transcripts Starts (PINTS)" dev_url: "https://github.com/hyulab/PINTS" From d2fe1b74162e7f6f89c41371e17c7b6727512cd7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:22:32 -0700 Subject: [PATCH 0669/2173] Update reframed to 1.5.0 (#44167) * Update reframed to 1.5.0 * Add run_exports to reframed. --------- Co-authored-by: Adam Caprez --- recipes/reframed/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/reframed/meta.yaml b/recipes/reframed/meta.yaml index c8db5c7200bad..5bc8f8eec8325 100644 --- a/recipes/reframed/meta.yaml +++ b/recipes/reframed/meta.yaml @@ -1,5 +1,5 @@ {% set name = "reframed" %} -{% set version = "1.4.0" %} +{% set version = "1.5.0" %} package: name: {{ name|lower }} @@ -7,12 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/reframed-{{ version }}.tar.gz - sha256: 5da99d68dc7ca8ce39cbeabc46f6158b0e82885d3432afb5ec675f1d9a2017be + sha256: 2f40e631080be7aa8f2ea1c1f4b1ffa5cf52e87e4279978b6c72c7bb690dc1c1 build: noarch: python script: {{ PYTHON }} -m pip install . -vv number: 0 + run_exports: + - {{ pin_subpackage('reframed', max_pin="x") }} requirements: host: From 1e8c8478944cab65d6c37cec68c8a0acce4afc5a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 16:35:28 -0700 Subject: [PATCH 0670/2173] Update hybracter to 0.3.0 (#44158) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index 14f18c8cdb326..b3c1078072223 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.2.1" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 2d696acaeb4999234ee5c7190ec9e63ee2c9c4bdea3e47e4d8363d44e458b7a0 + sha256: 71ed98a852e1153554eb78ba3c3dfb62fe1d9e9681ab71f948cedb8926659d8a build: number: 0 From b433de01a429ced871799dbf611f89a87f5dabc3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 18:15:22 -0700 Subject: [PATCH 0671/2173] Update physiofit to 3.3.1 (#44122) * Update physiofit to 3.3.1 * Update meta.yaml (#44127) Added <3.12 in python requirement --------- Co-authored-by: llegregam <75795040+llegregam@users.noreply.github.com> --- recipes/physiofit/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/physiofit/meta.yaml b/recipes/physiofit/meta.yaml index 319d30146fd90..4338f309dcecc 100644 --- a/recipes/physiofit/meta.yaml +++ b/recipes/physiofit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "physiofit" %} -{% set version = "3.3.0" %} +{% set version = "3.3.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/physiofit-{{ version }}.tar.gz - sha256: bf35004ab1d13b5a0f7ef8fca19c103271e79bb5ef5d54c81834895a7c411dbc + sha256: dc01bbf300f8dd19fadf5d9ed3032f37533cb28b9057a7ec434740de10e3d392 build: entry_points: @@ -20,11 +20,11 @@ build: requirements: host: - - python >=3.8,<3.9.7|>3.9.7 + - python >=3.8,<3.9.7|>3.9.7,<3.12 - poetry-core - pip run: - - python >=3.8,<3.9.7|>3.9.7 + - python >=3.8,<3.9.7|>3.9.7,<3.12 - pandas >=2.0.1 - numpy >=1.24.2 - scipy >=1.10.1 From e36348759f6a3d0e1b0d71749f82c60b403be55d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 18:15:44 -0700 Subject: [PATCH 0672/2173] Update get_homologues to 3.6.2 (#44134) * Update get_homologues to 3.6.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/get_homologues/meta.yaml | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/recipes/get_homologues/meta.yaml b/recipes/get_homologues/meta.yaml index 4b34c7901de2f..6146754cffe4e 100644 --- a/recipes/get_homologues/meta.yaml +++ b/recipes/get_homologues/meta.yaml @@ -1,6 +1,5 @@ - -{% set version = "3.6.1" %} -{% set sha256 = "22b126b45d79cd2f7489cf40c8a22738ecb9a034d2662e9ff82cb93a07d10af7" %} +{% set version = "3.6.2" %} +{% set sha256 = "882f5e94ad1ddcfec6b5ddf4502c946dbcf95a53adb3445a6aaf917ba6052cee" %} package: name: get_homologues @@ -9,42 +8,39 @@ package: build: number: 0 noarch: generic - #skip: True # [osx] script_env: - LC_ALL=POSIX + run_exports: + - {{ pin_subpackage('get_homologues', max_pin="x") }} source: url: https://github.com/eead-csic-compbio/get_homologues/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: - run: - wget - - perl - perl-gd - - r-base - r-gplots - r-dendextend - r-ape - r-factoextra - - blast - hmmer - diamond - - mcl + - mcl - cogtriangles - phylip -test: +test: source_files: - CHANGES.txt - "*.pl" - lib - bin - - db + - db commands: - get_homologues.pl -v @@ -53,14 +49,14 @@ test: about: home: https://github.com/eead-csic-compbio/get_homologues summary: "A versatile software package for pan-genome analysis, including GET_HOMOLOGUES and GET_HOMOLOGUES-EST" - license: GPL3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE.txt - extra: identifiers: - biotools:get_homologues - doi:https://doi.org/10.1128/AEM.02411-13 - - doi:https://doi.org/10.3389/fpls.2017.00184 + - doi:https://doi.org/10.3389/fpls.2017.00184 - doi:https://doi.org/10.1007/978-1-4939-1720-4_14 - doi:https://doi.org/10.1007/978-1-0716-2429-6_9 From ae223c9f70edce955ed549456f63e0f50d1fbb3a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 18:16:09 -0700 Subject: [PATCH 0673/2173] Update aniclustermap to 1.3.0 (#44139) * Update aniclustermap to 1.3.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/aniclustermap/meta.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/aniclustermap/meta.yaml b/recipes/aniclustermap/meta.yaml index 39002e9c0859d..dd5865cca6efc 100644 --- a/recipes/aniclustermap/meta.yaml +++ b/recipes/aniclustermap/meta.yaml @@ -1,5 +1,5 @@ {% set name = "aniclustermap" %} -{% set version = "1.2.0" %} +{% set version = "1.3.0" %} package: name: {{ name|lower }} @@ -7,19 +7,21 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/aniclustermap-{{ version }}.tar.gz - sha256: 82a831c35c04677a7708610fe705222b98b7b3f0e6f4d74de1d8e357b55ae61d + sha256: 67b909f1c987092b198227b2588ea4e634b6f46fe156f450a8d8741d0acd7bae build: entry_points: - ANIclustermap = aniclustermap.aniclustermap:main noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation number: 0 + run_exports: + - {{ pin_subpackage('aniclustermap', max_pin="x") }} requirements: host: - pip - - poetry + - poetry-core - python >=3.8 run: - python >=3.8 @@ -33,10 +35,8 @@ test: imports: - aniclustermap commands: - - pip check - ANIclustermap --help requires: - - pip - pytest source_files: - tests/ @@ -45,6 +45,7 @@ about: home: https://github.com/moshi4/ANIclustermap/ summary: A tool for drawing ANI clustermap between all-vs-all microbial genomes license: MIT + license_family: MIT license_file: LICENSE extra: From f7eef178c66c8d5441f613cd9d105a974ad26e39 Mon Sep 17 00:00:00 2001 From: Jessica Mattick <19544292+jmattick@users.noreply.github.com> Date: Wed, 8 Nov 2023 19:17:03 -0600 Subject: [PATCH 0674/2173] Update pbpigeon to v1.2.0 (#44173) * Update pbpigeon to v1.2.0 * Update meta.yaml --------- Co-authored-by: Jessica Mattick Co-authored-by: Thanh Lee --- recipes/pbpigeon/meta.yaml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/recipes/pbpigeon/meta.yaml b/recipes/pbpigeon/meta.yaml index ee74d485d69a8..20965d16c23e4 100644 --- a/recipes/pbpigeon/meta.yaml +++ b/recipes/pbpigeon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pbpigeon" %} -{% set version = "1.1.0" %} +{% set version = "1.2.0" %} package: name: {{ name }} @@ -7,17 +7,17 @@ package: source: - url: https://github.com/PacificBiosciences/pigeon/releases/download/v{{ version }}/pigeon - sha256: d35b090536ef2d9e9af5a6a5e91ccd87bc5214a275d88a145c73fdc74374c0f4 + sha256: 0202818fed1247d21b79bf58811402f7af2481b3731ebc1094b161cf03c0e009 build: # repackaged binaries skip: True # [osx] number: 0 - + run_exports: + - {{ pin_subpackage('pbpigeon', max_pin='x.x') }} requirements: build: - {{ compiler('cxx') }} - test: commands: - pigeon -h @@ -30,3 +30,8 @@ about: extra: recipe-maintainers: - jmattick + - armintoepfer + - pb-dseifert + skip-lints: + #repackaged binary + - should_be_noarch_generic From 38ef442654ceddd797edc455ecd0a80738a89eb8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 18:18:32 -0700 Subject: [PATCH 0675/2173] Update itsxpress to 2.0.1 (#44145) * Update itsxpress to 2.0.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/itsxpress/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/itsxpress/meta.yaml b/recipes/itsxpress/meta.yaml index 05ee7adc18aff..5339657193c68 100644 --- a/recipes/itsxpress/meta.yaml +++ b/recipes/itsxpress/meta.yaml @@ -1,8 +1,8 @@ {% set name = "itsxpress" %} -{% set version = "2.0.0" %} +{% set version = "2.0.1" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "3306cb809e4b8c69b93a795f0289dbf4b9d8b7ba653f34d94472a62b38f41f6e" %} +{% set hash_value = "b5797107ee3f21cbaba0b9625aa931741babdee3eeb5a3218a8b8bc9783e2e72" %} package: name: '{{ name|lower }}' @@ -17,7 +17,9 @@ build: number: 0 entry_points: - itsxpress=itsxpress.main:main - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv + run_exports: + - {{ pin_subpackage('itsxpress', max_pin="x") }} requirements: host: From 3ec0499edaee113de839907ba7cea135d6bd1509 Mon Sep 17 00:00:00 2001 From: entzian Date: Thu, 9 Nov 2023 02:20:58 +0100 Subject: [PATCH 0676/2173] Update to 0.2.0 (#44166) Co-authored-by: gentzian --- recipes/idemuxcpp/build.sh | 4 +++- recipes/idemuxcpp/meta.yaml | 16 +++++++++------- 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/recipes/idemuxcpp/build.sh b/recipes/idemuxcpp/build.sh index 5a89adf94d5f7..7e69267c6d7cc 100644 --- a/recipes/idemuxcpp/build.sh +++ b/recipes/idemuxcpp/build.sh @@ -1,6 +1,8 @@ #!/bin/sh -./configure --enable-tests --prefix="${PREFIX}" BAMTOOLS_CFLAGS="-I${PREFIX}/include/" BAMTOOLS_LIBS="-L${PREFIX}/lib/ -lbamtools" +export CXXFLAGS="-I${PREFIX}/include/bamtools ${CXXFLAGS}" +export LDFLAGS="-L${PREFIX}/lib/ -lbamtools ${LDFLAGS}" +./configure --enable-tests --prefix="${PREFIX}" make make install make check diff --git a/recipes/idemuxcpp/meta.yaml b/recipes/idemuxcpp/meta.yaml index 8cfa044440a7b..9c260e6708b31 100644 --- a/recipes/idemuxcpp/meta.yaml +++ b/recipes/idemuxcpp/meta.yaml @@ -1,6 +1,6 @@ {% set name = "idemuxcpp" %} -{% set version = "0.1.9" %} -{% set sha256 = "5037a5de72e975fe888593d570a1707fbbadc0f8732bc625b5b2698aa647415d" %} +{% set version = "0.2.0" %} +{% set sha256 = "0e44ed269b57b9577141c70361e6c5871ef3d76b302f9c8a4c0ff2d54f30bf01" %} package: name: {{ name }} @@ -11,7 +11,9 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('idemuxcpp', max_pin="x") }} requirements: build: @@ -19,12 +21,12 @@ requirements: - {{ compiler('cxx') }} host: - zlib - - boost-cpp - - bamtools + - boost-cpp >=1.55 + - bamtools >=2.5.1 run: - zlib - - boost-cpp - - bamtools + - boost-cpp >=1.55 + - bamtools >=2.5.1 test: commands: From d911c7a34aa0b2f622288b66e9868273938baf17 Mon Sep 17 00:00:00 2001 From: Stephan Schiffels Date: Thu, 9 Nov 2023 02:49:10 +0100 Subject: [PATCH 0677/2173] updated sequenceTools (#44171) Co-authored-by: Stephan Schiffels --- recipes/sequencetools/meta.yaml | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/recipes/sequencetools/meta.yaml b/recipes/sequencetools/meta.yaml index ca157c582926a..bc3b6d6b88426 100644 --- a/recipes/sequencetools/meta.yaml +++ b/recipes/sequencetools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.5.3" %} +{% set version = "1.5.3.2" %} package: name: sequencetools @@ -6,23 +6,25 @@ package: source: - url: https://github.com/stschiff/sequenceTools/releases/download/v{{ version }}/genoStats-linux # [linux] - md5: 9967a7ae908fe4f9609e85171d7f81ae # [linux] + md5: 50fd1595be89c375e0c0d86353b68aab # [linux] - url: https://github.com/stschiff/sequenceTools/releases/download/v{{ version }}/pileupCaller-linux # [linux] - md5: 3aa3e5c41c7a26f59f669d8b2a91eeee # [linux] + md5: 7e9e44f223f3b23283b2e846ae3eff92 # [linux] - url: https://github.com/stschiff/sequenceTools/releases/download/v{{ version }}/vcf2eigenstrat-linux # [linux] - md5: 190d13ea03bb45411afc71a4fd23ad21 # [linux] + md5: 88fe4a59b5a2df97794f67d7a4274e45 # [linux] - url: https://github.com/stschiff/sequenceTools/releases/download/v{{ version }}/genoStats-macOS # [osx] - md5: d267065a6d751df5278dc087329a6e08 # [osx] + md5: d4ad978d5956b02ffac9d91aa7779cf8 # [osx] - url: https://github.com/stschiff/sequenceTools/releases/download/v{{ version }}/pileupCaller-macOS # [osx] - md5: ae518ace450cee1f819aa28cd415857a # [osx] + md5: d1e10117bb7ef10c7f9bd43bd90c86af # [osx] - url: https://github.com/stschiff/sequenceTools/releases/download/v{{ version }}/vcf2eigenstrat-macOS # [osx] - md5: 7f22cb54d61af573a993dbd6aade17d5 # [osx] + md5: 015ce6ca8b99405f626665d4e9246ae1 # [osx] build: - number: 1 + number: 0 script: - "mkdir -p $PREFIX/bin" - "for TOOL in genoStats pileupCaller vcf2eigenstrat; do mv $TOOL-* $PREFIX/bin/$TOOL; chmod u+x $PREFIX/bin/$TOOL; done" + run_exports: + - {{ pin_subpackage("sequencetools", max_pin=None) }} requirements: From 20812f7935b4cac3652f08d5ded2050790bc82e9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 18:49:27 -0700 Subject: [PATCH 0678/2173] Update seqverify to 1.1.0 (#44170) * Update seqverify to 1.1.0 * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/seqverify/meta.yaml | 88 ++++++++++++++++++------------------- 1 file changed, 44 insertions(+), 44 deletions(-) diff --git a/recipes/seqverify/meta.yaml b/recipes/seqverify/meta.yaml index ebedfc6430943..f43ed2d87bda8 100644 --- a/recipes/seqverify/meta.yaml +++ b/recipes/seqverify/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.0.0" %} - -package: - name: seqverify - version: {{ version }} - -source: - url: https://github.com/mpiersonsmela/SeqVerify/archive/refs/tags/v1.0.0.tar.gz - sha256: 2db1194cdb51e9252936cf5b60e702cec3f170bc6ceeb7b3371745bddd4f39fc - -build: - noarch: generic - number: 0 - run_exports: - - {{ pin_subpackage('seqverify', max_pin="x") }} - -requirements: - run: - - bcftools - - blast - - bwa - - cnvpytor - - htslib - - idna - - igv =2.13.2 - - kraken2 - - matplotlib-base - - numpy - - openjdk =11 - - pip - - python =3.10 - - samtools - - scipy - - snpeff =5.1 - - snpsift =4.3.1t - -test: - commands: - - seqverify -h - -about: - home: https://github.com/mpiersonsmela/SeqVerify - license: GPL-3.0 - summary: Seqverify analyzes whole genome sequencing data for gene-editing verification. +{% set version = "1.1.0" %} + +package: + name: seqverify + version: {{ version }} + +source: + url: https://github.com/mpiersonsmela/SeqVerify/archive/refs/tags/v1.1.0.tar.gz + sha256: d6d9b1fc56bc7f7263d99d3e4f13e12a0e5ed0894c1ba70397805c46b5d34ec2 + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('seqverify', max_pin="x.x") }} + +requirements: + run: + - bcftools + - blast + - bwa + - cnvpytor + - htslib + - idna + - igv =2.13.2 + - kraken2 + - matplotlib-base + - numpy + - openjdk =11 + - pip + - python =3.10 + - samtools + - scipy + - snpeff =5.1 + - snpsift =4.3.1t + +test: + commands: + - seqverify -h + +about: + home: https://github.com/mpiersonsmela/SeqVerify + license: GPL-3.0 + summary: Seqverify analyzes whole genome sequencing data for gene-editing verification. From c6e406c7125a7abce3adef91d1d5760ae8b58b7b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 18:49:40 -0700 Subject: [PATCH 0679/2173] Update bioframe to 0.5.1 (#44169) --- recipes/bioframe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioframe/meta.yaml b/recipes/bioframe/meta.yaml index 4444dd9d7103c..3dd3614557adf 100644 --- a/recipes/bioframe/meta.yaml +++ b/recipes/bioframe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioframe" %} -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b593214db918ae5d7427f947a32bdfd71a1cda4273fcab84cf8e1f2113801487 + sha256: 416132f14334f3921d700a692bf94ea21161ca608e5e3b9a119f97c01012d578 build: noarch: python From 195a27f31872f75a611b4281d2ae7b9742a13b40 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Thu, 9 Nov 2023 10:50:20 +0900 Subject: [PATCH 0680/2173] Fix NaN issue in ColabFold 1.5.3 (#44164) --- recipes/colabfold/fix-jax-04-nan.patch | 20 ++++++++++++++++++++ recipes/colabfold/meta.yaml | 4 +++- 2 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 recipes/colabfold/fix-jax-04-nan.patch diff --git a/recipes/colabfold/fix-jax-04-nan.patch b/recipes/colabfold/fix-jax-04-nan.patch new file mode 100644 index 0000000000000..9065fc61d3154 --- /dev/null +++ b/recipes/colabfold/fix-jax-04-nan.patch @@ -0,0 +1,20 @@ +diff --git a/alphafold/model/modules.py b/alphafold/model/modules.py +index 73f9cdd..4ca8827 100644 +--- a/alphafold/model/modules.py ++++ b/alphafold/model/modules.py +@@ -672,6 +672,7 @@ class Attention(hk.Module): + logits = jnp.einsum('bqhc,bkhc->bhqk', q, k) + bias + if nonbatched_bias is not None: + logits += jnp.expand_dims(nonbatched_bias, axis=0) ++ logits = jnp.clip(logits, -1e8, 1e8) + weights = jax.nn.softmax(logits) + weighted_avg = jnp.einsum('bhqk,bkhc->bqhc', weights, v) + +@@ -771,6 +772,7 @@ class GlobalAttention(hk.Module): + k = jnp.einsum('bka,ac->bkc', m_data, k_weights) + bias = (1e9 * (q_mask[:, None, :, 0] - 1.)) + logits = jnp.einsum('bhc,bkc->bhk', q, k) + bias ++ logits = jnp.clip(logits, -1e8, 1e8) + weights = jax.nn.softmax(logits) + weighted_avg = jnp.einsum('bhk,bkc->bhc', weights, v) + diff --git a/recipes/colabfold/meta.yaml b/recipes/colabfold/meta.yaml index f5962e107e4bd..11697a3be4d8f 100644 --- a/recipes/colabfold/meta.yaml +++ b/recipes/colabfold/meta.yaml @@ -14,7 +14,7 @@ build: python -m pip install --no-deps --ignore-installed alphafold/ run_exports: - {{ pin_subpackage('colabfold', max_pin="x") }} - number: 0 + number: 1 source: - url: https://github.com/sokrypton/ColabFold/archive/refs/tags/v{{ cf_version }}.tar.gz @@ -23,6 +23,8 @@ source: - url: https://github.com/steineggerlab/alphafold/archive/refs/tags/v{{ af_version }}.tar.gz sha256: {{ af_hash }} folder: alphafold + patches: + - fix-jax-04-nan.patch requirements: host: From 7bfd171b7edc796917913af341286539e3b74b96 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 Nov 2023 21:26:50 -0700 Subject: [PATCH 0681/2173] Update parascopy to 1.13.9 (#44174) * Update parascopy to 1.13.9 * add run_exports * revert python pinning --------- Co-authored-by: joshuazhuang7 --- recipes/parascopy/build.sh | 4 ++-- recipes/parascopy/meta.yaml | 11 ++++++++--- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/recipes/parascopy/build.sh b/recipes/parascopy/build.sh index 81b104a3383e9..4afc56ed9f7d2 100644 --- a/recipes/parascopy/build.sh +++ b/recipes/parascopy/build.sh @@ -1,3 +1,4 @@ +#!/bin/bash rm -df freebayes git clone --recursive https://github.com/tprodanov/freebayes.git @@ -10,5 +11,4 @@ ninja -v cp freebayes "${PREFIX}/bin/_parascopy_freebayes" cd ../../ -$PYTHON -m pip install . --ignore-install --no-deps -vv - +$PYTHON -m pip install . --no-build-isolation --no-deps -vvv diff --git a/recipes/parascopy/meta.yaml b/recipes/parascopy/meta.yaml index d994ae440d302..b086855ecc5cb 100644 --- a/recipes/parascopy/meta.yaml +++ b/recipes/parascopy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "parascopy" %} -{% set version = "1.12.0" %} +{% set version = "1.13.9" %} package: name: {{ name|lower }} @@ -7,11 +7,15 @@ package: build: number: 0 - skip: true # [osx or py2k] + skip: True # [osx or py2k] + entry_points: + - parascopy=parascopy.entry_point:main + run_exports: + - {{ pin_subpackage('parascopy', max_pin="x") }} source: url: https://github.com/tprodanov/{{ name }}/archive/v{{ version }}.tar.gz - sha256: b25d998868814d52b29fbb6a2031d19e4aee106898b9df7470e2aba9f6cfe7d8 + sha256: d1f36bc37662e5eff8a49356f0c4710c6074708e4ae0b9d4c17c33e60ee232a3 requirements: build: @@ -57,5 +61,6 @@ test: about: home: https://github.com/tprodanov/parascopy license: MIT + license_family: MIT license_file: LICENSE summary: Calling paralog-specific copy number and sequence variants in duplicated genes using short-read whole-genome sequencing. From 335ef7818fdd8d10e2681c50b0f7bf49d9bb1643 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 Nov 2023 04:28:32 -0700 Subject: [PATCH 0682/2173] Update varlociraptor to 8.4.2 (#44184) --- recipes/varlociraptor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varlociraptor/meta.yaml b/recipes/varlociraptor/meta.yaml index f8e05d834e0b0..8fb5cf321e92c 100644 --- a/recipes/varlociraptor/meta.yaml +++ b/recipes/varlociraptor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.1" %} +{% set version = "8.4.2" %} package: name: varlociraptor @@ -11,7 +11,7 @@ build: source: url: https://github.com/varlociraptor/varlociraptor/archive/v{{ version }}.tar.gz - sha256: bbc5ef7eeb64cf578b0271d8a8319ed6f5bf9c178a08310f4394896205e92f95 + sha256: 41dd246d34e0e0d277681e9114bbc5bdfa95d0ef01b884be975a8f00bc3b492a requirements: build: From 06ab87a437b65c4e3a267798ef699473203d1803 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 Nov 2023 05:59:56 -0700 Subject: [PATCH 0683/2173] Update mehari to 0.16.0 (#44186) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index e3f56c7d2cc4e..f1c7743fafaa5 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.15.2" %} -{% set sha256 = "50e2c0fab299b94c5ca92ecf0ff726d56bcf69b4379a1dc2fdc58aa74a80d9b6" %} +{% set version = "0.16.0" %} +{% set sha256 = "bd2a67425ecc58f9adaf44a631bee90ef8a0eb1e36dec3f2f8e1ba21fd6acf89" %} package: name: mehari From 14010598c56b23e2a608a8d1fd2c742bfe86fae6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 Nov 2023 08:59:31 -0700 Subject: [PATCH 0684/2173] Update r-pipette to 0.15.0 (#44189) --- recipes/r-pipette/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-pipette/meta.yaml b/recipes/r-pipette/meta.yaml index 676e5fc893c6b..b88de4b723414 100644 --- a/recipes/r-pipette/meta.yaml +++ b/recipes/r-pipette/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.14.2" %} +{% set version = "0.15.0" %} {% set github = "https://github.com/acidgenomics/r-pipette" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 14f41aaed6afa3c0332282ca1a256774602ef7e12986afa82a09dd056ba4e5aa + sha256: 9948eb9d6cee54f4b72a6dd6bf2496816a9a0746cd73488c27ee360e9b33eb0b build: number: 0 From 1bc573038d7622bcb762be773fba73563e6d0472 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 Nov 2023 09:31:47 -0700 Subject: [PATCH 0685/2173] Update parascopy to 1.14.0 (#44190) --- recipes/parascopy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/parascopy/meta.yaml b/recipes/parascopy/meta.yaml index b086855ecc5cb..7a45a9c32060a 100644 --- a/recipes/parascopy/meta.yaml +++ b/recipes/parascopy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "parascopy" %} -{% set version = "1.13.9" %} +{% set version = "1.14.0" %} package: name: {{ name|lower }} @@ -15,7 +15,7 @@ build: source: url: https://github.com/tprodanov/{{ name }}/archive/v{{ version }}.tar.gz - sha256: d1f36bc37662e5eff8a49356f0c4710c6074708e4ae0b9d4c17c33e60ee232a3 + sha256: 2a1b9ec690f9686b437983af65bd43f8c2a1665ff710f76aae6bd2c78cf208ab requirements: build: From 20669fccef006c6217aa03981cc25dce536d039d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 Nov 2023 09:39:36 -0700 Subject: [PATCH 0686/2173] Update r-signac to 1.12.0 (#44163) --- recipes/r-signac/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-signac/meta.yaml b/recipes/r-signac/meta.yaml index 0427c385daf88..a3a41ca45a8f0 100644 --- a/recipes/r-signac/meta.yaml +++ b/recipes/r-signac/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.11.0' %} +{% set version = '1.12.0' %} package: name: r-signac @@ -8,7 +8,7 @@ source: url: - {{ cran_mirror }}/src/contrib/Signac_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/Signac/Signac_{{ version }}.tar.gz - sha256: 0daac539a4ca6d7f4c779fc06e77ffed4faca3e0689d3fb47d960edb4032f1c5 + sha256: 0a4f1e53bcb6c3ba1e3a8e0800d6c4e65983560ff1147a643b7109452374c937 build: number: 0 From 38337d05f536a037edd5fa5c8104dac7bb23f35d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 Nov 2023 09:48:14 -0700 Subject: [PATCH 0687/2173] Update ms-entropy to 1.0.4 (#44155) --- recipes/ms-entropy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms-entropy/meta.yaml b/recipes/ms-entropy/meta.yaml index ed54619e1658b..62fa5add4669a 100644 --- a/recipes/ms-entropy/meta.yaml +++ b/recipes/ms-entropy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms-entropy" %} -{% set version = "1.0.2" %} +{% set version = "1.0.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms_entropy-{{ version }}.tar.gz - sha256: 8780b4af0a19c2054b689095ebf99b0a6fc895dbad891b99703ea889088fbbaa + sha256: ccef60f5c6eba27bfe3734d6a22354232ea803368ac720cdc6e0e59ca631008b build: skip: true # [py<37] From 11b07e9d01f08eb962d57c22913da7dc9a01fc9a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 Nov 2023 09:48:47 -0700 Subject: [PATCH 0688/2173] Update dajin2 to 0.3.3 (#44153) --- recipes/dajin2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index 8d5e06cf489f9..29115833ac4b4 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "DAJIN2" %} -{% set version = "0.3.2" %} +{% set version = "0.3.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: 712a5d35244943ff1ddcb3ffb06bb41b1cd4ba4c0753ad12a7f79eaac244f088 + sha256: 1fe0f42e3dd79cf9e21f2c93706004c668440edd385ef112214fdfa8e9396a9f build: entry_points: From 2cc1439fe70aea346dd496d84df669cb0c759c18 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 Nov 2023 11:16:28 -0700 Subject: [PATCH 0689/2173] Update jbrowse2 to 2.8.0 (#44192) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 4a107ead1f045..862d582d90725 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.7.2" %} +{% set version = "2.8.0" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 8b43ea96d071a4dfa28458be20cc10b0e116fb7d5926565494f0e515cf09ba3a + sha256: 635c6003041251a33c2116bce4f0326e96a1c87b7995a0488a9f67b83ca71df8 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From 146c48719006758c20503ce005167162a0ce051f Mon Sep 17 00:00:00 2001 From: George Bouras <84495559+gbouras13@users.noreply.github.com> Date: Fri, 10 Nov 2023 04:47:21 +1030 Subject: [PATCH 0690/2173] correct plassembler dependencies (#44179) --- recipes/plassembler/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/plassembler/meta.yaml b/recipes/plassembler/meta.yaml index e10aca1a997f6..e7c18f6c2c70a 100644 --- a/recipes/plassembler/meta.yaml +++ b/recipes/plassembler/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 86167accca01b6e33ae4bff780c6ccbd8f208af41f605cbedc6c78272959f88a build: - number: 0 + number: 1 noarch: python entry_points: - plassembler = plassembler:main @@ -41,8 +41,8 @@ requirements: - biopython >=1.76 - alive-progress >=3.0.1 - requests >=2.25.1 - - canu - - dnaapler + - canu ==2.2 + - dnaapler >=0.4.0 test: imports: From 3364600197e8ed60f7357c0a8ede953b00b4acfc Mon Sep 17 00:00:00 2001 From: stuber Date: Thu, 9 Nov 2023 12:19:02 -0600 Subject: [PATCH 0691/2173] vsnp3 version 3.18 (#44178) Co-authored-by: Thanh Lee --- recipes/vsnp3/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/vsnp3/meta.yaml b/recipes/vsnp3/meta.yaml index c7f1f13a0f903..9fe286418fdbe 100644 --- a/recipes/vsnp3/meta.yaml +++ b/recipes/vsnp3/meta.yaml @@ -1,7 +1,7 @@ {% set user = "USDA-VS" %} {% set name = "vsnp3" %} -{% set version = "3.17" %} -{% set sha256 = "68f4dc521c57ba2418511d8649e9ed8698d93f096f2d9f76c50782ba66925625" %} +{% set version = "3.18" %} +{% set sha256 = "46c6d760d4e7ad6e437bbd1096cd9ae681a33c90c1be7c410439b0a1a0ba7769" %} package: name: {{ name|lower }} @@ -37,7 +37,7 @@ requirements: - regex >=2.5.110 - samtools >=1.14 - seqkit >=2.1.0 - - vcflib =1.0.9 + - vcflib =1.0.1 - vcftools =0.1.16 - sourmash >=4.2.4 - spades >=3.15.2 From 001d7ac79f30b759bd38864673ab62164a28c106 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 Nov 2023 11:29:31 -0700 Subject: [PATCH 0692/2173] Update flight-genome to 1.6.1 (#44181) --- recipes/flight-genome/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/flight-genome/meta.yaml b/recipes/flight-genome/meta.yaml index 2990b52651e74..f3c7dd35a939a 100644 --- a/recipes/flight-genome/meta.yaml +++ b/recipes/flight-genome/meta.yaml @@ -1,5 +1,5 @@ {% set name = "flight-genome" %} -{% set version = "1.6.0" %} +{% set version = "1.6.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c91a42b8164f46678bbc3a3d812de290c42898f1b38a544257afd5a829b60698 + sha256: 6bcd8e25ebbb5434050d31cdcc39062cb2f548020f853253569c70cdb0282503 build: number: 0 From 0d67eff7954159b9fcdc1d28996d567293a8369c Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Thu, 9 Nov 2023 18:48:58 +0000 Subject: [PATCH 0693/2173] Update SeqKit to 2.6.0 (#44191) * Update SeqKit to 2.6.0 * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/seqkit/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml index 28640fa95e85b..edc5173c6b1dc 100644 --- a/recipes/seqkit/meta.yaml +++ b/recipes/seqkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.1" %} +{% set version = "2.6.0" %} package: name: seqkit @@ -6,15 +6,16 @@ package: source: url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx] - md5: ace10918773a020528aa48cb3ed86b24 # [osx] + md5: 879359e899326e360e6109e39dd23ca4 # [osx] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux] - md5: b90ee92597254007b93b57980528b2b4 # [linux] + md5: 6fa9f5f405834bf54e34a3de280b260c # [linux] build: number: 0 skip: False - + run_exports: + - {{ pin_subpackage("seqkit", max_pin="x.x") }} test: commands: - seqkit version --help From 7a7aac311d1fac6e1ac4051a762c65a1f7c5a531 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 9 Nov 2023 21:28:34 +0100 Subject: [PATCH 0694/2173] Update r-monocle3 to 1.3.1 (#44138) * Update r-monocle3 to 1.3.1 * style: Fix linting * fix: Add v infront of version * Update dependencies * Fix max_pin https://github.com/bioconda/bioconda-recipes/pull/44138/files#r1388269344 Co-authored-by: thanhleviet --------- Co-authored-by: thanhleviet --- recipes/r-monocle3/meta.yaml | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/recipes/r-monocle3/meta.yaml b/recipes/r-monocle3/meta.yaml index 1614a1c1d9d71..f2d836c191569 100644 --- a/recipes/r-monocle3/meta.yaml +++ b/recipes/r-monocle3/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.0" %} +{% set version = "1.3.1" %} {% set github = "https://github.com/cole-trapnell-lab/monocle3" %} package: @@ -6,14 +6,16 @@ package: version: "{{ version }}" source: - url: "{{ github }}/archive/{{ version }}.tar.gz" - sha256: f09521a22b3584d000675e7ed659f2f41e823667bd019b38c52f6ab2ea654a00 + url: "{{ github }}/archive/v{{ version }}.tar.gz" + sha256: 30e86d5323ea22b302614813ecf102f26774b42710589671a1f1d51ef9ad183d build: - number: 5 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-monocle3', max_pin="x.x") }} requirements: build: @@ -28,18 +30,21 @@ requirements: - bioconductor-biocgenerics >=0.28 - bioconductor-delayedarray >=0.8 - bioconductor-delayedmatrixstats >=1.4 + - bioconductor-hdf5array - bioconductor-limma >=3.38.3 - bioconductor-s4vectors - bioconductor-summarizedexperiment >=1.11.5 - r-assertthat >=0.2.1 - r-dplyr >=0.8.0.1 - r-ggplot2 >=3.1.1 + - r-ggrastr - r-ggrepel >=0.8.1 - r-grr - r-htmlwidgets >=1.3 - r-igraph >=1.2.4 - r-irlba >=2.3.3 - r-leidenbase + - r-lme4 - r-lmtest >=0.9_36 - r-mass >=7.3_51.4 - r-matrix >=1.2_17 @@ -87,18 +92,21 @@ requirements: - bioconductor-biocgenerics >=0.28 - bioconductor-delayedarray >=0.8 - bioconductor-delayedmatrixstats >=1.4 + - bioconductor-hdf5array - bioconductor-limma >=3.38.3 - bioconductor-s4vectors - bioconductor-summarizedexperiment >=1.11.5 - r-assertthat >=0.2.1 - r-dplyr >=0.8.0.1 - r-ggplot2 >=3.1.1 + - r-ggrastr - r-ggrepel >=0.8.1 - r-grr - r-htmlwidgets >=1.3 - r-igraph >=1.2.4 - r-irlba >=2.3.3 - r-leidenbase + - r-lme4 - r-lmtest >=0.9_36 - r-mass >=7.3_51.4 - r-matrix >=1.2_17 From ccb238c3be76f70845c38810ef89798f8f2188a0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 Nov 2023 18:08:29 -0700 Subject: [PATCH 0695/2173] Update chopper to 0.7.0 (#44193) * Update chopper to 0.7.0 * Update meta.yaml adding run_exports --------- Co-authored-by: Wouter De Coster --- recipes/chopper/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/chopper/meta.yaml b/recipes/chopper/meta.yaml index 4132131c39dfa..d48214ed8d874 100644 --- a/recipes/chopper/meta.yaml +++ b/recipes/chopper/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.0" %} +{% set version = "0.7.0" %} package: name: chopper @@ -6,10 +6,12 @@ package: build: number: 0 + run_exports: + - {{ pin_subpackage('chopper', max_pin="x.x") }} source: url: https://github.com/wdecoster/chopper/archive/v{{ version }}.tar.gz - sha256: 5f327f6480a694afabaf23a6da75b347fcba126082a5b769cc4844c67d023491 + sha256: ff7e718084d16d4fa8ec40ede655d87dad5097e3e0f2d10cb278bcced02b586c requirements: build: From b40704e88c79da3a54bf60fdc76b751fab532bce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sinan=20U=C4=9Fur=20Umu?= Date: Fri, 10 Nov 2023 02:08:40 +0100 Subject: [PATCH 0696/2173] Update meta.yaml (#44185) * Update meta.yaml Hi, There are issues regarding the recent package update. I pinned some of the package versions. Thanks. Cheers, Sinan * Update meta.yaml --- recipes/cellsnake/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/cellsnake/meta.yaml b/recipes/cellsnake/meta.yaml index bf926aaacca29..ceafb17b3f864 100644 --- a/recipes/cellsnake/meta.yaml +++ b/recipes/cellsnake/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 2 entry_points: - cellsnake=cellsnake.command_line:main script: python -m pip install . -vv @@ -41,6 +41,8 @@ requirements: - python-kaleido - r-base ==4.2.2 - r-seurat ==4.3.0 + - r-seuratobject ==4.1.3 + - r-matrix <=1.5_4.1 - r-igraph ==1.3.4 - r-ggraph ==2.1.0 - r-clustree ==0.5.0 From bfe21d53947c69545c9e0905a4dc29ea78356073 Mon Sep 17 00:00:00 2001 From: Thom Griffioen Date: Fri, 10 Nov 2023 02:08:56 +0100 Subject: [PATCH 0697/2173] Update BLAST to 2.15.0 (#44183) * Update BLAST to 2.15.0 * Add SQLite3 compile-time dependency --- recipes/blast/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/blast/meta.yaml b/recipes/blast/meta.yaml index ee4070decd1e3..5706efbe329fb 100644 --- a/recipes/blast/meta.yaml +++ b/recipes/blast/meta.yaml @@ -1,6 +1,6 @@ {% set name = "blast" %} -{% set version = "2.14.1" %} -{% set sha256 = "712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e" %} +{% set version = "2.15.0" %} +{% set sha256 = "6918c370524c8d44e028bf491e8f245a895e07c66c77b261ce3b38d6058216e0" %} package: name: {{ name }} @@ -43,6 +43,7 @@ requirements: - entrez-direct - ncbi-vdb - curl + - sqlite =3 run: - zlib - bzip2 From 131605a096f3ad40d03703a773175891327c6147 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Thu, 9 Nov 2023 17:09:08 -0800 Subject: [PATCH 0698/2173] Update Augur dependencies for 23.1.1 (#44177) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Include dependency change for pyfastx¹ that was missed in the autobump PR² ¹ https://github.com/nextstrain/augur/commit/a7210930b6cbd617db3c16ff3bde4889762e2f96 ² https://github.com/bioconda/bioconda-recipes/pull/44150 --- recipes/augur/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index bc3674cd3735a..21d5c1cf2ebbe 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 1b6f8fb1f20c147d24806764761f8e977c8e100a58e04e06d3110bb72268518f build: - number: 0 + number: 1 noarch: python entry_points: - augur = augur.__main__:main @@ -33,11 +33,11 @@ requirements: - numpy >=1.0.0,<2 - packaging >=19.2 - pandas >=1.0.0,<2 - - pyfastx >=0.8.4,<0.9 + - pyfastx >=1.0.0,<3 - scipy >=1.0.0,<2 - treetime >=0.10.0,<0.12 - xopen[zstd] >=1.7.0,<2 - + - fasttree - iqtree - mafft From 56e288536c1b5c4bac0d2a29687629998e344328 Mon Sep 17 00:00:00 2001 From: Jessica Mattick <19544292+jmattick@users.noreply.github.com> Date: Thu, 9 Nov 2023 19:16:24 -0600 Subject: [PATCH 0699/2173] Update lima to v2.9.0 (#44195) Co-authored-by: Jessica Mattick --- recipes/lima/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/lima/meta.yaml b/recipes/lima/meta.yaml index 1f7c082142b4f..fd78fc100126b 100644 --- a/recipes/lima/meta.yaml +++ b/recipes/lima/meta.yaml @@ -1,5 +1,5 @@ {% set name = "lima" %} -{% set version = "2.7.1" %} +{% set version = "2.9.0" %} package: name: {{ name }} @@ -7,11 +7,13 @@ package: source: url: https://github.com/PacificBiosciences/barcoding/releases/download/v{{ version }}/lima.tar.gz - sha256: 388eb4746be3bf262e70c406f82519a8ef56e2a1891e9f2f3d7235ce04c23c7b + sha256: a13437bc7a90ab5df3c19eac44384de2a14370d0391586b5aa63a6478f9c2c53 build: number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('lima', max_pin='x.x') }} test: commands: From 2d4e3d0f1a73fb4b4653360e41b70ba59ad5432f Mon Sep 17 00:00:00 2001 From: Bede Constantinides Date: Fri, 10 Nov 2023 07:05:22 +0000 Subject: [PATCH 0700/2173] Update Hostile, pinning older bowtie2==2.4.5 (#44187) --- recipes/hostile/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/hostile/meta.yaml b/recipes/hostile/meta.yaml index 99f6769d0abb6..69b1aa9032cad 100644 --- a/recipes/hostile/meta.yaml +++ b/recipes/hostile/meta.yaml @@ -10,7 +10,9 @@ source: build: noarch: python - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('hostile', max_pin="x.x") }} entry_points: - hostile = hostile.cli:main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" @@ -21,7 +23,7 @@ requirements: - python >=3.10 - flit-core >=3.9.0 run: - - bowtie2 >=2.5.1 + - bowtie2 ==2.4.5 - defopt >=6.4.0 - gawk >=5.1.0 - httpx >=0.24.1 From 909f2065e9d7113d1c49281e275632407defa4f8 Mon Sep 17 00:00:00 2001 From: Ilya Flyamer Date: Fri, 10 Nov 2023 11:52:52 +0100 Subject: [PATCH 0701/2173] Update cooltools to 0.6.0 (#44161) * update recipe * add run_exports --- recipes/cooltools/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/cooltools/meta.yaml b/recipes/cooltools/meta.yaml index 3153df58c7360..ed36d3a9d6524 100644 --- a/recipes/cooltools/meta.yaml +++ b/recipes/cooltools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cooltools" %} -{% set version = "0.5.4" %} +{% set version = "0.6.0" %} package: name: "{{ name|lower }}" @@ -7,14 +7,16 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 24cd25a52c03f9f2473aa33dc6a4729f28856cc8812f3f4aa8f7e792877d9ef3 + sha256: ce970291b3b6b7d7abdd1c1fe374732491564866656e46e9a537cc7cf885a4a6 build: - number: 2 + number: 0 skip: True # [py <= 37] entry_points: - cooltools = cooltools.cli:cli script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('cooltools', max_pin="x.x") }} requirements: build: @@ -25,7 +27,7 @@ requirements: - python - numpy <1.24 run: - - bioframe >=0.3.3 + - bioframe >=0.4.1 - click >=7 - cooler >=0.9.1 - joblib From 29e36dc778bc4432b03eb270319ef39a9a41ede1 Mon Sep 17 00:00:00 2001 From: Ruben Vorderman Date: Fri, 10 Nov 2023 12:13:06 +0100 Subject: [PATCH 0702/2173] Add sequali recipe (#44199) --- recipes/sequali/meta.yaml | 55 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 recipes/sequali/meta.yaml diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml new file mode 100644 index 0000000000000..9d26f3ae111b8 --- /dev/null +++ b/recipes/sequali/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "sequali" %} +{% set version = "0.1.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: ed32729962b2f0631b7892ccfd783b86ab60fb2ab10d2045a42c353adb6eb679 + +build: + number: 0 + entry_points: + - sequali=sequali.__main__:main + - sequali-report=sequali.__main__:sequali_report + run_exports: + - {{ pin_subpackage('sequali', max_pin="x.x") }} + script: "{{ PYTHON }} -m pip install . -vv" + script_env: + - "CFLAGS=-mssse3" # [linux] + + +requirements: + build: + - "{{ compiler('c') }}" + - pip + host: + - python + run: + - pygal >=3.0.0 + - python + - tqdm + - xopen >=1.8.0 + +test: + imports: + - sequali + commands: + - sequali --help + - sequali-report --help + +about: + home: "https://github.com/rhpvorderman/sequali" + license: "GNU Affero General Public v3 or later (AGPLv3+)" + license_family: AGPL + license_file: LICENSE + summary: "Fast sequencing quality metrics" + doc_url: "https://github.com/rhpvorderman/sequali" + dev_url: "https://github.com/rhpvorderman/sequali" + +extra: + recipe-maintainers: + - rhpvorderman + From d89b58478b7a6c953827f8e4a79658f24f7ac2f0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 Nov 2023 04:44:45 -0700 Subject: [PATCH 0703/2173] Update assemblycomparator2 to 2.5.12 (#44197) * Update assemblycomparator2 to 2.5.11 * Update assemblycomparator2 to 2.5.12 --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index 4131a21c4050d..c10dfa3945b9e 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.9" %} +{% set version = "2.5.12" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3967e1f245cd7a4a4524bc3ec7e78dfe018c767ae4f57d678d20003cdd98ee2a + sha256: 96b28c2593878637b6587d5cd293b08ecef3260dc9dd332c8850851046ba0d9c build: From 852b7e186129af10bf1e2514d5be03e26ab9151d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 Nov 2023 04:45:15 -0700 Subject: [PATCH 0704/2173] Update mehari to 0.17.0 (#44201) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index f1c7743fafaa5..2d333b70b3999 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.16.0" %} -{% set sha256 = "bd2a67425ecc58f9adaf44a631bee90ef8a0eb1e36dec3f2f8e1ba21fd6acf89" %} +{% set version = "0.17.0" %} +{% set sha256 = "8d8514775d4ee3db726f32e346f7712c87effbbb6c975d6df27e81d2b08cf1f2" %} package: name: mehari From deefc53121fbb47f21936125a858e70d1201049d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 Nov 2023 08:11:14 -0700 Subject: [PATCH 0705/2173] Update oakvar to 2.9.57 (#44194) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index a1396c221aa56..ef18abc7fb403 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.56" %} -{% set sha256 = "fc46074f7deacf6809ba979fc97a5f65445558a43907800e9d5c15601911f31d" %} +{% set version = "2.9.57" %} +{% set sha256 = "af9d21a917da15f6bdbe218ee09eed8062e4b1615e3f890658ed7476036a5878" %} package: name: {{ name|lower }} From 67aa4b30df4fddd4ee5a12c60d71b6d45af2cee3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 Nov 2023 08:22:34 -0700 Subject: [PATCH 0706/2173] Update ena-webin-cli to 6.7.2 (#44204) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index f11c051dd940b..249da97616a98 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.7.1" %} -{% set sha256 = "f2c49ac1426ee804dec86cc062f071e695f4dfe7ad52234a20bc6495a4f387ec" %} +{% set version = "6.7.2" %} +{% set sha256 = "f45f9e54813711b6ea57130efae83a3381b2a3c66debd6d941fc1d9a85c69c6e" %} package: name: ena-webin-cli From 2f4d74b6315e6ee501c2e02235dcc68f4728ed60 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 Nov 2023 09:52:08 -0700 Subject: [PATCH 0707/2173] Update psims to 1.3.1 (#44156) --- recipes/psims/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psims/meta.yaml b/recipes/psims/meta.yaml index 38c81b54605da..b3012cb90ed31 100644 --- a/recipes/psims/meta.yaml +++ b/recipes/psims/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.3.0" %} -{% set sha256 = "0de9e1ae6b87177626f87639dc19555be7679bc6f5f29a7bdfff06e0b20f2b3e" %} +{% set version = "1.3.1" %} +{% set sha256 = "a6da07168737bdae3fdf0ee9e422be86990e004081c27027d50acecb3be8c248" %} package: name: "psims" From 7915598b8631c94affd41facf9de2cb84be8585c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 Nov 2023 09:52:17 -0700 Subject: [PATCH 0708/2173] Update gseapy to 1.1.0 (#44198) --- recipes/gseapy/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index d109a914827fd..b7e7775daa4ff 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -1,10 +1,10 @@ package: name: gseapy - version: "1.0.6" + version: "1.1.0" source: - url: https://files.pythonhosted.org/packages/9d/6e/02186263384ff5c50ff04957c3e5cd1f61ddb039457a8b7a7ae414b424dd/gseapy-1.0.6.tar.gz - sha256: 1e5faedd70ef9d3e9ca12d4b5d33f37b05e76c7e0c8c2c931514bfc2c47b6cab + url: https://files.pythonhosted.org/packages/6b/99/93b64bf596d9dee42cb338ffa557c0c2f327675c1f0e1148ff1115f76e35/gseapy-1.1.0.tar.gz + sha256: eba85ad99f55727bde7d1ac0172b29d5e07c8c879cdcbcc94c11df40a804ed8c build: entry_points: From 9473724be429ebfce1186e662841f6a9254463ae Mon Sep 17 00:00:00 2001 From: Alex Petty Date: Fri, 10 Nov 2023 10:53:43 -0600 Subject: [PATCH 0709/2173] Update r-saige to version 1.3.1 (#44065) * Update r-saige to version 1.3.1 * Add run_exports config. --- recipes/r-saige/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/r-saige/meta.yaml b/recipes/r-saige/meta.yaml index 36c6cb84a4a48..bfeb27810aad6 100644 --- a/recipes/r-saige/meta.yaml +++ b/recipes/r-saige/meta.yaml @@ -1,6 +1,6 @@ {% set name = "r-saige" %} -{% set version = "1.2.0" %} -{% set vcommit = "5fa0a2bda54656df1def789dd8c45ac513e3c21f" %} +{% set version = "1.3.1" %} +{% set vcommit = "92b6c6cd7f552d340cfc4b3b395574fbc598ee2e" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: source: url: https://github.com/saigegit/SAIGE/archive/{{ vcommit }}.tar.gz - sha256: da664896a14df5d09ccc45299e016f11b5a618132181e14edc885c58401fbf1d + sha256: c9d7da349c8eb3d6731ec8f7a989614f5d7a2e04f6ac058211cce8f4b0e60d3d patches: - patches/0001-use-shared-libs-in-makevars.patch @@ -17,6 +17,8 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-saige', max_pin="x") }} requirements: build: From 27459f72bef5ea1c76afe7a4488a596ddbd1203f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 Nov 2023 09:54:49 -0700 Subject: [PATCH 0710/2173] Update sirius-csifingerid to 5.8.5 (#44160) --- recipes/sirius-csifingerid/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sirius-csifingerid/meta.yaml b/recipes/sirius-csifingerid/meta.yaml index 09dbd0553ab9b..ef47cac572991 100644 --- a/recipes/sirius-csifingerid/meta.yaml +++ b/recipes/sirius-csifingerid/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "5.8.4" %} +{% set version = "5.8.5" %} {% set siriusDistDir = "sirius_gui_dist" %} package: @@ -15,7 +15,7 @@ build: source: - url: https://github.com/boecker-lab/sirius/archive/refs/tags/v{{ version }}.zip - sha256: 547abcafb297798b4fd4291889f1fbcf55b73f3fb97c95b2ec3a718eae0c5938 + sha256: 72bf7762f143740c6f2be06a268149e85787c97064586791348b8a27f9e9f5c8 requirements: build: From 9579cb356a3d68d6b76529b702977568afaf3b58 Mon Sep 17 00:00:00 2001 From: Stephan Schiffels Date: Fri, 10 Nov 2023 18:02:27 +0100 Subject: [PATCH 0711/2173] Update poseidon-xerxes to v1.0.0.2 (#44205) * Update poseidon-xerxes to v1.0.0.2 * updated checksums --- recipes/poseidon-xerxes/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/poseidon-xerxes/meta.yaml b/recipes/poseidon-xerxes/meta.yaml index 4f30fea73a4e9..f5211ec3ba3fa 100644 --- a/recipes/poseidon-xerxes/meta.yaml +++ b/recipes/poseidon-xerxes/meta.yaml @@ -1,13 +1,13 @@ -{% set version = "0.3.4.0" %} +{% set version = "1.0.0.2" %} package: name: poseidon-xerxes version: {{ version }} source: - - url: https://github.com/poseidon-framework/poseidon-analysis-hs/releases/download/v{{ version }}/xerxes-linux # [linux] - md5: 3e29ff53afbf436ec228052c8659383e # [linux] + - url: https://github.com/poseidon-framework/poseidon-analysis-hs/releases/download/v{{ version }}/xerxes-Linux # [linux] + md5: 4fd78ba70641fa521425cb2b8f30be0b # [linux] - url: https://github.com/poseidon-framework/poseidon-analysis-hs/releases/download/v{{ version }}/xerxes-macOS # [osx] - md5: 5271a2bf293724d896817e26877623fe # [osx] + md5: 44899bc8bd82d9cb81903de9b3bbb914 # [osx] build: number: 0 From c0c0961df68deb3f01e7a36cd83dee398e834c09 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 Nov 2023 10:02:42 -0700 Subject: [PATCH 0712/2173] Update pymlst to 2.1.5 (#44202) * Update pymlst to 2.1.5 * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/pymlst/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/pymlst/meta.yaml b/recipes/pymlst/meta.yaml index 986f1018ac122..e4ecec72d61bb 100644 --- a/recipes/pymlst/meta.yaml +++ b/recipes/pymlst/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pymlst" %} -{% set version = "2.1.4" %} +{% set version = "2.1.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/bvalot/pyMLST/archive/refs/tags/{{ version }}.tar.gz" - sha256: 4d165390f2c1b9eb3f0053a57f81d68f78c9fe756797daf0ac321c2a68e4c36b + sha256: 505a0a0e79645f385e13e33e8ecd054fa436cb60e6bbec6f25a513e21903faf6 build: noarch: python @@ -17,6 +17,8 @@ build: - wgmlst=pymlst.cmd:wg - clamlst=pymlst.cmd:cla script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: From cd491166ab54a119fe91aa4c964cb108cffd42ab Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 Nov 2023 10:48:21 -0700 Subject: [PATCH 0713/2173] Update hostile to 0.2.0 (#44206) --- recipes/hostile/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hostile/meta.yaml b/recipes/hostile/meta.yaml index 69b1aa9032cad..46a00d25e040e 100644 --- a/recipes/hostile/meta.yaml +++ b/recipes/hostile/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.0" %} +{% set version = "0.2.0" %} package: name: hostile @@ -6,11 +6,11 @@ package: source: url: https://pypi.io/packages/source/h/hostile/hostile-{{ version }}.tar.gz - sha256: 8fe1471c9aca5143a78162bb846b099a73071a74d37c133377a7eeba45494354 + sha256: 4edda5ad96a3f9feb0663e8b447299f4f57ab706ac2375946c5b4b314117e323 build: noarch: python - number: 1 + number: 0 run_exports: - {{ pin_subpackage('hostile', max_pin="x.x") }} entry_points: From 7367d63805360631d56fe18e43e9098585c463ab Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 Nov 2023 13:41:32 -0700 Subject: [PATCH 0714/2173] Update r-acidbase to 0.7.2 (#44217) --- recipes/r-acidbase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidbase/meta.yaml b/recipes/r-acidbase/meta.yaml index c37758af63053..5f697c4f9d056 100644 --- a/recipes/r-acidbase/meta.yaml +++ b/recipes/r-acidbase/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.1" %} +{% set version = "0.7.2" %} {% set github = "https://github.com/acidgenomics/r-acidbase" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 2237473f0b4577fd74266017940aeb0eb305812ba145ae7c56f1f821ebe10854 + sha256: 0e599ea7bcb5bc2f36f5f1a5a88f4b69c25120210ea69a48e92005d6ec2cd194 build: number: 0 From 01443729b4f19215ac97086be2541ea202f3f4a4 Mon Sep 17 00:00:00 2001 From: Patrick Blumenkamp Date: Sat, 11 Nov 2023 21:26:18 +0100 Subject: [PATCH 0715/2173] Update Curare to 0.5.0 (#44211) * update Curare to 0.5.0 * add spaces between package and version * add run_exports * add name in run_exports * add remove quotes around name * fix indentation * fix broken version number * remove spaces after = * define name globaly --------- Co-authored-by: Patrick Blumenkamp --- recipes/curare/meta.yaml | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/recipes/curare/meta.yaml b/recipes/curare/meta.yaml index c579d13c1e9f4..83dc705fef548 100644 --- a/recipes/curare/meta.yaml +++ b/recipes/curare/meta.yaml @@ -1,12 +1,13 @@ -{% set version = "0.4.5" %} +{% set name = "curare" %} +{% set version = "0.5.0" %} package: - name: curare + name: {{ name|lower }} version: {{ version }} source: url: https://github.com/pblumenkamp/Curare/archive/refs/tags/{{ version }}.tar.gz - sha256: 12049b34ed918b6a202307d45d281037073066b664a9eb41cf301f4618f4c84d + sha256: 13e5e209ad8158af3f7448c9a610fa2a64c201ec540e199373dc32e4f2a5ef1e build: number: 0 @@ -15,17 +16,19 @@ build: entry_points: - curare = curare.curare:main - curare_wizard = curare.curare_wizard:main + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: - - python >=3.9 + - python >=3.10 - pip run: - - snakemake=6.3 - - mamba=0.13 - - python=3.9 - - pyyaml=5.4.1 - - docopt=0.6.2 + - snakemake =7.32.3 + - mamba =1.5.3 + - python =3.10 + - pyyaml =6.0 + - docopt =0.6.2 test: imports: From aac8ba2a9338b5163af5b00df95508c5048c6fb8 Mon Sep 17 00:00:00 2001 From: Christiam Camacho Date: Sat, 11 Nov 2023 15:28:27 -0500 Subject: [PATCH 0716/2173] Update BLAST: add blastdb integrity check (#44212) * Add BLASTDB integrity check * Bump build number --- recipes/blast/meta.yaml | 2 +- recipes/blast/run_test.sh | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/recipes/blast/meta.yaml b/recipes/blast/meta.yaml index 5706efbe329fb..ac83310298c71 100644 --- a/recipes/blast/meta.yaml +++ b/recipes/blast/meta.yaml @@ -25,7 +25,7 @@ source: - normbase.patch build: - number: 0 + number: 1 run_exports: # Now, the point releases seem to be only bugfixes at least (but this definitely was not the # case up to v2.2.31) diff --git a/recipes/blast/run_test.sh b/recipes/blast/run_test.sh index 87432da8d0e85..e6f7a883f83e2 100755 --- a/recipes/blast/run_test.sh +++ b/recipes/blast/run_test.sh @@ -15,6 +15,11 @@ makeblastdb \ grep -q "added 3 sequences" echo PASS +echo -n 'Checking Database integrity... ' +blastdbcheck -full -dbtype nucl -db testdb | \ + grep -q "Result=SUCCESS" +echo PASS + echo -n 'Checking database version... ' blastdbcmd -info -db testdb -dbtype nucl | \ awk '/^BLASTDB Version/ {print $NF}' | \ From 96f01647057f99a76adc023475debf3649825227 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 11 Nov 2023 14:54:27 -0700 Subject: [PATCH 0717/2173] Update cooltools to 0.6.1 (#44203) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cooltools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cooltools/meta.yaml b/recipes/cooltools/meta.yaml index ed36d3a9d6524..13642309de7a2 100644 --- a/recipes/cooltools/meta.yaml +++ b/recipes/cooltools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cooltools" %} -{% set version = "0.6.0" %} +{% set version = "0.6.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: ce970291b3b6b7d7abdd1c1fe374732491564866656e46e9a537cc7cf885a4a6 + sha256: 1082186215c1215b1f1192b1c5dd2d103e0db6df3dca3a9e49ec15676f5c0adb build: number: 0 From 6ae69f161a06f91349391c0a6ffb178210d1e3a4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 11 Nov 2023 14:54:46 -0700 Subject: [PATCH 0718/2173] Update bohra to 2.3.3 (#44219) * Update bohra to 2.3.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/bohra/meta.yaml | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/recipes/bohra/meta.yaml b/recipes/bohra/meta.yaml index d1f8c10003049..a92628eea241e 100644 --- a/recipes/bohra/meta.yaml +++ b/recipes/bohra/meta.yaml @@ -1,6 +1,6 @@ {% set name = "bohra" %} -{% set version = "2.3.2" %} -{% set sha256 = "fcdcf59186493bf6f1272d717c7f0ed65fcf453b6461621d555eb5ad19558969" %} +{% set version = "2.3.3" %} +{% set sha256 = "8bb50d196057f2ab024a89dd2c025fd86603f5f165375c5fb20b6ae687f81637" %} package: name: "{{ name }}" @@ -15,7 +15,9 @@ build: number: 0 entry_points: - bohra=bohra.bohra:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('bohra', max_pin="x") }} requirements: host: @@ -23,6 +25,7 @@ requirements: - pip run: - python >=3.8 + - altair - biopython 1.81 - nextflow 22.10.6 - pandas 1.0.5 @@ -38,7 +41,7 @@ requirements: - perl-list-moreutils - perl-text-csv - perl-svg - + test: imports: - bohra @@ -48,10 +51,11 @@ test: about: home: "https://github.com/MDU-PHL/bohra" - license: "GNU General Public v3 (GPLv3)" + license: "GPL-3.0-or-later" license_family: "GPL3" license_file: "LICENSE.txt" summary: "Pipeline for analysing Illumina data for microbiological public health." + doc_url: "https://github.com/MDU-PHL/bohra/wiki" extra: recipe-maintainers: From 8c3411e1bf5c9b0fdffa3b347ee54a8c98748db7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 11 Nov 2023 14:55:05 -0700 Subject: [PATCH 0719/2173] Update fit_nbinom to 1.2 (#44222) * Update fit_nbinom to 1.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fit_nbinom/meta.yaml | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/recipes/fit_nbinom/meta.yaml b/recipes/fit_nbinom/meta.yaml index 9d12df1cc1da9..b4b3bd5093c28 100644 --- a/recipes/fit_nbinom/meta.yaml +++ b/recipes/fit_nbinom/meta.yaml @@ -1,24 +1,27 @@ -{% set version = "1.1" %} +{% set version = "1.2" %} + package: name: fit_nbinom version: '{{ version }}' source: url: 'https://github.com/joachimwolff/fit_nbinom/archive/{{ version }}.tar.gz' - sha256: d2a0c5e931152dfa32fee6a4d19aa8a24677c485d76f80c9ab0f15c18c8e5226 + sha256: ec4494292fb1282b3ed90afb1732cb5a81b9ea5f373b98fce006d978f556d1f8 build: - number: 2 - script: "python -m pip install --no-deps --ignore-installed ." + number: 0 + script: "{{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv" noarch: python + run_exports: + - {{ pin_subpackage('fit_nbinom', max_pin="x") }} requirements: host: - python run: - python - - numpy >=1.15 - - scipy >=1.2 + - numpy >=1.19 + - scipy >=1.10 test: imports: @@ -26,7 +29,9 @@ test: about: home: https://github.com/joachimwolff/fit_nbinom/ - license: GPL3 + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE summary: Script to fit negative binomial distributions via maximum likelihood estimation. From 05a26561c167aa60c00bfebbe36285e7c2737609 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 11 Nov 2023 15:30:14 -0700 Subject: [PATCH 0720/2173] Update scirpy to 0.14.0 (#44223) * Update scirpy to 0.14.0 * add run_exports * add license --------- Co-authored-by: joshuazhuang7 --- recipes/scirpy/LICENSE | 32 ++++++++++++++++++++++++++++++++ recipes/scirpy/meta.yaml | 22 ++++++++++++---------- 2 files changed, 44 insertions(+), 10 deletions(-) create mode 100644 recipes/scirpy/LICENSE diff --git a/recipes/scirpy/LICENSE b/recipes/scirpy/LICENSE new file mode 100644 index 0000000000000..ac2561aeab97c --- /dev/null +++ b/recipes/scirpy/LICENSE @@ -0,0 +1,32 @@ +BSD 3-Clause License + +Copyright (c) 2020 Gregor Sturm +Copyright (c) 2020 Tamas Szabo +Copyright (c) 2020 Francesca Finotello +Copyright (c) 2020 Institute of Bioinformatics, Medical University of Innsbruck +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/recipes/scirpy/meta.yaml b/recipes/scirpy/meta.yaml index 829194e9fdb3b..1d42f7a62616a 100644 --- a/recipes/scirpy/meta.yaml +++ b/recipes/scirpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "scirpy" %} -{% set version = "0.13.1" %} +{% set version = "0.14.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7d938e765acc767596f4a0f0ade29930ba21465e6afcbdc1207505949458c796 + sha256: 26a5a5374503925c1db16595ef67b1814a6389a4932edc2aa48607a47a00bf43 folder: "{{ name }}-{{ version }}" build: @@ -15,14 +15,15 @@ build: noarch: python script: - cd "{{ name }}-{{ version }}" - - "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + - "{{ PYTHON }} -m pip install . --no-build-isolation --no-deps -vvv" + run_exports: + - {{ pin_subpackage('scirpy', max_pin="x.x") }} requirements: host: - python >=3.9 - hatchling - hatch-vcs - run: - python >=3.9 - anndata >=0.9 @@ -43,7 +44,7 @@ requirements: - adjusttext >=0.7 - numba >=0.41.0 - pooch >=1.7.0 - + - pycairo >=1.20 # [win] test: imports: @@ -52,14 +53,15 @@ test: - pytest about: - home: https://icbi-lab.github.io/scirpy - dev_url: https://github.com/icbi-lab/scirpy - license: BSD-3 + home: https://scirpy.scverse.org/en/latest/ + dev_url: https://github.com/icbi-lab/scirpy + license: BSD-3-Clause license_family: BSD - summary: A Scanpy extension for analyzing single-cell T-cell and B-cell receptor (TCR/BCR) sequencing data. + license_file: LICENSE + summary: A Scanpy extension for analyzing single-cell T-cell and B-cell receptor (TCR/BCR) sequencing data. extra: recipe-maintainers: - grst identifiers: - - doi:10.1101/2020.04.10.035865 + - doi:10.1101/2020.04.10.035865 From 3074a2a4f8aedf827581f7a5fa2310f70efe92f1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 12 Nov 2023 04:07:59 -0700 Subject: [PATCH 0721/2173] Update perl-minion to 10.26 (#44208) --- recipes/perl-minion/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-minion/meta.yaml b/recipes/perl-minion/meta.yaml index 1ec373df99d8b..c492b93ae8a94 100644 --- a/recipes/perl-minion/meta.yaml +++ b/recipes/perl-minion/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-minion" %} -{% set version = "10.25" %} -{% set sha256 = "0be0a8375376889da04604696384c0cf98b2621d2650d9eb0307f6e4b940adad" %} +{% set version = "10.26" %} +{% set sha256 = "00c57a3ab909f29fc8c577eb05b7bcede2961e6727275b62acab74940d0cc3a0" %} package: name: {{ name }} From ea97ae9a79fa857e6df406cbfd6e3206f4858a40 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 12 Nov 2023 04:08:15 -0700 Subject: [PATCH 0722/2173] Update vsearch to 2.25.0 (#44213) --- recipes/vsearch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index 43c39d7f1c2a9..227abadd8cca4 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.24.0" %} -{% set sha256 = "036c3a5c7827958446e56155d750d22d03d460a53237c37fa6541208dc0bdca1" %} +{% set version = "2.25.0" %} +{% set sha256 = "b7e25638924e56591d7c6ac3a959795000439937f5b566be7f06457bb31f91a9" %} package: name: vsearch From 5027e1db8550fee82b795b37380a1fdaab951dff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 12 Nov 2023 04:11:52 -0700 Subject: [PATCH 0723/2173] Update seqscreen to 4.3 (#44218) * Update seqscreen to 4.3 * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/seqscreen/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/seqscreen/meta.yaml b/recipes/seqscreen/meta.yaml index 4633ef222e344..9c8cbdf6eb2a8 100644 --- a/recipes/seqscreen/meta.yaml +++ b/recipes/seqscreen/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.2" %} +{% set version = "4.3" %} package: name: seqscreen @@ -6,12 +6,13 @@ package: source: url: 'https://gitlab.com/treangenlab/seqscreen/-/archive/v{{version}}/seqscreen-v{{version}}.tar.gz' - sha256: 16bd9f647360449e1d50fad938a1958b4dae7429a373afca531a3b64178e2659 + sha256: c859657e965e9898bec702c7c1c4624478cbe640219c21a0139af9dd137c5d3a build: noarch: generic number: 0 - + run_exports: + - {{ pin_subpackage("seqscreen", max_pin="x.x") }} requirements: run: - scipy From e2690c000643956f5496d1bdc55e334b301248d3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 12 Nov 2023 04:13:45 -0700 Subject: [PATCH 0724/2173] Update omamer to 2.0.2 (#44216) --- recipes/omamer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/omamer/meta.yaml b/recipes/omamer/meta.yaml index ff8007093ef01..d7a0f90833459 100644 --- a/recipes/omamer/meta.yaml +++ b/recipes/omamer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "omamer" %} -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/omamer-{{ version }}.tar.gz - sha256: 749ccd0f3f1dad48b00651c7298f8e83c08e1bceef288ff53068dd8abda705f5 + sha256: 2cd75d7771333c9a611b274285eb662c19ea50c38a2ae0a2748a3b821be67dae build: entry_points: From cfa8163b6774a1f716f4ea0a7cdef49e4d9a2363 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 12 Nov 2023 04:13:56 -0700 Subject: [PATCH 0725/2173] Update oakvar to 2.9.58 (#44214) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index ef18abc7fb403..70cc2f1379a14 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.57" %} -{% set sha256 = "af9d21a917da15f6bdbe218ee09eed8062e4b1615e3f890658ed7476036a5878" %} +{% set version = "2.9.58" %} +{% set sha256 = "b616699f6fd3d9f57e9e01eaca17ffb6e38c6cb9f324b2beff97fb3332541239" %} package: name: {{ name|lower }} From 7a5fc1bad78c7f5baf1391df60812d2d7b8c134f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20P=C5=99=C3=ADhoda?= Date: Sun, 12 Nov 2023 12:14:18 +0100 Subject: [PATCH 0726/2173] Bump deepbgc to 0.1.31 (#44220) * Bump deepbgc to 0.1.31 * Use build number 0 * Add run_exports --- recipes/deepbgc/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/deepbgc/meta.yaml b/recipes/deepbgc/meta.yaml index 16f1f936817d3..e2fc7ea4a628a 100644 --- a/recipes/deepbgc/meta.yaml +++ b/recipes/deepbgc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "deepbgc" %} -{% set version = "0.1.30" %} # remember to update sha256 hash as well +{% set version = "0.1.31" %} # remember to update sha256 hash as well {% set file_ext = "tar.gz" %} package: @@ -8,14 +8,16 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.{{ file_ext }} - sha256: '676d03171087d7ca6187be304dae4e4aaabcdd33ee5b88363a33f28c7a8bd602' + sha256: 'f294736ca63790a0429a2802457774da9c07e0b42dee8b2963f42f77ccb06255' build: noarch: python - number: 2 + number: 0 entry_points: - deepbgc = deepbgc.main:main script: python setup.py install --single-version-externally-managed --record=record.txt + run_exports: + - {{ pin_subpackage('deepbgc', max_pin="x.x") }} requirements: host: From d4ff1a8b7fe1abc218f59de822035aac466ee668 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 12 Nov 2023 17:37:44 -0700 Subject: [PATCH 0727/2173] Update capcruncher to 0.3.8 (#44229) --- recipes/capcruncher/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/capcruncher/meta.yaml b/recipes/capcruncher/meta.yaml index 8bda4d9f2f501..e1b742d58f4fa 100644 --- a/recipes/capcruncher/meta.yaml +++ b/recipes/capcruncher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "capcruncher" %} -{% set version = "0.3.7" %} +{% set version = "0.3.8" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/capcruncher-{{ version }}.tar.gz - sha256: 70d5a4f70ba165681c605de66562020ae65de6c3546d4b4534edf7bc1ab8cb2c + sha256: 6124d6e7ff0ff269b434c1cd38bbc6e7bf69ff737024aa411f58d1ce5384d2e7 build: number: 0 From 5a0f167e3c03d6a9ab847e92dabfc729c3b37e57 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 13 Nov 2023 04:02:43 -0700 Subject: [PATCH 0728/2173] Update gimbleprep to 0.0.2b5 (#44236) --- recipes/gimbleprep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gimbleprep/meta.yaml b/recipes/gimbleprep/meta.yaml index 426d7e1e5a82a..dc28547728e74 100644 --- a/recipes/gimbleprep/meta.yaml +++ b/recipes/gimbleprep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gimbleprep" %} -{% set version = "0.0.2b4" %} +{% set version = "0.0.2b5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/LohseLab/gimbleprep/archive/refs/tags/v{{ version }}.tar.gz - sha256: 4b67ae856ab99450d6720a8e30bbbc418f024c73476ae130da2b9dcc8aee3c62 + sha256: 6b9f893ba61fbd27577f87b561b7e2dad609589edfa62e63b6d2517b468bd953 build: noarch: python From ef2314323e816a99933370e35be3fc22b46b524e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 13 Nov 2023 04:03:23 -0700 Subject: [PATCH 0729/2173] Update singlem to 0.15.1 (#44233) --- recipes/singlem/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/singlem/meta.yaml b/recipes/singlem/meta.yaml index 66ff4e4fb31c6..b7d0b36334738 100644 --- a/recipes/singlem/meta.yaml +++ b/recipes/singlem/meta.yaml @@ -1,5 +1,5 @@ {% set name = "singlem" %} -{% set version = "0.15.0" %} +{% set version = "0.15.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: c13d17bcb2df0e840a8b0cf136e1433f231d8df43c519dc8a6b4a86d7e496464 + sha256: 98a84252e22460aebdeee6e43e21f157a56158e312b780a1be9fc8a41ee7ac32 build: number: 0 From 67a3b7bf2d450f56463a917400a711cb3d39a736 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 13 Nov 2023 04:06:25 -0700 Subject: [PATCH 0730/2173] Update bohra to 2.3.4 (#44232) --- recipes/bohra/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bohra/meta.yaml b/recipes/bohra/meta.yaml index a92628eea241e..89ab861961742 100644 --- a/recipes/bohra/meta.yaml +++ b/recipes/bohra/meta.yaml @@ -1,6 +1,6 @@ {% set name = "bohra" %} -{% set version = "2.3.3" %} -{% set sha256 = "8bb50d196057f2ab024a89dd2c025fd86603f5f165375c5fb20b6ae687f81637" %} +{% set version = "2.3.4" %} +{% set sha256 = "d68a4815c0ae63012029dd3745517b4b831c2e9150b45a0a4acf10ddfb85b7ee" %} package: name: "{{ name }}" From f70b47bf49f66e42e6443a79a8ffa26df060bd05 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 13 Nov 2023 05:54:29 -0700 Subject: [PATCH 0731/2173] Update earlgrey to 3.2.1 (#44237) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index 187a257bbae45..c3b27765175c5 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "3.2" %} -{% set sha256 = "2a6423bcc267fc6c4287d7b8e29484ba216a305d6c3aa9d994d474962a64abca" %} +{% set version = "3.2.1" %} +{% set sha256 = "38c4a85276164b3efc1b59fb2f6580357dc697d54b3b4649b29b200c6141dc69" %} package: name: {{ name|lower }} From f3bc65adb4ee43c2aed0de86f5aa7f8a669df71f Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Mon, 13 Nov 2023 11:43:06 -0500 Subject: [PATCH 0732/2173] Add annembed v0.1.1 (#44230) * Add annembed v0.1.1 * Add annembed v0.1.1 --- recipes/annembed/build.sh | 8 ++++++++ recipes/annembed/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 recipes/annembed/build.sh create mode 100644 recipes/annembed/meta.yaml diff --git a/recipes/annembed/build.sh b/recipes/annembed/build.sh new file mode 100644 index 0000000000000..f4634f476014f --- /dev/null +++ b/recipes/annembed/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --features intel-mkl-static --verbose --path . --root $PREFIX diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml new file mode 100644 index 0000000000000..c1a1ff1c642b6 --- /dev/null +++ b/recipes/annembed/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "0.1.1" %} + +package: + name: annembed + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('annembed', max_pin="x.x") }} + skip: True # [osx] +source: + url: https://github.com/jianshu93/annembed/archive/v{{ version }}.tar.gz + sha256: 7d428dd4ac630de7f6ab75e74f7261f1017eae77065f4e678ddde62771253da4 + +requirements: + build: + - {{ compiler("cxx") }} + - {{ compiler('c') }} + - rust >=1.39 + - make + - cmake + +test: + commands: + - annembed -h + +about: + home: https://github.com/jean-pierreBoth/gsearch + license: MIT + summary: annembed is an ultra-fast and scalable non-linear dimension reduction algorithm (similar to UMAP or t-SNE) for large-scale biological data + +extra: + maintainers: + - Jean Pierre-Both + - Jianshu Zhao From dbab9019c7f361e2972d2b12113a83c6b435268a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 13 Nov 2023 11:50:10 -0700 Subject: [PATCH 0733/2173] Update perl-math-bigint to 2.001000 (#44243) --- recipes/perl-math-bigint/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-math-bigint/meta.yaml b/recipes/perl-math-bigint/meta.yaml index 215290cbdcac4..fa0887c33e784 100644 --- a/recipes/perl-math-bigint/meta.yaml +++ b/recipes/perl-math-bigint/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-math-bigint" %} -{% set version = "2.000000" %} -{% set sha256 = "7d111a47431294db99cd130ff8586e88f0e9b64b4e7fb3bb3e15dec5fd14f1c7" %} +{% set version = "2.001000" %} +{% set sha256 = "0a1cf05d85282be4019f93a947bd8b820c7d11a91ffde560eaed31dddf4ba622" %} package: name: {{ name }} From 12611e7746e6c5dcaca3eb1627150fbe04743501 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 13 Nov 2023 11:53:18 -0700 Subject: [PATCH 0734/2173] Update last to 1513 (#44234) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index c8c8a65658219..d7a542b9ae271 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1512" %} +{% set version = "1513" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: ed367c7eb8403a41ec43386e1c401d9dba9d7967427d24db3d95ed1919c6783e + sha256: 596d364fa87ba61555645cdaa2dcbe5f2babd38aad0aeb4dfa305a69caf40a07 build: number: 0 From f3f571651b59931652b988ed1ed5efa79620d277 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Mon, 13 Nov 2023 20:47:32 +0100 Subject: [PATCH 0735/2173] New recipe: bedgovcf (#44239) * add bedgovcf * fix for osx? --- recipes/bedgovcf/build.sh | 4 ++++ recipes/bedgovcf/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 recipes/bedgovcf/build.sh create mode 100644 recipes/bedgovcf/meta.yaml diff --git a/recipes/bedgovcf/build.sh b/recipes/bedgovcf/build.sh new file mode 100644 index 0000000000000..c5c869f01eb7d --- /dev/null +++ b/recipes/bedgovcf/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +chmod a+x bedgovcf* +mkdir -p $PREFIX/bin +cp bedgovcf* $PREFIX/bin/bedgovcf \ No newline at end of file diff --git a/recipes/bedgovcf/meta.yaml b/recipes/bedgovcf/meta.yaml new file mode 100644 index 0000000000000..8fd41cd2aadef --- /dev/null +++ b/recipes/bedgovcf/meta.yaml @@ -0,0 +1,36 @@ +{% set version = '0.1.0' %} +{% set name = 'bedgovcf' %} + +package: + name: {{ name }} + version: {{ version }} + +source: + - url: https://github.com/nvnieuwk/bedgovcf/releases/download/{{ version }}/bedgovcf-{{ version }}-darwin-amd64.tar.gz # [osx-amd64] + md5: 9e57370c3b7eced5da92cd11dc1984e5 # [osx] + - url: https://github.com/nvnieuwk/bedgovcf/releases/download/{{ version }}/bedgovcf-{{ version }}-linux-amd64.tar.gz # [linux] + md5: bbe8e249c655a276657c6602524f7e39 # [linux] + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + run: + - tabix + +test: + commands: + - "{{ name }} --help" + - bgzip -h + +extra: + skip-lints: + - should_be_noarch_generic # uses per platform binaries + - should_not_be_noarch_source # uses binaries + +about: + home: https://github.com/nvnieuwk/bedgovcf + license: MIT + summary: A simple tool to convert BED files to VCF files From b67fedae5bbdc6365a961110d25be6167bfd570f Mon Sep 17 00:00:00 2001 From: Michael Uhl Date: Mon, 13 Nov 2023 22:05:04 +0100 Subject: [PATCH 0736/2173] Rbpbench v04 (#44227) * add rbpbench meta yaml * add run exports * update recipe to rbpbench v04 * rerun tests * rerun tests * Restrict python to <3.12 * Restrict python to <=3.11 in host and run * Update meta.yaml --- recipes/rbpbench/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/rbpbench/meta.yaml b/recipes/rbpbench/meta.yaml index 986258197fc9b..bcd1e1886d7ed 100644 --- a/recipes/rbpbench/meta.yaml +++ b/recipes/rbpbench/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RBPBench" %} -{% set version = "0.3" %} -{% set sha256 = "b119b8cfd8a81d4db8af4c66c60b7b482bb7476bafd3a4206bf8b01f280e3f10" %} +{% set version = "0.4" %} +{% set sha256 = "c5fc49bd3801e68170ca624edfc5ab3041d17a5d1814958178ece6e5066aa7b7" %} package: name: {{ name|lower }} @@ -19,9 +19,10 @@ build: requirements: host: - - python + - python <3.12 - pip run: + - python <3.12 - logomaker - markdown - meme From bd9663e60217c5cbd91ca7d405fdeccfaff7b5a6 Mon Sep 17 00:00:00 2001 From: Dirk-Jan <72025902+dirkjanvw@users.noreply.github.com> Date: Tue, 14 Nov 2023 06:32:13 +0100 Subject: [PATCH 0737/2173] Update FastANI (#44241) --- recipes/fastani/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/fastani/meta.yaml b/recipes/fastani/meta.yaml index 976936ec9f8b7..c24fad941222f 100644 --- a/recipes/fastani/meta.yaml +++ b/recipes/fastani/meta.yaml @@ -7,7 +7,9 @@ package: version: {{ version }} build: - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('fastani', max_pin="x") }} source: url: https://github.com/ParBLiSS/{{ name }}/archive/v{{ version }}.tar.gz @@ -22,14 +24,15 @@ requirements: host: - zlib - gsl >=2.6, <2.7.1 - - openmp + - openmp # [linux] + - llvm-openmp # [osx] - clangdev # [osx] - libcxx >=4.0 # [osx] run: - zlib - gsl - libcxx >=4.0 # [osx] - - openmp >=4.0 # [osx] + - llvm-openmp >=4.0 # [osx] test: commands: From e23cc34d9cfae2d7bd58eeedc79754e7a51a5923 Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Mon, 13 Nov 2023 23:34:21 -0600 Subject: [PATCH 0738/2173] Update megalodon version (#44240) --- recipes/megalodon/meta.yaml | 28 ++++++++++++++++------------ 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/recipes/megalodon/meta.yaml b/recipes/megalodon/meta.yaml index de3fb1f4ee6e7..9056a14a6a404 100644 --- a/recipes/megalodon/meta.yaml +++ b/recipes/megalodon/meta.yaml @@ -1,55 +1,58 @@ {% set name = "megalodon" %} -{% set version = "2.4.1" %} -{% set hash = "c67de21120407258019498cd704892573f687576edbb3d4d4c5bb4b48aa56e7c" %} +{% set version = "2.5.0" %} +{% set sha256 = "60ad1f1191b86d9a1423dcb9c934c7577cf1ce083689337646937be2538953a3" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/nanoporetech/megalodon/archive/{{ version }}.tar.gz - sha256: {{ hash }} + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/megalodon-{{ version }}.tar.gz + sha256: {{ sha256 }} build: - number: 2 + skip: true # [py2k or py < 36] entry_points: - megalodon = megalodon.__main__:_main - megalodon_extras = megalodon_extras.__main__:_main - skip: True # [py2k or py == 39] - script: "{{ PYTHON }} -m pip install . -vv" + script: {{ PYTHON }} -m pip install . --no-deps -vv + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: - {{ compiler('c') }} host: - - cython - python + - setuptools >=38.3 + - cython >=0.25.2,<3 + - pyscaffold >=3.2a0,<3.3a0 - pip - numpy >=1.9.0 - - setuptools # [osx] run: - python - - setuptools - h5py >=2.2.1 - numpy >=1.9.0 - scipy >=1.1.0 - mappy >=2.16 - pysam >=0.15 - ont-fast5-api >=3.2 - - tqdm + - tqdm >=2.17 - scikit-learn - seaborn test: imports: - megalodon + - megalodon_extras commands: - megalodon --help - megalodon_extras --help about: home: https://github.com/nanoporetech/megalodon - license: Mozilla Public License 2.0 + license: Oxford Nanopore Technologies PLC. Public License Version 1.0 license_family: OTHER license_file: LICENCE.txt summary: Nanopore modified base and sequence variant detection. @@ -59,3 +62,4 @@ about: extra: recipe-maintainers: - marcus1487 + - npavlovikj From a155f86e1418366a97e0cd002434d43a8045a12d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 03:43:25 -0700 Subject: [PATCH 0739/2173] Update msstitch to 3.15 (#44256) --- recipes/msstitch/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/msstitch/meta.yaml b/recipes/msstitch/meta.yaml index fcdf6b910863d..671d97d9e7f86 100644 --- a/recipes/msstitch/meta.yaml +++ b/recipes/msstitch/meta.yaml @@ -1,10 +1,10 @@ package: name: msstitch - version: "3.14" + version: "3.15" source: - url: https://files.pythonhosted.org/packages/5b/ac/b7043fda0400f4618ea2f5394ee0d091bc4f0eb47804681519d94bcf7a32/msstitch-3.14.tar.gz - sha256: 0a2badd83ac8b64c9d8795dfcdd8f4d42568f58a4f0d33a719176850e826681b + url: https://files.pythonhosted.org/packages/f1/66/91e1682699ece4f2ed937d627171eba012f721336f7f8425750240791898/msstitch-3.15.tar.gz + sha256: 3e33b84031a5ccb06f497ef5457a17254bd4830f3e5c26661184467ae8701777 build: noarch: python From 89b02ed1180d10206a835277748acafd3954e9dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 03:49:45 -0700 Subject: [PATCH 0740/2173] Update bohra to 2.3.6 (#44253) * Update bohra to 2.3.5 * Update bohra to 2.3.6 --- recipes/bohra/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bohra/meta.yaml b/recipes/bohra/meta.yaml index 89ab861961742..1ba1ae27f4825 100644 --- a/recipes/bohra/meta.yaml +++ b/recipes/bohra/meta.yaml @@ -1,6 +1,6 @@ {% set name = "bohra" %} -{% set version = "2.3.4" %} -{% set sha256 = "d68a4815c0ae63012029dd3745517b4b831c2e9150b45a0a4acf10ddfb85b7ee" %} +{% set version = "2.3.6" %} +{% set sha256 = "3d51bfe235ae95dbe2c020a7f538375b49694b35480263e7c9b07972fdce221c" %} package: name: "{{ name }}" From 23b271b48f2c69d22c48573d9e7fbe5845188146 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 03:50:02 -0700 Subject: [PATCH 0741/2173] Update goalign to 0.3.7 (#44254) --- recipes/goalign/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/goalign/meta.yaml b/recipes/goalign/meta.yaml index e5fb7a3eaed45..6821e4de56ec7 100644 --- a/recipes/goalign/meta.yaml +++ b/recipes/goalign/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.6" %} +{% set version = "0.3.7" %} {% set name = "goalign" %} package: @@ -13,7 +13,7 @@ build: source: - url: https://github.com/evolbioinfo/{{name}}/archive/v{{ version }}.tar.gz - sha256: f0dba3674bef72a2a01f0c50a967c30176d952d99487c6c8fab8281bccb8ec20 + sha256: ae88553b45944f104486aa2c71161820ac9125f3628bb494ee76bfea3e75142e folder: src/github.com/evolbioinfo/{{name}}/ requirements: From 94db841fd2437eb4ed90f7f25ebeb78d3762fce2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 03:50:25 -0700 Subject: [PATCH 0742/2173] Update hybracter to 0.4.0 (#44252) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index b3c1078072223..017e17b1d2c9e 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.3.0" %} +{% set version = "0.4.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 71ed98a852e1153554eb78ba3c3dfb62fe1d9e9681ab71f948cedb8926659d8a + sha256: b65bbd2be4a7259b9676a36277bb6c086c84a91307510626b53970b41aa42838 build: number: 0 From 9c73760ca28b13e5daeb4b7c12b39b87b3038a4f Mon Sep 17 00:00:00 2001 From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Date: Tue, 14 Nov 2023 11:10:37 -0500 Subject: [PATCH 0743/2173] Update hmmer to version 3.4 (#44259) --- recipes/hmmer/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/hmmer/meta.yaml b/recipes/hmmer/meta.yaml index 1184ba02f7240..f6561a1f17117 100644 --- a/recipes/hmmer/meta.yaml +++ b/recipes/hmmer/meta.yaml @@ -1,13 +1,16 @@ package: name: hmmer - version: "3.3.2" + version: "3.4" source: - url: http://eddylab.org/software/hmmer/hmmer-3.3.2.tar.gz - sha256: 92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69 + url: http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz + sha256: ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3 build: - number: 4 + number: 0 + run_exports: + # commands/options have been removed or replaced between minor versions + - {{ pin_subpackage('hmmer', max_pin="x.x") }} requirements: build: From aa0f98cdb9a699e5e95070ce3e88baa82d91b679 Mon Sep 17 00:00:00 2001 From: Jessica Mattick <19544292+jmattick@users.noreply.github.com> Date: Tue, 14 Nov 2023 10:12:00 -0600 Subject: [PATCH 0744/2173] Update pbtk to v3.1.1 (#44249) Co-authored-by: Jessica Mattick --- recipes/pbtk/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/pbtk/meta.yaml b/recipes/pbtk/meta.yaml index b690d3fc50aa3..6192456fd7a53 100644 --- a/recipes/pbtk/meta.yaml +++ b/recipes/pbtk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbtk" %} -{% set version = "3.1.0" %} -{% set sha256 = "00d03f07071c1926282fe9de460ed9f505fe4caf5691ffd5df6a422ab5a2fc81" %} +{% set version = "3.1.1" %} +{% set sha256 = "4dbe08d880a4b54d7c84ecdf9849feead71ac5330277a66f57a2915447169814" %} package: name: {{ name }} @@ -26,6 +26,8 @@ extra: build: number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('pbtk', max_pin='x.x') }} test: commands: From 77b3590bd6aad7da4df10831fbafbfcedbc28bac Mon Sep 17 00:00:00 2001 From: Jessica Mattick <19544292+jmattick@users.noreply.github.com> Date: Tue, 14 Nov 2023 10:13:30 -0600 Subject: [PATCH 0745/2173] Update pbskera to v1.2.0 (#44248) Co-authored-by: Jessica Mattick --- recipes/pbskera/meta.yaml | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/recipes/pbskera/meta.yaml b/recipes/pbskera/meta.yaml index 557d1cfb69500..39a8c65d89706 100644 --- a/recipes/pbskera/meta.yaml +++ b/recipes/pbskera/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbskera" %} -{% set version = "1.1.0" %} -{% set pbskera_sha256 = "950fece28fb38f7043673c38a55f57606fe6e8be14784f9d3bbec222ca4acc9c" %} +{% set version = "1.2.0" %} +{% set pbskera_sha256 = "0385ab4d67377cd6ed596eccd5df973c03d78561db639d84f9ff557332f745be" %} package: name: {{ name }} @@ -18,10 +18,16 @@ about: extra: recipe-maintainers: - zeeev + - jmattick + skip-lints: + #repackaged binary + - should_be_noarch_generic build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('pbskera', max_pin='x.x') }} test: commands: From 58a86a195f56e962de788956da258a79ed871a06 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 14 Nov 2023 16:31:26 +0000 Subject: [PATCH 0746/2173] Add seqerakit recipe (#44260) * Add seqerakit recipe * Add run_exports * Add tower cli dependency --- recipes/seqerakit/meta.yaml | 47 +++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/seqerakit/meta.yaml diff --git a/recipes/seqerakit/meta.yaml b/recipes/seqerakit/meta.yaml new file mode 100644 index 0000000000000..2365bbc9f5f5c --- /dev/null +++ b/recipes/seqerakit/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "seqerakit" %} +{% set version = "0.4.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqerakit-{{ version }}.tar.gz + sha256: e37979e4ea5c7767b9d521fbdf09a06f62e44536a7260c5db711e952102df8d3 + +build: + entry_points: + - seqerakit=seqerakit.cli:main + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + +requirements: + host: + - python >=3.8,<4.0 + - pip + run: + - python >=3.8,<4.0 + - pyyaml >=6.0.0 + - tower-cli >=0.9.0 + +test: + imports: + - seqerakit + commands: + - pip check + - seqerakit --help + requires: + - pip + +about: + home: https://github.com/seqeralabs/seqera-kit + summary: Automate creation of Seqera Platform resources + license: Apache-2.0 + license_file: LICENSE.txt + +extra: + recipe-maintainers: + - pinin4fjords From 865ce853906cb4671946e3ceda0fcea4c93c49c4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 18:25:28 -0700 Subject: [PATCH 0747/2173] Update ncbi-datasets-pylib to 15.28.0 (#44269) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 46955df4b6c6b..2b600cab8f3b3 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.27.1" %} -{% set sha256 = "81417faef837b2276ffb40aa3ee078c9aec54d6ff6c51db13bb950cc6ac19d8c" %} +{% set version = "15.28.0" %} +{% set sha256 = "d0650b656a21bc7dccdbe7b6dd49b11e9776c4bd0b9836eb2e661d0a719659ed" %} package: name: {{ name|lower }} From c36f7e6c290e42471e147a5b57715f4f8ee667e2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 19:03:36 -0700 Subject: [PATCH 0748/2173] Update captus to 0.9.99 (#44261) --- recipes/captus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/captus/meta.yaml b/recipes/captus/meta.yaml index df3ba80239977..175d459cfe48b 100644 --- a/recipes/captus/meta.yaml +++ b/recipes/captus/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.9.98" %} -{% set sha256 = "b35d31d6c9c9ed2c2753f5e83346945f64357a00d3859236cda83f774320aeb9" %} +{% set version = "0.9.99" %} +{% set sha256 = "cb12443b948ed74b10c0d75b83aef49e719c609a0cb2715ef6af96e838fb4bb2" %} package: name: captus From 890435ff730462087a2ee00d5537438f627dfb9b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 19:03:52 -0700 Subject: [PATCH 0749/2173] Update pybiolib to 1.1.1527 (#44258) * Update pybiolib to 1.1.1518 * Update pybiolib to 1.1.1525 * Update pybiolib to 1.1.1527 * Update meta.yaml --------- Co-authored-by: Thanh Lee Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pybiolib/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 712aacd6db1e8..268db70c3f6b3 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1514" %} +{% set version = "1.1.1527" %} package: name: {{ name|lower }} @@ -7,14 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: fbef1e55c3ff2d0bf55f3fca1bb38033f1f2e5de5a85b552f69d00eb2ae45192 + sha256: 8b7471274604ac6e10c47b52a6e6ae50cc87eb4f22facba485d03d354461b2a3 build: noarch: python script: {{ PYTHON }} -m pip install . -vv number: 0 run_exports: - - {{ pin_subpackage('pybiolib', max_pin="x") }} + - {{ pin_subpackage('pybiolib', max_pin="x.x") }} requirements: host: From f9f8c9d65c0078bb490ee986ac21bf74dde32784 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 19:04:31 -0700 Subject: [PATCH 0750/2173] Update biocommons.seqrepo to 0.6.6 (#44244) * Update biocommons.seqrepo to 0.6.6 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/biocommons.seqrepo/meta.yaml | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/recipes/biocommons.seqrepo/meta.yaml b/recipes/biocommons.seqrepo/meta.yaml index af439c7613fe4..f70cee72ac83a 100644 --- a/recipes/biocommons.seqrepo/meta.yaml +++ b/recipes/biocommons.seqrepo/meta.yaml @@ -1,6 +1,5 @@ {% set name = "biocommons.seqrepo" %} -{% set version = "0.6.5" %} - +{% set version = "0.6.6" %} package: name: {{ name|lower }} @@ -8,28 +7,29 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/biocommons.seqrepo-{{ version }}.tar.gz - sha256: af9d1120fdef58025f1f8da02b0d184bb4a5a8a9299433f6020998d45992b29d + sha256: 655eb8a2b6e3d4564ef2cbfaa2db6415ccb066f9fd786bd4b3303bbba00e752a build: number: 0 noarch: python entry_points: - seqrepo = biocommons.seqrepo.cli:main - script: {{ PYTHON }} -m pip install . -vv --no-deps + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('biocommons.seqrepo', max_pin="x.x") }} requirements: host: - pip - - python >=3.6 + - python >=3.9 - pytest-runner - - cython - setuptools-scm - - wheel run: - bioutils >0.4 - coloredlogs + - ipython - pysam - - python >=3.6 + - python >=3.9 - requests - requests-html - six @@ -43,12 +43,11 @@ test: commands: #- pip check #requests-html 0.10.0 requires bs4, which is not installed - seqrepo --help - requires: - - pip about: home: https://github.com/biocommons/biocommons.seqrepo license: Apache-2.0 + license_family: APACHE license_file: LICENSE summary: Python package for writing and reading a local collection of biological sequences. From 4c9f50ece01983038894987578a4cf29a37da131 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 19:05:21 -0700 Subject: [PATCH 0751/2173] Update oakvar to 2.9.59 (#44265) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 70cc2f1379a14..b46211480983d 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.58" %} -{% set sha256 = "b616699f6fd3d9f57e9e01eaca17ffb6e38c6cb9f324b2beff97fb3332541239" %} +{% set version = "2.9.59" %} +{% set sha256 = "4cda1e2dacaadbc6f89985356a7aaa02ec16928eb40b62bdd8336a110cb2029d" %} package: name: {{ name|lower }} From 01e8027ed0e445b3f8ce22ae777494459835b935 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 19:05:53 -0700 Subject: [PATCH 0752/2173] Update picard-slim to 3.1.1 (#44267) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/picard-slim/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/picard-slim/meta.yaml b/recipes/picard-slim/meta.yaml index ad9557fe4a43b..c8de8e67a58e6 100644 --- a/recipes/picard-slim/meta.yaml +++ b/recipes/picard-slim/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.1.0" %} -{% set sha256 = "ea79ca6279a5e818cb6fa68a3476dde799c7ea03ffe52a26a3ca68c71ef28559" %} +{% set version = "3.1.1" %} +{% set sha256 = "15c79f51fd0ac001049f9dd7b9bac1dbdf759dcb0230a89c7f6d1f246e8bbab4" %} package: name: picard-slim From d012829219c8bb20f41327164b8eb1528a34e418 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 19:06:05 -0700 Subject: [PATCH 0753/2173] Update picard to 3.1.1 (#44266) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/picard/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/picard/meta.yaml b/recipes/picard/meta.yaml index f074f62a32c82..d8dfd44a2f90e 100644 --- a/recipes/picard/meta.yaml +++ b/recipes/picard/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.1.0" %} -{% set sha256 = "ea79ca6279a5e818cb6fa68a3476dde799c7ea03ffe52a26a3ca68c71ef28559" %} +{% set version = "3.1.1" %} +{% set sha256 = "15c79f51fd0ac001049f9dd7b9bac1dbdf759dcb0230a89c7f6d1f246e8bbab4" %} package: name: picard From 780aa488fcf3d67626a181038d85613caa9f5205 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 19:08:34 -0700 Subject: [PATCH 0754/2173] Update hic2cool to 1.0.1 (#44268) * Update hic2cool to 1.0.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/hic2cool/meta.yaml | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/recipes/hic2cool/meta.yaml b/recipes/hic2cool/meta.yaml index eb524e89673b7..b06d8470690e2 100644 --- a/recipes/hic2cool/meta.yaml +++ b/recipes/hic2cool/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hic2cool" %} -{% set version = "0.8.3" %} -{% set sha256 = "2fa1557df8b1b3eddc06df394649e69c0f1f40f1a0c951b26c16c0d3ff81a41e" %} +{% set version = "1.0.1" %} +{% set sha256 = "f1f1ffeeec8788819e6ae4b4d1236ba4349dceb98aa4a0b0b3068af30c2a6434" %} package: name: {{ name|lower }} @@ -12,24 +12,26 @@ source: build: noarch: python - number: 2 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('hic2cool', max_pin="x") }} requirements: host: - - python - - setuptools + - python >=3.8,<3.10 + - poetry-core >=1.0.0 - numpy >=1.10.1 - scipy - pandas - - cooler>=0.8.5 + - cooler >=0.8.5 - h5py >=2.8.0 run: - python - numpy >=1.10.1 - scipy - pandas - - cooler>=0.8.5 + - cooler >=0.8.5 - h5py >=2.8.0 test: @@ -43,4 +45,4 @@ about: license: MIT license_family: MIT license_file: LICENSE.txt - summary: "A converter between .hic files (from juicer) and .cool files (for cooler)." + summary: "A converter between .hic files (from juicer) and single-resolution or multi-resolution .cool files (for cooler)." From e8d994a835528f83507dedee1a6ebca232f12911 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 19:38:05 -0700 Subject: [PATCH 0755/2173] Update deeparg to 1.0.3 (#44225) * Update deeparg to 1.0.3 * add run_exports * edit python dependency * edit tests * limit tqdm to <4.65 * edit home URL and add note on tqdm pinning --------- Co-authored-by: joshuazhuang7 --- recipes/deeparg/meta.yaml | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/recipes/deeparg/meta.yaml b/recipes/deeparg/meta.yaml index 8ec26a83b8fcf..3cc4e6b275213 100644 --- a/recipes/deeparg/meta.yaml +++ b/recipes/deeparg/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.2" %} +{% set version = "1.0.3" %} package: name: deeparg @@ -6,12 +6,16 @@ package: source: url: https://pypi.io/packages/source/d/deeparg/DeepARG-{{version}}.tar.gz - sha256: 921835da1ec8a6caea1c6df0070dcda9fc0fe3b2681e2c5f3c7996c99b96bfe8 + sha256: 17eb351db9ff38d7f078a22aa614923c6cf5adcc632057edf7816d731655d55c build: - script: python -m pip install . + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv noarch: python - number: 1 + number: 0 + entry_points: + - deeparg = deeparg.entry:main + run_exports: + - {{ pin_subpackage('deeparg', max_pin="x") }} requirements: host: @@ -24,7 +28,8 @@ requirements: - joblib >=0.14.1 - biopython >=1.68 - ete3 >=3.1.2 - - tqdm >=4.62.3 + # tqdm pinning to <4.65 can be removed once https://github.com/gaarangoa/deeparg/issues/1 is resolved. + - tqdm >=4.62.3,<4.65 - nolearn >=0.6.1 - lasagne >=0.1 - scikit-learn >=0.19.2 @@ -41,7 +46,7 @@ test: - deeparg -h about: - home: https://bitbucket.org/gusphdproj/deeparg-ss/ + home: https://github.com/gaarangoa/deeparg license: MIT license_family: MIT license_file: "LICENSE.txt" From 5f98d9edfcbdaafba5f99a597074a35093c195f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20P=C5=99=C3=ADhoda?= Date: Wed, 15 Nov 2023 03:40:36 +0100 Subject: [PATCH 0756/2173] Use flask<3 in biophi (#44257) * Use flask<3 in biophi * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/biophi/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/biophi/meta.yaml b/recipes/biophi/meta.yaml index 8fea66bd29ef7..c207209df1acb 100644 --- a/recipes/biophi/meta.yaml +++ b/recipes/biophi/meta.yaml @@ -10,10 +10,12 @@ source: build: noarch: python - number: 1 + number: 2 entry_points: - biophi = biophi.common.cli.main:main script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + run_exports: + - {{ pin_subpackage("biophi", max_pin="x.x") }} requirements: host: @@ -28,7 +30,8 @@ requirements: - hmmer >=3.1 - click >=7 - sqlalchemy <2 # BioPhi is currently incompatible with SQLAlchemy 2.0 Engine - - flask >=2.1 + - flask <3 + - werkzeug <3 - redis-py - celery - requests From e272d54bc2824236dfa17323d603392248eb4da2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 19:40:55 -0700 Subject: [PATCH 0757/2173] Update ms-entropy to 1.1.1 (#44250) --- recipes/ms-entropy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms-entropy/meta.yaml b/recipes/ms-entropy/meta.yaml index 62fa5add4669a..1acfdcb572439 100644 --- a/recipes/ms-entropy/meta.yaml +++ b/recipes/ms-entropy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms-entropy" %} -{% set version = "1.0.4" %} +{% set version = "1.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms_entropy-{{ version }}.tar.gz - sha256: ccef60f5c6eba27bfe3734d6a22354232ea803368ac720cdc6e0e59ca631008b + sha256: ec2df69651049853e0b9d645abb1f0f3f4042e8d79bf8bc8997ba3c52b116525 build: skip: true # [py<37] From 763fef5911bbcc293323e7454f57307738e81077 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 19:41:26 -0700 Subject: [PATCH 0758/2173] Update dxpy to 0.364.0 (#44246) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 1faed26dfbf60..3838e4ec85068 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.363.0" %} +{% set version = "0.364.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 0da6f5c783f5614220d8962969eacc73767a991c0656a238c403a48f2b0dc3f1 + sha256: 1c3c18281261e4e3ce8566f44d61f017c3e9231a848940ba99ff2827a4f0fc06 build: number: 0 From 592da6e9a31901d3016ae56f68bed19769d0abf0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 14 Nov 2023 20:38:58 -0700 Subject: [PATCH 0759/2173] Update bigscape to 1.1.6 (#44255) * Update bigscape to 1.1.6 * add run_exports * revert python pinning * remove scikit-learn pinning * edit tests --------- Co-authored-by: joshuazhuang7 --- recipes/bigscape/meta.yaml | 25 +++++++++++++++++++------ 1 file changed, 19 insertions(+), 6 deletions(-) diff --git a/recipes/bigscape/meta.yaml b/recipes/bigscape/meta.yaml index cb0f0d73a88c7..78c95f18aa48d 100644 --- a/recipes/bigscape/meta.yaml +++ b/recipes/bigscape/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.5" %} -{% set sha256 = "ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7" %} +{% set version = "1.1.6" %} +{% set sha256 = "c38f633d4f1c5b9034c9ee2c96a14b7994884e2fc005fbead219068a618580a4" %} package: name: bigscape @@ -12,24 +12,37 @@ source: build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv" + script: "{{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv" + entry_points: + - bigscape=bigscape.__main__:main + run_exports: + - {{ pin_subpackage('bigscape', max_pin="x") }} requirements: host: - python ==3.7 + - pip run: - python ==3.7 - hmmer - biopython - fasttree - networkx - - scikit-learn ==0.19.2 + - numpy + - scikit-learn + - scipy test: commands: - - 'bigscape.py --version' + - 'bigscape --version' about: home: https://github.com/medema-group/BiG-SCAPE - license: GNU Affero v3 + license: AGPL-3.0-or-later + license_file: LICENSE summary: Biosynthetic Genes Similarity Clustering and Prospecting Engine. + doc_url: https://github.com/medema-group/BiG-SCAPE/wiki + +extra: + identifiers: + - doi:10.1038/s41589-019-0400-9 From 6e778cadd2cd607530e38abd3d8b73b7d12fa572 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 01:56:50 -0700 Subject: [PATCH 0760/2173] Update seqerakit to 0.4.2 (#44271) --- recipes/seqerakit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seqerakit/meta.yaml b/recipes/seqerakit/meta.yaml index 2365bbc9f5f5c..55ab0994c9ae5 100644 --- a/recipes/seqerakit/meta.yaml +++ b/recipes/seqerakit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqerakit" %} -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqerakit-{{ version }}.tar.gz - sha256: e37979e4ea5c7767b9d521fbdf09a06f62e44536a7260c5db711e952102df8d3 + sha256: 442423a80aa80e77a8c47f2b6f6876e0c872e649e43a017c14abf17f55e86169 build: entry_points: From cbc60c3af5a7aef3e5b5e8ac114b9790097190b6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 03:03:37 -0700 Subject: [PATCH 0761/2173] Update sequali to 0.2.0 (#44275) --- recipes/sequali/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index 9d26f3ae111b8..f49120d7e89ac 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sequali" %} -{% set version = "0.1.0" %} +{% set version = "0.2.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: ed32729962b2f0631b7892ccfd783b86ab60fb2ab10d2045a42c353adb6eb679 + sha256: 7fbe9a053d0a4529fdf937bf474334125c8828c692447f0356926ee735dcef68 build: number: 0 From 883fe227065a9354c6afe42e558612324244fbdb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 07:47:09 -0700 Subject: [PATCH 0762/2173] Update ananse to 0.5.0 (#44277) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update ananse to 0.5.0 * Update meta.yaml * Update meta.yaml * fix run_exports --------- Co-authored-by: Siebren Frölich <48289046+siebrenf@users.noreply.github.com> --- recipes/ananse/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/ananse/meta.yaml b/recipes/ananse/meta.yaml index eaeca43054cd3..f6d2cfe02bade 100644 --- a/recipes/ananse/meta.yaml +++ b/recipes/ananse/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.1" %} +{% set version = "0.5.0" %} package: name: ananse @@ -6,12 +6,14 @@ package: source: url: https://github.com/vanheeringen-lab/ANANSE/releases/download/v{{ version }}/ANANSE-{{ version }}.tar.gz - sha256: 4b8c63294c0ddf85247a3394e68756ce928d0d89a6d4b3e613dd6175a7bd31d5 + sha256: 3c623ba6df0e824238ce3d381bcbf9e2991654c18d7180e63d05951bb509e747 build: number: 0 noarch: python script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_subpackage("ananse", max_pin="x.x") }} requirements: host: @@ -20,7 +22,7 @@ requirements: run: - python >=3.7 - adjusttext - - dask + - dask <=2023.9.1 - genomepy >=0.14.0 - gimmemotifs-minimal >=0.18.0 - loguru @@ -28,7 +30,7 @@ requirements: - networkx - numpy >=1.6 - openpyxl - - pandas + - pandas <2 - pybedtools - pydot >=1.4.1 - pygraphviz >=1.7 From e4bea7015382f49db4012c295e723cc7f42fdddd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 08:54:30 -0700 Subject: [PATCH 0763/2173] Update deeparg to 1.0.4 (#44272) --- recipes/deeparg/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/deeparg/meta.yaml b/recipes/deeparg/meta.yaml index 3cc4e6b275213..2da747b7cb601 100644 --- a/recipes/deeparg/meta.yaml +++ b/recipes/deeparg/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.3" %} +{% set version = "1.0.4" %} package: name: deeparg @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/d/deeparg/DeepARG-{{version}}.tar.gz - sha256: 17eb351db9ff38d7f078a22aa614923c6cf5adcc632057edf7816d731655d55c + sha256: 85df343a76b19b109b02d0b7784b39132531712e8f0a0fc87091f98bdacdd30d build: script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv From 3f6359740f69b629410ded3a439a8ac3e0866ecd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 08:54:53 -0700 Subject: [PATCH 0764/2173] Update sylph to 0.4.1 (#44281) --- recipes/sylph/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sylph/meta.yaml b/recipes/sylph/meta.yaml index c3703e9973199..4ef0837272ca2 100644 --- a/recipes/sylph/meta.yaml +++ b/recipes/sylph/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.0" %} +{% set version = "0.4.1" %} package: name: sylph @@ -11,7 +11,7 @@ build: source: url: https://github.com/bluenote-1577/sylph/archive/v{{ version }}.tar.gz - sha256: 66fae78c240ffc514fe784dce8783d63e8551a7de1486c95083367956ef33d8f + sha256: fd405d34e8ebd5a0f09a85631864b330594a29e30fd3509e7f4873f2946046a6 requirements: build: From 155f03fa04ac5985370ffb35aefbdfed24fce906 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 08:55:38 -0700 Subject: [PATCH 0765/2173] Update mehari to 0.17.1 (#44278) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 2d333b70b3999..0eb4a6a8123f6 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.17.0" %} -{% set sha256 = "8d8514775d4ee3db726f32e346f7712c87effbbb6c975d6df27e81d2b08cf1f2" %} +{% set version = "0.17.1" %} +{% set sha256 = "cdb7e68f88df1439e8e05ffd4d9ebf011195700ae1936ea32cdd1bd65202bab0" %} package: name: mehari From b55f0cd0bc13c99ca3e8e87277d74dd94ae06322 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 08:56:00 -0700 Subject: [PATCH 0766/2173] Update oakvar to 2.9.60 (#44273) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index b46211480983d..993ab46ba1a87 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.59" %} -{% set sha256 = "4cda1e2dacaadbc6f89985356a7aaa02ec16928eb40b62bdd8336a110cb2029d" %} +{% set version = "2.9.60" %} +{% set sha256 = "a9b0ea9fbd3535933b71c9b693e3714179b8db19102e68b66f776a7e3e72adb0" %} package: name: {{ name|lower }} From 1077281758460e7938da04710628f3ab541c823b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 09:44:14 -0700 Subject: [PATCH 0767/2173] Update seq2science to 1.2.1 (#44282) --- recipes/seq2science/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seq2science/meta.yaml b/recipes/seq2science/meta.yaml index 324f9c1a2392d..dd78a09be0e26 100644 --- a/recipes/seq2science/meta.yaml +++ b/recipes/seq2science/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.0" %} +{% set version = "1.2.1" %} package: name: seq2science @@ -6,7 +6,7 @@ package: source: url: https://github.com/vanheeringen-lab/seq2science/archive/v{{ version }}.tar.gz - sha256: 074d19142ff9b9d0c92abf053b9784949309ff878712974c61d6964d26183508 + sha256: f4543413118f9bdf69e1143f14708f4debf2f1089952569d55a1ca539d676bff build: noarch: python From c9f8f019b90aa239bb64ff767322cfa46cee71fd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 13:44:05 -0700 Subject: [PATCH 0768/2173] Update monsda to 1.2.0 (#44284) --- recipes/monsda/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/monsda/meta.yaml b/recipes/monsda/meta.yaml index ef47e02a73861..1ae416497703e 100644 --- a/recipes/monsda/meta.yaml +++ b/recipes/monsda/meta.yaml @@ -1,6 +1,6 @@ {% set name = "MONSDA" %} -{% set version = "1.1.1" %} -{% set sha256 = "6f4d389c848aa89722b267104344a3a82317e763166cade88511f3b79d3c099e" %} +{% set version = "1.2.0" %} +{% set sha256 = "375984684d9852fe8c466d65a44e13b1cfb593fdbe9aee6b7340bcf15796b47d" %} package: name: "{{ name|lower }}" From 277bb9baa1eafa14f5b63a220df74c92511dfc32 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 15:05:34 -0700 Subject: [PATCH 0769/2173] Update alignoth to 0.11.0 (#44285) --- recipes/alignoth/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/alignoth/meta.yaml b/recipes/alignoth/meta.yaml index e795d8fb5e4de..20b848d111860 100644 --- a/recipes/alignoth/meta.yaml +++ b/recipes/alignoth/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.10.0" %} +{% set version = "0.11.0" %} package: name: alignoth @@ -14,7 +14,7 @@ build: source: url: https://github.com/koesterlab/alignoth/archive/v{{ version }}.tar.gz - sha256: 0f0a2a78c8a4d840957fc91ce1d3d2d598e773b1d0df3a8af0435f6a7b9eb2bf + sha256: b7df1ee950b274c8f1fdfe75b806f47b23a0a9bd8bf2db7b6b762f84a6295f91 requirements: build: From cc4005137038ce09ac34f28e70b1cd3153c9525d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 16:10:25 -0700 Subject: [PATCH 0770/2173] Update seqfu to 1.20.2 (#44270) * Update seqfu to 1.20.1 * Nim < 2.0.0 * Update meta.yaml * max_pin to x.x * Update seqfu to 1.20.2 * Update meta.yaml * Update meta.yaml * add gcc * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml --------- Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com> Co-authored-by: Thanh Lee --- recipes/seqfu/build.sh | 18 +++++++++++++++++- recipes/seqfu/meta.yaml | 13 ++++++++----- 2 files changed, 25 insertions(+), 6 deletions(-) diff --git a/recipes/seqfu/build.sh b/recipes/seqfu/build.sh index 2a8873e4fdee2..41e15120f4793 100644 --- a/recipes/seqfu/build.sh +++ b/recipes/seqfu/build.sh @@ -5,8 +5,24 @@ set -euxo pipefail echo "--- NIM BUILD ---" nim --version echo "----------" -nimble --version + + + +echo " Setting environment variables" +# Fix zlib +export CFLAGS="$CFLAGS -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" +export CPATH=${PREFIX}/include + +echo "GXX: $GXX" +echo "GCC: $GCC" echo "----------" +echo "Patching makefile" +# Trying to fix build when gcc or g++ are required +sed -i 's/gcc/$(GCC)/g' Makefile +sed -i 's/g++/$(GXX)/g' Makefile +sed -i '1iGCC ?= gcc' Makefile +sed -i '1iGXX ?= g++' Makefile if [[ $OSTYPE == "darwin"* ]]; then export HOME="/Users/distiller" diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml index 8b598e46b5be9..c0f03f2958763 100644 --- a/recipes/seqfu/meta.yaml +++ b/recipes/seqfu/meta.yaml @@ -1,6 +1,6 @@ {% set name = "seqfu" %} -{% set version = "1.20.0" %} -{% set sha256 = "d076f636eb7195c1607af403f3497963892471f60832f6f497370750fcbeb074" %} +{% set version = "1.20.2" %} +{% set sha256 = "a7e5f2bdf0810d4b4d4a00a7f25522e8e3df7d5acf96742d2b63fb93da04ac8e" %} package: name: {{ name }} @@ -11,15 +11,18 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 + skip: True # Let's skip MacOS until we find out more run_exports: - - {{ pin_subpackage(name, max_pin="x") }} + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: - {{ compiler('c') }} - - nim + - {{ compiler('cxx') }} + - nim >=2.0.0 - make + - zlib host: - zlib - pcre From 8c0cbc81b55280ecdea18e31f60f9a22947d179d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 17:36:37 -0700 Subject: [PATCH 0771/2173] Update earlgrey to 3.2.2 (#44280) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index c3b27765175c5..ac9e6b4c4d999 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "3.2.1" %} -{% set sha256 = "38c4a85276164b3efc1b59fb2f6580357dc697d54b3b4649b29b200c6141dc69" %} +{% set version = "3.2.2" %} +{% set sha256 = "dfb561005413b60426e12dc894622da25f3bcb604e8a986c23a8d72eddaec9e0" %} package: name: {{ name|lower }} From 5fca64da36b1db09dffd967ecee0b4b7fc9037cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 17:36:52 -0700 Subject: [PATCH 0772/2173] Update deeplcretrainer to 0.2.8 (#44274) --- recipes/deeplcretrainer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/deeplcretrainer/meta.yaml b/recipes/deeplcretrainer/meta.yaml index 62673714c4b3d..5d602ecfa1aa3 100644 --- a/recipes/deeplcretrainer/meta.yaml +++ b/recipes/deeplcretrainer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DeepLCRetrainer" %} -{% set version = "0.2.1" %} -{% set sha256 = "1f042a003146c81e023f47e7d53e20d1f888dcdb7325618555227ab1073e47b1" %} +{% set version = "0.2.8" %} +{% set sha256 = "73a9052d186921df42cfefce6215ee50f2a0abb3c4b1cef4a67126a59dfa7c9b" %} package: name: {{ name|lower }} From c4c244a4aadf2ad9067ada164aa7e8e88a5e2dfb Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Thu, 16 Nov 2023 11:56:25 +1100 Subject: [PATCH 0773/2173] Update Metaphor dependencies (#44279) * Pin Python version - Use Python<=3.12 for now, see snakemake/snakemake#2480 for discussion * Bump build number --- recipes/metaphor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metaphor/meta.yaml b/recipes/metaphor/meta.yaml index c4ca52342d920..53267b80f5cc6 100644 --- a/recipes/metaphor/meta.yaml +++ b/recipes/metaphor/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 36c089a427a4fba0ed8768b2bbfc8312bd53d0f51b357b715ab1fe7a2b33dfe1 build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -25,7 +25,7 @@ requirements: - jinja2 - networkx - pandas - - python >=3.9 + - python >=3.9,<3.12 - pyyaml - requests - snakemake >=7.5 From 77c1dd09484cab01a3b8e4d56504b61525029aef Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 19:11:47 -0700 Subject: [PATCH 0774/2173] Update treeswift to 1.1.38 (#44286) * Update treeswift to 1.1.38 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/treeswift/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/treeswift/meta.yaml b/recipes/treeswift/meta.yaml index 29ddb697dd74e..1affe755cfa1c 100644 --- a/recipes/treeswift/meta.yaml +++ b/recipes/treeswift/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.37" %} +{% set version = "1.1.38" %} package: name: "treeswift" @@ -6,12 +6,14 @@ package: source: url: https://pypi.io/packages/source/t/treeswift/treeswift-{{ version }}.tar.gz - sha256: d7899104428cbb157027099fbe2fbaec1e87870ae48d561a6075a29498827b6b + sha256: 04da31d2fae71f01a8cd6ecd54e77e068b9267d55c0f70f6d4c644f692d3652d build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('treeswift', max_pin="x") }} requirements: host: @@ -30,3 +32,4 @@ about: license_family: GPL3 license_file: LICENSE summary: "TreeSwift: Fast tree module for Python 2 and 3" + dev_url: https://github.com/niemasd/TreeSwift From efe7b3bb910051bc6208369dced56a4684cf2113 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 23:10:41 -0700 Subject: [PATCH 0775/2173] Update flight-genome to 1.6.2 (#44288) * Update flight-genome to 1.6.2 * Fix flight-genome command (#44291) --------- Co-authored-by: Samuel Aroney <41124903+AroneyS@users.noreply.github.com> --- recipes/flight-genome/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/flight-genome/meta.yaml b/recipes/flight-genome/meta.yaml index f3c7dd35a939a..98ec30f242755 100644 --- a/recipes/flight-genome/meta.yaml +++ b/recipes/flight-genome/meta.yaml @@ -1,5 +1,5 @@ {% set name = "flight-genome" %} -{% set version = "1.6.1" %} +{% set version = "1.6.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 6bcd8e25ebbb5434050d31cdcc39062cb2f548020f853253569c70cdb0282503 + sha256: d07b920f3a6bfabb6190d27eb2cbe8ad8a1ddb40b0cbf62104d3adbb71c484a2 build: number: 0 @@ -31,7 +31,7 @@ test: imports: - flight commands: - - flight --help + - flight --version about: home: "https://github.com/rhysnewell/flight" From 89770511861548f9e4f2b6a02d121c53d4bdfe74 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 15 Nov 2023 23:15:56 -0700 Subject: [PATCH 0776/2173] Update rosella to 0.5.1 (#44289) --- recipes/rosella/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rosella/meta.yaml b/recipes/rosella/meta.yaml index e112f18d75e8e..792250cabb4fe 100644 --- a/recipes/rosella/meta.yaml +++ b/recipes/rosella/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} {% set name = "rosella" %} -{% set hash = "f89a41facff14d45220fe04cf412d42272913070ac702678446d70e33252aeb8" %} +{% set hash = "6fa50c3c82a0e792ad9e44abb814992753732d169e99f74b228a834d822f1a8c" %} package: name: rosella From 470deab5d10f85b2d3d37e2b337193f03de7f8d7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 02:23:13 -0700 Subject: [PATCH 0777/2173] Update gget to 0.28.1 (#44226) * Update gget to 0.28.0 * add run_exports * add bs4 * Update gget to 0.28.1 * add requests * add pandas * add ipython * add mysql-connector-python * add matplotlib-base * add tqdm * add remaining dependencies [hopefully] to host --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/gget/meta.yaml | 29 ++++++++++++----------------- 1 file changed, 12 insertions(+), 17 deletions(-) diff --git a/recipes/gget/meta.yaml b/recipes/gget/meta.yaml index b388fc82f3150..7bbfb969bd6a1 100644 --- a/recipes/gget/meta.yaml +++ b/recipes/gget/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gget" %} -{% set version = "0.27.9" %} -{% set sha256 = "4a04f11e8829b4e0001d0b1bd4c5039fcf7a2f6776770f0b40819acde4c1c5b2" %} +{% set version = "0.28.1" %} +{% set sha256 = "83b01d44c45e6ae89a377f45ab0e7e08071f2358a64e7872f4936c1cbd3ece73" %} package: name: "{{ name|lower }}" @@ -13,29 +13,24 @@ source: build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation -vvv . + run_exports: + - {{ pin_subpackage('gget', max_pin="x.x") }} requirements: - build: - - python >=3.6 - - pip - - setuptools host: - python >=3.6 - - numpy >=1.17.2 - - pandas >=1.0.0 + - pip + - bs4 - requests >=2.22.0 + - pandas >=1.0.0 - ipython - - matplotlib-base - mysql-connector-python >=8.0.5,<=8.0.29 - - beautifulsoup4 >=4.10.0 - - ipywidgets + - matplotlib-base - tqdm - - py3Dmol >=1.8.0 - - curl + - ipywidgets - lxml - - openmm ==7.5.1 - - openai + - numpy >=1.17.2 run: - python >=3.6 - numpy >=1.17.2 @@ -52,7 +47,7 @@ requirements: - lxml - openmm ==7.5.1 - openai - + test: commands: - {{ name }} ref --help From e8b33c025e057e82db018ffc68fb2f771c33dfe8 Mon Sep 17 00:00:00 2001 From: Chun-Hui Gao Date: Thu, 16 Nov 2023 18:36:12 +0800 Subject: [PATCH 0778/2173] typo in README (#44235) typo --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index eedda1c1b8582..046ac7a353fcc 100644 --- a/README.md +++ b/README.md @@ -6,8 +6,8 @@ [![Gitter](https://badges.gitter.im/bioconda/bioconda-recipes.svg)](https://gitter.im/bioconda/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) [Conda](http://anaconda.org) is a platform- and language-independent package -manager that sports easy distribution, installation and version management of -software. The [bioconda channel](https://anaconda.org/bioconda) is a Conda +manager that supports easy distribution, installation and version management of +software. The [bioconda channel](https://anaconda.org/bioconda) is a Conda channel providing bioinformatics related packages for **Linux** and **Mac OS**. This repository hosts the corresponding recipes. From 0251bf889d7b3db39bcd6c39d44830ba794d9aae Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 04:37:21 -0700 Subject: [PATCH 0779/2173] Update mimseq to 1.3.8 (#44292) --- recipes/mimseq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mimseq/meta.yaml b/recipes/mimseq/meta.yaml index b57cbcc8dcb9e..8ed6c9100ae08 100644 --- a/recipes/mimseq/meta.yaml +++ b/recipes/mimseq/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mimseq" %} -{% set version = "1.3.7" %} +{% set version = "1.3.8" %} package: name: mimseq @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8eff7406b75f3bc25b40c32b15087dcf97b02aa58e0ed779c258533a9ea401ce + sha256: 1d2a76c4f45d2388c7c5eb7112c3446e41cd8a9663949c4c76d14df0abd42ae5 build: run_exports: From 7ef77757badbd34b1624692b260c3aca064ce516 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 04:38:49 -0700 Subject: [PATCH 0780/2173] Update squigulator to 0.2.2 (#44293) --- recipes/squigulator/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/squigulator/meta.yaml b/recipes/squigulator/meta.yaml index 3e77d7e68e208..cdb6c3d60102f 100644 --- a/recipes/squigulator/meta.yaml +++ b/recipes/squigulator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "squigulator" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/hasindu2008/squigulator/releases/download/v{{ version }}/squigulator-v{{ version }}-release.tar.gz - sha256: c6019bb6fed55d9f4b875185b8fb12afd2052150d23d41d6fcb0f7a6149d8a80 + sha256: c1159c71ab04623e678c265081a2b0fc6b790b5cc86260deac1646d87c180e35 build: number: 0 From a07939edbc3f71c4daaf5de353658068752271b0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 04:41:36 -0700 Subject: [PATCH 0781/2173] Update oakvar to 2.9.62 (#44290) * Update oakvar to 2.9.61 * Update oakvar to 2.9.62 --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 993ab46ba1a87..26ef8420ae976 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.60" %} -{% set sha256 = "a9b0ea9fbd3535933b71c9b693e3714179b8db19102e68b66f776a7e3e72adb0" %} +{% set version = "2.9.62" %} +{% set sha256 = "c62cc2754e2284d69a256169bf9e92bcf868470f28ad61471fdb0d965495c241" %} package: name: {{ name|lower }} From 569cb1e8854cca67435f9c518716c044a50e398e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 04:43:41 -0700 Subject: [PATCH 0782/2173] Update ncbi-datasets-pylib to 15.29.0 (#44287) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 2b600cab8f3b3..90dc0bf4d1b3b 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.28.0" %} -{% set sha256 = "d0650b656a21bc7dccdbe7b6dd49b11e9776c4bd0b9836eb2e661d0a719659ed" %} +{% set version = "15.29.0" %} +{% set sha256 = "6b49e4afe1362e64c4e639e34e21fc1e3c72eb473db41b5113f71f1504f9723c" %} package: name: {{ name|lower }} From 2b0c363f8ffb0e796693d42e998c8cae2ab8bbb5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 05:13:56 -0700 Subject: [PATCH 0783/2173] Update r-liger to 1.0.1 (#44180) * Update r-liger to 1.0.1 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Thanh Lee Co-authored-by: Christian Brueffer --- recipes/r-liger/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/r-liger/meta.yaml b/recipes/r-liger/meta.yaml index ff011ae791908..47619e1464082 100644 --- a/recipes/r-liger/meta.yaml +++ b/recipes/r-liger/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.0.0' %} +{% set version = '1.0.1' %} package: name: r-liger @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/rliger_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/rliger/rliger_{{ version }}.tar.gz - sha256: b905643e6609b051bd257c5d6998c7ba03d19700b804d022224f8f037ce50dbf + sha256: 5a48c8c18c66c3b692d99ff7eb1595acd4659595cc633c09c55e3f4f44094b74 build: - number: 5 + number: 0 script: R CMD INSTALL --build . rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage("r-liger", max_pin="x.x") }} requirements: build: @@ -44,11 +46,11 @@ requirements: - r-uwot - r-hdf5r - r-plyr - - r-riverplot - r-snow - r-psych - r-rcppeigen - r-rann + - r-scattermore >=0.7 run: - r-base - r-fnn @@ -72,12 +74,12 @@ requirements: - r-mclust - r-patchwork - r-plyr - - r-riverplot - r-snow - r-psych - r-rcppeigen - r-rann - r-reticulate + - r-scattermore >=0.7 - openjdk >=6 - umap-learn From ba5ad2f7da6da22529aee4af4bc9ea5a2aecbb7c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 18:46:55 -0700 Subject: [PATCH 0784/2173] Update ribodetector to 0.2.8 (#44300) * Update ribodetector to 0.2.8 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/ribodetector/meta.yaml | 25 ++++++++++++++++--------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/recipes/ribodetector/meta.yaml b/recipes/ribodetector/meta.yaml index 1121acb70e5a7..18cd605993a9c 100644 --- a/recipes/ribodetector/meta.yaml +++ b/recipes/ribodetector/meta.yaml @@ -1,24 +1,29 @@ -{% set version = "0.2.7" %} +{% set version = "0.2.8" %} package: name: ribodetector version: {{ version }} source: - url: https://files.pythonhosted.org/packages/d8/66/f1f7445866fe5a80058eace33a4d1888ab9531cf42b08ce9a764c993902a/ribodetector-0.2.7.tar.gz - sha256: 39633b2642eb961f61a827f7733acfe0de95e43a66749c6c46ddecd910e602d2 + url: https://files.pythonhosted.org/packages/88/e7/4b7bb1a97093600cf0ca66399b91262dcdbe77eeafa06ef07e9f3eb04e53/ribodetector-0.2.8.tar.gz + sha256: 9da4b60b09321e0261cb97f51d209bda21573e810820290ecc39d70690a57aff build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + entry_points: + - ribodetector = ribodetector.detect:main + - ribodetector_cpu = ribodetector.detect_cpu:main + run_exports: + - {{ pin_subpackage('ribodetector', max_pin="x.x") }} requirements: host: - pip - - python >=3.8 + - python >=3.8,<=3.10 run: - - python >=3.8 + - python >=3.8,<=3.10 - pandas - numpy - tqdm @@ -34,9 +39,11 @@ test: - ribodetector_cpu --help about: - home: https://github.com/hzi-bifo/RiboDetector - license: GPL-3 - summary: Accurate and rapid RiboRNA sequences Detector based on deep learning + home: https://github.com/hzi-bifo/RiboDetector + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: Accurate and rapid RiboRNA sequences Detector based on deep learning extra: recipe-maintainers: From 9125c6d4708f9383c7ea70205e80620bff04cd0e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 18:47:12 -0700 Subject: [PATCH 0785/2173] Update ndex2 to 3.6.0 (#44298) * Update ndex2 to 3.6.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/ndex2/meta.yaml | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/recipes/ndex2/meta.yaml b/recipes/ndex2/meta.yaml index 29d3f36ab8cbb..de8e93c6e67c0 100644 --- a/recipes/ndex2/meta.yaml +++ b/recipes/ndex2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ndex2" %} -{% set version = "3.5.1" %} +{% set version = "3.6.0" %} package: @@ -8,12 +8,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ndex2-{{ version }}.tar.gz" - sha256: "e4bfecf0f75c4d1f22cf59f6f04af458defa82946d1baabec494553fd4936e92" + sha256: "d6e95ba33747c59ae47d32ebce55837f17d001f776ea811a70b9e716592d2d1e" build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('ndex2', max_pin="x") }} requirements: host: @@ -36,15 +38,12 @@ test: imports: - ndex2 - ndex2cx - commands: - - pip check - requires: - - pip about: home: "https://github.com/ndexbio/ndex2-client" summary: "Nice CX Python includes a client and a data model." license: BSD-3-Clause + license_family: BSD license_file: LICENSE.txt dev_url: "https://github.com/ndexbio/ndex2-client" doc_url: "https://github.com/ndexbio/ndex2-client/blob/master/README.rst" From 387596de73fe00936e4b2483e3191bee4ca56287 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 18:47:29 -0700 Subject: [PATCH 0786/2173] Update planemo to 0.75.18 (#44294) --- recipes/planemo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 743c623d6ba16..1d659535dbf15 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "planemo" %} -{% set version = "0.75.17" %} -{% set sha256 = "451da7eb82c8e1f6ab5ea854a765b6b4551327e5b374e7e991d33323f0c46aea" %} +{% set version = "0.75.18" %} +{% set sha256 = "a38c7edef459fd6daaba1f9d63da6ad5b3e39b7a6d62aecd0f71395ae56e6629" %} package: name: {{ name|lower }} From 495819a0939cb7f460d84f578bd4100b926ce326 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 18:47:49 -0700 Subject: [PATCH 0787/2173] Update curare to 0.5.1 (#44295) --- recipes/curare/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/curare/meta.yaml b/recipes/curare/meta.yaml index 83dc705fef548..961edaf9848d9 100644 --- a/recipes/curare/meta.yaml +++ b/recipes/curare/meta.yaml @@ -1,5 +1,5 @@ {% set name = "curare" %} -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/pblumenkamp/Curare/archive/refs/tags/{{ version }}.tar.gz - sha256: 13e5e209ad8158af3f7448c9a610fa2a64c201ec540e199373dc32e4f2a5ef1e + sha256: bf1d47c889b90bb33b5b5353b87d8486a23321394a928e863510c6ac2e8eb0c7 build: number: 0 From a00f6330897e06dc3aac343e0f8a51d4744952a8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 18:49:48 -0700 Subject: [PATCH 0788/2173] Update gget to 0.28.2 (#44301) --- recipes/gget/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gget/meta.yaml b/recipes/gget/meta.yaml index 7bbfb969bd6a1..0c155d5a9aec3 100644 --- a/recipes/gget/meta.yaml +++ b/recipes/gget/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gget" %} -{% set version = "0.28.1" %} -{% set sha256 = "83b01d44c45e6ae89a377f45ab0e7e08071f2358a64e7872f4936c1cbd3ece73" %} +{% set version = "0.28.2" %} +{% set sha256 = "2bc24c484e26fdd25646f66089e08edf101c344e9ddb9aaeb1484fac3e1d2a99" %} package: name: "{{ name|lower }}" From b34a6241426d7ea23603cdc994252d350a1f5d1b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 19:32:59 -0700 Subject: [PATCH 0789/2173] Update alfred to 0.2.8 (#44299) * Update alfred to 0.2.8 * add run_exports --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/alfred/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/alfred/meta.yaml b/recipes/alfred/meta.yaml index 674c9fff68aee..a1d0b9d8a4038 100644 --- a/recipes/alfred/meta.yaml +++ b/recipes/alfred/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.7" %} -{% set sha256 = "fa2b9bc47e1f716471684b0467b35c5f1b6f1b36ffd35608d13f4d1f138d6fc1" %} +{% set version = "0.2.8" %} +{% set sha256 = "5d2583249728184aedd0165e936496a02833221c44eec2243f20ea315fa525e9" %} package: name: alfred @@ -10,7 +10,9 @@ source: sha256: '{{ sha256 }}' build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('alfred', max_pin="x.x") }} requirements: build: From d8eacf826d9dbed9798d25c48360ee5dd11edae1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 16 Nov 2023 19:34:50 -0700 Subject: [PATCH 0790/2173] Update viralmsa to 1.1.39 (#44302) --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index d134a5f1ceb9e..a5b203d7f9c7b 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.38" %} +{% set version = "1.1.39" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: 1100b08575ad6335d9aff3423315419f05a08ffeab82d42cb3333aa9298f533b + sha256: 00ff79a0b106cef69e7afaec8e16d2789ed5fb6243817588abcedfd4435269bb requirements: run: From 254b62e51fd1ce9ead7cdecb5c0557e00d599afa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 17 Nov 2023 02:56:00 -0700 Subject: [PATCH 0791/2173] Update lorax to 0.3.9 (#44308) --- recipes/lorax/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/lorax/meta.yaml b/recipes/lorax/meta.yaml index b774f1994a4ef..904907ef97879 100644 --- a/recipes/lorax/meta.yaml +++ b/recipes/lorax/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.8" %} -{% set sha256 = "a12755ed0007f8aa7aea4ae8f84bdb839d46c34ad535d83acc62dac33444d70d" %} +{% set version = "0.3.9" %} +{% set sha256 = "f4fa1f92f75d53af696225a42c3b1ee689a78eee41c09040146da9692a34fd6f" %} package: name: lorax From 176c59accf96194a49123e0dadba35919e03b508 Mon Sep 17 00:00:00 2001 From: Tobias Rausch Date: Fri, 17 Nov 2023 11:52:28 +0100 Subject: [PATCH 0792/2173] Update tracy to v0.7.6 (#44306) --- recipes/tracy/meta.yaml | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/recipes/tracy/meta.yaml b/recipes/tracy/meta.yaml index 9bcf56d87130d..6a8f5ac375bd9 100644 --- a/recipes/tracy/meta.yaml +++ b/recipes/tracy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.5" %} -{% set sha256 = "f53ddc40f1ab212d530324b7535896ee5400d8f9bd22d08fa8c3aaa103b0ea2c" %} +{% set version = "0.7.6" %} +{% set sha256 = "68bb079d9c05c98d7de1bf044e6c4da6a409d8f2abc8b96038b1782bc5497c5e" %} package: name: tracy @@ -13,7 +13,10 @@ source: git_rev: a654b57 build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage("tracy", max_pin="x.x") }} + requirements: build: @@ -55,3 +58,6 @@ extra: skip-lints: - uses_vcs_url - missing_hash + identifiers: + - doi:10.1186/s12864-020-6635-8 + - biotools:Gear-Genomics From 70f141c720ecd3cc739d2f0a6f1b9945e7d30239 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 17 Nov 2023 06:48:20 -0700 Subject: [PATCH 0793/2173] Update genoboo to 0.4.9 (#44312) --- recipes/genoboo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genoboo/meta.yaml b/recipes/genoboo/meta.yaml index 1dccadf084b90..4c0cd5d175a2c 100644 --- a/recipes/genoboo/meta.yaml +++ b/recipes/genoboo/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'genoboo' %} -{% set version = '0.4.8' %} -{% set sha256 = '09a3a5e520aae725eb7bf428490668dce02e89433dcd989f603d4393ad82b127' %} +{% set version = '0.4.9' %} +{% set sha256 = '5d8116ae6ed31d727ff96f405d1f173dde35ac98d0eaf6f6a5f10e9328d65466' %} package: name: {{ name|lower }} From 42a3aa88f4897c5efe72e08ca6c31df3c4166fc8 Mon Sep 17 00:00:00 2001 From: Vijini Mallawaarachchi Date: Sat, 18 Nov 2023 00:26:26 +1030 Subject: [PATCH 0794/2173] Add reneo v0.2.0 (#44309) * Add reneo v0.2.0 * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/reneo/meta.yaml | 52 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/reneo/meta.yaml diff --git a/recipes/reneo/meta.yaml b/recipes/reneo/meta.yaml new file mode 100644 index 0000000000000..78b5f9f67c1bf --- /dev/null +++ b/recipes/reneo/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "reneo" %} +{% set version = "0.2.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://github.com/Vini2/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" + sha256: 69a19c0043e722453da1a0c7fe280998707f30d05c555afcbdff0174115e574b + +build: + number: 0 + noarch: python + entry_points: + - reneo=reneo.__main__:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('reneo', max_pin="x") }} + +requirements: + host: + - python <3.11 + - pip + run: + - python <3.11 + - snakemake-minimal >=7.14.0 + - pyyaml >=6.0 + - click >=8.1.3 + - jinja2 >=3.0.2 + - mamba <1.4.2 + - metasnek >=0.0.5 + - snaketool-utils >=0.0.3 + +test: + commands: + - reneo --help + +about: + home: "https://github.com/Vini2/phables" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Reneo: Unraveling Viral Genomes from Metagenomes" + description: | + Reneo recovers high-quality genomes from viral communities (including both prokaryotic and eukaryotic viruses) found within metagenomes. + doc_url: "https://github.com/Vini2/reneo" + dev_url: "https://github.com/Vini2/reneo" + +extra: + recipe-maintainers: + - Vini2 From 062d268b9811ed3136af3f6437c6fe156952663f Mon Sep 17 00:00:00 2001 From: Vlad Savelyev Date: Fri, 17 Nov 2023 16:12:19 +0100 Subject: [PATCH 0795/2173] MultiQC 1.18 (#44318) --- recipes/multiqc/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index 9eeb34ce7ab11..5bcd8cc95d825 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.17" %} +{% set version = "1.18" %} package: name: multiqc @@ -6,10 +6,10 @@ package: source: url: https://github.com/ewels/MultiQC/archive/v{{ version }}.tar.gz - sha256: f28268e50ef57dbc330ba40eb8dcbb2b86029bc4542dd420fe180c914c284d34 + sha256: a6b1409607a05ecac452c2f8cd76167afca5d8f3df0b71f02e88d6f809f82d3c build: - number: 1 + number: 0 entry_points: - multiqc=multiqc.__main__:run_multiqc noarch: python @@ -36,6 +36,7 @@ requirements: - networkx >=2.5.1 - numpy - packaging + - pyaml-env - pyyaml >=4 - requests - rich >=10 From 20dbde8e0cc9a9cb6b4478333f63024983a920c7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 17 Nov 2023 09:54:18 -0700 Subject: [PATCH 0796/2173] Update gapmm2 to 23.11.3 (#44305) --- recipes/gapmm2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gapmm2/meta.yaml b/recipes/gapmm2/meta.yaml index 85b65281456ef..d1dc84eb881d0 100644 --- a/recipes/gapmm2/meta.yaml +++ b/recipes/gapmm2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gapmm2" %} -{% set version = "0.2.0" %} +{% set version = "23.11.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/gapmm2-{{ version }}.tar.gz - sha256: 185faa005babf32d5c1a0eab2032af8d7d370aa297643362b9673075c67cd2d6 + sha256: da058706e9e71a786ed6b35686a67ee53090258c8f16f7b2c07451cf85e05ddb build: number: 0 From efc1a91f2f75d3c595f02e4749c91d897c69ffae Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Sat, 18 Nov 2023 01:10:59 -0800 Subject: [PATCH 0797/2173] Update Ampliconsuite to 1.1.0 (#44325) --- recipes/ampliconsuite/build.sh | 6 ++++-- recipes/ampliconsuite/meta.yaml | 17 ++++++++--------- 2 files changed, 12 insertions(+), 11 deletions(-) diff --git a/recipes/ampliconsuite/build.sh b/recipes/ampliconsuite/build.sh index 2e0bd4e37c1ec..cf34795dc10cd 100644 --- a/recipes/ampliconsuite/build.sh +++ b/recipes/ampliconsuite/build.sh @@ -5,9 +5,8 @@ set -ex # we have to slightly reorganize the AA src files to make everything work mv ampliconarchitectlib/src/*.py ampliconarchitectlib/ -# add init for ampliconarchitect and ampliconclassifier tools, so they can be imported by AmpliconSuite-pipeline +# add init for ampliconarchitect, so it can be imported by AmpliconSuite-pipeline touch ampliconarchitectlib/__init__.py -touch ampliconclassifierlib/__init__.py # make the bin dir if it doesn't exist mkdir -p $PREFIX/bin @@ -16,6 +15,9 @@ mkdir -p $PREFIX/bin # setup.py will handle this in the next release cp AmpliconSuite-pipeline.py ${PREFIX}/bin/AmpliconSuite-pipeline.py cp GroupedAnalysisAmpSuite.py ${PREFIX}/bin/GroupedAnalysisAmpSuite.py +cp amplicon_classifier.py ${PREFIX}/bin/amplicon_classifier.py +cp feature_similarity.py ${PREFIX}/bin/feature_similarity.py +cp make_results_table.py ${PREFIX}/bin/make_results_table.py # Python command to install the package. $PYTHON setup.py install --install-data aa_data_repo/ --single-version-externally-managed --record=record.txt diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml index 3e7ec878b2a59..e7a4ba1f85188 100644 --- a/recipes/ampliconsuite/meta.yaml +++ b/recipes/ampliconsuite/meta.yaml @@ -1,7 +1,7 @@ {% set name="ampliconsuite" %} -{% set AS_version="1.0.0" %} +{% set AS_version="1.1.0" %} {% set AA_version="1.3.r6" %} -{% set AC_version="0.5.4" %} +{% set AC_version="1.0.0" %} package: name: {{ name }} @@ -11,15 +11,12 @@ source: # the sha256 sum is generated by doing # $ wget -O- [URL] | shasum -a 256 - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz - sha256: 7503c0545015a8891a716870f17c32d6f0f8806a92613640872ec9fd72a6bab7 + sha256: 9fd2d0f5bbdc0c60dd60ec38cef7cac1fd2253ce9b644360dbdefadd2c8af29b - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz sha256: cc21a52d9853cd5e0b5b9374773a6ea24191241b9b9cf1d71e2a928ab3d97f01 folder: ampliconarchitectlib - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz - sha256: 92684566d58187d8ef9f7990310793376ab39469fb925dd37f057dc236909faa - folder: ampliconclassifierlib - - + sha256: d1f35e17827947f657892b08c93c9694e9b33947e30d45e8e515084a5c96638d build: noarch: python @@ -50,11 +47,13 @@ requirements: test: commands: - AmpliconSuite-pipeline.py -v -# - amplicon_classifier.py -v # will be exposed in future builds + - amplicon_classifier.py -v + - feature_similarity.py -h + - make_results_table.py -h imports: - paalib - ampliconarchitectlib - - ampliconclassifierlib + - ampclasslib about: home: https://github.com/AmpliconSuite From a59e2733606b6b7864a5abb2eacd8746df1e2706 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 18 Nov 2023 03:49:52 -0700 Subject: [PATCH 0798/2173] Update viralmsa to 1.1.40 (#44328) --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index a5b203d7f9c7b..1a41b2d896121 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.39" %} +{% set version = "1.1.40" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: 00ff79a0b106cef69e7afaec8e16d2789ed5fb6243817588abcedfd4435269bb + sha256: eb61ebad514448b5eebb675a19bfe91b622c7d825fb11528c8331aa9d3d7222d requirements: run: From 3c113595265d2c9b36d208d7aa5e36a3e2480238 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 18 Nov 2023 03:50:24 -0700 Subject: [PATCH 0799/2173] Update xengsort to 2.0.2 (#44317) --- recipes/xengsort/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/xengsort/meta.yaml b/recipes/xengsort/meta.yaml index dfa270926fc3b..0950c1283bbf4 100644 --- a/recipes/xengsort/meta.yaml +++ b/recipes/xengsort/meta.yaml @@ -1,5 +1,5 @@ {% set name = "xengsort" %} -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 2eff6e76d5f1da2e0bad705b040d2cdf7dd2b2dbd74bb23a378676717a1d064c + sha256: 58540e42d86b943dc00e0d4b3b3131fb2dd26286b03228bf8a08553911a18052 build: number: 0 From 99d8e4666837d6010e56fac72302eb450c780006 Mon Sep 17 00:00:00 2001 From: Bede Constantinides Date: Sat, 18 Nov 2023 10:51:07 +0000 Subject: [PATCH 0800/2173] Update PAML to 4.10.7 (#44315) * Update PAML to 4.10.7 * Run exports --- recipes/paml/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/paml/meta.yaml b/recipes/paml/meta.yaml index 33a39a03b3389..1509d22de4f07 100644 --- a/recipes/paml/meta.yaml +++ b/recipes/paml/meta.yaml @@ -1,17 +1,19 @@ {% set name = "PAML" %} -{% set version = "4.10.6" %} -{% set sha256 = "d6437f04ee233209e1ded83addbfe65d1363185877a03ba7924ce81f9ebc7777" %} +{% set version = "4.10.7" %} +{% set sha256 = "0f29e768b3797b69eadc6332c3d046d8727702052d56c3b729883626c0a5a4e3" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/abacus-gene/paml/archive/v{{ version }}.tar.gz + url: https://github.com/abacus-gene/paml/archive/{{ version }}.tar.gz sha256: {{ sha256 }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('paml', max_pin="x.x") }} requirements: build: From 6667229c116627a4732e05d933128c5effd14238 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 18 Nov 2023 03:51:24 -0700 Subject: [PATCH 0801/2173] Update snakemake-interface-common to 1.14.3 (#44314) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 6b89e7aa82e39..55c7ce56fd11d 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.14.2" %} +{% set version = "1.14.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 377aa7760220f92deade72473cd9409b8715eaa2cd6f76b1965e035a5556ffe2 + sha256: 1ea9486d26841c169a85d9955ff9e8a3b720d9d64fda357d70e87b3cd70eeeee build: noarch: python From b078a2017868fe5318420a1672a552bd4041589f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 18 Nov 2023 03:51:42 -0700 Subject: [PATCH 0802/2173] Update virheat to 0.6 (#44311) --- recipes/virheat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/virheat/meta.yaml b/recipes/virheat/meta.yaml index 9b41c34d5d907..18cd21c835db9 100644 --- a/recipes/virheat/meta.yaml +++ b/recipes/virheat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "virheat" %} -{% set version = "0.5.4" %} +{% set version = "0.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/virheat-{{ version }}.tar.gz - sha256: 7e1264b2652ba044c7b52a9da5a58771ee82e0cc18d1e278a335dec16cc4e877 + sha256: 7005f5cfbab4aebc425457ef48607dbce5784c9319518f5d7cba3318b45587ba build: entry_points: From af4ece9ad90c8637f9a2f05a4b8a28d1d17ed4e5 Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Sat, 18 Nov 2023 12:40:41 +0000 Subject: [PATCH 0803/2173] Update SeqKit to v2.6.1 (#44329) --- recipes/seqkit/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml index edc5173c6b1dc..845a461c51f7a 100644 --- a/recipes/seqkit/meta.yaml +++ b/recipes/seqkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.6.0" %} +{% set version = "2.6.1" %} package: name: seqkit @@ -6,10 +6,10 @@ package: source: url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx] - md5: 879359e899326e360e6109e39dd23ca4 # [osx] + md5: c3596d65d5fa973a7c65485a97d735ac # [osx] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux] - md5: 6fa9f5f405834bf54e34a3de280b260c # [linux] + md5: c48e7806a03cb9e3f2c1a091c9113908 # [linux] build: number: 0 From 056c0bf7181785ea5a5f5db5fe1b9a73bc49256e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 18 Nov 2023 11:19:38 -0700 Subject: [PATCH 0804/2173] Update annonars to 0.25.0 (#44331) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 906b402fd2f00..23ceef1467a0d 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.24.5" %} +{% set version = "0.25.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 8e66712ff006206eeb55ef4c3342b38b1f30bfb414951bfeb9269d7c3ee7c5f4 + sha256: 1b07ae7a833cc3cd2dd7f501d1f9318d45f528b2990559946ca669451ec29909 requirements: build: From c0abcffd660a421ecece2f3e012e6bb2594f9528 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 18 Nov 2023 11:35:19 -0700 Subject: [PATCH 0805/2173] Update cutesv to 2.1.0 (#44303) * Update cutesv to 2.1.0 * Update cutesv to 2.1.0 * run_exports * add scitkit-learn and scipy --------- Co-authored-by: Thanh Lee Co-authored-by: joshuazhuang7 --- recipes/cutesv/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/cutesv/meta.yaml b/recipes/cutesv/meta.yaml index 6f61dca55da15..957edae2caec5 100644 --- a/recipes/cutesv/meta.yaml +++ b/recipes/cutesv/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.3" %} +{% set version = "2.1.0" %} package: name: cutesv @@ -6,12 +6,14 @@ package: source: url: https://github.com/tjiangHIT/cuteSV/archive/cuteSV-v{{ version }}.tar.gz - sha256: b29115148636c551976ec6e97d03f4da9e2fd4e81a2ea4b8b2b817afb9bbbd52 + sha256: c2d072e8c3c1a2a8ec52abe63ffc796d0e023385e850c4ead6e3a18c14f173d3 build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation -vvv . + run_exports: + - {{ pin_subpackage("cutesv", max_pin="x.x") }} requirements: host: @@ -24,6 +26,8 @@ requirements: - pysam >=0.15.0 - python >=3 - pyvcf + - scikit-learn + - scipy test: commands: From 13d766a2792d7a2945e5c5cd3ad13fe54d1a3310 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 18 Nov 2023 12:59:31 -0700 Subject: [PATCH 0806/2173] Update tn93 to 1.0.12 (#44323) * Update tn93 to 1.0.12 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/tn93/meta.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/tn93/meta.yaml b/recipes/tn93/meta.yaml index 1cf70e3eadd75..dd24eb3675cba 100644 --- a/recipes/tn93/meta.yaml +++ b/recipes/tn93/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.9" %} +{% set version = "1.0.12" %} package: name: tn93 @@ -6,10 +6,12 @@ package: source: url: https://github.com/veg/tn93/archive/v{{ version }}.tar.gz - sha256: de22038b3a0129a6a8f72bff300bb349c815d530566de8cd15febc1e73cf7768 + sha256: d60281b1b4375bff585bcfae57be6938606500a656682249da3e10ce222b889d build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('tn93', max_pin="x") }} requirements: build: @@ -19,8 +21,6 @@ requirements: - llvm-openmp # [osx] - libgomp # [linux] - cmake - host: - run: test: commands: @@ -29,5 +29,6 @@ test: about: home: https://github.com/veg/tn93 license: MIT + license_family: MIT license_file: LICENSE summary: This is a simple program meant to compute pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance. From 535d825386dcc410411a50fd7fd8bee1e0747380 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 18 Nov 2023 13:35:37 -0700 Subject: [PATCH 0807/2173] Update flams to 1.1.0 (#44321) * Update flams to 1.1.0 * edit tests * add pandas * fix tzdata pinning --------- Co-authored-by: joshuazhuang7 --- recipes/flams/meta.yaml | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/recipes/flams/meta.yaml b/recipes/flams/meta.yaml index c63f1c3d4e67d..bf037b77909e7 100644 --- a/recipes/flams/meta.yaml +++ b/recipes/flams/meta.yaml @@ -1,5 +1,5 @@ {% set name = "flams" %} -{% set version = "1.0.1" %} +{% set version = "1.1.0" %} package: name: {{ name|lower }} @@ -7,13 +7,13 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/flams-{{ version }}.tar.gz - sha256: fe553630ba355bf111b84e3a23081e360568472a01d4b366cefd8a3e13186006 + sha256: c67a3c0807d050ad17bbdcaa51ea04268d4a9cc062dd17ca9ef0b3c484614558 build: entry_points: - FLAMS = flams.flams:main noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -21,7 +21,6 @@ build: requirements: host: - python >=3.10 - - setuptools - pip run: - python >=3.10 @@ -34,20 +33,23 @@ requirements: - numpy ==1.24.3 - requests ==2.31.0 - urllib3 ==2.0.2 + - pandas ==2.1.2 + - python-dateutil ==2.8.2 + - pytz ==2023.3.post1 + - six ==1.16.0 + - tzdata ==2023c test: imports: - flams commands: - - pip check - FLAMS --help - requires: - - pip about: home: https://github.com/hannelorelongin/FLAMS summary: Find Lysine Acylation & other Modification Sites license: MIT + license_family: MIT license_file: LICENSE extra: From db1786c1d5a61fd504560f3d9dae615748cc55ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 19 Nov 2023 08:05:22 -0700 Subject: [PATCH 0808/2173] Update mehari to 0.18.0 (#44333) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 0eb4a6a8123f6..46ad0951133fa 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.17.1" %} -{% set sha256 = "cdb7e68f88df1439e8e05ffd4d9ebf011195700ae1936ea32cdd1bd65202bab0" %} +{% set version = "0.18.0" %} +{% set sha256 = "da2941ad65a4b9278eeec79cba812b15f579cb104ad6e73debb51ad1d1a3fe2e" %} package: name: mehari From 2695c494a99c52ea6da4555220298bf746ce10bb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 19 Nov 2023 08:53:52 -0700 Subject: [PATCH 0809/2173] Update mehari to 0.18.1 (#44334) * Update mehari to 0.18.0 * Update mehari to 0.18.1 --------- Co-authored-by: Manuel Holtgrewe --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 46ad0951133fa..038d7016447de 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.18.0" %} -{% set sha256 = "da2941ad65a4b9278eeec79cba812b15f579cb104ad6e73debb51ad1d1a3fe2e" %} +{% set version = "0.18.1" %} +{% set sha256 = "e25bed84505f1de7826680dc7e054c8596f46d054c1cfbcf74f29fe94229484f" %} package: name: mehari From 802f88c2ae6f4a19b7fa4d2dcfa61d8c75434457 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 19 Nov 2023 11:57:00 -0700 Subject: [PATCH 0810/2173] Update hicexplorer to 3.7.3 (#44322) * Update hicexplorer to 3.7.3 * Update meta.yaml --------- Co-authored-by: Joachim Wolff --- recipes/hicexplorer/meta.yaml | 45 +++++++++++++++++++---------------- 1 file changed, 24 insertions(+), 21 deletions(-) diff --git a/recipes/hicexplorer/meta.yaml b/recipes/hicexplorer/meta.yaml index c123fdc53fa78..4ee9927c54e42 100644 --- a/recipes/hicexplorer/meta.yaml +++ b/recipes/hicexplorer/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.7.2" %} +{% set version = "3.7.3" %} package: name: hicexplorer @@ -6,47 +6,49 @@ package: source: url: https://github.com/deeptools/HiCExplorer/archive/{{ version }}.tar.gz - sha256: dca71065dd4e549d578db96870b8d650b48f3dc852918ef19a345f436f612037 + sha256: db80bb90772795e603136b781f7dc81659509977e1e86dea7b298490cab73444 build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps -vv" noarch: python + run_exports: + - {{ pin_subpackage('hicexplorer', max_pin="x.x") }} requirements: host: - - python >=3.6 + - python >=3.8 - pip run: - - python >=3.6 + - python >=3.8 - numpy >=1.19 - - scipy >=1.5 - - matplotlib-base >=3.1.* - - ipykernel >=5.3.0 + - scipy >=1.10 + - matplotlib-base >=3.6 + - ipykernel >=6.25.2 - pysam - intervaltree - biopython - pytables - pybigwig - - pandas >=1.1.* + - pandas >=2.0 - jinja2 - - cooler >=0.8.10 + - cooler >=0.9.3 - future - unidecode - - hicmatrix >=15 - - cooler - - pygenometracks >=3.5 + - hicmatrix >=17 + - cooler >=0.9.3 + - pygenometracks >=3.8 - hic2cool >=0.8.3 - - fit_nbinom >=1.1 + - fit_nbinom >=1.2 - krbalancing >=0.0.5 - psutil - - pybedtools >=0.8 - - tqdm >=4.50 - - hyperopt >=0.2.4 - - python-graphviz >=0.14 - - scikit-learn >=0.23.2 - - imbalanced-learn >=0.7.* - - cleanlab >=0.1 + - pybedtools >=0.9 + - tqdm >=4.66 + - hyperopt >=0.2.7 + - python-graphviz >=0.20 + - scikit-learn >=1.3.1 + - imbalanced-learn >=0.11 + - cleanlab >=2.5 test: imports: @@ -104,4 +106,5 @@ extra: identifiers: - doi:10.1093/nar/gky504 - doi:10.1093/nar/gkaa220 + - doi:10.1093/gigascience/giac061 - usegalaxy-eu:hicexplorer_hicplotviewpoint From 460d7f9d42cbe5c30f56b680726146f54e440a63 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 19 Nov 2023 13:49:09 -0700 Subject: [PATCH 0811/2173] Update pybiolib to 1.1.1530 (#44320) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 268db70c3f6b3..81a71c0537ab8 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1527" %} +{% set version = "1.1.1530" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 8b7471274604ac6e10c47b52a6e6ae50cc87eb4f22facba485d03d354461b2a3 + sha256: 853fb7cb5dd2ef57c59109ef554b81becf5ba0b555f8648e4eb33ec368c716df build: noarch: python From 8d8c20099fe4437ffdc648e83cbbc2585ab3dc4e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 19 Nov 2023 13:49:28 -0700 Subject: [PATCH 0812/2173] Update oakvar to 2.9.64 (#44332) * Update oakvar to 2.9.63 * Update oakvar to 2.9.64 --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 26ef8420ae976..5dadb2f52affa 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.62" %} -{% set sha256 = "c62cc2754e2284d69a256169bf9e92bcf868470f28ad61471fdb0d965495c241" %} +{% set version = "2.9.64" %} +{% set sha256 = "16395f8aaeb6b79ce30c86be1c7535b91778d0d4941d65fe93a92dbd6db9414b" %} package: name: {{ name|lower }} From c114d6d612dc50d16d5f50acf8dfbfb9f5306527 Mon Sep 17 00:00:00 2001 From: Andreas Grigorjew Date: Mon, 20 Nov 2023 01:25:29 +0200 Subject: [PATCH 0813/2173] Rebuild: emerald 1.2.1 (#42930) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [emerald] Patch integrated in newest version * [emerald] Fix MacOS compiling issue * [emerald] Remove functional.patch * [emerald] update build.sh * [emerald] remove std::filesystem from code --------- Co-authored-by: Andreas Grigorjew Co-authored-by: Marcel Martin Co-authored-by: Björn Grüning --- recipes/emerald/functional.patch | 12 ------- recipes/emerald/meta.yaml | 6 ++-- recipes/emerald/no_filesystem.patch | 55 +++++++++++++++++++++++++++++ 3 files changed, 57 insertions(+), 16 deletions(-) delete mode 100644 recipes/emerald/functional.patch create mode 100644 recipes/emerald/no_filesystem.patch diff --git a/recipes/emerald/functional.patch b/recipes/emerald/functional.patch deleted file mode 100644 index d3c6ea235b805..0000000000000 --- a/recipes/emerald/functional.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/alpha_safe_paths.cpp b/alpha_safe_paths.cpp -index d5e42bc..a5a9620 100644 ---- src/alpha_safe_paths.cpp -+++ src/alpha_safe_paths.cpp -@@ -8,6 +8,7 @@ - #include - - #include "alpha_safe_paths.h" -+#include - #include "optimal_paths.h" - - diff --git a/recipes/emerald/meta.yaml b/recipes/emerald/meta.yaml index a3a3a9f121783..9e7f883929b5f 100644 --- a/recipes/emerald/meta.yaml +++ b/recipes/emerald/meta.yaml @@ -9,12 +9,10 @@ source: url: https://github.com/algbio/emerald/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} patches: - - functional.patch + - no_filesystem.patch build: - number: 0 - # Needs 10.15 or later - skip: True # [osx] + number: 1 run_exports: - {{ pin_subpackage('emerald', max_pin="x") }} diff --git a/recipes/emerald/no_filesystem.patch b/recipes/emerald/no_filesystem.patch new file mode 100644 index 0000000000000..f6adebee62651 --- /dev/null +++ b/recipes/emerald/no_filesystem.patch @@ -0,0 +1,55 @@ +diff --git a/src/main.cpp b/src/main.cpp +index 90b11ed..40e71f8 100644 +--- a/src/main.cpp ++++ b/src/main.cpp +@@ -6,10 +6,10 @@ + #include + #include + #include +-#include + #include + #include + #include ++#include + + #include + #include +@@ -19,8 +19,6 @@ + #include "optimal_paths.h" + #include "draw_subgraph.h" + +-namespace fs = std::filesystem; +- + int64_t print_usage(char **argv, int64_t help) { + std::cout << "Usage: " << argv[0] << " -f -o [arguments]\n\n"; + std::cout << "Optional arguments:\n"; +@@ -48,6 +46,11 @@ int64_t print_usage(char **argv, int64_t help) { + return help; + } + ++bool file_exists(const std::string &filename) { ++ struct stat buffer; ++ return (stat (filename.c_str(), &buffer) == 0); ++} ++ + struct Protein { + std::string descriptor; + std::string sequence; +@@ -120,7 +123,7 @@ void run_case(const int64_t j, std::vector &output) { + + if (print_alignments > 0) { + std::string subop_fasta_file = "suboptimal_" + file_without_path_and_ending + '_' + std::to_string(i) + ".fasta"; +- for (int fidx = 1; fs::exists(fs::path(subop_fasta_file)); fidx++) { ++ for (int fidx = 1; file_exists(subop_fasta_file); fidx++) { + subop_fasta_file = "suboptimal_" + file_without_path_and_ending + '_' + std::to_string(i) + '(' + std::to_string(fidx) + ").fasta"; + } + alignments_into_fasta(print_alignments, d, a, b, subop_fasta_file); +@@ -313,7 +316,7 @@ int main(int argc, char **argv) { + return print_usage(argv, 1); + } + +- if (drawgraph && !fs::exists(fs::path(drawgraph_dir))) { ++ if (drawgraph && !file_exists(drawgraph_dir)) { + std::cerr << "Error: directory " << drawgraph_dir << " does not exist.\n"; + return 2; + } From 78e6a87368ed73b97883cb68d8d93bc1c38c5706 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 19 Nov 2023 23:00:37 -0700 Subject: [PATCH 0814/2173] Update aviary to 0.8.3 (#44342) * Update aviary to 0.8.3 * aviary: Update deps. --------- Co-authored-by: Ben Woodcroft --- recipes/aviary/meta.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/aviary/meta.yaml b/recipes/aviary/meta.yaml index 7e5d8bbcd7ace..eba258abc566c 100644 --- a/recipes/aviary/meta.yaml +++ b/recipes/aviary/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.8.2" %} +{% set version = "0.8.3" %} {% set name = "aviary" %} -{% set sha256 = "0f3299acc2586a1cca5a1c6588d63bc1bcf613a1feac91534ea9b532957f0ba1" %} +{% set sha256 = "c484f2bef8ac783e2fbb93270b8a8e034e1139eef2bf641ccfa3a4f17e78abcb" %} package: name: aviary @@ -22,9 +22,9 @@ requirements: - python >=3.8 - pip run: - - python >=3.8 - - snakemake >=6.0.5, <=7.17 - - ruamel.yaml >=0.15.99 # needs to be explicit + - python >=3.8,<=3.11 + - snakemake >=7.0.0,<=7.32.3 + - ruamel.yaml >=0.15.99 - numpy - pandas - biopython @@ -32,6 +32,7 @@ requirements: - pigz =2.6 - parallel - bbmap + - extern test: commands: From 275a5efb3f289982d1102f20313c66317850fdcd Mon Sep 17 00:00:00 2001 From: Dirk-Jan <72025902+dirkjanvw@users.noreply.github.com> Date: Mon, 20 Nov 2023 11:53:30 +0100 Subject: [PATCH 0815/2173] Update Pantools v4.2.3 recipe (#44182) * make bcftools and busco linux specific * replace build in requirements section by host --- recipes/pantools/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/pantools/meta.yaml b/recipes/pantools/meta.yaml index bd623054fb43f..a178e072c607c 100644 --- a/recipes/pantools/meta.yaml +++ b/recipes/pantools/meta.yaml @@ -12,12 +12,12 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage("pantools", max_pin="x") }} requirements: - build: + host: - openjdk =8 - maven - jq @@ -32,13 +32,13 @@ requirements: - blast - mash =2.3 - fastani - #- busco =5 #causes conflicts on macOS + - busco =5 # [linux] - r-base >=3.5.0 - r-ggplot2 - r-ape - graphviz - aster =1.3 - #- bcftools >=1.12 #causes conflicts on macOS + - bcftools >=1.12 # [linux] - tabix test: @@ -68,7 +68,6 @@ extra: If you want to overwrite it you can specify these values directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with "pantools -Xms512m -Xmx1g". - NB: Both `BUSCO` and `bcftools` are dependencies of PanTools but they are not included in this recipe due to conflicts on MacOS. identifiers: - doi:https://doi.org/10.1093/bioinformatics/btw455 - doi:https://doi.org/10.1186/s12859-018-2362-4 From 420178b00a45eaed279c4591964aac7581a6ff3b Mon Sep 17 00:00:00 2001 From: Mikko Rautiainen Date: Mon, 20 Nov 2023 13:36:30 +0200 Subject: [PATCH 0816/2173] Update MBG to version 1.0.16 (#44345) --- recipes/mbg/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/mbg/meta.yaml b/recipes/mbg/meta.yaml index a294ea3ab2f91..0ba6a59d45aed 100644 --- a/recipes/mbg/meta.yaml +++ b/recipes/mbg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MBG" %} -{% set version = "1.0.15" %} +{% set version = "1.0.16" %} package: name: {{ name|lower }} @@ -7,14 +7,16 @@ package: source: - url: https://github.com/maickrau/{{ name }}/files/11663997/{{ name }}.tar.gz - sha256: 8df3a3169f5f3ca099b71306b80e39e170413e536a4317cee38851e12ddf1653 + url: https://github.com/maickrau/{{ name }}/files/13408153/{{ name }}.tar.gz + sha256: b51f1013c72baed3f2f725bb605e98eb290df285afae7ba219b1cadd9791a50e patches: - version.patch - osx_availability.patch # [osx] build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('mbg', max_pin="x.x") }} requirements: build: From 635a17e4c609e4a2bf3ef80fea87b25dc386a220 Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Mon, 20 Nov 2023 06:38:16 -0500 Subject: [PATCH 0817/2173] Update gsearch v0.1.5 (#44343) --- recipes/gsearch/build_failure.osx-64.yaml | 104 ---------------------- recipes/gsearch/meta.yaml | 14 +-- 2 files changed, 9 insertions(+), 109 deletions(-) delete mode 100644 recipes/gsearch/build_failure.osx-64.yaml diff --git a/recipes/gsearch/build_failure.osx-64.yaml b/recipes/gsearch/build_failure.osx-64.yaml deleted file mode 100644 index 2e8b5279f9afc..0000000000000 --- a/recipes/gsearch/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: a757e7bcf784bac32f841424569be0135f9947f99404b0c044e4f2fab56298f4 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - f32 - f64 - note: required by a bound in probminhash::superminhasher::SuperMinHash - --> /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/probminhash-0.1.8/src/superminhasher.rs:92:28 - | - 92 | pub struct SuperMinHash { - | ^^^^^ required by this bound in SuperMinHash - - error[E0277]: the trait bound probminhash::superminhasher::NoHashHasher: Hash is not satisfied - --> /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/kmerutils-0.0.7/src/sketching/seqminhash.rs:24:24 - | - 24 | let mut sminhash : SuperMinHash= SuperMinHash::new(sketch_size, &bh); - | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ the trait Hash is not implemented for probminhash::superminhasher::NoHashHasher - | - note: required by a bound in probminhash::superminhasher::SuperMinHash - --> /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/probminhash-0.1.8/src/superminhasher.rs:92:38 - | - 92 | pub struct SuperMinHash { - | ^^^^ required by this bound in SuperMinHash - - error[E0277]: the trait bound u32: num::Float is not satisfied - --> /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/kmerutils-0.0.7/src/sketching/seqminhash.rs:24:57 - | - 24 | let mut sminhash : SuperMinHash= SuperMinHash::new(sketch_size, &bh); - | ^^^^^^^^^^^^^^^^^ the trait num::Float is not implemented for u32 - | - = help: the following other types implement trait num::Float: - f32 - f64 - note: required by a bound in probminhash::superminhasher::SuperMinHash::::new - --> /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/probminhash-0.1.8/src/superminhasher.rs:113:10 - | - 113 | impl SuperMinHash { - | ^^^^^ required by this bound in SuperMinHash::::new - - error[E0277]: the trait bound probminhash::superminhasher::NoHashHasher: Hash is not satisfied - --> /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/kmerutils-0.0.7/src/sketching/seqminhash.rs:24:57 - | - 24 | let mut sminhash : SuperMinHash= SuperMinHash::new(sketch_size, &bh); - | ^^^^^^^^^^^^^^^^^ the trait Hash is not implemented for probminhash::superminhasher::NoHashHasher - | - note: required by a bound in probminhash::superminhasher::SuperMinHash::::new - --> /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/probminhash-0.1.8/src/superminhasher.rs:113:53 - | - 113 | impl SuperMinHash { - | ^^^^ required by this bound in SuperMinHash::::new - - error[E0277]: the trait bound u32: num::Float is not satisfied - --> /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/kmerutils-0.0.7/src/sketching/seqminhash.rs:24:57 - | - 24 | let mut sminhash : SuperMinHash= SuperMinHash::new(sketch_size, &bh); - | ^^^^^^^^^^^^ the trait num::Float is not implemented for u32 - | - = help: the following other types implement trait num::Float: - f32 - f64 - note: required by a bound in probminhash::superminhasher::SuperMinHash - --> /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/probminhash-0.1.8/src/superminhasher.rs:92:28 - | - 92 | pub struct SuperMinHash { - | ^^^^^ required by this bound in SuperMinHash - - error[E0277]: the trait bound probminhash::superminhasher::NoHashHasher: Hash is not satisfied - --> /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/kmerutils-0.0.7/src/sketching/seqminhash.rs:24:57 - | - 24 | let mut sminhash : SuperMinHash= SuperMinHash::new(sketch_size, &bh); - | ^^^^^^^^^^^^ the trait Hash is not implemented for probminhash::superminhasher::NoHashHasher - | - note: required by a bound in probminhash::superminhasher::SuperMinHash - --> /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/probminhash-0.1.8/src/superminhasher.rs:92:38 - | - 92 | pub struct SuperMinHash { - | ^^^^ required by this bound in SuperMinHash - - Some errors have detailed explanations: E0107, E0277. - For more information about an error, try rustc --explain E0107. - error: could not compile kmerutils due to 7 previous errors - - Caused by: - process didn't exit successfully: rustc --crate-name kmerutils --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/.cargo/registry/src/github.com-1ecc6299db9ec823/kmerutils-0.0.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' -C metadata=e577b0b5627b4f68 -C extra-filename=-e577b0b5627b4f68 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps --extern bloom=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libbloom-b042290736fb2c21.rmeta --extern clap=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libclap-0e5c203b73694e8c.rmeta --extern crossbeam=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libcrossbeam-26e83c0342dd1b90.rmeta --extern cuckoofilter=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libcuckoofilter-7b2b60a32aee81ef.rmeta --extern env_logger=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libenv_logger-1a3c6c9b35203a91.rmeta --extern fnv=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libfnv-36ca22b81d6ef64e.rmeta --extern fxhash=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libfxhash-ceb1768b1b16ddcd.rmeta --extern histogram=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libhistogram-3a70a6b2fa5b3eb5.rmeta --extern hnsw_rs=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libhnsw_rs-7b7760b4e8956c7a.rmeta --extern indexmap=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libindexmap-684ec2db7e8e2771.rmeta --extern lazy_static=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/liblazy_static-a938bfd90d819d09.rmeta --extern log=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/liblog-62ef23b456af1749.rmeta --extern metrohash=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libmetrohash-4249c76a367913c5.rmeta --extern multimap=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libmultimap-27eb9f8b808ad9e4.rmeta --extern ndarray=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libndarray-4a8af6554346deca.rmeta --extern needletail=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libneedletail-74093466191669cd.rlib --extern num=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libnum-722dbb8692acf49f.rmeta --extern num_cpus=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libnum_cpus-2975b7a552267876.rmeta --extern parking_lot=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libparking_lot-de9b1db1c4952286.rmeta --extern probminhash=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libprobminhash-50fe35d6dd33ee8b.rmeta --extern rand=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/librand-3b86af9d9169e472.rmeta --extern rand_distr=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/librand_distr-b1483d48a6743dd1.rmeta --extern rand_xorshift=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/librand_xorshift-3b32a0de8818658d.rmeta --extern rand_xoshiro=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/librand_xoshiro-3fb444d2c1067b8d.rmeta --extern rayon=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/librayon-7fa37c0bbc464749.rmeta --extern redis=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libredis-482eb422382e614d.rmeta --extern serde=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libserde-3963c483b06466c2.rmeta --extern serde_json=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libserde_json-5dac48cd2776f9c6.rmeta --extern wavelet_matrix=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libwavelet_matrix-a852f4963c7d12bd.rmeta --extern wyhash=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libwyhash-cbb0fc501026a983.rmeta --extern xdr_codec=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/deps/libxdr_codec-a37dee4acd904d76.rmeta --cap-lints allow -L native=/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target/release/build/bzip2-sys-25122d71c3cd00dd/out/lib -L native=/usr/local/Cellar/xz/5.4.3/lib (exit status: 1) - warning: build failed, waiting for other jobs to finish... - error: failed to compile gsearch v0.0.12 (/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work), intermediate artifacts can be found at /opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/target - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/gsearch_1685356475155/work/conda_build.sh']' returned non-zero exit status 101. -# Last 100 lines of the build log. diff --git a/recipes/gsearch/meta.yaml b/recipes/gsearch/meta.yaml index 61ba716dfb67a..72eb49f2cb25f 100644 --- a/recipes/gsearch/meta.yaml +++ b/recipes/gsearch/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.4" %} +{% set version = "0.1.5" %} package: name: gsearch @@ -7,11 +7,11 @@ package: build: number: 0 run_exports: - - {{ pin_subpackage('gsearch', max_pin="x") }} + - {{ pin_subpackage('gsearch', max_pin="x.x") }} skip: True # [osx] source: - url: https://github.com/jean-pierreBoth/gsearch/archive/v{{ version }}.tar.gz - sha256: f5ae10b46dbc81604723fe8460dfe71215d49d33f605c06f124ab1935f74d893 + url: https://github.com/jianshu93/gsearch/archive/v{{ version }}.tar.gz + sha256: d25e6a8353b79da1fd3e2fafa49461e4be3352bdedd48fb2dcdfe12c76aa100f requirements: build: @@ -28,4 +28,8 @@ test: about: home: https://github.com/jean-pierreBoth/gsearch license: MIT - summary: gsearch is an ultra-fast and scalable microbial genome search program based on MinHash-like metric and graph-based approximate nearest neighbor search + summary: gsearch is an ultra-fast and scalable microbial genome search program based on MinHash-like metrics and graph-based approximate nearest neighbor search +extra: + maintainers: + - Jean Pierre-Both + - Jianshu Zhao From 2f6e425b8e5bd2c5f8b856164a6e0ae6a470dd0e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 05:54:20 -0700 Subject: [PATCH 0818/2173] Update monsda to 1.2.1 (#44353) --- recipes/monsda/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/monsda/meta.yaml b/recipes/monsda/meta.yaml index 1ae416497703e..abbdf7e347767 100644 --- a/recipes/monsda/meta.yaml +++ b/recipes/monsda/meta.yaml @@ -1,6 +1,6 @@ {% set name = "MONSDA" %} -{% set version = "1.2.0" %} -{% set sha256 = "375984684d9852fe8c466d65a44e13b1cfb593fdbe9aee6b7340bcf15796b47d" %} +{% set version = "1.2.1" %} +{% set sha256 = "ccb30c5a047a6f0bf0a8b074697ddc1c72052b0c85dcd76a7c3e1f78f7a133f2" %} package: name: "{{ name|lower }}" From d4547a708da5e69460c19150ed2a7bf54cd42371 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 06:04:00 -0700 Subject: [PATCH 0819/2173] Update thapbi-pict to 1.0.4 (#44352) --- recipes/thapbi-pict/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 833f3a572cddd..43e04010dd3bc 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.3" %} +{% set version = "1.0.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: b27551dd862ed090f110296f0d8a05f8e3ea2443bb3c81403b9353ec3ae17b1b + sha256: b845cca32700d0e62e13e148b0a759d0822958738109ff7bf1ab6bad7c89bf52 build: noarch: python From baf735e46d0cb7043d7e11ab6ffc8ae91de1dd11 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 07:01:17 -0700 Subject: [PATCH 0820/2173] Update annonars to 0.26.0 (#44354) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 23ceef1467a0d..55ba834efbd0a 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.25.0" %} +{% set version = "0.26.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 1b07ae7a833cc3cd2dd7f501d1f9318d45f528b2990559946ca669451ec29909 + sha256: 31b49f1f0d4d19038cd3c9817480c4eefc5fe27a117a30164981d2b302845759 requirements: build: From 762f1ae76ae966326d8bea9dba7bf0a9b10c48ad Mon Sep 17 00:00:00 2001 From: Nate Date: Mon, 20 Nov 2023 06:22:54 -0800 Subject: [PATCH 0821/2173] Add bacpage recipe (#44215) * updated metadata * Linting * run_exports? * Tested and passing * Use SPDX identifiers * Removed majority of pins --- recipes/bacpage/meta.yaml | 61 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 recipes/bacpage/meta.yaml diff --git a/recipes/bacpage/meta.yaml b/recipes/bacpage/meta.yaml new file mode 100644 index 0000000000000..7183c904056a0 --- /dev/null +++ b/recipes/bacpage/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "2023.11.10.1" %} + +package: + name: bacpage + version: {{ version }} + +source: + url: https://github.com/CholGen/bacpage/archive/refs/tags/{{ version }}.tar.gz + sha256: 7a62278131407195a8f7555a92ed2d86ca7e63366bac6d280dac337e5f5218c5 + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed ." + run_exports: + - {{ pin_subpackage('bacpage') }} + +requirements: + host: + - python <3.12,>=3.9 + - pip + run: + - python <3.12,>=3.9 + - bc + - bcftools =1.17 + - bedtools + - biopython + - bwa + - emboss + - fastqc + - iqtree + - multiqc + - pandas + - qualimap + - samtools =1.17 + - snakemake-minimal + - snp-sites + - fastp + - lighter + - flash + - unicycler + - prokka + - quast + - abricate + +test: + commands: + - bacpage -h + - bacpage version + - bacpage example "$(mktemp -d)" + +about: + home: https://github.com/CholGen/bacpage + license: "GPL-3.0-or-later" + license_file: LICENSE + summary: An easy-to-use pipeline for the assembly and analysis of bacterial genomes + + +extra: + recipe-maintainers: + - watronfire From aeae6cf926eff056395e93a383ddbf80be7fc7e3 Mon Sep 17 00:00:00 2001 From: Thanh Lee Date: Mon, 20 Nov 2023 15:31:31 +0000 Subject: [PATCH 0822/2173] Add Centrifuger (#44338) * add centrifuger * add zlib * typo * fix test --- recipes/centrifuger/build.sh | 12 ++++++++++ recipes/centrifuger/meta.yaml | 44 +++++++++++++++++++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 recipes/centrifuger/build.sh create mode 100644 recipes/centrifuger/meta.yaml diff --git a/recipes/centrifuger/build.sh b/recipes/centrifuger/build.sh new file mode 100644 index 0000000000000..5198e76cc7426 --- /dev/null +++ b/recipes/centrifuger/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +export LDFLAGS="-L$PREFIX/lib" +export CPATH=${PREFIX}/include + +mkdir -p $PREFIX/bin + +make CXX=$CXX RELEASE_FLAGS="$CXXFLAGS" +chmod +x centrifuger-download +chmod +x centrifuger-kreport +chmod +x centrifuger-inspect + +cp {centrifuger,centrifuger-build,centrifuger-download,centrifuger-kreport,centrifuger-inspect} $PREFIX/bin diff --git a/recipes/centrifuger/meta.yaml b/recipes/centrifuger/meta.yaml new file mode 100644 index 0000000000000..a25ea6d2ebf32 --- /dev/null +++ b/recipes/centrifuger/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "centrifuger" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +source: + url: https://github.com/mourisl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 88d8e9031caa9298a2ea0c3a7a4d4a8a2a569dcc32cf6f795a13cdf03612aa49 + +requirements: + build: + - zlib + - make + - {{ compiler('cxx') }} + host: + - zlib + run: + - zlib + - perl + - wget + - tar + - python + +test: + commands: + - centrifuger -v | grep 'Centrifuger v' + - centrifuger-inspect 2>&1 | grep 'Required' + + +about: + home: https://github.com/mourisl/centrifuger + license: MIT + summary: 'Lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.' + +extra: + identifiers: + - doi:10.1101/2023.11.15.567129 From 4a9a4b2acf70c03f945d8d41648f0610a92a2a1a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 09:46:28 -0700 Subject: [PATCH 0823/2173] Update nanometa-live to 0.4.0 (#44336) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update nanometa-live to 0.4.0 * Update meta.yaml --------- Co-authored-by: Andreas Sjödin --- recipes/nanometa-live/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/nanometa-live/meta.yaml b/recipes/nanometa-live/meta.yaml index 2a4c4083c716b..d2c9332d1ed55 100644 --- a/recipes/nanometa-live/meta.yaml +++ b/recipes/nanometa-live/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanometa-live" %} -{% set version = "0.3.1" %} +{% set version = "0.4.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/FOI-Bioinformatics/nanometa_live/archive/{{ version }}.tar.gz - sha256: 8511a86d3ea689ca0abec0c45b814a98ac0fd2c67dfd25d3a660aae50a3c0c6b + sha256: 2c19b9df861391bbee842fbd6e92db43a3585bd881ab9cb8dfbc16d20bb06ae6 build: number: 0 @@ -45,6 +45,7 @@ requirements: - fastp >=0.23.2 - ruamel.yaml >=0.17.32 - ncbi-datasets-cli >=15.20.0 + - tqdm >=4.62.3 test: commands: From 511a4d3646ad5f09b6d4469815627579bc76f0f2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 13:29:23 -0700 Subject: [PATCH 0824/2173] Update pybiolib to 1.1.1533 (#44356) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 81a71c0537ab8..8eebe8d714756 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1530" %} +{% set version = "1.1.1533" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 853fb7cb5dd2ef57c59109ef554b81becf5ba0b555f8648e4eb33ec368c716df + sha256: 666e4f0f60012951b2a1e98468df99256fda01df7442cc0cb1830ca1a3d2a160 build: noarch: python From a047134e6942f5a512c43476d917c12dc88d5ef6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 13:45:48 -0700 Subject: [PATCH 0825/2173] Update taxmyphage to 0.2.4 (#44359) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index ec427135f67eb..ed901718bfef5 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.2.3" %} +{% set version = "0.2.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: 3eb12912217fd1020230756cf4d266922f98af7fbb2485ad69c7dc333f3bf6f0 + sha256: a8267f8c2af478876e000edd595d58153d9c5d2b497ca61a667858a3d434b061 build: entry_points: From 218e52f68bfb071f7705f2a246936af18bc6234e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 13:46:07 -0700 Subject: [PATCH 0826/2173] Update varvamp to 0.9.5 (#44350) --- recipes/varvamp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varvamp/meta.yaml b/recipes/varvamp/meta.yaml index c523c95c14113..9d6ea2b324986 100644 --- a/recipes/varvamp/meta.yaml +++ b/recipes/varvamp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varvamp" %} -{% set version = "0.9.4" %} +{% set version = "0.9.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/varvamp-{{ version }}.tar.gz - sha256: 1b5a0a40235ab295a961c7136a5eb3127e1e70f96887dc70ca7b7b7614bcf4b0 + sha256: 9d6d0d5dc6095aab8920089fd730595ec33bdd43a7de6309bdce84e7870dca4b build: entry_points: From 5c2f4d64df223f95233dafd143687040968e66df Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 13:46:30 -0700 Subject: [PATCH 0827/2173] Update genmod to 3.8.1 (#44355) --- recipes/genmod/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genmod/meta.yaml b/recipes/genmod/meta.yaml index fd4a3b92d4cb6..1cd3b5465f5b2 100644 --- a/recipes/genmod/meta.yaml +++ b/recipes/genmod/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genmod" %} -{% set version = "3.8.0" %} +{% set version = "3.8.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e057cb2e630a3e16eeb63735ab604cc5315998a4a89993d57f03680c3fd8c9f3 + sha256: d21f072f6c4a34479bc0f1633bd7a15b04a04c87f63f28457dce58615a0a7f14 build: number: 0 From 46a1fba89b77557ba7eb6937eaea71212dca789a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 13:46:43 -0700 Subject: [PATCH 0828/2173] Update perl-minion to 10.27 (#44357) --- recipes/perl-minion/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-minion/meta.yaml b/recipes/perl-minion/meta.yaml index c492b93ae8a94..bca6af67b1818 100644 --- a/recipes/perl-minion/meta.yaml +++ b/recipes/perl-minion/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-minion" %} -{% set version = "10.26" %} -{% set sha256 = "00c57a3ab909f29fc8c577eb05b7bcede2961e6727275b62acab74940d0cc3a0" %} +{% set version = "10.27" %} +{% set sha256 = "c8c5c64d4b3ac8359ed78227b47992bd6ccc3496110849cef228191f895ceb54" %} package: name: {{ name }} From 7e89566dd2e81b65d015dacc8d95214aed193caf Mon Sep 17 00:00:00 2001 From: mzytnicki <34034101+mzytnicki@users.noreply.github.com> Date: Mon, 20 Nov 2023 21:46:56 +0100 Subject: [PATCH 0829/2173] Update to mmquant 1.0.9 (#44351) --- recipes/mmquant/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mmquant/meta.yaml b/recipes/mmquant/meta.yaml index 0ddba5d1823be..9e281487b471e 100644 --- a/recipes/mmquant/meta.yaml +++ b/recipes/mmquant/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mmquant" %} -{% set version = "1.0.7" %} +{% set version = "1.0.9" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ build: source: url: https://bitbucket.org/mzytnicki/multi-mapping-counter/get/{{ version }}.tar.gz - sha256: 077ec5c470e653a97da01399cf47e75de41c234d708db75c7d1bdb0e77f7e6bb + sha256: 208852b8efa85d9bf5b88906dde329d0c312a90897c7b00481c87116a12ea2eb requirements: build: From 7922d0d6013ec43516c816b32fa3de9c2b924bb9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 13:47:10 -0700 Subject: [PATCH 0830/2173] Update koverage to 0.1.7 (#44349) --- recipes/koverage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/koverage/meta.yaml b/recipes/koverage/meta.yaml index 951b2bf6ce1d3..385acafa06329 100644 --- a/recipes/koverage/meta.yaml +++ b/recipes/koverage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "koverage" %} -{% set version = "0.1.6" %} +{% set version = "0.1.7" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 66da69ae446f89a30429f30437a95dccd909e8147f3260c1df88ca486a8139f4 + sha256: 75561037d21f1577200b659d097ef72ccb305f2cf5323eabda5d86cee15916ff build: noarch: python From 28c2198ba3f6328d834fae113825da6485f94608 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 13:48:02 -0700 Subject: [PATCH 0831/2173] Update snakemake-interface-executor-plugins to 8.0.2 (#44348) * Update snakemake-interface-executor-plugins to 8.0.0 * Update snakemake-interface-executor-plugins to 8.0.2 --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index 1e3188eee8369..3b97d69376c22 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "7.0.3" %} +{% set version = "8.0.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: ace3c8c9fdc80ce8f612af3d372a6e2e40bf10b031b2539660d5a37075dc257d + sha256: e7838042762b8946cbfae62887ee8ad9b7273e2c3296199c6385c8c2805934c6 build: noarch: python From c6fee3841358c73e058fd82d63bd002a37fb8b9d Mon Sep 17 00:00:00 2001 From: Mikko Rautiainen Date: Mon, 20 Nov 2023 22:48:25 +0200 Subject: [PATCH 0832/2173] Update GraphAligner to version 1.0.18 (#44346) * Update GraphAligner to version 1.0.18 * fix for osx compilation issue --- recipes/graphaligner/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/graphaligner/meta.yaml b/recipes/graphaligner/meta.yaml index c4977bd3f8f8b..ff837db9ff3f9 100644 --- a/recipes/graphaligner/meta.yaml +++ b/recipes/graphaligner/meta.yaml @@ -1,19 +1,21 @@ {% set name = "GraphAligner" %} -{% set version = "1.0.17b" %} +{% set version = "1.0.18" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/maickrau/{{ name }}/files/10706255/{{ name }}.tar.gz - sha256: b0eb5531bf111f808feeaf35045d43b7d81f75d87003458c7415622c9e3006ad + url: https://github.com/maickrau/{{ name }}/files/13412859/{{ name }}.tar.gz + sha256: 69d248332c1df732b74571f9910d3390bfeb48165fb9d99a892ec0a71ab1291f patches: - version.patch - linux_link.patch # [linux] build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('graphaligner', max_pin="x.x") }} requirements: build: From b6b353b84af2e9c00a1bf5ddd063a39ed63207a0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 16:56:59 -0700 Subject: [PATCH 0833/2173] Update dnaio to 1.1.0 (#44364) --- recipes/dnaio/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/dnaio/meta.yaml b/recipes/dnaio/meta.yaml index 93ac5a5829be8..d98d56e78497e 100644 --- a/recipes/dnaio/meta.yaml +++ b/recipes/dnaio/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "1.0.1" %} +{% set version = "1.1.0" %} package: name: dnaio version: {{ version }} source: - url: https://files.pythonhosted.org/packages/45/65/29b0648880cc84906c5e66433b89cd63f1b001fe46c33761091302dd65ea/dnaio-1.0.1.tar.gz - sha256: 48cb0a8763d91aee329414f7756ee635dd78f6c059d5dbd0de78fb3b15f8a32a + url: https://files.pythonhosted.org/packages/c6/67/d07ada36ad76198197cee7deea862ee568aa255adc8b6f93535f5bf00da8/dnaio-1.1.0.tar.gz + sha256: 7ecdfb3de3fd82c69b9750ba66202edc095610646d0720961ca7308af4ee8c45 build: number: 0 From 17ba38223baf13d0431f8c841bab8991b4c0f3d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 17:06:27 -0700 Subject: [PATCH 0834/2173] Update bifrost to 1.3.1 (#43579) * Update bifrost to 1.3.0 * add run_exports * Update bifrost to 1.3.0 * Update bifrost to 1.3.1 --------- Co-authored-by: joshuazhuang7 Co-authored-by: Thanh Lee --- recipes/bifrost/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/bifrost/meta.yaml b/recipes/bifrost/meta.yaml index 86e8668780e78..5ca33f7b6ee0d 100644 --- a/recipes/bifrost/meta.yaml +++ b/recipes/bifrost/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bifrost" %} -{% set version = "1.2.1" %} +{% set version = "1.3.1" %} package: name: {{ name|lower }} @@ -7,10 +7,13 @@ package: source: url: https://github.com/pmelsted/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: fe93080ef3ea71ff009fc206b5c17dd40fbfd18293000621a83d7d947dfedf1a + sha256: d6a9baacddba8e9508336c5adff15a8a482774c724fc0710392fed7bb9ad1e8b build: number: 0 + # v1.3.0 breaks Bifrost Index File (.bfi) compatibility with previous Bifrost versions + run_exports: + - {{ pin_subpackage('bifrost', max_pin="x.x") }} requirements: build: From abe08db8a2cea6fc49bf57c82c0009caf0fe2c87 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 17:49:34 -0700 Subject: [PATCH 0835/2173] Update pairtools to 1.0.3 (#44361) * Update pairtools to 1.0.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/pairtools/meta.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/pairtools/meta.yaml b/recipes/pairtools/meta.yaml index 71df1535aacad..43d9a7bf44b70 100644 --- a/recipes/pairtools/meta.yaml +++ b/recipes/pairtools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pairtools" %} -{% set version = "1.0.2" %} +{% set version = "1.0.3" %} package: name: {{ name|lower }} @@ -7,13 +7,15 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: af031b369b9d99ecd6388b2c116425a9d5c6fdb98146d44d5d013c92b3704917 + sha256: 12b482f04d66a01b80ababfb4b6d37959f7995c29f4bb1640f1102d8566d478f build: - number: 1 + number: 0 skip: True # [osx or py<37] entry_points: - pairtools = pairtools.cli:cli + run_exports: + - {{ pin_subpackage('pairtools', max_pin="x") }} requirements: build: @@ -21,7 +23,7 @@ requirements: - {{ compiler('cxx') }} host: - python - - setuptools + - pip - cython - numpy - pysam >=0.19 @@ -44,7 +46,6 @@ requirements: test: imports: - pairtools - commands: # click requires a unicode locale - pairtools --help From 755a4e921d3004aad767ccd29a6126631313a80a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 17:51:14 -0700 Subject: [PATCH 0836/2173] Update runjob to 2.10.6 (#44341) * Update runjob to 2.10.6 * add run_exports * remove batchcompute --------- Co-authored-by: joshuazhuang7 --- recipes/runjob/meta.yaml | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/recipes/runjob/meta.yaml b/recipes/runjob/meta.yaml index 76d1832ef7fc5..b72d313a2fd04 100644 --- a/recipes/runjob/meta.yaml +++ b/recipes/runjob/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.10.5" %} +{% set version = "2.10.6" %} {% set bc = "batchcompute" %} {% set bcv = "2.1.7" %} @@ -8,20 +8,23 @@ package: source: url: https://github.com/yodeng/runjob/archive/v{{ version }}.tar.gz - sha256: 82e96404a91ee6f5d9daa67af329d5e8b680860f08681e7b5b24a20b29e67811 + sha256: bb87cc67abeafd3374d5668d2eacee5e64d0949205fac274b7b715e464680fbe build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install -vv --no-deps . https://pypi.io/packages/source/{{ bc[0] }}/{{ bc }}/{{ bc }}-{{ bcv }}.tar.gz + script: {{ PYTHON }} -m pip install -vvv --no-deps --no-build-isolation . https://pypi.io/packages/source/{{ bc[0] }}/{{ bc }}/{{ bc }}-{{ bcv }}.tar.gz + entry_points: + - runjob = runjob.qsub:main + run_exports: + - {{ pin_subpackage('runjob', max_pin="x") }} requirements: host: - pip - - python >=2.7.10,<3.11 + - python >=3.5 run: - - pip - - python >=2.7.10,<3.11 + - python >=3.5 - psutil >=5.7.0 - ratelimiter >=1.2.0 - prettytable >=3.2.0 @@ -37,5 +40,7 @@ test: about: home: https://github.com/yodeng/runjob license: MIT + license_family: MIT + license_file: LICENSE summary: "Manage jobs or pipeline of bioinfomation." description: "Runjob is a program for managing a group of related bioinformatic jobs or pipelines running on a compute cluster." From ba05bfbd4001b937da15a00eb17732b0d9a670e2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 20 Nov 2023 18:40:28 -0700 Subject: [PATCH 0837/2173] Update hybkit to 0.3.4 (#44362) * Update hybkit to 0.3.4 * add typing_extensions * add typing_extensions to run section * add hybkit to host too --------- Co-authored-by: joshuazhuang7 --- recipes/hybkit/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/hybkit/meta.yaml b/recipes/hybkit/meta.yaml index ddc325d389599..e350da1a32f29 100644 --- a/recipes/hybkit/meta.yaml +++ b/recipes/hybkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybkit" %} -{% set version = "0.3.3" %} +{% set version = "0.3.4" %} package: name: {{ name|lower }} @@ -7,11 +7,11 @@ package: source: url: https://github.com/RenneLab/hybkit/archive/v{{ version }}.tar.gz - sha256: a0999de963da6ee87668104c126647a7968e7be06445da62d256c9b7d15d9bc1 + sha256: 6f42b1e116dd668b5fd2847691bc6b78cf641f9c1aae91ca752e6df6d18022cd build: noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps -vvv run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} number: 0 @@ -22,10 +22,12 @@ requirements: - pip - matplotlib-base - biopython + - typing_extensions run: - python >=3.8 - matplotlib-base - biopython + - typing_extensions test: imports: @@ -44,7 +46,8 @@ test: about: home: https://github.com/RenneLab/hybkit - license: GPL-3.0 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Hybkit toolkit and Python3 API chimeric genomic data analysis from proximity ligation methods. From 77c0f6872f7cbb97ac1f8094dad4bb4a7d2c397c Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 21 Nov 2023 00:16:00 -0600 Subject: [PATCH 0838/2173] Add recipe for peaks2utr v1.2.0 (#44366) --- recipes/peaks2utr/LICENSE | 674 ++++++++++++++++++++++++++++++++++++ recipes/peaks2utr/meta.yaml | 52 +++ 2 files changed, 726 insertions(+) create mode 100644 recipes/peaks2utr/LICENSE create mode 100644 recipes/peaks2utr/meta.yaml diff --git a/recipes/peaks2utr/LICENSE b/recipes/peaks2utr/LICENSE new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/peaks2utr/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/peaks2utr/meta.yaml b/recipes/peaks2utr/meta.yaml new file mode 100644 index 0000000000000..fde63cc700b3b --- /dev/null +++ b/recipes/peaks2utr/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "peaks2utr" %} +{% set version = "1.2.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/peaks2utr-{{ version }}.tar.gz + sha256: 9b7058f96455fb00c595759a92ab1c16bbaab4ec81658c89f37977cc1f4bb7c5 + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('peaks2utr', max_pin="x") }} + +requirements: + host: + - python >=3.8,<3.12 + - wheel + - pip + run: + - python >=3.8,<3.12 + - requests + - gffutils ==0.10.1 + - pysam + - macs2 ==2.2.9.1 + - numpy >=1.21.4 + - tqdm + - asgiref + - psutil + - pybedtools + - typing-extensions + - importlib-resources + - zipp + +test: + imports: + - peaks2utr + +about: + home: https://github.com/haessar/peaks2utr + summary: A robust, parallelized Python CLI for annotating three_prime_UTR + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + +extra: + identifiers: + - doi:10.1093/bioinformatics/btad112 From fb6b4f40bdb4b1a78df4f4a37e0204179434a157 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 04:07:45 -0700 Subject: [PATCH 0839/2173] Update srnaminer to 1.1.2 (#44375) --- recipes/srnaminer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/srnaminer/meta.yaml b/recipes/srnaminer/meta.yaml index 5182cf37602f6..6aab8d70881e2 100644 --- a/recipes/srnaminer/meta.yaml +++ b/recipes/srnaminer/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.1" %} +{% set version = "1.1.2" %} package: name: srnaminer @@ -6,7 +6,7 @@ package: source: url: "https://github.com/kli28/sRNAminer/releases/download/v{{ version }}/sRNAminer_v{{ version }}.tar.gz" - sha256: 6da0c89ca2a3a5d5994fc6ef1356039e20189480d91cef8804c02b7337c54ba4 + sha256: ad01e31f155d4160b8d0db35909fb38737a62fdc1678775fc64ff6f6fd7e6c84 build: number: 0 From fca028c6a45d610a8df606167decb803350318bc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 04:08:03 -0700 Subject: [PATCH 0840/2173] Update plassembler to 1.5.0 (#44367) --- recipes/plassembler/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/plassembler/meta.yaml b/recipes/plassembler/meta.yaml index e7c18f6c2c70a..85b1484bc031b 100644 --- a/recipes/plassembler/meta.yaml +++ b/recipes/plassembler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "plassembler" %} -{% set version = "1.4.1" %} +{% set version = "1.5.0" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 86167accca01b6e33ae4bff780c6ccbd8f208af41f605cbedc6c78272959f88a + sha256: 35496f09241e9c5eb45e66146e0c24b1e77598c84a61db8bc9fbf0d11c3db5d5 build: - number: 1 + number: 0 noarch: python entry_points: - plassembler = plassembler:main From d5dfdac353ec4d215d5ad6e051a16b62e5f11c3b Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Tue, 21 Nov 2023 13:24:33 +0100 Subject: [PATCH 0841/2173] Updating sentieon to 202308.01 (#44378) --- recipes/sentieon/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sentieon/meta.yaml b/recipes/sentieon/meta.yaml index 5d10d110578d9..2660842aebff9 100644 --- a/recipes/sentieon/meta.yaml +++ b/recipes/sentieon/meta.yaml @@ -1,11 +1,11 @@ -{% set version="202308" %} +{% set version="202308.01" %} package: name: sentieon version: {{ version }} source: - url: https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-{{ version }}.tar.gz # [linux64] - sha256: d663067f46e499c23819e344cf548fdc362abbf94d3ef086a2e655c072ebe0d6 # [linux64] + sha256: 047899a2b4247adaace82032a6fe269a57f70b1c9ecbc84d77914f902a714d50 # [linux64] patches: # [linux64] # Fix driver scripts so they resolves location including symlinks - sentieon_symlinks.patch # [linux64] From 9951f3b47b49400b90070379d72228dd24a48df5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 07:51:16 -0700 Subject: [PATCH 0842/2173] Update pybiolib to 1.1.1535 (#44383) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 8eebe8d714756..cd010da5adf9c 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1533" %} +{% set version = "1.1.1535" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 666e4f0f60012951b2a1e98468df99256fda01df7442cc0cb1830ca1a3d2a160 + sha256: 7b0885a8228bc18b0be4d71abc5cdfb68a600965159f83892c87059477b498d7 build: noarch: python From 9590c4f85211dc1919bb0794261b9b99a1293ce4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 07:52:12 -0700 Subject: [PATCH 0843/2173] Update captus to 1.0.0 (#44379) --- recipes/captus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/captus/meta.yaml b/recipes/captus/meta.yaml index 175d459cfe48b..44207123a1eea 100644 --- a/recipes/captus/meta.yaml +++ b/recipes/captus/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.9.99" %} -{% set sha256 = "cb12443b948ed74b10c0d75b83aef49e719c609a0cb2715ef6af96e838fb4bb2" %} +{% set version = "1.0.0" %} +{% set sha256 = "2ecdab60cc0ce9b422e66e325a4746a04f2700c8b477790458217f0c9d0b8adb" %} package: name: captus From 5fd95319341233fb91bbe366532b224cbf72b255 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 07:53:11 -0700 Subject: [PATCH 0844/2173] Update annonars to 0.26.1 (#44374) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 55ba834efbd0a..3484a39ac6ef3 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.26.0" %} +{% set version = "0.26.1" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 31b49f1f0d4d19038cd3c9817480c4eefc5fe27a117a30164981d2b302845759 + sha256: 8dc37b0e6574d1bc294cb4651f33cd5be079865dfce7aa41b6acdfb2653bd7dc requirements: build: From 00c94df0c196b88aa0ddb5809072ee938b5d0eab Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 07:53:30 -0700 Subject: [PATCH 0845/2173] Update mehari to 0.20.0 (#44372) * Update mehari to 0.19.1 * Update mehari to 0.20.0 --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 038d7016447de..f2f3d05dc9cff 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.18.1" %} -{% set sha256 = "e25bed84505f1de7826680dc7e054c8596f46d054c1cfbcf74f29fe94229484f" %} +{% set version = "0.20.0" %} +{% set sha256 = "dc9c3d485a1d0fb6af143395026d7c218177ce463dde9f4d2b063883de9e094d" %} package: name: mehari From da71ac5c6576ad2c7eacf85cbcacec7b6eeb797b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 08:18:13 -0700 Subject: [PATCH 0846/2173] Update hapog to 1.3.7 (#44385) --- recipes/hapog/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hapog/meta.yaml b/recipes/hapog/meta.yaml index e48194763caff..525046c08f7e6 100644 --- a/recipes/hapog/meta.yaml +++ b/recipes/hapog/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.6" %} +{% set version = "1.3.7" %} package: name: hapog @@ -12,7 +12,7 @@ build: source: url: https://github.com/institut-de-genomique/HAPO-G/archive/refs/tags/{{ version }}.tar.gz - sha256: "af982ad482386f8e77a11f1db3afd356677c94f9883245bb689025d6aa7db9c4" + sha256: "727ff2a712b046c7787ac2bb599a7e3808f70219d6b7e22ddfc5942ba38c5841" requirements: build: From 70eb1540a6c5b44d06e7c3ae6a3b43456631e1fd Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Tue, 21 Nov 2023 10:42:10 -0500 Subject: [PATCH 0847/2173] Update gsearch v0.1.5 with SIMD (#44363) * Update gsearch v0.1.5 * Update gsearch v0.1.5 SIMD * Update gsearch v0.1.6 --- recipes/gsearch/build.sh | 2 +- recipes/gsearch/meta.yaml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gsearch/build.sh b/recipes/gsearch/build.sh index c4f31ae3a4136..255e702c00317 100644 --- a/recipes/gsearch/build.sh +++ b/recipes/gsearch/build.sh @@ -5,4 +5,4 @@ export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" # build statically linked binary with Rust -RUST_BACKTRACE=1 cargo install --features annembed_intel-mkl --verbose --path . --root $PREFIX +RUST_BACKTRACE=1 cargo install --features annembed_intel-mkl,simdeez_f --verbose --path . --root $PREFIX diff --git a/recipes/gsearch/meta.yaml b/recipes/gsearch/meta.yaml index 72eb49f2cb25f..e705912ca1f85 100644 --- a/recipes/gsearch/meta.yaml +++ b/recipes/gsearch/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.5" %} +{% set version = "0.1.6" %} package: name: gsearch @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/gsearch/archive/v{{ version }}.tar.gz - sha256: d25e6a8353b79da1fd3e2fafa49461e4be3352bdedd48fb2dcdfe12c76aa100f + sha256: e57b53617e325195699d3e3a8e68acc7172775466ce8be37516df60dd71fbd12 requirements: build: From b00b665858b1f015af883bf0897404160a08d72e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 08:53:05 -0700 Subject: [PATCH 0848/2173] Update assemblycomparator2 to 2.5.13 (#44386) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index c10dfa3945b9e..64a212e6ad2ab 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.12" %} +{% set version = "2.5.13" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 96b28c2593878637b6587d5cd293b08ecef3260dc9dd332c8850851046ba0d9c + sha256: 7a8b8d547f6454782aed0e5aecdb2a1f299d909170cd64e32c286b6e032fd141 build: From ee568000a86e9bb46d856cf37fe47f4007b87430 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 09:11:37 -0700 Subject: [PATCH 0849/2173] Update matchms to 0.24.0 (#44387) --- recipes/matchms/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 967e9e49a80c5..6db06343038dc 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.23.1" %} +{% set version = "0.24.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 0cee3013e6f6fd09dd4b9d41d96130c9e2273b31bc6b36d2cea666dcfdbf6f2e + sha256: e62b1591782b01c3ef83850245609d85e3d612a7f7c350b4fc2ad067d8bc9d15 build: number: 0 From da5168e75c58660d33845af22de84845dd78c7a8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 11:13:56 -0700 Subject: [PATCH 0850/2173] Update annonars to 0.27.0 (#44391) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 3484a39ac6ef3..851f9f1ccc75b 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.26.1" %} +{% set version = "0.27.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 8dc37b0e6574d1bc294cb4651f33cd5be079865dfce7aa41b6acdfb2653bd7dc + sha256: 0e679d1623e0280083131f36c30800a12d4c3c543151ce17841ebe40d7357f7f requirements: build: From e8d2d1f1dc17a746805a9c5b3085a68d3d31f45a Mon Sep 17 00:00:00 2001 From: Marc Sturm Date: Tue, 21 Nov 2023 20:08:53 +0100 Subject: [PATCH 0851/2173] Update of ngs-bits to version 2023_11 (#44382) * Updated ngs-bits to version 2018_10 * Updated ngs-bits to version 2023_11 --- recipes/ngs-bits/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ngs-bits/meta.yaml b/recipes/ngs-bits/meta.yaml index 9dab49582fbad..5fa12dddf0aa1 100755 --- a/recipes/ngs-bits/meta.yaml +++ b/recipes/ngs-bits/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2023_09" %} +{% set version = "2023_11" %} package: name: ngs-bits @@ -11,7 +11,7 @@ build: source: url: https://github.com/imgag/ngs-bits/releases/download/{{ version }}/ngs-bits-{{ version }}.tgz - sha256: cdceef2945a8b586dd8e3acf8edd7703c8c0f201f6ad8fdbfb2b8bf11bfea775 + sha256: bb994eb9a74043fa173a3b0ee6b9eafdf3e7b1aeb1ebcc2ba3e73888e1e61fa4 requirements: build: From 4d5758db3ac77ec227d6be27bd123b35f9a435b4 Mon Sep 17 00:00:00 2001 From: pirovc <4673375+pirovc@users.noreply.github.com> Date: Tue, 21 Nov 2023 20:09:18 +0100 Subject: [PATCH 0852/2173] update ganon to v2.0.0 (#44384) --- recipes/ganon/build_failure.linux-64.yaml | 104 ---------------------- recipes/ganon/conda_build_config.yaml | 5 -- recipes/ganon/meta.yaml | 18 ++-- 3 files changed, 9 insertions(+), 118 deletions(-) delete mode 100644 recipes/ganon/build_failure.linux-64.yaml delete mode 100644 recipes/ganon/conda_build_config.yaml diff --git a/recipes/ganon/build_failure.linux-64.yaml b/recipes/ganon/build_failure.linux-64.yaml deleted file mode 100644 index dd58888dbf700..0000000000000 --- a/recipes/ganon/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: a2de07a72a0165afc0ea398c58f57f70672ea2ba5795360cbe18e9637a3a0e23 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:711:24: error: template argument 1 is invalid - 711 | std::integral(mate))>>), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:717:53: error: template argument 1 is invalid - 717 | if constexpr (std::integral(mate))>> || - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:717:24: error: template argument 1 is invalid - 717 | if constexpr (std::integral(mate))>> || - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:718:102: error: template argument 1 is invalid - 718 | detail::is_type_specialisation_of_v(mate))>, std::optional>) - | ^ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:718:110: error: 'optional' is not a member of 'std' - 718 | detail::is_type_specialisation_of_v(mate))>, std::optional>) - | ^~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:718:110: note: 'std::optional' is defined in header ''; did you forget to '#include '? - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:731:99: error: 'optional' is not a member of 'std' - 731 | !detail::is_type_specialisation_of_v, std::optional>) - | ^~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:731:99: note: 'std::optional' is defined in header ''; did you forget to '#include '? - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:761:9: error: 'ref_offset' was not declared in this scope; did you mean 'seqan3::field::ref_offset'? - 761 | if (ref_offset.has_value() && (ref_offset.value() 1) < 0) - | ^~~~~~~~~~ - | seqan3::field::ref_offset - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/record.hpp:84:5: note: 'seqan3::field::ref_offset' declared here - 84 | ref_offset, //!< Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value. - | ^~~~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:786:50: error: 'flag' was not declared in this scope; did you mean 'seqan3::field::flag'? - 786 | stream_it.write_number(static_cast(flag)); - | ^~~~ - | seqan3::field::flag - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/record.hpp:87:5: note: 'seqan3::field::flag' declared here - 87 | flag, //!< The alignment flag (bit information), uint16_t value. - | ^~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:795:107: error: 'optional' is not a member of 'std' - 795 | else if constexpr (detail::is_type_specialisation_of_v, std::optional>) - | ^~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:795:107: note: 'std::optional' is defined in header ''; did you forget to '#include '? - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:815:28: error: 'ref_offset' was not declared in this scope; did you mean 'seqan3::field::ref_offset'? - 815 | stream_it.write_number(ref_offset.value_or(-1) 1); - | ^~~~~~~~~~ - | seqan3::field::ref_offset - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/record.hpp:84:5: note: 'seqan3::field::ref_offset' declared here - 84 | ref_offset, //!< Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value. - | ^~~~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:818:50: error: 'mapq' was not declared in this scope; did you mean 'seqan3::field::mapq'? - 818 | stream_it.write_number(static_cast(mapq)); - | ^~~~ - | seqan3::field::mapq - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/record.hpp:89:5: note: 'seqan3::field::mapq' declared here - 89 | mapq, //!< The mapping quality of the seqan3::field::seq alignment, usually a Phred-scaled score. - | ^~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:821:29: error: 'cigar_vector' was not declared in this scope; did you mean 'rna5_vector'? - 821 | if (!std::ranges::empty(cigar_vector)) - | ^~~~~~~~~~~~ - | rna5_vector - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:850:57: error: template argument 1 is invalid - 850 | if constexpr (std::integral(mate))>>) - | ^~~~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:850:24: error: template argument 1 is invalid - 850 | if constexpr (std::integral(mate))>>) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:854:106: error: template argument 1 is invalid - 854 | else if constexpr (detail::is_type_specialisation_of_v(mate))>, std::optional>) - | ^ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:854:114: error: 'optional' is not a member of 'std' - 854 | else if constexpr (detail::is_type_specialisation_of_v(mate))>, std::optional>) - | ^~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:854:114: note: 'std::optional' is defined in header ''; did you forget to '#include '? - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:870:97: error: template argument 1 is invalid - 870 | if constexpr (detail::is_type_specialisation_of_v(mate))>, std::optional>) - | ^ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:870:105: error: 'optional' is not a member of 'std' - 870 | if constexpr (detail::is_type_specialisation_of_v(mate))>, std::optional>) - | ^~~~~~~~ - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:870:105: note: 'std::optional' is defined in header ''; did you forget to '#include '? - /opt/conda/conda-bld/ganon_1686048214748/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/seqan3/io/sam_file/format_sam.hpp:890:33: error: 'tag_dict' was not declared in this scope - 890 | write_tag_fields(stream_it, tag_dict, separator); - | ^~~~~~~~ - make[2]: *** [src/CMakeFiles/ganon-build-lib.dir/build.make:90: src/CMakeFiles/ganon-build-lib.dir/ganon-build/GanonBuild.cpp.o] Error 1 - make[1]: *** [CMakeFiles/Makefile2:122: src/CMakeFiles/ganon-build-lib.dir/all] Error 2 - make: *** [Makefile:146: all] Error 2 - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ganon_1686048214748/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/ganon/conda_build_config.yaml b/recipes/ganon/conda_build_config.yaml deleted file mode 100644 index ad3cc199a8195..0000000000000 --- a/recipes/ganon/conda_build_config.yaml +++ /dev/null @@ -1,5 +0,0 @@ -# SeqAn3.1.0 doesn does not build with newer compilers (max gcc10) -cxx_compiler_version: - - 10 # [linux] -c_compiler_version: - - 10 # [linux] diff --git a/recipes/ganon/meta.yaml b/recipes/ganon/meta.yaml index fca3385be9015..a2aa06fab08cb 100755 --- a/recipes/ganon/meta.yaml +++ b/recipes/ganon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ganon" %} -{% set version = "1.9.0" %} +{% set version = "2.0.0" %} package: name: "{{ name|lower }}" @@ -8,7 +8,7 @@ package: source: - folder: ganon url: https://github.com/pirovc/{{ name }}/archive/{{ version }}.tar.gz - sha256: 551cb35f2c9f38ad74a2fc45e9810db5dac7ecc8a50680083fb42235d7b8d9c3 + sha256: 065013bbc4d8817c1895793fcf41c9f68c9f36cae590ded005b389e3cc8941d6 - folder: robin-hood-hashing url: https://github.com/martinus/robin-hood-hashing/archive/refs/tags/3.11.3.tar.gz sha256: dcf2b7fa9ef9dd0c67102d94c28e8df3effbe1845e0ed1f31f4772ca5e857fc4 @@ -23,10 +23,10 @@ requirements: build: - make - {{ compiler('cxx') }} - - cmake >=3.14 + - cmake >=3.4 host: - bzip2 - - seqan3 ==3.1.0 + - seqan3 ==3.3.0 - catch2 ==2.* - cxxopts >=2.2.0 - python @@ -49,7 +49,7 @@ requirements: - curl - diffutils - zlib - - raptor ==3.0.0 + - raptor ==3.0.1 test: commands: @@ -59,11 +59,11 @@ test: about: home: https://github.com/pirovc/ganon - summary: "ganon classifies DNA sequences against large sets of genomic reference sequences efficiently" + summary: "ganon2 classifies genomic sequences against large sets of references efficiently," description: | - ganon classifies DNA sequences against large sets of genomic sequences efficiently, - with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and - hierarchical classification, customized reporting and more + ganon2 classifies genomic sequences against large sets of references efficiently, + with integrated download and update of databases (refseq/genbank), taxonomic profiling + (ncbi/gtdb), binning and hierarchical classification, customized reporting and more license: MIT License license_family: MIT license_file: {{ SRC_DIR }}/ganon/LICENSE From ed6d32760f182f2da57f9372d3af5660c57e4886 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 12:11:03 -0700 Subject: [PATCH 0853/2173] Update upimapi to 1.12.3 (#44389) --- recipes/upimapi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/upimapi/meta.yaml b/recipes/upimapi/meta.yaml index 307b66976c236..5c952176f1640 100644 --- a/recipes/upimapi/meta.yaml +++ b/recipes/upimapi/meta.yaml @@ -1,6 +1,6 @@ {% set name = "upimapi" %} -{% set version = "1.12.2" %} -{% set sha256 = "8fc5f19b56bb215c8204778837ae0dd8fda1918af215cb0ece01970cd58f3f00" %} +{% set version = "1.12.3" %} +{% set sha256 = "2cb9fe4a345bd6a80437af7400d09446eaf6da56ed632757d8c957d3a57de4cd" %} package: name: {{ name|lower }} From 85293134cef54154f8e573046372dc4835628ba2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 13:16:15 -0700 Subject: [PATCH 0854/2173] Update ultraplex to 1.2.9 (#44207) * Update ultraplex to 1.2.7 * add run_exports * Update ultraplex to 1.2.8 * add setuptools_scm * Update ultraplex to 1.2.9 * Update meta.yaml (#44335) * Update meta.yaml ultraplex fails with python >= 3.10 * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update recipes/ultraplex/meta.yaml revert skip: statement to include python > 3.9 * Update recipes/ultraplex/meta.yaml remove python pinning in host --------- Co-authored-by: joshuazhuang7 Co-authored-by: Charlotte Capitanchik Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ultraplex/meta.yaml | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/recipes/ultraplex/meta.yaml b/recipes/ultraplex/meta.yaml index 16f5134c8718d..68e00272ed7de 100644 --- a/recipes/ultraplex/meta.yaml +++ b/recipes/ultraplex/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ultraplex" %} -{% set version = "1.2.5" %} +{% set version = "1.2.9" %} package: name: "{{ name|lower }}" @@ -7,13 +7,17 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 13fcb6bcbb20c1765a544869171dff4f31a930b77ebb44bed6a6000c4ea9a3b4 - + sha256: 7b1efa09a421590907c7e5177eb9e4837deade89c237b961bcf2f7edfa9f2e90 build: - number: 2 - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + number: 0 skip: True # [py < 37 or py > 39] + script: + - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" + entry_points: + - ultraplex = ultraplex.__main__:main + run_exports: + - {{ pin_subpackage('ultraplex', max_pin="x") }} requirements: build: @@ -22,12 +26,14 @@ requirements: - pip - python - cython - - setuptools_scm + - setuptools-scm >8 run: - python - xopen >=1.0.0 - dnaio >=0.5.0 - pigz + - multiprocess + - setuptools_scm >8 test: imports: @@ -39,8 +45,10 @@ about: home: "https://github.com/ulelab/ultraplex.git" license: MIT license_family: MIT + license_file: LICENSE summary: "fastq demultiplexer" extra: recipe-maintainers: - Delayed-Gitification + - CharlotteAnne From b67bcec4466d85c7230c2ee44f99a6cea39a6f52 Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Tue, 21 Nov 2023 12:58:00 -0800 Subject: [PATCH 0855/2173] Update qualimap to v2.3 (#44360) * Update qualimap to v2.3 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/qualimap/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/qualimap/meta.yaml b/recipes/qualimap/meta.yaml index 33d1b6e7bc9b9..ef8d7f3885d21 100644 --- a/recipes/qualimap/meta.yaml +++ b/recipes/qualimap/meta.yaml @@ -1,14 +1,16 @@ package: name: qualimap - version: "2.2.2d" + version: "2.3" source: - url: https://bitbucket.org/kokonech/qualimap/downloads/qualimap-build-11-11-19.tar.gz - md5: a9afa75339f8b67f75706ec46095d08c + url: https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip + md5: dfe659cb950b7902ee5c57aeab35eaff build: - number: 2 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('qualimap', max_pin="x") }} requirements: run: @@ -27,7 +29,7 @@ test: about: home: http://qualimap.bioinfo.cipf.es/ - license: GPLv2 + license: GPL-2.0-or-later license_file: LICENSE summary: Quality control of alignment sequencing data and its derivatives like feature counts From 819943f9da5f42600b63a09e6fe2676cc1e95f16 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 13:58:06 -0700 Subject: [PATCH 0856/2173] Update perl-math-bigint to 2.001001 (#44392) --- recipes/perl-math-bigint/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-math-bigint/meta.yaml b/recipes/perl-math-bigint/meta.yaml index fa0887c33e784..f9e6c046f450d 100644 --- a/recipes/perl-math-bigint/meta.yaml +++ b/recipes/perl-math-bigint/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-math-bigint" %} -{% set version = "2.001000" %} -{% set sha256 = "0a1cf05d85282be4019f93a947bd8b820c7d11a91ffde560eaed31dddf4ba622" %} +{% set version = "2.001001" %} +{% set sha256 = "d9ce4697c40ac59f4b6fc3a474a69aa40f9e7ccc35eb7053d8d9aa69ac2fa9ba" %} package: name: {{ name }} From b52c6162d3da35c38fa7e31753daad88ef746d06 Mon Sep 17 00:00:00 2001 From: Nathan Weeks <1800812+nathanweeks@users.noreply.github.com> Date: Tue, 21 Nov 2023 20:15:03 -0500 Subject: [PATCH 0857/2173] Set binary_relocation: False for lima to fix EL8 segfault (#44388) --- recipes/lima/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/lima/meta.yaml b/recipes/lima/meta.yaml index fd78fc100126b..53d51fabd39ef 100644 --- a/recipes/lima/meta.yaml +++ b/recipes/lima/meta.yaml @@ -10,8 +10,9 @@ source: sha256: a13437bc7a90ab5df3c19eac44384de2a14370d0391586b5aa63a6478f9c2c53 build: - number: 0 + number: 1 skip: True # [osx] + binary_relocation: False run_exports: - {{ pin_subpackage('lima', max_pin='x.x') }} From 3c6bd2b973ef984069cc1dc9a7aa0035346fb56a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 18:15:17 -0700 Subject: [PATCH 0858/2173] Update pydeseq2 to 0.4.2 (#44390) --- recipes/pydeseq2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pydeseq2/meta.yaml b/recipes/pydeseq2/meta.yaml index 77cbc6a90283b..1b3e199caec5f 100644 --- a/recipes/pydeseq2/meta.yaml +++ b/recipes/pydeseq2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pydeseq2" %} -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pydeseq2-{{ version }}.tar.gz - sha256: f437f8176783ebedffdb43d987cecabd729f2f1fc42d4da9b34da53b5ee84f7e + sha256: b2e8878dccf4e5562c4c1f0efd64e1c93e83ba51642c20bcae0384a2da2cc819 build: noarch: python From 03e8ef370a11ab34d3404a6b569441de50a8e65b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 18:15:33 -0700 Subject: [PATCH 0859/2173] Update dxpy to 0.365.0 (#44395) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 3838e4ec85068..ce62cf169e98b 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.364.0" %} +{% set version = "0.365.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 1c3c18281261e4e3ce8566f44d61f017c3e9231a848940ba99ff2827a4f0fc06 + sha256: 234efe289c71da5069cb7e42f569c9dbff922e270267365d8b36798fd541240c build: number: 0 From ecc20499799710f571f6a1b2ad2636462194908e Mon Sep 17 00:00:00 2001 From: yodeng Date: Wed, 22 Nov 2023 09:15:52 +0800 Subject: [PATCH 0860/2173] Add hpcblast recipe (#44380) --- recipes/hpcblast/meta.yaml | 42 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 recipes/hpcblast/meta.yaml diff --git a/recipes/hpcblast/meta.yaml b/recipes/hpcblast/meta.yaml new file mode 100644 index 0000000000000..0596424abf221 --- /dev/null +++ b/recipes/hpcblast/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.0.2" %} + +package: + name: hpcblast + version: {{ version }} + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install -vvv . + entry_points: + - hpc-blast = hpcblast.main:main + run_exports: + - {{ pin_subpackage('hpcblast', max_pin="x") }} + +source: + url: https://github.com/yodeng/hpc-blast/archive/v{{ version }}.tar.gz + sha256: 71f3fa343dc553fa447af26474e90204843abe395a98ff27cf88f0cb3ba9ca21 + +requirements: + host: + - python >=3.5 + - pip + run: + - python >=3.5 + - pip + - runjob >=2.10.5 + - blast + +test: + imports: + - hpcblast + commands: + - hpc-blast --version + +about: + home: https://github.com/yodeng/hpc-blast + license: MIT + license_family: MIT + license_file: LICENSE + summary: "A wrapper for NCBI-BLAST+ suite which provides a simple and efficient method to accelerate the blast search" + description: "hpcblast provides a simple and efficient method for running the NCBI-BLAST+ suite program in localhost or the HPC environment (Sun Grid Engine). It splits the input sequence file and run all chunked tasks in parallel to accelerate the blast search speed. When there are many sequences in the input file for blast comparison and the running speed is slow, using hpcblast can significantly improve the performance. All of this can be easy done only by adding the hpc-blast command at the head of your blast command line." From 833a5bae77aa295f4793bb168753283eb2a8125b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 18:16:18 -0700 Subject: [PATCH 0861/2173] Update r-grain to 1.4.1 (#44393) --- recipes/r-grain/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-grain/meta.yaml b/recipes/r-grain/meta.yaml index 56a8bae3d728e..18c6cd5efde07 100644 --- a/recipes/r-grain/meta.yaml +++ b/recipes/r-grain/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.4.0' %} +{% set version = '1.4.1' %} package: name: r-grain @@ -8,7 +8,7 @@ source: url: - {{ cran_mirror }}/src/contrib/gRain_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/gRain/gRain_{{ version }}.tar.gz - sha256: c0ccd33448fff881aea6b09927da99af37be63f4795abe4c65591fbbcbb09690 + sha256: d9f926aa876270ab4ae156a70703ec8ccd384cc6a7bfe5de4d1de3ef9e056485 build: number: 0 From 93649b5c78a1a3f6c2d017df5e9eb3a7564754bf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 21 Nov 2023 18:16:30 -0700 Subject: [PATCH 0862/2173] Update assemblycomparator2 to 2.5.14 (#44396) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index 64a212e6ad2ab..350463aca94b1 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.13" %} +{% set version = "2.5.14" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 7a8b8d547f6454782aed0e5aecdb2a1f299d909170cd64e32c286b6e032fd141 + sha256: d95f39d996330ab72ceffc5e8aa17b9348b39478fd2a4bfd01ca960adff2d20e build: From fecbf5e6022e6f052ada0687a5756a067fe5e3cc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 01:53:06 -0700 Subject: [PATCH 0863/2173] Update annonars to 0.28.0 (#44398) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 851f9f1ccc75b..0f366977f09dd 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.27.0" %} +{% set version = "0.28.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 0e679d1623e0280083131f36c30800a12d4c3c543151ce17841ebe40d7357f7f + sha256: 464026c76b759fc24e4ec60c5e2a83f64549f07f5176661cacb8792046af1c70 requirements: build: From 4892cd9a7542d52a04db7c698581e82325720c72 Mon Sep 17 00:00:00 2001 From: Rlibouban <127295521+rlibouba@users.noreply.github.com> Date: Wed, 22 Nov 2023 11:46:42 +0100 Subject: [PATCH 0864/2173] Update Braker v3.0.3 to v3.0.6 (#44296) * Update Braker v3.0.3 to v3.0.6 * error - run_exports * update meta.yaml * Download file version error * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/braker3/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/braker3/meta.yaml b/recipes/braker3/meta.yaml index dec3752a3c767..963a2bf73bdde 100644 --- a/recipes/braker3/meta.yaml +++ b/recipes/braker3/meta.yaml @@ -1,13 +1,12 @@ {% set name = "BRAKER3" %} -{% set version = "3.0.3" %} -{% set sha256 = "3cb65c3bc51abc2a5217927c04a65739062e59c54e938504520993a193a671b4" %} +{% set version = "3.0.6" %} +{% set sha256 = "2609410c597a95017966c88bdc1787c44494caf9a2b2242a7a849fee6484282b" %} package: name: "{{ name|lower }}" version: "{{ version }}" - source: -- url: https://github.com/Gaius-Augustus/BRAKER/archive/refs/tags/v{{ version }}.tar.gz +- url: https://github.com/Gaius-Augustus/BRAKER/archive/refs/tags/v3.06.tar.gz sha256: {{ sha256 }} - url: https://github.com/Gaius-Augustus/TSEBRA/archive/refs/tags/v.1.1.1.tar.gz sha256: 0426c243888135ee3fd6ea0ca9f37eb4af03dd117498165257fa756f59d49ce9 @@ -16,6 +15,8 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('braker3', max_pin='x') }} requirements: run: From ac5a93bb77167a4d6cf315ffe172595732f61a6d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 05:25:38 -0700 Subject: [PATCH 0865/2173] Update thapbi-pict to 1.0.5 (#44404) --- recipes/thapbi-pict/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 43e04010dd3bc..d1eca3abad919 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.4" %} +{% set version = "1.0.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: b845cca32700d0e62e13e148b0a759d0822958738109ff7bf1ab6bad7c89bf52 + sha256: c7e42668397ac37b869b2c5774e721635e892ebb99eefc014d634b090d9f7c08 build: noarch: python From ad3ba723a7abbde2518049c258efe6a00614e948 Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Wed, 22 Nov 2023 13:40:23 +0100 Subject: [PATCH 0866/2173] Add BOMS to bioconda. (#44358) * Added recipe for boms. * Added run_exports to build. * Added homepage. * Removed pip check from boms recipe. * Update recipes/boms/meta.yaml Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> --------- Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> --- recipes/boms/meta.yaml | 54 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 recipes/boms/meta.yaml diff --git a/recipes/boms/meta.yaml b/recipes/boms/meta.yaml new file mode 100644 index 0000000000000..7097126eefac7 --- /dev/null +++ b/recipes/boms/meta.yaml @@ -0,0 +1,54 @@ +{% set name = "boms" %} +{% set version = "1.0.5" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 75187e1e78ac9eacda923dee3943936625676f2382859636448f14a64e57ea54 + +build: + run_exports: + - {{ pin_subpackage('boms', max_pin="x.x") }} + skip: true # [osx or py<39] + script: {{ PYTHON }} -m pip install . -vv --no-build-isolation + number: 0 + +requirements: + build: + - {{ compiler('cxx') }} + - {{ compiler('c') }} + host: + - python + - setuptools >=61.0 + - wheel + - pybind11 >=2.11.0 + - requests + - pip + - mkl-service + run: + - python + - numpy + - mkl + - mkl-service + - scipy + - matplotlib-base + - scikit-learn + +test: + imports: + - boms + requires: + - pip + +about: + summary: Cell Segmentation for Spatial Transcriptomics Data using BOMS + home: https://github.com/ocimakamboj/boms + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - FloWuenne From a6d53b95de3ca10ffaac8f709c236c7bfc0716a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Siebren=20Fr=C3=B6lich?= <48289046+siebrenf@users.noreply.github.com> Date: Wed, 22 Nov 2023 14:02:25 +0100 Subject: [PATCH 0867/2173] Added run_exports to meta.yaml (#44402) --- recipes/genomepy/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/genomepy/meta.yaml b/recipes/genomepy/meta.yaml index 87a26d0ebd98b..f82088f838ea9 100644 --- a/recipes/genomepy/meta.yaml +++ b/recipes/genomepy/meta.yaml @@ -9,9 +9,11 @@ source: sha256: c550e32fbafd67ae4ce3792356459fd6658de70ab8820a735a8a815238643be9 build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_subpackage('genomepy', max_pin="x.x") }} requirements: host: From b91fc439f85d44d8915af2b33fcac31d794203c9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 07:57:20 -0700 Subject: [PATCH 0868/2173] Update annonars to 0.29.0 (#44408) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 0f366977f09dd..6230dae83d476 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.28.0" %} +{% set version = "0.29.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 464026c76b759fc24e4ec60c5e2a83f64549f07f5176661cacb8792046af1c70 + sha256: d38396661da5088274427a8b95137ff5addd0d239c67bc66c5a2fab0e76136c5 requirements: build: From 2f6b16ab61b8ef26311c71b7c49ee0907458b186 Mon Sep 17 00:00:00 2001 From: Mikko Rautiainen Date: Wed, 22 Nov 2023 17:56:17 +0200 Subject: [PATCH 0869/2173] Update ribotin to version 1.2 (#44401) * Update ribotin to version 1.2 --- recipes/ribotin/build.sh | 1 + recipes/ribotin/meta.yaml | 8 +++++--- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/ribotin/build.sh b/recipes/ribotin/build.sh index f8a7b9acf6352..21514ab5ec912 100644 --- a/recipes/ribotin/build.sh +++ b/recipes/ribotin/build.sh @@ -8,3 +8,4 @@ cp bin/ribotin-verkko $PREFIX/bin mkdir -p $PREFIX/share/${PKG_NAME}-${PKG_VERSION} cp template_seqs/rDNA_one_unit.fasta $PREFIX/share/${PKG_NAME}-${PKG_VERSION}/rDNA_one_unit.fasta cp template_seqs/chm13_rDNAs.fa $PREFIX/share/${PKG_NAME}-${PKG_VERSION}/chm13_rDNAs.fa +cp template_seqs/rDNA_annotation.gff3 $PREFIX/share/${PKG_NAME}-${PKG_VERSION}/rDNA_annotation.gff3 diff --git a/recipes/ribotin/meta.yaml b/recipes/ribotin/meta.yaml index 60fb11c2a511e..360feb7cd003d 100644 --- a/recipes/ribotin/meta.yaml +++ b/recipes/ribotin/meta.yaml @@ -1,19 +1,21 @@ {% set name = "ribotin" %} -{% set version = "1.1" %} +{% set version = "1.2" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/maickrau/{{ name }}/files/12247664/{{ name }}.tar.gz - sha256: 811e242cefcdbeeb34119a12c00a7370196229326d62bd09e750a1e919cba88b + url: https://github.com/maickrau/{{ name }}/files/13435950/{{ name }}.tar.gz + sha256: 88d7be40dc641b96ef6f36cd2e464e8d65395ab50158efa1d2d49203b42ffa79 patches: - makefile.patch build: number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('ribotin', max_pin="x.x") }} requirements: build: From 32ebe6f4cf9136888fa2e08a998d7dfd1f258979 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 09:03:09 -0700 Subject: [PATCH 0870/2173] Update mehari to 0.21.0 (#44410) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index f2f3d05dc9cff..ed61e18bbf4d7 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.20.0" %} -{% set sha256 = "dc9c3d485a1d0fb6af143395026d7c218177ce463dde9f4d2b063883de9e094d" %} +{% set version = "0.21.0" %} +{% set sha256 = "ce849731697f834b64da6a6fd1007666c98fb6c21def5a00d57d247dfc91555e" %} package: name: mehari From b5fbca45023a41c4f59946586fcebb54321e939c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 10:04:14 -0700 Subject: [PATCH 0871/2173] Update annonars to 0.29.1 (#44411) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 6230dae83d476..e2ce1adfad3eb 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.29.0" %} +{% set version = "0.29.1" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: d38396661da5088274427a8b95137ff5addd0d239c67bc66c5a2fab0e76136c5 + sha256: 20eb6206d53d31e6fcb8f497db83b39d66dd4d0d468b23843b646e47bfbc2053 requirements: build: From 99dd9a7d620d2379acb5cba140203d111c6218bf Mon Sep 17 00:00:00 2001 From: John Lees Date: Wed, 22 Nov 2023 17:53:04 +0000 Subject: [PATCH 0872/2173] Update poppunk to v2.6.1 (#44406) * Update poppunk to v2.6.1 * Add run_exports * Reset build to 0 * idiot copy paste --------- Co-authored-by: Sam Horsfield <57448593+samhorsfield96@users.noreply.github.com> --- recipes/poppunk/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index aa2b9c61d2062..a321fb07a79a0 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.6.0" %} +{% set version = "2.6.1" %} {% set name = "PopPUNK" %} package: @@ -7,10 +7,10 @@ package: source: url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 9060e0f09e99c1cd34662fb4b6c4b28e4344c0e3d00e983a7be8b60591ad92ec + sha256: 1f993aa7cda94a578ecd71be27c3e013707389d96c8dc0ddaa020284ca508799 build: - number: 1 + number: 0 skip: true # [py < 38] script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" entry_points: @@ -22,6 +22,8 @@ build: - poppunk_mandrake = PopPUNK.mandrake:main - poppunk_info = PopPUNK.info:main - poppunk_lineages_from_strains = PopPUNK.lineages:main + run_exports: + - {{ pin_subpackage("poppunk", max_pin="x") }} requirements: build: From 22234068fbe1c5e6dc3b060339cde31d9c323d30 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 11:18:55 -0700 Subject: [PATCH 0873/2173] Update flams to 1.1.2 (#44399) --- recipes/flams/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/flams/meta.yaml b/recipes/flams/meta.yaml index bf037b77909e7..8e3788910a7bd 100644 --- a/recipes/flams/meta.yaml +++ b/recipes/flams/meta.yaml @@ -1,5 +1,5 @@ {% set name = "flams" %} -{% set version = "1.1.0" %} +{% set version = "1.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/flams-{{ version }}.tar.gz - sha256: c67a3c0807d050ad17bbdcaa51ea04268d4a9cc062dd17ca9ef0b3c484614558 + sha256: b1a62f8ba443800afcaa8bed70b4d93b1c0e2631d0d6a7eae9064a8368403b0e build: entry_points: From e0f6870751d77d561300b5c03d77998eced56139 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 11:19:07 -0700 Subject: [PATCH 0874/2173] Update pbsim3 to 3.0.1 (#44403) --- recipes/pbsim3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbsim3/meta.yaml b/recipes/pbsim3/meta.yaml index 36243c12f136e..5a166dcaeb058 100644 --- a/recipes/pbsim3/meta.yaml +++ b/recipes/pbsim3/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbsim3" %} -{% set version = "3.0.0" %} -{% set sha256 = "949ac8bcc2832d5b775da1766de19bdbdd97bd69b1543231ccd16688b46f7972" %} +{% set version = "3.0.1" %} +{% set sha256 = "4d2d0cabc1adfd1ade0cde983fb37f7e8af477c0fd7b09ef3e753742b89cc541" %} package: name: {{ name }} From 1e282bc9fdd26e201f7b8d90e9cebc32af6471b0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 11:20:15 -0700 Subject: [PATCH 0875/2173] Update earlgrey to 4.0 (#44412) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index ac9e6b4c4d999..c5f6be97ed3f6 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "3.2.2" %} -{% set sha256 = "dfb561005413b60426e12dc894622da25f3bcb604e8a986c23a8d72eddaec9e0" %} +{% set version = "4.0" %} +{% set sha256 = "317e058d2a09261ae68cec96a5af8cafefb05d9b060be869f0280cb66b0b81ac" %} package: name: {{ name|lower }} From 8aa4e5059e072cb40f76efc7044f96cde9784831 Mon Sep 17 00:00:00 2001 From: Linelle <48773001+abueg@users.noreply.github.com> Date: Wed, 22 Nov 2023 13:21:54 -0500 Subject: [PATCH 0876/2173] Update merquryfk dependencies (#44397) * add fastk and R packages to merquryfk meta.yaml R package version minimums used are copied from the merqury package's meta.yaml * bump build number --- recipes/merquryfk/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/merquryfk/meta.yaml b/recipes/merquryfk/meta.yaml index ba6212b78d301..09f7118cbb63f 100644 --- a/recipes/merquryfk/meta.yaml +++ b/recipes/merquryfk/meta.yaml @@ -13,7 +13,7 @@ source: - patch build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("merquryfk", max_pin="x") }} @@ -27,6 +27,12 @@ requirements: - bzip2 - zlib - libcurl + run: + - fastk + - r-base >=4 + - r-argparse >=2.0.1 + - r-ggplot2 >=3.3.2 + - r-scales >=1.1.1 test: commands: From e14644c25a1d7b45159169ba818ffadabfc1ea6b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 11:22:32 -0700 Subject: [PATCH 0877/2173] Update piranha-polio to 1.2.2 (#44409) --- recipes/piranha-polio/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/piranha-polio/meta.yaml b/recipes/piranha-polio/meta.yaml index f02a40a7be400..9692a7158684e 100644 --- a/recipes/piranha-polio/meta.yaml +++ b/recipes/piranha-polio/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} package: name: piranha-polio @@ -6,7 +6,7 @@ package: source: url: https://github.com/polio-nanopore/piranha/archive/refs/tags/{{ version }}.tar.gz - sha256: a0c8e145868946664a9a1be07ae94cca514c63f06ce7e70e2a5dde660f2b228c + sha256: 458f9d2e1021a8643a7bf2f2f8f695c36bb025744bfed588c27777f8afe536c7 build: number: 0 From 23d81e5928f54c14e9dc2fd90e01bc57f79411f8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 12:31:27 -0700 Subject: [PATCH 0878/2173] Update sequali to 0.3.0 (#44407) --- recipes/sequali/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index f49120d7e89ac..fcc9e14b627a8 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sequali" %} -{% set version = "0.2.0" %} +{% set version = "0.3.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7fbe9a053d0a4529fdf937bf474334125c8828c692447f0356926ee735dcef68 + sha256: b194d2d993f61431085b43196d8d829a58cff3ae91cd6cceeefff7dbc1dd5321 build: number: 0 From 7e9e2908ee8d2f604b2edcf18b7ef269482253d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 16:46:14 -0700 Subject: [PATCH 0879/2173] Update iphop to 1.3.3 (#44368) * Update iphop to 1.3.3 * add run_exports * add perl-json * try removing perl-bioperl pinning --------- Co-authored-by: joshuazhuang7 --- recipes/iphop/build.sh | 2 +- recipes/iphop/meta.yaml | 16 ++++++++++++---- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/recipes/iphop/build.sh b/recipes/iphop/build.sh index f2f441a01a60a..200275ba0f084 100644 --- a/recipes/iphop/build.sh +++ b/recipes/iphop/build.sh @@ -1,5 +1,5 @@ echo " === Start build" -${PYTHON} -m pip install . -vv +${PYTHON} -m pip install . --no-deps --no-build-isolation -vvv echo "Pip install done - now adjusting the library paths" for CHANGE in "activate" "deactivate" do diff --git a/recipes/iphop/meta.yaml b/recipes/iphop/meta.yaml index cf598bdda53c6..df7fd52d2da88 100644 --- a/recipes/iphop/meta.yaml +++ b/recipes/iphop/meta.yaml @@ -1,5 +1,5 @@ {% set name = "iphop" %} - {% set version = "1.3.2" %} + {% set version = "1.3.3" %} package: name: "{{ name|lower }}" @@ -7,11 +7,13 @@ package: source: url: https://bitbucket.org/srouxjgi/iphop/downloads/{{ name }}-{{ version }}.tar.gz - sha256: 1d4678c4ee8d47b798c0b105e156c382585f07aeac528ba9b7f3a2dc5d1d3ed3 + sha256: dfa42bcd31a076b213a97e105a5ddc8725531f7a5e069ba2645789f6adcfb85e build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage('iphop', max_pin="x") }} requirements: build: @@ -22,7 +24,7 @@ requirements: - numpy 1.23.* - tensorflow 2.7.* - perl <6 - - perl-bioperl <=1.7 + - perl-bioperl - blast 2.12.* - biopython 1.79.* - scikit-learn 0.22.* @@ -44,6 +46,12 @@ test: about: home: "https://bitbucket.org/srouxjgi/iphop/" license: Modified GPL v3 - license_family: GPL + license_family: GPL3 license_file: LICENSE.txt summary: "Predict host genus from genomes of uncultivated phages." + +extra: + identifiers: + - doi:10.1371/journal.pbio.3002083 + recipe-maintainers: + - simroux From a50336adda7519eb7adbfd51cf54b08e920cad48 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 22 Nov 2023 16:46:47 -0700 Subject: [PATCH 0880/2173] Update hostile to 0.3.0 (#44414) --- recipes/hostile/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hostile/meta.yaml b/recipes/hostile/meta.yaml index 46a00d25e040e..6265bcf8bd3a4 100644 --- a/recipes/hostile/meta.yaml +++ b/recipes/hostile/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.0" %} +{% set version = "0.3.0" %} package: name: hostile @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/h/hostile/hostile-{{ version }}.tar.gz - sha256: 4edda5ad96a3f9feb0663e8b447299f4f57ab706ac2375946c5b4b314117e323 + sha256: e18678827d2b010487d77bb56a7115137a067ce9827c911bd567e364166a5ea4 build: noarch: python From 8c53c2b763aef73515e4f9c40747ba64ed5be98c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Siebren=20Fr=C3=B6lich?= <48289046+siebrenf@users.noreply.github.com> Date: Thu, 23 Nov 2023 00:47:27 +0100 Subject: [PATCH 0881/2173] Added run_exports to meta.yaml (#44405) --- recipes/gimmemotifs/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/gimmemotifs/meta.yaml b/recipes/gimmemotifs/meta.yaml index d4aa790fba52f..7811f1aef805b 100644 --- a/recipes/gimmemotifs/meta.yaml +++ b/recipes/gimmemotifs/meta.yaml @@ -9,7 +9,11 @@ source: sha256: 8e7d23a898174a962c845b22433a74e3ddde619c5d77f3a5b5dbfb8fa61e7351 build: - number: 4 + number: 5 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('gimmemotifs', max_pin="x.x") }} + - {{ pin_subpackage('gimmemotifs-minimal', max_pin="x.x") }} outputs: - name: gimmemotifs-minimal From 0caad08b411bf9ddf12a627bb05349f92e89ffcd Mon Sep 17 00:00:00 2001 From: benzoid Date: Thu, 23 Nov 2023 07:38:56 +0000 Subject: [PATCH 0882/2173] Update Jalview to 2.11.3.0 (#44297) --- recipes/jalview/build.sh | 6 ++ recipes/jalview/jalview.sh | 176 ++++++++++++++++++++++++++++++++----- recipes/jalview/meta.yaml | 19 ++-- 3 files changed, 170 insertions(+), 31 deletions(-) mode change 100644 => 100755 recipes/jalview/build.sh mode change 100644 => 100755 recipes/jalview/jalview.sh diff --git a/recipes/jalview/build.sh b/recipes/jalview/build.sh old mode 100644 new mode 100755 index 3dc643c4f5b51..cb17e2ed52032 --- a/recipes/jalview/build.sh +++ b/recipes/jalview/build.sh @@ -21,6 +21,12 @@ gradle -PJAVA_VERSION=11 -PINSTALLATION="bioconda (build $PKG_BUILDNUM)" -PJALVI # copy jalview jar to target cp -vR build/libs/jalview-all-$PKG_VERSION-j11.jar $JALVIEWDIR/jalview-all-j11.jar +# copy jalview logo to target +LOGO=$SRC_DIR/utils/channels/release/images/jalview_logo.png +if [ -e "$LOGO" ]; then + cp "$LOGO" $JALVIEWDIR/jalview_logo.png +fi + # copy wrapper and make executable cp $RECIPE_DIR/jalview.sh $JALVIEWDIR/. chmod +x $JALVIEWDIR/jalview.sh; diff --git a/recipes/jalview/jalview.sh b/recipes/jalview/jalview.sh old mode 100644 new mode 100755 index 9c2daa1582bdc..1f35b44d829af --- a/recipes/jalview/jalview.sh +++ b/recipes/jalview/jalview.sh @@ -3,49 +3,177 @@ ############################### # Wrapper for Jalview # -# Note, in order to run commandline-only calls use -# -nodisplay +# 2023-08-16 Jalview 2.11.3.0 has new command line arguments +# Old command line arguments are currently detected and actioned +# but are no longer supported and will be removed at a later date. +# +# See +# Jalview -> Help -> Documentation -> Command Line -> introduction and reference +# or +# https://www.jalview.org/help/html/features/clarguments.html +# for details of the new command line arguments. +# +# Note, in order to run commandline-only calls use +# --headless # # By default, this wrapper executes java -version to determine the JRE version -# Set JALVIEW_JRE=j1.8 or JALVIEW_JRE=j11 to skip the version check +# Set JALVIEW_JRE=j1.8 or JALVIEW_JRE=j11 to skip the version check. # # By default, this wrapper does NOT restrict the memory consumption of Jalview. # Set eg. JALVIEW_MAXMEM=1g to set the maximal memory of Jalview's VM # +# This script is maintained in the Jalview repository in utils/conda/jalview.sh ############################### -# ARG1 saved to check whether we need "-open" later -ARG1=$1 +declare -a ARGS=("${@}") + +# this function is because there's no readlink -f in Darwin/macOS +function readlinkf() { + FINDFILE="$1" + FILE="${FINDFILE}" + PREVFILE="" + C=0 + MAX=100 # just in case we end up in a loop + FOUND=0 + while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do + PREVFILE="${FILE}" + FILE="$(readlink "${FILE}")" + if [ -z "${FILE}" ]; then + # the readlink is empty means we've arrived at the script, let's canonicalize with pwd + FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")" + FOUND=1 + elif [ "${FILE#/}" = "${FILE}" ]; then + # FILE is not an absolute path link, we need to add the relative path to the previous dir + FILE="$(dirname "${PREVFILE}")/${FILE}" + fi + C=$((C+1)) + done + if [ "${FOUND}" -ne 1 ]; then + echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2 + exit 1 + fi + echo "${FILE}" +} + +ISMACOS=0 +if [ "$( uname -s )" = "Darwin" ]; then + ISMACOS=1 +fi -# Find original directory of bash script, resolving symlinks -# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 -SOURCE="${BASH_SOURCE[0]}" -while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink - DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +# check for headless mode +HEADLESS=0 +GUI=0 +HELP=0 +DEBUG=0 +for RAWARG in "${@}"; do + ARG="${RAWARG%%=*}" + case "${ARG}" in + --headless|--output|--image|--structureimage) + HEADLESS=1 + ;; + --help|--help-*|--version|-h) + HELP=1 + ;; + --gui) + GUI=1 + ;; + --debug) + DEBUG=1 + ;; + esac + + if [ "${HELP}" = 1 ]; then + # --help takes precedence + HEADLESS=1 + GUI=0 + elif [ "${GUI}" = 1 ]; then + # --gui takes precedence over --headless + HEADLESS=0 + fi done -DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script + +declare -a JVMARGS=() + +# set vars for being inside the macos App Bundle +if [ "${ISMACOS}" = 1 ]; then +# MACOS ONLY + DIR="$(dirname "$(readlinkf "$0")")" + if [ -e "${DIR}/jalview_logo.png" ]; then + JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${DIR}/jalview_logo.png" ) + fi +else +# NOT MACOS + DIR="$(dirname "$(readlink -f "$0")")" +fi + +if [ "${HEADLESS}" = 1 ]; then + # this suppresses the Java icon appearing in the macOS Dock and maybe other things in other OSes + JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" ) +fi + +JAVA=java # decide which jalview jar to launch - either 'j11' or 'j1.8' if [[ "$JALVIEW_JRE" != "j11" && "$JALVIEW_JRE" != "j1.8" ]]; then JALVIEW_JRE="j11" # if java 8 is installed we pick the j1.8 build - if [[ $( java -version 2>&1 | grep '"1.8' ) != "" ]]; then JALVIEW_JRE=j1.8; fi + if [[ $( "${JAVA}" -version 2>&1 | grep '"1.8' ) != "" ]]; then + JALVIEW_JRE="j1.8" + fi fi +JARPATH="${DIR}/jalview-all-${JALVIEW_JRE}.jar" + # check if memory maximum is set and if so forward to java-based jalview call -if [ -z "$JALVIEW_MAXMEM" ]; then - VMMAXMEM="" -else - VMMAXMEM="-Xmx${JALVIEW_MAXMEM}" +if [ \! -z "$JALVIEW_MAXMEM" ]; then + JVMARGS=( "${JVMARGS[@]}" "-Xmx${JALVIEW_MAXMEM}" ) +fi + +# WINDOWS ONLY (Cygwin or WSL) +# change paths for Cygwin or Windows Subsystem for Linux (WSL) +if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid + if [ "$(uname -o)" = "Cygwin" ]; then + # CYGWIN + JARPATH="$(cygpath -pw "${JARPATH}")" + # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~' + ARGS=() + for ARG in "${@}"; do + if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then + ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" ) + else + ARGS=( "${ARGS[@]}" "${ARG}" ) + fi + done + elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then + # WSL + JARPATH="$(wslpath -aw "${JARPATH}")" + ARGS=() + for ARG in "${@}"; do + if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then + # annoyingly wslpath does not work if the file doesn't exist! + ARGBASENAME="$(basename "${ARG}")" + ARGDIRNAME="$(dirname "${ARG}")" + ARGS=( "${ARGS[@]}" "$(wslpath -aw "${ARGDIRNAME}")\\${ARGBASENAME}" ) + else + ARGS=( "${ARGS[@]}" "${ARG}" ) + fi + done + JAVA="${JAVA}.exe" + fi +fi + +# get console width -- three ways to try, just in case +if command -v tput 2>&1 >/dev/null; then + COLUMNS=$(tput cols) 2>/dev/null +elif command -v stty 2>&1 >/dev/null; then + COLUMNS=$(stty size | cut -d" " -f2) 2>/dev/null +elif command -v resize 2>&1 >/dev/null; then + COLUMNS=$(resize -u | grep COLUMNS= | sed -e 's/.*=//;s/;//') 2>/dev/null fi +JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" ) -# check to see if $1 is set and is not start of other cli set args -OPEN="" -if [ -n "$ARG1" -a "$ARG1" = "${ARG1#-}" ]; then - # first argument exists and does not start with a "-" - OPEN="-open" +if [ "${DEBUG}" = 1 ]; then + echo Shell running: \""${JAVA}"\" \""${JVMARGS[@]}"\" -jar \""${JARPATH}"\" "${ARGS[@]}" fi -java $VMMAXMEM -jar $DIR/jalview-all-${JALVIEW_JRE}.jar $OPEN ${@}; +"${JAVA}" "${JVMARGS[@]}" -jar "${JARPATH}" "${ARGS[@]}" diff --git a/recipes/jalview/meta.yaml b/recipes/jalview/meta.yaml index 6516dff6d1884..cf4e2c84b77f9 100644 --- a/recipes/jalview/meta.yaml +++ b/recipes/jalview/meta.yaml @@ -1,16 +1,19 @@ -{% set version = "2.11.2.7" %} +{% set name = "jalview" %} +{% set version = "2.11.3.0" %} package: - name: jalview + name: {{ name|lower }} version: {{ version }} build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage( name, max_pin="x.x") }} source: url: https://www.jalview.org/source/jalview_{{ version|replace(".", "_") }}.tar.gz - sha256: "a71c3bfff51c85ccd9080dd123b09131faa262c307fc887c0fe0c53ca5a19579" + sha256: "a3eb2832d221dc1c25cc75e4ea60823479027462c993b53aa3d085c1a9bf766a" requirements: build: @@ -23,13 +26,13 @@ requirements: # Jalview 2.11.1.4 can run as 1.8 or java 11+ # Version number reference: https://github.com/conda/conda/issues/6948#issuecomment-369360906 # A bug with OpenJDK 11.0.9.1+1 makes Jalview crash on macOS. Fixed with later versions of OpenJDK. - - openjdk >=8.0.192,!=11.0.9.*,<12 + - openjdk >=8.0.192,!=9.*,!=10.*,!=11.0.9.*,<12 - xorg-libxtst - psutil test: commands: - - jalview -help + - jalview --help about: @@ -46,7 +49,9 @@ about: extra: notes: | - This wrapper and installation is primarily for commandline-only use. + This wrapper and installation is primarily for commandline use. Set JALVIEW_JRE=j1.8 or JALVIEW_JRE=j11 to specify the java runtime if you need jalview to start up as quickly as possible Set JALVIEW_MAXMEM=2g to restrict jalviews maximal memory consumption (here to 2G RAM). Otherwise 90% of physical memory - (capped at 32G) is allocated. Memory allocation can also be set in Tools->Preferences->Startup. + (capped at 32G) is allocated. Memory allocation can also be set in Tools->Preferences->Startup or specified with command- + line arguments --jvmmempc=90 (percentage of total physical memory, default 90) and --jvmmemmax=2g (set a different cap, + default 32G if total physical memory can be detected or 8G if total physical memory cannot be detected). From af9633a987770550473b6859e31426c98f4fcfd9 Mon Sep 17 00:00:00 2001 From: Peter Diakumis Date: Thu, 23 Nov 2023 19:09:40 +1100 Subject: [PATCH 0883/2173] bump mosdepth v0.3.5 -> v0.3.6 (#44418) --- recipes/mosdepth/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/mosdepth/meta.yaml b/recipes/mosdepth/meta.yaml index a637559a8e272..a4a4b1000eeec 100755 --- a/recipes/mosdepth/meta.yaml +++ b/recipes/mosdepth/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.5" %} +{% set version = "0.3.6" %} package: name: mosdepth From 6f05be7cb442ea3943d5a40c2b8131c1cd8b67ba Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 23 Nov 2023 02:10:04 -0700 Subject: [PATCH 0884/2173] Update ska2 to 0.3.5 (#44420) --- recipes/ska2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ska2/meta.yaml b/recipes/ska2/meta.yaml index 53d1b819c1333..bd250923fcb6e 100644 --- a/recipes/ska2/meta.yaml +++ b/recipes/ska2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ska2" %} -{% set version = "0.3.4" %} +{% set version = "0.3.5" %} package: name: {{ name|lower}} @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/ska.rust/archive/v{{ version }}.tar.gz - sha256: 65a60e74ac061ab15d8c982cfd446e0b39d01deca353f52d978d811a412e9834 + sha256: 507290aef6ec268e2b5098b60a208dddfc690f1c029e50b68eb5169ba3b1c9f0 build: number: 0 From 4a2368a07d1f3bc7cdc10439a7860aa8cd1fca1a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 23 Nov 2023 05:57:40 -0700 Subject: [PATCH 0885/2173] Update nanometa-live to 0.4.1 (#44425) --- recipes/nanometa-live/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanometa-live/meta.yaml b/recipes/nanometa-live/meta.yaml index d2c9332d1ed55..ab801d6964c57 100644 --- a/recipes/nanometa-live/meta.yaml +++ b/recipes/nanometa-live/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanometa-live" %} -{% set version = "0.4.0" %} +{% set version = "0.4.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/FOI-Bioinformatics/nanometa_live/archive/{{ version }}.tar.gz - sha256: 2c19b9df861391bbee842fbd6e92db43a3585bd881ab9cb8dfbc16d20bb06ae6 + sha256: bc241b82277b641df9d419cb014a80a223a5f2db47a596925663589d8dbda5c2 build: number: 0 From a6a6409dab7b518e0fb1d5dfc1b078cd7860cb55 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 23 Nov 2023 06:00:35 -0700 Subject: [PATCH 0886/2173] Update annonars to 0.29.2 (#44426) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index e2ce1adfad3eb..1d0c56eac5cee 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.29.1" %} +{% set version = "0.29.2" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 20eb6206d53d31e6fcb8f497db83b39d66dd4d0d468b23843b646e47bfbc2053 + sha256: 5acc5382811fec1324519f33efbe7b04ba563df5e49a3e345c963933da15610c requirements: build: From c1eaa711df8f0c5035ea5683a9e508ba6d689ac6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 23 Nov 2023 06:26:28 -0700 Subject: [PATCH 0887/2173] Update genoboo to 0.4.10 (#44422) --- recipes/genoboo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genoboo/meta.yaml b/recipes/genoboo/meta.yaml index 4c0cd5d175a2c..3a910a856e5e5 100644 --- a/recipes/genoboo/meta.yaml +++ b/recipes/genoboo/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'genoboo' %} -{% set version = '0.4.9' %} -{% set sha256 = '5d8116ae6ed31d727ff96f405d1f173dde35ac98d0eaf6f6a5f10e9328d65466' %} +{% set version = '0.4.10' %} +{% set sha256 = 'd65c113dc6a515b8b07906ebf0bd8cc167704335f582b27b8cae2a3097f857aa' %} package: name: {{ name|lower }} From 01e32e200cbbfddf16bb241251fbe3f8eb80be83 Mon Sep 17 00:00:00 2001 From: Lidong Date: Thu, 23 Nov 2023 22:14:06 +0800 Subject: [PATCH 0888/2173] Update spagrn to v1.0.7 (#44381) * add spagrn * add spagrn * add spagrn * remove zip * update v1.0.7 * add run_export * fixed bugs * fixed bugs * update GPL --- recipes/spagrn/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/spagrn/meta.yaml b/recipes/spagrn/meta.yaml index e2a810f486bc8..e8dff8d51ed68 100644 --- a/recipes/spagrn/meta.yaml +++ b/recipes/spagrn/meta.yaml @@ -1,18 +1,20 @@ {% set name = "SpaGRN" %} -{% set version = "1.0.4" %} +{% set version = "1.0.7" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: http://www.bgiocean.com/SpaGRN/spatialGRN.tar.gz - sha256: a92f59f3c4095eef33f3b615932e9cbaa182ff80296265a4cbe030ec321a3e7e + url: https://www.bgiocean.com/SpaGRN/SpaGRN.tar.gz + sha256: ac60ca83b69c483eb7b717e82d8a2ab3add0237919e610ac8d9e8ec9a1aca67c build: noarch : python number: 0 script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed ." + run_exports: + - {{ pin_subpackage('spagrn', max_pin="x.x") }} requirements: host: @@ -43,8 +45,8 @@ test: - spagrn about: - home: https://github.com/iprada/Circle-Map - license: GNU General Public License v3.0 + home: https://github.com/BGI-Qingdao/SpaGRN + license: GPL-3.0-or-later license_family: GPL3 summary: A comprehensive tool to infer TF-centered, spatial gene regulatory networks for the spatially resolved transcriptomics (SRT) data. From 0855546a134e8106f2625e830222ef817a803c4e Mon Sep 17 00:00:00 2001 From: benzoid Date: Thu, 23 Nov 2023 17:32:59 +0000 Subject: [PATCH 0889/2173] Update Jalview version to 2.3.11.1 (#44424) --- recipes/jalview/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/jalview/meta.yaml b/recipes/jalview/meta.yaml index cf4e2c84b77f9..5701dd1f676e1 100644 --- a/recipes/jalview/meta.yaml +++ b/recipes/jalview/meta.yaml @@ -1,5 +1,5 @@ {% set name = "jalview" %} -{% set version = "2.11.3.0" %} +{% set version = "2.11.3.1" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ build: source: url: https://www.jalview.org/source/jalview_{{ version|replace(".", "_") }}.tar.gz - sha256: "a3eb2832d221dc1c25cc75e4ea60823479027462c993b53aa3d085c1a9bf766a" + sha256: "d70338e1f8f0aca01c26484c1cbc9693067b3858c326c1de360a24a0fe5c7078" requirements: build: @@ -23,7 +23,7 @@ requirements: - openjdk 11 - xorg-libxtst run: - # Jalview 2.11.1.4 can run as 1.8 or java 11+ + # Jalview 2.11.* can run as 1.8/8 or java 11 # Version number reference: https://github.com/conda/conda/issues/6948#issuecomment-369360906 # A bug with OpenJDK 11.0.9.1+1 makes Jalview crash on macOS. Fixed with later versions of OpenJDK. - openjdk >=8.0.192,!=9.*,!=10.*,!=11.0.9.*,<12 From c43761f593064afe3c981e206128d2a3fef6918b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 23 Nov 2023 10:40:45 -0700 Subject: [PATCH 0890/2173] Update pybiolib to 1.1.1542 (#44427) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index cd010da5adf9c..fa711ee6e5ed1 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1535" %} +{% set version = "1.1.1542" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 7b0885a8228bc18b0be4d71abc5cdfb68a600965159f83892c87059477b498d7 + sha256: b12069e53df0510d4c9ec6b32619d8ed446c050627325059b388921805a0a4b9 build: noarch: python From d756bc038ca15ba0eb09400c668100b1143f8918 Mon Sep 17 00:00:00 2001 From: Dirk-Jan <72025902+dirkjanvw@users.noreply.github.com> Date: Thu, 23 Nov 2023 18:42:05 +0100 Subject: [PATCH 0891/2173] update pantools to 4.3.0 (#44430) --- recipes/pantools/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/pantools/meta.yaml b/recipes/pantools/meta.yaml index a178e072c607c..49c0210b7a1cb 100644 --- a/recipes/pantools/meta.yaml +++ b/recipes/pantools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PanTools" %} -{% set version = "4.2.3" %} -{% set sha256 = "a406f451e263dd90351905dfeadeefe3a16d2bd152afe224ab073f76fe3a7923" %} +{% set version = "4.3.0" %} +{% set sha256 = "8cef87de8aadf2555e97dc78d32bee92cc2ca069bdd4637d4cb7c1b41681cbf1" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 0 run_exports: - {{ pin_subpackage("pantools", max_pin="x") }} @@ -25,21 +25,24 @@ requirements: - python >=3.7 - openjdk =8 - mcl - - kmc =3.0.1 + - kmc >=3.1.0 - mafft - iqtree - fasttree - blast - mash =2.3 - fastani - - busco =5 # [linux] + - busco =5 - r-base >=3.5.0 - r-ggplot2 - r-ape - graphviz - aster =1.3 - - bcftools >=1.12 # [linux] + - bcftools >=1.12 - tabix + - pal2nal >=14.1 + - paml >=4.10.6 + - r-cowplot >=1.1.1 test: commands: From 19bcfdb4e10c69f2c265c7e960472410739001ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Siebren=20Fr=C3=B6lich?= <48289046+siebrenf@users.noreply.github.com> Date: Thu, 23 Nov 2023 23:47:24 +0100 Subject: [PATCH 0892/2173] Update anansnake to 0.1.0 (#44429) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update anansnake to 0.1.0 * add run_exports * Update meta.yaml --------- Co-authored-by: Andreas Sjödin --- recipes/anansnake/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/anansnake/meta.yaml b/recipes/anansnake/meta.yaml index d69e1fcab01f4..6823e53bf21c2 100644 --- a/recipes/anansnake/meta.yaml +++ b/recipes/anansnake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.0.1" %} +{% set version = "0.1.0" %} package: @@ -7,21 +7,23 @@ package: source: url: https://github.com/vanheeringen-lab/anansnake/releases/download/{{ version }}/anansnake-{{ version }}.tar.gz - sha256: 4b2e71102aa3d9ee316ca569ae8c1da7332a6e5dfe7a9ee48bbd169cd074c7dd + sha256: baafb8a89c14e15965916968ac55994594c2f51426a3806f7b2cd8b212cb4fa7 build: number: 0 noarch: python script: {{ PYTHON }} -m pip install . -vv + run_exports: + - {{ pin_subpackage('anansnake', max_pin="x.x") }} requirements: host: + - python - pip - hatchling >=1.5.0 - - python =3.8 run: - - python =3.8 - - seq2science =0.9.7 + - python + - seq2science =1.2.1 test: commands: From add1b81dea29845a6010c124b6044090fee92007 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 23 Nov 2023 15:48:50 -0700 Subject: [PATCH 0893/2173] Update kb-python to 0.28.0 (#44416) * Update kb-python to 0.28.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/kb-python/meta.yaml | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/recipes/kb-python/meta.yaml b/recipes/kb-python/meta.yaml index c89906dcedc5b..9cc58afa65d9a 100644 --- a/recipes/kb-python/meta.yaml +++ b/recipes/kb-python/meta.yaml @@ -1,5 +1,5 @@ {% set name = "kb-python" %} -{% set version = "0.27.3" %} +{% set version = "0.28.0" %} package: name: {{ name|lower }} @@ -7,20 +7,24 @@ package: source: url: https://github.com/pachterlab/kb_python/archive/v{{ version }}.tar.gz - sha256: 87739a0cead3d762fb4fbdb9de10a5df78274f16f6b701b5479d62d169736e8f + sha256: ed3d655f6e60d87be5b5b013ffc54e68a943f2997b70ba4f7b3e8a1c83bd2b8a patches: config.py.patch build: - number: 1 + number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + entry_points: + - kb=kb_python.main:main + run_exports: + - {{ pin_subpackage('kb-python', max_pin="x.x") }} requirements: host: - - python >=3.6 + - python >=3.7 - pip run: - - python >=3.6 + - python >=3.7 - anndata >=0.6.22.post1 - h5py >=2.10.0 - jinja2 >2.10.1 @@ -37,6 +41,7 @@ requirements: - kallisto >=0.46.2 - bustools >=0.40.0 - requests >=2.22.0 + - typing-extensions >=3.7.4 test: commands: @@ -46,10 +51,10 @@ test: about: home: https://github.com/pachterlab/kb_python - license: BSD + license: BSD-2-Clause license_file: LICENSE license_family: BSD - summary: "A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing " + summary: "A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing" dev_url: https://github.com/pachterlab/kb_python doc_url: https://www.kallistobus.tools/ From c9714ccec06f6589c4eedf82e1e3eb82d3504b72 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 23 Nov 2023 15:49:11 -0700 Subject: [PATCH 0894/2173] Update ngs-tools to 1.8.5 (#44415) * Update ngs-tools to 1.8.5 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/ngs-tools/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ngs-tools/meta.yaml b/recipes/ngs-tools/meta.yaml index 3010acb88d6ca..8bd5ac25b52c8 100644 --- a/recipes/ngs-tools/meta.yaml +++ b/recipes/ngs-tools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ngs-tools" %} -{% set version = "1.8.4" %} +{% set version = "1.8.5" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "8c54fe3f3a85f2c3e9c185e389ac83bb2bb4c76cf2bb1204e90d33d241f91f98" + sha256: "380e236a101c5b1ac3c0fcdbcc908a210179b6ef2a93fbea9f4eb0ec2edc1de0" build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: From f94dde12afe7442062d6311adfa0a6109b7cdc2c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 23 Nov 2023 16:20:39 -0700 Subject: [PATCH 0895/2173] Update strobealign to 0.12.0 (#44434) * Update strobealign to 0.12.0 * Update meta.yaml --------- Co-authored-by: Marcel Martin --- recipes/strobealign/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/strobealign/meta.yaml b/recipes/strobealign/meta.yaml index 1551cd502b0a0..11fa5f4b70fe5 100644 --- a/recipes/strobealign/meta.yaml +++ b/recipes/strobealign/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.11.0" %} +{% set version = "0.12.0" %} package: name: strobealign @@ -6,10 +6,12 @@ package: build: number: 0 + run_exports: + - {{ pin_subpackage("strobealign", max_pin="x.x") }} source: url: https://github.com/ksahlin/strobealign/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9f2e5fc87ca377392006550bd2f0c76b54ee0d98d8f851310ebf9df59a23051d + sha256: 1ea8d081ee172b5444578bcbf261d130ea6744d9cbfc76154121e17f405ea975 requirements: build: From 289d942589894332bd388b6c1dd07c4f29860949 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 24 Nov 2023 01:23:02 -0700 Subject: [PATCH 0896/2173] Update illumina-interop to 1.3.0 (#44432) * Update illumina-interop to 1.3.0 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/illumina-interop/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 3c1538db42a2e..7d469d9e3a067 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.4" %} +{% set version = "1.3.0" %} {% set sha256 = "0335f20a6d46b3c57a7dd1c337594b156bc1e7558f44cb981f1100f396929baa" %} package: @@ -6,12 +6,14 @@ package: version: '{{version}}' build: - number: 2 + number: 0 skip: true # [osx] - + run_exports: + - {{ pin_subpackage('illumina-interop', max_pin="x.x") }} + source: url: https://github.com/Illumina/interop/archive/v{{version}}.tar.gz - sha256: e10ee79f476d40f40a1d4c73074ea58088d82700239b1a2ae9633235afe894c3 + sha256: 982770eeb271d7111d7215f5102e7c09b198686e84d4f1c7dc256df64bd0a3ca requirements: build: From 95f783a93adae5a50a384ed9f4245227d1518432 Mon Sep 17 00:00:00 2001 From: mjohnpayne Date: Fri, 24 Nov 2023 19:23:44 +1100 Subject: [PATCH 0897/2173] Add dodge to bioconda (#44421) * Update stecfinder to 1.1.1 * Update stecfinder to 1.1.1 * Update meta.yaml * Create dodge meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * fix license description --------- Co-authored-by: Thanh Lee --- recipes/dodge/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 recipes/dodge/meta.yaml diff --git a/recipes/dodge/meta.yaml b/recipes/dodge/meta.yaml new file mode 100644 index 0000000000000..5e1278b3e5998 --- /dev/null +++ b/recipes/dodge/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "0.1.0" %} +{% set name = "dodge" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/LanLab/{{ name }}/archive/v{{ version }}.tar.gz + sha256: 6897fa29651f3ea9f404f73da8a8d0e2981e2f4e3b9a44a1252fb74a2b908a7a + +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_subpackage('dodge', max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - scikit-learn >=1.0 + - pandas >=1.3 + +about: + home: https://github.com/LanLab/dodge + license: GPL-3.0-or-later + license_file: LICENSE + summary: Dynamic Outbreak Detection for Genomic Epidemiology. Automated point source bacterial outbreak detection using cumulative long term genomic surveillance. + +test: + commands: + - dodge --help From dcf0bc879e20b4a977112860588fcb24a5bec063 Mon Sep 17 00:00:00 2001 From: Stephen Shank Date: Fri, 24 Nov 2023 03:25:20 -0500 Subject: [PATCH 0898/2173] Update HyPhy to 2.5.57 (#44417) * Bump HyPhy to 2.5.57. * run_exports --------- Co-authored-by: Thanh Lee --- recipes/hyphy/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/hyphy/meta.yaml b/recipes/hyphy/meta.yaml index 36c09881912f9..a22a1c4664913 100644 --- a/recipes/hyphy/meta.yaml +++ b/recipes/hyphy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.5.50" %} -{% set sha256 = "c7597db75275cf017a64719d3134c5a0dca38e04c2e70b9d518f49bbb5f83032" %} +{% set version = "2.5.57" %} +{% set sha256 = "5412331ff40b58fa69f34ad67f3431e662e9c2002f5d035f47225f26b8e3533c" %} package: name: hyphy @@ -10,8 +10,9 @@ source: sha256: '{{ sha256 }}' build: - number: 2 - + number: 0 + run_exports: + - {{ pin_subpackage("hyphy", max_pin="x.x") }} requirements: build: - make From 45a65e31fa57e653f6bd2f021ebc5272a2eb373a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 24 Nov 2023 01:57:38 -0700 Subject: [PATCH 0899/2173] Update annonars to 0.29.3 (#44438) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 1d0c56eac5cee..893374c890a25 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.29.2" %} +{% set version = "0.29.3" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5acc5382811fec1324519f33efbe7b04ba563df5e49a3e345c963933da15610c + sha256: 962af5eedbbc1abb2e3819c79268d1d535573910c2532d352af5709425a1eec4 requirements: build: From 608cbc9908deb29083c3169af62fbb5e791c82b0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 24 Nov 2023 05:06:42 -0700 Subject: [PATCH 0900/2173] Update gunc to 1.0.6 (#44428) * Update gunc to 1.0.6 * run_exports * Change python build version --------- Co-authored-by: Thanh Lee Co-authored-by: Anthony Fullam --- recipes/gunc/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/gunc/meta.yaml b/recipes/gunc/meta.yaml index 81134c4d3bcb6..4bcb86e8d4d81 100644 --- a/recipes/gunc/meta.yaml +++ b/recipes/gunc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gunc" %} -{% set version = "1.0.5" %} +{% set version = "1.0.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 2b60dc57aba4a990622389905b5a089dd708437d5310e67549ecc71906222dbe + sha256: 6c8d6ffc658d130e59b39709da521fc5689c85ad84f4ec6d381dda5efbb16475 build: number: 0 @@ -15,11 +15,13 @@ build: - gunc = gunc.gunc:main script: "{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps" noarch: python + run_exports: + - {{ pin_subpackage("gunc", max_pin="x.x") }} requirements: host: - pip - - python >=3.6 + - python >=3.6,<3.12 run: - prodigal - diamond 2.0.4 From b85f1db90492107bc402ea5653f74186f296cd8e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 24 Nov 2023 05:39:41 -0700 Subject: [PATCH 0901/2173] Update hostile to 0.4.0 (#44441) --- recipes/hostile/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hostile/meta.yaml b/recipes/hostile/meta.yaml index 6265bcf8bd3a4..4f8c76370bf62 100644 --- a/recipes/hostile/meta.yaml +++ b/recipes/hostile/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.0" %} +{% set version = "0.4.0" %} package: name: hostile @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/h/hostile/hostile-{{ version }}.tar.gz - sha256: e18678827d2b010487d77bb56a7115137a067ce9827c911bd567e364166a5ea4 + sha256: dd003b09a7f17a8fc126bc81c2b402d1ab5946916f1f55dbcffa4c9c3014a56a build: noarch: python From 7523e9a9322078508072350a831b0c3a1f5b50c2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 24 Nov 2023 08:57:19 -0700 Subject: [PATCH 0902/2173] Update annonars to 0.29.4 (#44444) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 893374c890a25..8c824925da4c2 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.29.3" %} +{% set version = "0.29.4" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 962af5eedbbc1abb2e3819c79268d1d535573910c2532d352af5709425a1eec4 + sha256: 7394aecf2d9c4f33e63e071c973b4176b6be75db653bb10ebb130acceda5a50c requirements: build: From 953b2d139bfd981b7e6d7ebae4327c0708765c6a Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Fri, 24 Nov 2023 18:19:12 +0000 Subject: [PATCH 0903/2173] Update TaxonKit to v0.15.1 (#44443) --- recipes/taxonkit/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/taxonkit/meta.yaml b/recipes/taxonkit/meta.yaml index a6eb8dbb5129f..ebb8e35f5e385 100644 --- a/recipes/taxonkit/meta.yaml +++ b/recipes/taxonkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.15.0" %} +{% set version = "0.15.1" %} package: name: taxonkit @@ -6,12 +6,14 @@ package: build: number: 0 + run_exports: + - {{ pin_subpackage('taxonkit', max_pin='x.x') }} source: - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_darwin_amd64.tar.gz # [osx] - md5: 8d0bff0dfa6ee699fe8bd9ed7ec060bb # [osx] + md5: cc61492e7642ecf6e0708fb934de7e5f # [osx] - url: https://github.com/shenwei356/taxonkit/releases/download/v{{ version }}/taxonkit_linux_amd64.tar.gz # [linux] - md5: 6bc9ebeb76476173eeacaf72c4636af7 # [linux] + md5: c40825316860d0a23a51fb782561eef7 # [linux] test: commands: From d97b37a6cf1d3864f7f782293a41e3f4076b1b05 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Fri, 24 Nov 2023 19:32:02 +0000 Subject: [PATCH 0904/2173] Pin numpy version in matchms (#44446) * Pin numpy version in matchms * Update meta.yaml * Update meta.yaml --- recipes/matchms/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 6db06343038dc..20b110efe079c 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e62b1591782b01c3ef83850245609d85e3d612a7f7c350b4fc2ad067d8bc9d15 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps -vvv" noarch: python run_exports: @@ -27,14 +27,14 @@ requirements: - matplotlib-base - networkx - numba >=0.47 - - numpy + - numpy <1.25 - pickydict >=0.4.0 - pyteomics >=4.6 - python >=3.8 - pyyaml - rdkit >=2020.03.1 - requests - - scipy >=1.4.0 + - scipy >=1.4.0, <1.11 - sparsestack >=0.4.1 - tqdm - pillow =9.5 From 6c0fdff5205407bf341ccdc9db7e30ae0839ad5c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 24 Nov 2023 12:33:08 -0700 Subject: [PATCH 0905/2173] Update vsearch to 2.26.0 (#44445) --- recipes/vsearch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index 227abadd8cca4..168605a711a7a 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.25.0" %} -{% set sha256 = "b7e25638924e56591d7c6ac3a959795000439937f5b566be7f06457bb31f91a9" %} +{% set version = "2.26.0" %} +{% set sha256 = "960b9b2693fa20a9547367b585542dae1cc93de78bdaea66d6904f14b8216d17" %} package: name: vsearch From c6ede28dbb44e8b00812ae60e66112e1e3b868ec Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 24 Nov 2023 12:34:57 -0700 Subject: [PATCH 0906/2173] Update pydeseq2 to 0.4.3 (#44440) --- recipes/pydeseq2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pydeseq2/meta.yaml b/recipes/pydeseq2/meta.yaml index 1b3e199caec5f..a15262ff69be7 100644 --- a/recipes/pydeseq2/meta.yaml +++ b/recipes/pydeseq2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pydeseq2" %} -{% set version = "0.4.2" %} +{% set version = "0.4.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pydeseq2-{{ version }}.tar.gz - sha256: b2e8878dccf4e5562c4c1f0efd64e1c93e83ba51642c20bcae0384a2da2cc819 + sha256: 694f4fa1d390304488cd55b317204b21cb1d724a60ebb167a6973138d0f05faf build: noarch: python From 8269db8e969ce2992652aaff9af564beee8b354c Mon Sep 17 00:00:00 2001 From: Hasindu Gamaarachchi Date: Sat, 25 Nov 2023 06:36:01 +1100 Subject: [PATCH 0907/2173] add slow5curl (#44436) --- recipes/slow5curl/build.sh | 5 +++++ recipes/slow5curl/meta.yaml | 40 +++++++++++++++++++++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 recipes/slow5curl/build.sh create mode 100644 recipes/slow5curl/meta.yaml diff --git a/recipes/slow5curl/build.sh b/recipes/slow5curl/build.sh new file mode 100644 index 0000000000000..ab6342d1471b4 --- /dev/null +++ b/recipes/slow5curl/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash +scripts/install-zstd.sh +make CC=$CC zstd_local=../zstd/lib +mkdir -p $PREFIX/bin +cp slow5curl $PREFIX/bin/slow5curl diff --git a/recipes/slow5curl/meta.yaml b/recipes/slow5curl/meta.yaml new file mode 100644 index 0000000000000..4830b0486ce78 --- /dev/null +++ b/recipes/slow5curl/meta.yaml @@ -0,0 +1,40 @@ +{% set name = "slow5curl" %} +{% set version = "0.2.0" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/BonsonW/slow5curl/releases/download/v{{ version }}/slow5curl-v{{ version }}-release.tar.gz + sha256: 11eac212e3452fb91e158999d0c5b186ac238d5580e3a9696a87590c21206bd3 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('slow5curl', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + host: + - zlib + - wget + - curl + run: + - zlib + - curl + +test: + commands: + - slow5curl --help + - slow5curl --version + +about: + home: https://github.com/BonsonW/slow5curl + license: MIT + license_file: LICENSE + summary: Tool for accessing remote BLOW5 files. + description: 'slow5curl is a command line tool for fetching reads from remote BLOW5 files, which is built on top of slow5lib and libcurl.' + From fe1885af589869d62f6a5f8a13ef780c02f62f0d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 24 Nov 2023 12:37:20 -0700 Subject: [PATCH 0908/2173] Update singlem to 0.16.0 (#44435) --- recipes/singlem/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/singlem/meta.yaml b/recipes/singlem/meta.yaml index b7d0b36334738..009d1a627814f 100644 --- a/recipes/singlem/meta.yaml +++ b/recipes/singlem/meta.yaml @@ -1,5 +1,5 @@ {% set name = "singlem" %} -{% set version = "0.15.1" %} +{% set version = "0.16.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 98a84252e22460aebdeee6e43e21f157a56158e312b780a1be9fc8a41ee7ac32 + sha256: 64e43a6a40795d68ff5aed7dfff9a94532b862f25a28c27de7d588d64a8c7f79 build: number: 0 From 59e538981ddd4929b498ddbe9743012e1c02f59b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 25 Nov 2023 04:01:15 -0700 Subject: [PATCH 0909/2173] Update cptac to 1.5.8 (#44449) --- recipes/cptac/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cptac/meta.yaml b/recipes/cptac/meta.yaml index 715c3afce8b96..bb81951f69797 100644 --- a/recipes/cptac/meta.yaml +++ b/recipes/cptac/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cptac" %} -{% set version = "1.5.7" %} +{% set version = "1.5.8" %} package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 824e255f63b003479cda300c141b60f482c0b0e6dbd0dbd2489b64c1e470d070 + sha256: c30d3faf666454c208a103620a094bdb6fea607953305ad48ee069bb7e6e6783 build: number: 0 From c1e7378fefb1fb495869cc922aa93a5330879724 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 25 Nov 2023 04:02:29 -0700 Subject: [PATCH 0910/2173] Update pybiolib to 1.1.1558 (#44439) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index fa711ee6e5ed1..6ca4eae58f02b 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1542" %} +{% set version = "1.1.1558" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: b12069e53df0510d4c9ec6b32619d8ed446c050627325059b388921805a0a4b9 + sha256: fe8c0f7aa6f6fa45a93956aab198769a4e8ec0dd0a7f330bf52e9f4e9ab87370 build: noarch: python From 80816b599ea9c84c3376734eaa80febe4ffe8aaa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 25 Nov 2023 04:03:08 -0700 Subject: [PATCH 0911/2173] Update parascopy to 1.14.1 (#44423) * Update parascopy to 1.14.1 * add construct --------- Co-authored-by: joshuazhuang7 --- recipes/parascopy/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/parascopy/meta.yaml b/recipes/parascopy/meta.yaml index 7a45a9c32060a..f83ef261d7f2e 100644 --- a/recipes/parascopy/meta.yaml +++ b/recipes/parascopy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "parascopy" %} -{% set version = "1.14.0" %} +{% set version = "1.14.1" %} package: name: {{ name|lower }} @@ -15,7 +15,7 @@ build: source: url: https://github.com/tprodanov/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 2a1b9ec690f9686b437983af65bd43f8c2a1665ff710f76aae6bd2c78cf208ab + sha256: a475086faeea706448db866ca8c504b3c17f3988a67fd8c174f1a334bd4bb4f1 requirements: build: @@ -42,6 +42,7 @@ requirements: - bwa >=0.7 - intervaltree >=3.0 - tabixpp + - construct test: commands: From d65171a51dc5a4a7fab282d2941ff5ffc58adba8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 25 Nov 2023 09:13:10 -0700 Subject: [PATCH 0912/2173] Update vsearch to 2.26.1 (#44455) --- recipes/vsearch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index 168605a711a7a..fdfb483ba13ff 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.26.0" %} -{% set sha256 = "960b9b2693fa20a9547367b585542dae1cc93de78bdaea66d6904f14b8216d17" %} +{% set version = "2.26.1" %} +{% set sha256 = "dc8513376405fc01ca3742624177113752870b05bb682fe1bf62d190d0a696bd" %} package: name: vsearch From 8df22ff08fd43ac82e82eeb798a1347e87212c40 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 25 Nov 2023 09:13:47 -0700 Subject: [PATCH 0913/2173] Update pyfastx to 2.0.2 (#44453) --- recipes/pyfastx/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyfastx/meta.yaml b/recipes/pyfastx/meta.yaml index 081706c3e0a2b..9006bae819474 100644 --- a/recipes/pyfastx/meta.yaml +++ b/recipes/pyfastx/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pyfastx" %} -{% set version = "2.0.1" %} -{% set sha256 = "93aff63ce88bc5cfe7152d8dcb3f2164356bcd8f95a68fb20af107e59a7f9b55" %} +{% set version = "2.0.2" %} +{% set sha256 = "763bb59f58d7884cad8a15ff8b0f0bbc5e29f867a4260d1e5ed9ecb2035ac70b" %} package: name: {{ name|lower }} From 1f478049663c8f174ff464cdb3ea925f4cb8319a Mon Sep 17 00:00:00 2001 From: Akihiro Kuno Date: Sun, 26 Nov 2023 01:14:56 +0900 Subject: [PATCH 0914/2173] Update the recipe of cstag-cli (#44454) * Update the recipe of cstag-cli * The recipe build number was incremented to 1 --- recipes/cstag-cli/meta.yaml | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/recipes/cstag-cli/meta.yaml b/recipes/cstag-cli/meta.yaml index 1b5137e130e57..91ec7c11fb99e 100644 --- a/recipes/cstag-cli/meta.yaml +++ b/recipes/cstag-cli/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python script: {{ PYTHON }} -m pip install . -vv - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name|lower, max_pin='x.x') }} @@ -23,17 +23,8 @@ requirements: - pip run: - python >=3.7.0,<4.0.0 + - pysam >=0.19.0 - cstag >=0.6.2 - ############################# - ### for pysam==0.19.1 ##### - - pysam ==0.19.1 - - bzip2 <2.0a0 - - libdeflate <1.11.0a0 - - libcurl <8.0a0 - - openssl <1.1.2a - - xz <5.3.0a0 - - zlib <1.3.0a0 - ############################# test: imports: From 7cf3f703703ac84ac8ffff3828313de2d899e50d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 25 Nov 2023 12:48:07 -0700 Subject: [PATCH 0915/2173] Update trtools to 5.1.0 (#44419) * Update trtools to 5.1.0 * add run_exports * add pyfaidx --------- Co-authored-by: joshuazhuang7 --- recipes/trtools/meta.yaml | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/recipes/trtools/meta.yaml b/recipes/trtools/meta.yaml index 822e6ccd0d326..2cb2ddd5fe79f 100644 --- a/recipes/trtools/meta.yaml +++ b/recipes/trtools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trtools" %} -{% set version = "5.0.2" %} +{% set version = "5.1.0" %} package: name: "{{ name|lower }}" @@ -7,9 +7,9 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: bdfb102dc207b6bade1859b394bf65c44f380c5d52b2dbefe52506cf0b563b64 + sha256: 22472f1983614c15780d7ec6de845095a2a7f6cb4be049942f38f6f9b1a7e359 -build: +build: noarch: python entry_points: - dumpSTR=trtools.dumpSTR:run @@ -18,8 +18,12 @@ build: - compareSTR=trtools.compareSTR:run - qcSTR=trtools.qcSTR:run - associaTR=trtools.associaTR:run - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + - prancSTR = trtools.prancSTR:run + - simTR = trtools.simTR:run + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" number: 0 + run_exports: + - {{ pin_subpackage('trtools', max_pin="x") }} requirements: host: @@ -36,6 +40,7 @@ requirements: - scikit-learn >=0.23.1 - scipy >=1.4.1 - statsmodels >=0.13.5 + - pyfaidx test: imports: @@ -65,7 +70,7 @@ about: license: MIT license_family: MIT license_file: LICENSE.txt - summary: Toolkit for genome-wide analysis of tandem repeats https://trtools.readthedocs.io/ + summary: Toolkit for genome-wide analysis of tandem repeats doc_url: https://trtools.readthedocs.io/ dev_url: https://github.com/gymreklab/TRTools From ff82bbd6d59428297f28a73754a88e6aff0b91e3 Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Sat, 25 Nov 2023 14:49:29 -0500 Subject: [PATCH 0916/2173] Update annembed v0.1.2 (#44452) * Update annembed v0.1.2 * Update annembed v0.1.2 --- recipes/annembed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml index c1a1ff1c642b6..5a2b606fcd0b3 100644 --- a/recipes/annembed/meta.yaml +++ b/recipes/annembed/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: annembed @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/annembed/archive/v{{ version }}.tar.gz - sha256: 7d428dd4ac630de7f6ab75e74f7261f1017eae77065f4e678ddde62771253da4 + sha256: 68d08b42f06d873a3b301cb609530cb1072cd97cd8ccefa8d0331d857f692352 requirements: build: From 12bf6ae78c5cf6d6853c0cc0b50062b75321571c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 25 Nov 2023 13:44:10 -0700 Subject: [PATCH 0917/2173] Update sequana to 0.16.1 (#44448) * Update sequana to 0.16.1 * deprecated --------- Co-authored-by: joshuazhuang7 --- recipes/sequana/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/sequana/meta.yaml b/recipes/sequana/meta.yaml index 7d3be2bd989d7..7e25a04a05c6a 100644 --- a/recipes/sequana/meta.yaml +++ b/recipes/sequana/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.15.4" %} -{% set sha256 = "b394fc148a67de70959189b9053ef42dbb82a99857920825b8db0ed1a28097cd" %} +{% set version = "0.16.1" %} +{% set sha256 = "5a519ca7156109c044cce41b6414e750dd5a257c11f78fc443abf8c2f6652b48" %} {% set name = "sequana" %} package: @@ -19,6 +19,7 @@ build: - sequana_taxonomy=sequana.scripts.taxonomy:main - sequana_coverage=sequana.scripts.coverage:main - sequana_start_pipeline=sequana.scripts.start_pipeline:main + - sequana_substractor=sequana.scripts.substractor:main script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" run_exports: - {{ pin_subpackage('sequana', max_pin="x") }} @@ -37,6 +38,7 @@ requirements: - colormap - cookiecutter <2 - cython + - deprecated - docutils - easydev >=0.11.1 - gseapy @@ -53,6 +55,7 @@ requirements: - pykwalify - pysam >=0.16 - python >=3.8 + - rich-click - ruamel.yaml >=0.16.0 - scikit-learn - scipy From 601b043c7ff2d7c9a9f164b07dbb8655aebb6118 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 25 Nov 2023 13:44:30 -0700 Subject: [PATCH 0918/2173] Update shortstack to 4.0.3 (#44456) * Update shortstack to 4.0.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/shortstack/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/shortstack/meta.yaml b/recipes/shortstack/meta.yaml index cb346e90fd51a..b676bb43042fa 100644 --- a/recipes/shortstack/meta.yaml +++ b/recipes/shortstack/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ShortStack" %} -{% set version = "4.0.2" %} -{% set sha256 = "049db4495f1e9c8d5fc9d23e3d6974205096135609812ab9f68e71bdd53f24a6" %} +{% set version = "4.0.3" %} +{% set sha256 = "d9990910f4359b881f5fe417ac7ab365ee2599d4bfa22844172d4e22a5ff9489" %} package: name: {{ name|lower }} @@ -13,6 +13,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('shortstack', max_pin="x") }} requirements: run: From 77cbae659085ce177b54263240046c174516d9a3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 26 Nov 2023 05:14:45 -0700 Subject: [PATCH 0919/2173] Update monsda to 1.2.2 (#44460) --- recipes/monsda/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/monsda/meta.yaml b/recipes/monsda/meta.yaml index abbdf7e347767..d923fef7e8211 100644 --- a/recipes/monsda/meta.yaml +++ b/recipes/monsda/meta.yaml @@ -1,6 +1,6 @@ {% set name = "MONSDA" %} -{% set version = "1.2.1" %} -{% set sha256 = "ccb30c5a047a6f0bf0a8b074697ddc1c72052b0c85dcd76a7c3e1f78f7a133f2" %} +{% set version = "1.2.2" %} +{% set sha256 = "677ce6d6c880f022dfd70b5dddb62d2ffdb21c2816a0930ec2a712e786adc4c3" %} package: name: "{{ name|lower }}" From 10a96804fc7aaaf229e6a7fe373afb49f7b6f217 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 26 Nov 2023 05:24:36 -0700 Subject: [PATCH 0920/2173] Update seqerakit to 0.4.3 (#44459) --- recipes/seqerakit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seqerakit/meta.yaml b/recipes/seqerakit/meta.yaml index 55ab0994c9ae5..50c14231d18bf 100644 --- a/recipes/seqerakit/meta.yaml +++ b/recipes/seqerakit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqerakit" %} -{% set version = "0.4.2" %} +{% set version = "0.4.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqerakit-{{ version }}.tar.gz - sha256: 442423a80aa80e77a8c47f2b6f6876e0c872e649e43a017c14abf17f55e86169 + sha256: bd71a6e7933ce362606c4abb2ddd8bc6de533b56e9a97ec457c52bba964baea9 build: entry_points: From 6ebfc3677da0503389d2f3b675806c7f154bc064 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 26 Nov 2023 14:47:58 -0700 Subject: [PATCH 0921/2173] Update kaiju to 1.10.0 (#44458) * Update kaiju to 1.10.0 * add run_exports * Update build.sh --------- Co-authored-by: joshuazhuang7 Co-authored-by: Thanh Lee --- recipes/kaiju/build.sh | 17 +---------------- recipes/kaiju/meta.yaml | 14 +++++++++----- 2 files changed, 10 insertions(+), 21 deletions(-) diff --git a/recipes/kaiju/build.sh b/recipes/kaiju/build.sh index bfea0a0feddf6..18d6b28918644 100755 --- a/recipes/kaiju/build.sh +++ b/recipes/kaiju/build.sh @@ -14,19 +14,4 @@ cd $SRC_DIR/src/ make CC=${CC} CXX=${CXX} cd $SRC_DIR/bin/ -cp kaiju-addTaxonNames $PREFIX/bin -cp kaiju-convertNR $PREFIX/bin -cp kaiju-gbk2faa.pl $PREFIX/bin -cp kaiju $PREFIX/bin -cp kaiju2krona $PREFIX/bin -cp kaiju2table $PREFIX/bin -cp kaijup $PREFIX/bin -cp kaijux $PREFIX/bin -cp kaiju-multi $PREFIX/bin -cp kaiju-makedb $PREFIX/bin -cp kaiju-mergeOutputs $PREFIX/bin -cp kaiju-mkbwt $PREFIX/bin -cp kaiju-mkfmi $PREFIX/bin -cp kaiju-convertMAR.py $PREFIX/bin -cp kaiju-taxonlistEuk.tsv $PREFIX/bin -cp kaiju-excluded-accessions.txt $PREFIX/bin +cp kaiju* $PREFIX/bin diff --git a/recipes/kaiju/meta.yaml b/recipes/kaiju/meta.yaml index e6eecd026bb1f..a12694188896f 100644 --- a/recipes/kaiju/meta.yaml +++ b/recipes/kaiju/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.9.2" %} +{% set version = "1.10.0" %} package: name: kaiju @@ -6,12 +6,14 @@ package: source: url: https://github.com/bioinformatics-centre/kaiju/archive/v{{ version }}.tar.gz - sha256: 58d922358dfa4a608be888ec5c9e615b45b1e4be50615429183b0c5355e89c78 + sha256: 328c85ee1d5e4eafb18b8dd0bcf26b6ba88ba15ab4f14443ac643cd7e6675267 build: - number: 3 + number: 0 no_link: - bin/kaiju-makedb.sh + run_exports: + - {{ pin_subpackage('kaiju', max_pin="x") }} requirements: build: @@ -32,10 +34,12 @@ test: - kaiju 2>&1 | grep "Kaiju {{ version }}" about: - home: http://kaiju.binf.ku.dk/ - license: GNU GPL v3 + home: https://kaiju.binf.ku.dk/ + license: GPL-3.0-or-later + license_family: GPL3 summary: 'Fast and sensitive taxonomic classification for metagenomics' license_file: LICENSE + dev_url: https://github.com/bioinformatics-centre/kaiju extra: identifiers: From f3ff8091e8aba19d25ad73d2a2c6dfa12a9e521d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 26 Nov 2023 14:48:10 -0700 Subject: [PATCH 0922/2173] Update bioconda-utils to 2.10.0 (#44461) --- recipes/bioconda-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index 22d380d54a236..709431ae41c1f 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.9.0" %} -{% set sha256 = "f11c5971ff2b618b61bea8f9e7ebd2b53e41739aa794c0d1c6af82e8c030e31c" %} +{% set version = "2.10.0" %} +{% set sha256 = "06c0560de53105c08b1ac2fad15c828980002ba3b5a19ca61fd2520227fe614b" %} package: name: bioconda-utils From 674c683c88b72d99c0ffa889679ef71a98c8dd4c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 26 Nov 2023 17:27:43 -0700 Subject: [PATCH 0923/2173] Update zol to 1.3.12 (#44464) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index 756440cacb87d..d8adaf92a1ed7 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.11" %} +{% set version = "1.3.12" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: ad0871f5922f74a4a5c9c8c73b6c0b3f8d0f59b4cbe752eb751ae9c96a11cfe1 + sha256: 978ad91679037239ca0b0762c0755b25e80777680ac998ddc316362b0406598b build: number: 0 From 43b9f07a1e3de261716d0ba52226a2e28300dd80 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 26 Nov 2023 17:59:40 -0700 Subject: [PATCH 0924/2173] Update versionix to 0.2.3 (#44463) * Update versionix to 0.2.3 * add rich-click --------- Co-authored-by: joshuazhuang7 --- recipes/versionix/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/versionix/meta.yaml b/recipes/versionix/meta.yaml index c4521bdef86ad..eac216c2f4759 100644 --- a/recipes/versionix/meta.yaml +++ b/recipes/versionix/meta.yaml @@ -1,5 +1,5 @@ {% set name = "versionix" %} -{% set version = "0.2.2" %} +{% set version = "0.2.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/versionix-{{ version }}.tar.gz - sha256: a0c215b827b17213ab3bc8980c55ccd4b0f5a5bc42e61cda6338cdf6fd61b6b9 + sha256: b8a83f09615ffb233115d64cbb42a193a187f62ce9f8769d3900cfbcc2e085c1 build: entry_points: @@ -26,6 +26,7 @@ requirements: run: - python >=3.8.0 - click >=8.1.7 + - rich-click test: imports: From c3f9a2117d5fda822b482599bfcbbc526a09d051 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 26 Nov 2023 20:34:02 -0700 Subject: [PATCH 0925/2173] Update zol to 1.3.14 (#44466) * Update zol to 1.3.14 * Update meta.yaml --------- Co-authored-by: Rauf Salamzade --- recipes/zol/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index d8adaf92a1ed7..8919b24f24453 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.12" %} +{% set version = "1.3.14" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 978ad91679037239ca0b0762c0755b25e80777680ac998ddc316362b0406598b + sha256: 1a37c3b397f0da6c0a62ceb577a5c576487f5ec3d7d61c2cfb914593f4d39f9b build: number: 0 @@ -35,6 +35,7 @@ requirements: - diamond =2.0.15 - pyrodigal - prodigal + - prodigal-gv - pyhmmer - pandas >=2.0 - xlsxwriter >=3.0.3 From 33c21a3818b7590197d9ac97eacea5fe90081c11 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 27 Nov 2023 05:14:34 -0700 Subject: [PATCH 0926/2173] Update leviosam2 to 0.4.2 (#44468) * Update leviosam2 to 0.4.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/leviosam2/meta.yaml | 27 ++++++++++++++++++--------- 1 file changed, 18 insertions(+), 9 deletions(-) diff --git a/recipes/leviosam2/meta.yaml b/recipes/leviosam2/meta.yaml index b0f02ae515205..b039512101d06 100644 --- a/recipes/leviosam2/meta.yaml +++ b/recipes/leviosam2/meta.yaml @@ -1,15 +1,17 @@ -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: - name: leviosam2 - version: {{ version }} + name: leviosam2 + version: {{ version }} source: url: https://github.com/milkschen/leviosam2/archive/refs/tags/v{{ version }}.tar.gz - sha256: ff971aef064f3717230e300ee833486d1be98d87367bb235d9680223c5e0e77c + sha256: c0901f7e78e092058116a0b013286d4c452caeeaee778a24eb13301d08e56e30 build: number: 0 + run_exports: + - {{ pin_subpackage('leviosam2', max_pin="x.x") }} requirements: build: @@ -26,10 +28,17 @@ requirements: - zlib >=1.2.11,<1.3.0a0 test: - commands: + commands: - leviosam2 -h about: - home: "https://github.com/milkschen/leviosam2" - license: MIT - license_file: LICENSE - summary: "Fast and accurate coordinate conversion between assemblies" + home: "https://github.com/milkschen/leviosam2" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Fast and accurate coordinate conversion between assemblies" + doc_url: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md" + +extra: + identifiers: + - doi:10.1093/bioinformatics/btab396 + - doi:10.1101/2022.04.27.489683 From dd256371bf8a4ca534035d446380d7329527690b Mon Sep 17 00:00:00 2001 From: Akihiro Kuno Date: Mon, 27 Nov 2023 21:15:22 +0900 Subject: [PATCH 0927/2173] Update a recipe of DAJIN2 (#44470) --- recipes/dajin2/meta.yaml | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index 29115833ac4b4..9d98f0440c51c 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -14,7 +14,7 @@ build: - DAJIN2=DAJIN2.main:execute noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 0 + number: 1 run_exports: - {{ pin_subpackage('dajin2', max_pin="x.x") }} @@ -24,16 +24,6 @@ requirements: - pip run: - python - ############################# - ### for pysam==0.19.1 ##### - - pysam ==0.19.1 - - bzip2 <2.0a0 - - libdeflate <1.11.0a0 - - libcurl <8.0a0 - - openssl <1.1.2a - - xz <5.3.0a0 - - zlib <1.3.0a0 - ############################# - numpy >=1.20.0 - scipy >=1.6.0 - pandas >=1.0.0 @@ -42,6 +32,7 @@ requirements: - statsmodels >=0.13.5 - scikit-learn >=1.0.0 - mappy >=2.24 + - pysam >=0.19.0 - flask >=2.2.0 - waitress >=2.1.0 - jinja2 >=3.1.0 From 30cf249243f214e41b7661e73809bfb3dd6379bd Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Mon, 27 Nov 2023 15:27:16 +0000 Subject: [PATCH 0928/2173] update csvtk to v0.29.0 (#44476) --- recipes/csvtk/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/csvtk/meta.yaml b/recipes/csvtk/meta.yaml index 14412fbdb90cb..f81d3b38c5053 100644 --- a/recipes/csvtk/meta.yaml +++ b/recipes/csvtk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.28.0" %} +{% set version = "0.29.0" %} package: name: csvtk @@ -7,13 +7,13 @@ package: build: number: 0 run_exports: - - {{ pin_subpackage('csvtk', max_pin='x') }} + - {{ pin_subpackage('csvtk', max_pin='x.x') }} source: - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_amd64.tar.gz # [osx] - md5: 4e6bbb301e73d5122b9e364206182130 # [osx] + md5: 055172fe0ce888cdbbe11c3c03846aa4 # [osx] - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux] - md5: 58aaf68fdd39969a184a1b2d582ff40f # [linux] + md5: ac796feaa66514b0b5eb9b21df81c22b # [linux] test: commands: From 94a056089e51eb52e217240730338203b7e7d31c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 27 Nov 2023 08:40:14 -0700 Subject: [PATCH 0929/2173] Update zol to 1.3.15 (#44474) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index 8919b24f24453..c290db062ef25 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.14" %} +{% set version = "1.3.15" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 1a37c3b397f0da6c0a62ceb577a5c576487f5ec3d7d61c2cfb914593f4d39f9b + sha256: a745b5e02fd5cb7516b284622fab8181c70b56f4067ddce7ff282b66a2799e79 build: number: 0 From 5c9de2aa28fb31e61f68c0b3db97a2bedf5a4141 Mon Sep 17 00:00:00 2001 From: Arya Massarat <23412689+aryarm@users.noreply.github.com> Date: Mon, 27 Nov 2023 12:44:08 -0800 Subject: [PATCH 0930/2173] Update trtools to 5.1.1 (#44483) --- recipes/trtools/meta.yaml | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/recipes/trtools/meta.yaml b/recipes/trtools/meta.yaml index 2cb2ddd5fe79f..f0431f6c1f2ec 100644 --- a/recipes/trtools/meta.yaml +++ b/recipes/trtools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trtools" %} -{% set version = "5.1.0" %} +{% set version = "5.1.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 22472f1983614c15780d7ec6de845095a2a7f6cb4be049942f38f6f9b1a7e359 + sha256: e3b107d3d4a2ba2f0df49c382df911ab79bfbdf04aa15c84d3093bed67e4220d build: noarch: python @@ -40,7 +40,8 @@ requirements: - scikit-learn >=0.23.1 - scipy >=1.4.1 - statsmodels >=0.13.5 - - pyfaidx + - pyfaidx >=0.5.3 + - ART >=2016.06.05 test: imports: @@ -51,6 +52,8 @@ test: - trtools.mergeSTR - trtools.qcSTR - trtools.statSTR + - trtools.prancSTR + - trtools.simTR - trtools.utils requires: - bcftools @@ -64,6 +67,8 @@ test: - statSTR --help - compareSTR --help - qcSTR --help + - prancSTR --help + - simTR --help about: home: http://github.com/gymreklab/TRTools @@ -77,3 +82,4 @@ about: extra: recipe-maintainers: - LiterallyUniqueLogin + - aryarm From 448de83c8970c422cf9678357a5e57458cad7880 Mon Sep 17 00:00:00 2001 From: Ian Fiddes Date: Mon, 27 Nov 2023 13:46:33 -0800 Subject: [PATCH 0931/2173] Update: multiple python versions for pytrf (#44283) * multiple python versions for pytrf * fix build * try different setups for osx vs linux, since osx was working before * wrong variable name * python versions in both osx and linux * reviewer comments --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pytrf/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/pytrf/meta.yaml b/recipes/pytrf/meta.yaml index 92846f4d81cd6..14cbbf40ed6d3 100644 --- a/recipes/pytrf/meta.yaml +++ b/recipes/pytrf/meta.yaml @@ -11,7 +11,8 @@ source: sha256: "{{ sha256 }}" build: - number: 0 + number: 1 + skip: True # [py < 36] script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" run_exports: - {{ pin_subpackage("pytrf", max_pin="x.x") }} @@ -21,9 +22,9 @@ requirements: - {{ compiler('c') }} host: - pip - - python >=3.6,<3.12 + - python run: - - python >=3.6,<3.12 + - python test: imports: From 8bf6f71bb90fe2ee42490db112d9c993b02677cd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 27 Nov 2023 18:27:11 -0700 Subject: [PATCH 0932/2173] Update visor to 1.1.2.1 (#44472) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update visor to 1.1.2.1 * Update deps and add run_export --------- Co-authored-by: Tomás Di Domenico --- recipes/visor/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/visor/meta.yaml b/recipes/visor/meta.yaml index 32de871baf975..ef36b8029c154 100644 --- a/recipes/visor/meta.yaml +++ b/recipes/visor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "VISOR" %} -{% set version = "1.1.2" %} +{% set version = "1.1.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/davidebolo1993/VISOR/archive/v{{ version }}.tar.gz - sha256: 90a33f99a05374d58072a129f40a84972bf34a0a65db501216daa607af64322b + sha256: 8cb8c21414c70f037263b70d217ed89532ffa26ca0a50ea0a239e5a87c1d6b0e build: entry_points: @@ -15,6 +15,8 @@ build: noarch: python script: {{ PYTHON }} -m pip install . -vv number: 0 + run_exports: + - {{ pin_subpackage('visor', max_pin="x") }} requirements: host: @@ -29,7 +31,7 @@ requirements: - pysam >=0.15.0 - python - pywgsim >=0.3.3 - - badread >=0.2.0 + - badread >=0.4.0 - minimap2 >=2.17 - samtools >=1.9 From 08642c84aed5294d5f417143630ce2c3c4c7d53a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 27 Nov 2023 19:36:02 -0700 Subject: [PATCH 0933/2173] Update bakta to 1.9.0 (#44480) * Update bakta to 1.9.0 * Update dependency versions --------- Co-authored-by: Oliver Schwengers --- recipes/bakta/meta.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml index 62c28ce4236ba..0730c2c00cc20 100644 --- a/recipes/bakta/meta.yaml +++ b/recipes/bakta/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.8.2" %} +{% set version = "1.9.0" %} package: name: bakta @@ -6,11 +6,11 @@ package: source: url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz - sha256: 'ebeab3f3d6fd437aea736bcb1ec37e7c75f6127fd0202c706ac1c6b006ec65b9' + sha256: '30e9584a5e027cb07bb52ff4fd95008cc2c83c99747b38c79ccb026ba0674781' build: noarch: python - number: 1 + number: 0 script: python -m pip install --no-deps --ignore-installed . entry_points: - bakta = bakta.main:main @@ -31,15 +31,15 @@ requirements: - requests >=2.25.1 - alive-progress ==3.0.1 - pyyaml >=6.0 - - pyrodigal >=2.1.0, <3.0 + - pyrodigal >=3.1.0 - trnascan-se >=2.0.11 - aragorn >=1.2.41 - infernal >=1.1.4 - piler-cr - - pyhmmer >=0.10.0 - - diamond >=2.0.14 - - blast >=2.12.0 - - ncbi-amrfinderplus >=3.11.2 + - pyhmmer >=0.10.4 + - diamond >=2.1.8 + - blast >=2.14.0 + - ncbi-amrfinderplus >=3.11.26 - circos >=0.69.8 test: From 6862512bc5febae861ff12bfb4f1b8d6067dcf9e Mon Sep 17 00:00:00 2001 From: John Lees Date: Tue, 28 Nov 2023 02:36:26 +0000 Subject: [PATCH 0934/2173] Bump poppunk to v2.6.2 (#44477) --- recipes/poppunk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index a321fb07a79a0..09f1470304214 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.6.1" %} +{% set version = "2.6.2" %} {% set name = "PopPUNK" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 1f993aa7cda94a578ecd71be27c3e013707389d96c8dc0ddaa020284ca508799 + sha256: c554fbc8b322836771acd6b2c0d13bb516227cf96dd8d85680b619472897082f build: number: 0 From 8c7d8bbb3d77dca8dd3da65b30666cfc7fcc39eb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 27 Nov 2023 19:38:20 -0700 Subject: [PATCH 0935/2173] Update snakemake-interface-common to 1.14.4 (#44471) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 55c7ce56fd11d..b99011ecde299 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.14.3" %} +{% set version = "1.14.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 1ea9486d26841c169a85d9955ff9e8a3b720d9d64fda357d70e87b3cd70eeeee + sha256: 9a5ab67dcb5298dccb5b19c60c61b80071358700be1b506515b87820e4d1d916 build: noarch: python From a7ac9bb33d8dd42bcd1b8297d284af40db1adbea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 27 Nov 2023 19:38:45 -0700 Subject: [PATCH 0936/2173] Update pyrodigal to 3.2.1 (#44475) * Update pyrodigal to 3.2.0 * Update pyrodigal to 3.2.1 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pyrodigal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyrodigal/meta.yaml b/recipes/pyrodigal/meta.yaml index 53c5b56be6855..79aae4b1a1021 100644 --- a/recipes/pyrodigal/meta.yaml +++ b/recipes/pyrodigal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrodigal" %} -{% set version = "3.1.1" %} +{% set version = "3.2.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1ccb0304c4a4257cd87e862286870095d9e5fd8cd5d2662ff7ae5368d1221895 + sha256: 7c0bb83eafa888bdc5d931fb3a1f6abc35247f96abc3f9e557a0109e85cbdd35 build: number: 0 From 58e9668b54a6317fc879139430481014b2780524 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 27 Nov 2023 19:39:14 -0700 Subject: [PATCH 0937/2173] Update pyrodigal-gv to 0.3.0 (#44478) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pyrodigal-gv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyrodigal-gv/meta.yaml b/recipes/pyrodigal-gv/meta.yaml index 2423c6bb8e5b3..40ce691ce8f0e 100644 --- a/recipes/pyrodigal-gv/meta.yaml +++ b/recipes/pyrodigal-gv/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrodigal-gv" %} -{% set version = "0.2.0" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pyrodigal_gv-{{ version }}.tar.gz - sha256: 8dc78704ba2021534e4a3f880063760450f12f2f4393835587d3fe4b0982851d + sha256: f111719d7f4670e5e01cb8e98fd22e48514b035776f7e156aa0dc111b5ec2fc4 build: script: {{ PYTHON }} -m pip install . --ignore-installed --use-pep517 --no-deps -vvv From c5d22a35625c7d0bfd439b61ccfba205978c322c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 00:59:29 -0700 Subject: [PATCH 0938/2173] Update gtotree to 1.8.4 (#44491) --- recipes/gtotree/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gtotree/meta.yaml b/recipes/gtotree/meta.yaml index 8b35139659846..8bdeeae00ce5f 100644 --- a/recipes/gtotree/meta.yaml +++ b/recipes/gtotree/meta.yaml @@ -1,5 +1,5 @@ {% set name = "GToTree" %} -{% set version = "1.8.3" %} +{% set version = "1.8.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/AstrobioMike/GToTree/archive/v{{ version }}.tar.gz - sha256: 432fdfd735cca427a10033c6edd75123e42a5be02f456524760eed6a76f6906b + sha256: 8a20b168b1174d2f54059d3b8273e41d1358df2200338e54adce65d3848a7893 build: number: 0 From a4893fd8d6cd1f9bf840d3abc87d4f6f6cbdd386 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 02:33:37 -0700 Subject: [PATCH 0939/2173] Update hybracter to 0.4.1 (#44490) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index 017e17b1d2c9e..4fd336ec8d85d 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.4.0" %} +{% set version = "0.4.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: b65bbd2be4a7259b9676a36277bb6c086c84a91307510626b53970b41aa42838 + sha256: 934eb7cc5024a4aac40e6f239a371cd2f1c987361d0c423f27cb24cc65b39217 build: number: 0 From fbb940f1dda092dccc1be028bde0b914a1ffa1e1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 03:39:53 -0700 Subject: [PATCH 0940/2173] Update ncbi-datasets-pylib to 15.30.0 (#44487) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 90dc0bf4d1b3b..4d247664fdebd 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.29.0" %} -{% set sha256 = "6b49e4afe1362e64c4e639e34e21fc1e3c72eb473db41b5113f71f1504f9723c" %} +{% set version = "15.30.0" %} +{% set sha256 = "44a5579bd7122659c0ee8641b1118060d86e5e9e3fba5a220e44b457dbc616ff" %} package: name: {{ name|lower }} From 2713db9d7770c4c69861cdaedeac161909408dab Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 11:04:35 -0700 Subject: [PATCH 0941/2173] Update flye to 2.9.3 (#44497) * Update flye to 2.9.3 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/flye/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/flye/meta.yaml b/recipes/flye/meta.yaml index 7a4d3c1671303..708a33bcce936 100644 --- a/recipes/flye/meta.yaml +++ b/recipes/flye/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.9.2" %} +{% set version = "2.9.3" %} package: name: flye @@ -6,11 +6,12 @@ package: source: url: https://github.com/fenderglass/Flye/archive/{{ version }}.tar.gz - sha256: 4b9534b912c805d44b83d497b40102bed807678b82be62667129bf1641676402 + sha256: 09580390ed0558c131ca0b836a2374d3cc7993cba2a6500024c2ee1d96666edc build: - number: 2 - + number: 0 + run_exports: + - {{ pin_subpackage("flye", max_pin="x.x") }} requirements: build: - {{ compiler('cxx') }} From 4c8928667fb4aeaa3de8bc7fe107e9117f914a60 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 12:03:25 -0700 Subject: [PATCH 0942/2173] Update tissuumaps to 3.2 (#44486) * Update tissuumaps to 3.2 * Update tissuumaps to 3.2 --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index bbcd525f51fe5..8763cabd920d0 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.1.1.6" %} +{% set version = "3.2" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: dd416e1f763aa6d5605ff5ebfe01f6be16f475400ac0835c803a620c84e57a3d + sha256: 82ecde593a748ac7e0a438d6322e026405b6a758dbdcb83b1fc81d2c7b13a1e2 build: number: 0 From 493498d1042fd0a0a411b179d7490a7ea7989478 Mon Sep 17 00:00:00 2001 From: Nils Hoffmann <3309580+nilshoffmann@users.noreply.github.com> Date: Tue, 28 Nov 2023 20:04:53 +0100 Subject: [PATCH 0943/2173] Update jgoslin to latest Maven central release 2.2.0 (#44492) * Updated jgoslin to latest Maven central release 2.2.0 * Added run_exports pin subpackage to resolve linter error. --- recipes/jgoslin/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/jgoslin/meta.yaml b/recipes/jgoslin/meta.yaml index 9f84d3fbf5cea..60d90ac4ae819 100644 --- a/recipes/jgoslin/meta.yaml +++ b/recipes/jgoslin/meta.yaml @@ -1,6 +1,6 @@ # Do not forget to update the version string in the jgoslin.py file {% set name = "jgoslin" %} -{% set version = "2.0.2" %} +{% set version = "2.2.0" %} package: name: jgoslin @@ -9,10 +9,12 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('jgoslin', max_pin="x") }} source: - url: https://repo1.maven.org/maven2/org/lifs-tools/jgoslin-cli/2.0.2/{{ name }}-cli-{{ version }}-bin.zip - sha256: cb6950bbcb68074acf65cfd875807684a9fd818811a7b1c8e4acbab1ae947751 + url: https://repo1.maven.org/maven2/org/lifs-tools/jgoslin-cli/2.2.0/{{ name }}-cli-{{ version }}-bin.zip + sha256: 0228017d3efaf09d27f3240fdda2b82a5a4c2f4327ac04367803caa06fb26192 requirements: run: From 22185ad23b74fd6068949b7a337d18e59b401af8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 12:05:38 -0700 Subject: [PATCH 0944/2173] Update taxmyphage to 0.2.5 (#44494) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index ed901718bfef5..3a674b7be117b 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.2.4" %} +{% set version = "0.2.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: a8267f8c2af478876e000edd595d58153d9c5d2b497ca61a667858a3d434b061 + sha256: eac2db71a3f17afa180e111e30cced38987c781237f23f4165f13fb0b249900b build: entry_points: From a99560bdcd40ffbb537abb702a4952c62c520628 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 12:07:40 -0700 Subject: [PATCH 0945/2173] Update ncbi-vdb to 3.0.9 (#44506) --- recipes/ncbi-vdb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-vdb/meta.yaml b/recipes/ncbi-vdb/meta.yaml index 6c12a7a1154e9..5a3e7c36fa4c9 100644 --- a/recipes/ncbi-vdb/meta.yaml +++ b/recipes/ncbi-vdb/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.0.8" %} +{% set version = "3.0.9" %} package: name: ncbi-vdb @@ -12,7 +12,7 @@ build: source: url: https://github.com/ncbi/ncbi-vdb/archive/{{ version }}.tar.gz - sha256: f8c0168a3e8454b6faf8e996fb074dd26bf161362168d316ebb22bb173fa2251 + sha256: 26c94e5259b0c7e98fdaa1e93d41201df29ffff56946dd19464c6a0cfb584f92 folder: ncbi-vdb requirements: From 3bef398cc93b35677c97aeca6dd2a624b8a1b752 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 12:08:48 -0700 Subject: [PATCH 0946/2173] Update flams to 1.1.3 (#44503) --- recipes/flams/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/flams/meta.yaml b/recipes/flams/meta.yaml index 8e3788910a7bd..4ead7da071881 100644 --- a/recipes/flams/meta.yaml +++ b/recipes/flams/meta.yaml @@ -1,5 +1,5 @@ {% set name = "flams" %} -{% set version = "1.1.2" %} +{% set version = "1.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/flams-{{ version }}.tar.gz - sha256: b1a62f8ba443800afcaa8bed70b4d93b1c0e2631d0d6a7eae9064a8368403b0e + sha256: b028cd8e131add01eb012ded0ae7c48bf361f36ae14b477a3d193fc0da4ea5fa build: entry_points: From 1863031f201a3dc139e709cccecac04aab10f257 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 13:47:49 -0700 Subject: [PATCH 0947/2173] Update sra-tools to 3.0.9 (#44504) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/sra-tools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sra-tools/meta.yaml b/recipes/sra-tools/meta.yaml index 06282e322df9e..1059721198b5b 100644 --- a/recipes/sra-tools/meta.yaml +++ b/recipes/sra-tools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sra-tools" %} -{% set version = "3.0.8" %} -{% set sha256 = "c722e1c96eb6775962ed250fdbd443357beed386ae3587534cf1835dcf604b66" %} +{% set version = "3.0.9" %} +{% set sha256 = "41159b817fb7649e42b41b3ca37bb3346d4fcb27049737d8a3bca5091ad74bb5" %} package: name: {{ name }} From d0ed06775e99d7534162e6d37a592dc2be2e01e3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 13:48:07 -0700 Subject: [PATCH 0948/2173] Update ncbi-vdb-py to 3.0.9 (#44505) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ncbi-vdb-py/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-vdb-py/meta.yaml b/recipes/ncbi-vdb-py/meta.yaml index 434531c2bce34..270c44e2b6586 100644 --- a/recipes/ncbi-vdb-py/meta.yaml +++ b/recipes/ncbi-vdb-py/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.0.8" %} -{% set sha256 = "f8c0168a3e8454b6faf8e996fb074dd26bf161362168d316ebb22bb173fa2251" %} +{% set version = "3.0.9" %} +{% set sha256 = "26c94e5259b0c7e98fdaa1e93d41201df29ffff56946dd19464c6a0cfb584f92" %} package: name: ncbi-vdb-py From 5d49e8159eb6e3d971d3da5692f4f31aee609918 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 16:49:57 -0700 Subject: [PATCH 0949/2173] Update genomad to 1.7.2 (#44507) --- recipes/genomad/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genomad/meta.yaml b/recipes/genomad/meta.yaml index cf128b29475fb..c50a69c57ed96 100644 --- a/recipes/genomad/meta.yaml +++ b/recipes/genomad/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genomad" %} -{% set version = "1.7.1" %} +{% set version = "1.7.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d435b72c401d7dc1755a5fc120601bca756db475232c0ebf32ea673b43da83f7 + sha256: fd63b39c47da0fb896ab18dca8138cb1dd37f334c41c04a06b3a3fba6face5be build: number: 0 From 8a15d981deb8e365daee51bf56c16d1d34530ec1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 19:38:46 -0700 Subject: [PATCH 0950/2173] Update gotree to 0.4.5 (#44500) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/gotree/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gotree/meta.yaml b/recipes/gotree/meta.yaml index c61821f1cda02..f828bc85efeff 100644 --- a/recipes/gotree/meta.yaml +++ b/recipes/gotree/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.4" %} +{% set version = "0.4.5" %} {% set name = "gotree" %} package: @@ -13,7 +13,7 @@ build: source: - url: https://github.com/evolbioinfo/{{name}}/archive/v{{ version }}.tar.gz - sha256: 9888bf5ca0f1ff97d069610ca10b4b1fc7ed4d3b1d72fd93fcf342ff6c9c0557 + sha256: 317a881fc8465e45c991dac9c1fbf95031e8c8cb7fe65a1f4de1c0c1c91e9026 folder: src/github.com/evolbioinfo/{{name}}/ requirements: From 3b94cc7c6ae7f2feceedd82b1b75ad526c9b794e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 19:39:16 -0700 Subject: [PATCH 0951/2173] Update guidemaker to 0.4.2 (#44509) * Update guidemaker to 0.4.2 * edit python version pinning --------- Co-authored-by: joshuazhuang7 --- recipes/guidemaker/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/guidemaker/meta.yaml b/recipes/guidemaker/meta.yaml index e7d5548ecd883..0101eb6b5f4c8 100644 --- a/recipes/guidemaker/meta.yaml +++ b/recipes/guidemaker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} {% set name = "GuideMaker" %} -{% set sha256 = "f26b4c98d3eede37dbc121087e9a38115612a7e7b3e3e04a2a6b02f1ed44e4be" %} +{% set sha256 = "8766e3fa2443a09c270e06af5162e1d323b840b85789ba9b92efb4d51ed4b833" %} {% set user = "USDA-ARS-GBRU" %} package: @@ -16,18 +16,18 @@ build: noarch: python entry_points: - guidemaker=guidemaker.cli:main - script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . -vvv run_exports: - {{ pin_subpackage('guidemaker', max_pin="x") }} requirements: host: - pip - - python >=3.6 + - python >=3.8,<3.12 - biopython >=1.79 run: - pip - - python >=3.6 + - python >=3.8,<3.12 - biopython >=1.79 - numpy >=1.11 - pybedtools >=0.8.2 @@ -42,17 +42,20 @@ requirements: - streamlit_tags >=1.2.6 - pdoc3 - onnxruntime >=1.8.1 + - importlib-resources >=6.0 test: commands: - guidemaker --version about: - home: https://github.com/USDA-ARS-GBRU/GuideMaker + home: https://guidemaker.app.scinet.usda.gov/ license: 'CC0-1.0' license_family: 'PUBLIC-DOMAIN' license_file: LICENSE.txt summary: 'GuideMaker: Software to design gRNAs pools in non-model genomes and CRISPR-Cas systems' + doc_url: https://guidemaker.org/ + dev_url: https://github.com/USDA-ARS-GBRU/GuideMaker extra: recipe-maintainers: From 9506a5161ae6321e90ec49409f039e815bbfcf00 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 20:20:42 -0700 Subject: [PATCH 0952/2173] Update lamassemble to 1.6.2 (#44510) * Update lamassemble to 1.6.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/lamassemble/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/lamassemble/meta.yaml b/recipes/lamassemble/meta.yaml index b9c7ef92c2680..bba6f006b581d 100644 --- a/recipes/lamassemble/meta.yaml +++ b/recipes/lamassemble/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.6.1" %} +{% set version = "1.6.2" %} package: name: lamassemble @@ -6,12 +6,14 @@ package: source: url: https://gitlab.com/mcfrith/lamassemble/-/archive/{{ version }}/lamassemble-{{ version }}.tar.gz - sha256: 2c99401d0b1126fff1e0a0e70a2a0ad10a78e840d2a3a15bae122d823cb88cf9 + sha256: 4d578d829f7d65a8e227fe6a4c5bb906d1423a15967ac209423acfcf7d2eed8c build: number: 0 noarch: python - script: python -m pip install . --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('lamassemble', max_pin="x") }} requirements: host: @@ -28,6 +30,7 @@ test: about: home: https://gitlab.com/mcfrith/lamassemble - summary: Merge overlapping "long" DNA reads into a consensus sequence + summary: 'Merge overlapping "long" DNA reads into a consensus sequence' license: MIT + license_family: MIT license_file: LICENSE From b27ad7d4154495893e207c0cee016f977e893a81 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 20:52:51 -0700 Subject: [PATCH 0953/2173] Update snipit to 1.2 (#44499) * Update snipit to 1.2 * add run_exports --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snipit/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/snipit/meta.yaml b/recipes/snipit/meta.yaml index 2683fdd4fae04..6145586560291 100644 --- a/recipes/snipit/meta.yaml +++ b/recipes/snipit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snipit" %} -{% set version = "1.1.2" %} +{% set version = "1.2" %} package: name: "{{ name|lower }}" @@ -7,14 +7,16 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e798e22d99ef1675034a1a12a87c39642a0c71dded2170e53efca58d6e2b9475 + sha256: 92e4395a23ef5e55ae753868723daa3e68d5803a10db6ae27fc6722a99bcc708 build: number: 0 noarch: python entry_points: - snipit=snipit.command:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" + run_exports: + - {{ pin_subpackage('snipit', max_pin="x") }} requirements: host: @@ -35,7 +37,7 @@ test: about: home: "https://github.com/aineniamh/snipit" - license: GNU General Public License v3 (GPLv3) + license: GPL-3.0-or-later license_family: GPL3 license_file: LICENSE summary: Visualize snps relative to a reference sequence From 63083bbd0b24eae747618be897de48cb1b080ca2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 28 Nov 2023 21:11:38 -0700 Subject: [PATCH 0954/2173] Update synapseclient to 3.2.0 (#44501) * Update synapseclient to 3.2.0 * add opentelemetry-api * add opentelemetry-sdk * add opentelemetry-exporter-otlp --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/synapseclient/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/synapseclient/meta.yaml b/recipes/synapseclient/meta.yaml index 5d5376fe5e1dc..3b475ae73277e 100644 --- a/recipes/synapseclient/meta.yaml +++ b/recipes/synapseclient/meta.yaml @@ -1,5 +1,5 @@ {% set name = "synapseclient" %} -{% set version="3.1.1" %} +{% set version = "3.2.0" %} package: name: {{ name|lower }} @@ -7,14 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/synapseclient-{{ version }}.tar.gz - sha256: ab78a1202725d22c21f92798191c1862e779b2b31c01ff06f59789bb05fa1174 + sha256: 87c91f03dbca7074efd18144325df07db24e07ea92e0b7c8691aaec46c28329a build: noarch: python entry_points: - synapse = synapseclient.__main__:main number: 0 - script: {{ PYTHON }} -m pip install . --no-deps -vvv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv run_exports: - {{ pin_subpackage('synapseclient', max_pin="x") }} @@ -31,6 +31,9 @@ requirements: - backports.csv - deprecated >=1.2.4 - keyring >=15.0.0 + - opentelemetry-api + - opentelemetry-sdk + - opentelemetry-exporter-otlp run_constrained: - pandas >=0.25.0 - pysftp >=0.2.8 @@ -45,6 +48,7 @@ test: about: home: https://www.synapse.org license: Apache-2.0 + license_family: APACHE summary: Python client for Synapse description: | A client for Synapse, a collaborative compute space that allows From aa2f48bab29d875bf0106635676502468ad6e8e7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 03:44:31 -0700 Subject: [PATCH 0955/2173] Update seqerakit to 0.4.4 (#44511) --- recipes/seqerakit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seqerakit/meta.yaml b/recipes/seqerakit/meta.yaml index 50c14231d18bf..097bb053c1fe8 100644 --- a/recipes/seqerakit/meta.yaml +++ b/recipes/seqerakit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqerakit" %} -{% set version = "0.4.3" %} +{% set version = "0.4.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqerakit-{{ version }}.tar.gz - sha256: bd71a6e7933ce362606c4abb2ddd8bc6de533b56e9a97ec457c52bba964baea9 + sha256: 04e4f7b930efd3b3581c56e7774696db00625124893ebb9969aaa7fd3cd7959f build: entry_points: From b0665c998aa47e41627417d8fc6d07deeb2402ec Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 04:58:53 -0700 Subject: [PATCH 0956/2173] Update bakta to 1.9.1 (#44513) --- recipes/bakta/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml index 0730c2c00cc20..98a9068bd9875 100644 --- a/recipes/bakta/meta.yaml +++ b/recipes/bakta/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.9.0" %} +{% set version = "1.9.1" %} package: name: bakta @@ -6,7 +6,7 @@ package: source: url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz - sha256: '30e9584a5e027cb07bb52ff4fd95008cc2c83c99747b38c79ccb026ba0674781' + sha256: 'd8eb7ea1321ad6884002cfac670c33031b8dfa219a62b90c556f7cf402a64fe4' build: noarch: python From 5fb9f9e3f5a6b25818d3acf0ba1e71ba6eaf9eda Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 06:44:20 -0700 Subject: [PATCH 0957/2173] Update r-goalie to 0.7.6 (#44496) --- recipes/r-goalie/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-goalie/meta.yaml b/recipes/r-goalie/meta.yaml index adf24485490bf..92a46d939565b 100644 --- a/recipes/r-goalie/meta.yaml +++ b/recipes/r-goalie/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.5" %} +{% set version = "0.7.6" %} {% set github = "https://github.com/acidgenomics/r-goalie" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 8810a75efb99fa923d8fd5e08b1d6f7fb0926684578fbdf125a8228ab9002e14 + sha256: c2894758e58c994813deaa3767916bdd4ca0ffac111fc88159cc766f54cd4a1b build: number: 0 From 85fe13f5cb4014777476451a56f3a606f605b9dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 07:34:07 -0700 Subject: [PATCH 0958/2173] Update genoboo to 0.4.11 (#44515) --- recipes/genoboo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genoboo/meta.yaml b/recipes/genoboo/meta.yaml index 3a910a856e5e5..c7ad9fc8ac572 100644 --- a/recipes/genoboo/meta.yaml +++ b/recipes/genoboo/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'genoboo' %} -{% set version = '0.4.10' %} -{% set sha256 = 'd65c113dc6a515b8b07906ebf0bd8cc167704335f582b27b8cae2a3097f857aa' %} +{% set version = '0.4.11' %} +{% set sha256 = '3511b73acccacd07cf15dc30f70fbb8907f65cefeb7caa82e63a9dda2dab664a' %} package: name: {{ name|lower }} From ea27b1b032c61a14c5bd30023aa1b48fa6367706 Mon Sep 17 00:00:00 2001 From: Tobias Baril <46785187+TobyBaril@users.noreply.github.com> Date: Wed, 29 Nov 2023 15:56:30 +0100 Subject: [PATCH 0959/2173] Update earlgrey meta.yaml (#44473) * Add citation to description in meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/earlgrey/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index c5f6be97ed3f6..e32b0e6d5229e 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('earlgrey', max_pin='x') }} @@ -59,5 +59,9 @@ about: description: | Earl Grey is a full-automated transposable element (TE) annotation pipeline, leveraging the most widely-used tools and combining these with a consensus - elongation process to better define de novo consensus sequences when - annotating new genome assemblies. + elongation process (BEAT) to better define de novo consensus sequences when + annotating new genome assemblies. + +extra: + identifiers: + - doi:10.1101/2022.06.30.498289 From ecdebc8b5b56dff5df2321758c07c5ad521cd69d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 10:36:55 -0700 Subject: [PATCH 0960/2173] Update r-grbase to 2.0.1 (#44519) --- recipes/r-grbase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-grbase/meta.yaml b/recipes/r-grbase/meta.yaml index ca535310bec96..f00657d4a41c5 100644 --- a/recipes/r-grbase/meta.yaml +++ b/recipes/r-grbase/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '2.0.0' %} +{% set version = '2.0.1' %} package: name: r-grbase @@ -8,7 +8,7 @@ source: url: - {{ cran_mirror }}/src/contrib/gRbase_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/gRbase/gRbase_{{ version }}.tar.gz - sha256: 9b90c4615f103369a8a4500f53800e4fde9948770ce465ce7a950433d46fd942 + sha256: 1ee49352854954b469bd23eeb1b044b54fe622c4f214d8291f57bc1444c781a9 build: number: 0 From e78db25b910ff94b7601ea89d745e39aac0f5198 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 12:45:51 -0700 Subject: [PATCH 0961/2173] Update psm-utils to 0.7.2 (#44522) --- recipes/psm-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psm-utils/meta.yaml b/recipes/psm-utils/meta.yaml index 1f6d413af873c..e2767e8637fc8 100644 --- a/recipes/psm-utils/meta.yaml +++ b/recipes/psm-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "psm-utils" %} -{% set version = "0.7.1" %} -{% set sha256 = "b4d1a6da74cb0fe7601b5f9c106826a3dfb8d85011e23bcc18ce022bafa4fc16" %} +{% set version = "0.7.2" %} +{% set sha256 = "a6b892f3ca6dfb8c2b298e0788c79965d754e84e7049c560b52263b096b82a17" %} package: name: {{ name|lower }} From 3a44e32824366cef55c74d9aba9f424a2ba9b762 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 17:43:40 -0700 Subject: [PATCH 0962/2173] Update naibr-plus to 0.5.2 (#44514) --- recipes/naibr-plus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/naibr-plus/meta.yaml b/recipes/naibr-plus/meta.yaml index 886ae5ad3b0cd..1fde0ed5de8bc 100644 --- a/recipes/naibr-plus/meta.yaml +++ b/recipes/naibr-plus/meta.yaml @@ -1,5 +1,5 @@ {% set name = "naibr-plus" %} -{% set version = "0.5.1" %} +{% set version = "0.5.2" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/pontushojer/NAIBR/releases/download/v{{ version }}/naibr-{{ version }}.tar.gz - sha256: 62629ee70fb68c0299e7e5464c528b4a91c778176b86ad6abf6e1d4f00967fdb + sha256: 9e79f808fbd2847f6286ffe8f9c4dbd3b1b9bc2a07c06c32ffc87ab15b2ae899 build: number: 0 From 69b0a8e3046c3f254c8a16f4b8e348b03c99d1d2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 17:43:50 -0700 Subject: [PATCH 0963/2173] Update taxmyphage to 0.2.6 (#44516) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index 3a674b7be117b..0d0b81c087803 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.2.5" %} +{% set version = "0.2.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: eac2db71a3f17afa180e111e30cced38987c781237f23f4165f13fb0b249900b + sha256: 1058adb02296ec0493b21dedd899447a144804230a4e13f4c98f94dcc0548076 build: entry_points: From 5567a572d2f8120e3ccb994dc9085687745c4c09 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 17:44:09 -0700 Subject: [PATCH 0964/2173] Update earlgrey to 4.0.1 (#44517) --- recipes/earlgrey/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index e32b0e6d5229e..8e70a6bccefe2 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0" %} -{% set sha256 = "317e058d2a09261ae68cec96a5af8cafefb05d9b060be869f0280cb66b0b81ac" %} +{% set version = "4.0.1" %} +{% set sha256 = "75910863a12f77ca864eba55e4375ad6dfb1bb548b15324296109eab90c817cd" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('earlgrey', max_pin='x') }} From 615279528e924267106fb0e3c2f6f574197e11d2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 17:44:29 -0700 Subject: [PATCH 0965/2173] Update galaxy-files to 23.1.2 (#44526) --- recipes/galaxy-files/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml index 047f835c6c4da..54b29aec44cb5 100644 --- a/recipes/galaxy-files/meta.yaml +++ b/recipes/galaxy-files/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.1.1" %} -{% set sha256 = "830937bc1bf201da5c1c4e68981adf265ecbfad2cb1b8924349debe3523d5eab" %} +{% set version = "23.1.2" %} +{% set sha256 = "426a57051264b17dcd1e78c442fd8b09d8548f30ff55baac46eb13bfc6e2e6d5" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From f705ccc9e22e4c0383021527b66e4ca11be41d5b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 17:44:44 -0700 Subject: [PATCH 0966/2173] Update galaxy-objectstore to 23.1.2 (#44527) --- recipes/galaxy-objectstore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml index 2cf198441566b..589aa6780596d 100644 --- a/recipes/galaxy-objectstore/meta.yaml +++ b/recipes/galaxy-objectstore/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.1.1" %} -{% set sha256 = "1a4c5132944462b665b51af2539a07ec7e36bca9ea178de247204dece3d2c43a" %} +{% set version = "23.1.2" %} +{% set sha256 = "0058ee7c17e59d361f92bddad4a3c24e76fb75a43d0ca0a5711a084a01490478" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From fe177f409d1f28e74dd10c58e22e263293749dbf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 17:45:13 -0700 Subject: [PATCH 0967/2173] Update medaka to 1.11.2 (#44533) --- recipes/medaka/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 96f01ac731ff9..130e59ae53756 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -1,6 +1,6 @@ {% set name = "Medaka" %} -{% set version = "1.11.1" %} -{% set sha256 = "4440762a17ddd66806ddbd7c3218140caa234b96a8c919ed54d7243d3e4a5dd1" %} +{% set version = "1.11.2" %} +{% set sha256 = "8dcb9941ead369b0a8715db80a3375b50a1ad8b58ea12009222b1d70f39cfb07" %} # Bot PRs - Always review requirements.txt for new release package: From 225c6a4d4ea94c487d7891c0dcd15c2e6372453b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 18:07:32 -0700 Subject: [PATCH 0968/2173] Update anglerfish to 0.6.0 (#44518) * Update anglerfish to 0.6.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/anglerfish/meta.yaml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/recipes/anglerfish/meta.yaml b/recipes/anglerfish/meta.yaml index f93c689dee9fc..ee4d25f033fc1 100644 --- a/recipes/anglerfish/meta.yaml +++ b/recipes/anglerfish/meta.yaml @@ -1,5 +1,5 @@ {% set name = "anglerfish" %} -{% set version = "0.5.0" %} +{% set version = "0.6.0" %} package: name: "{{ name|lower }}" @@ -7,25 +7,25 @@ package: source: url: "https://pypi.io/packages/source/b/bio-{{ name }}/bio-{{ name }}-{{ version }}.tar.gz" - sha256: 7c6b41e1220f805cc5f9f571d2fc8781f7159ff7cf788385706ec9e37bffbf4e + sha256: b67a0c77680f85ebdf88622382bb271655e807c60dc3bdcd01997d336e6574fa build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + entry_points: + - anglerfish=anglerfish.anglerfish:anglerfish + run_exports: + - {{ pin_subpackage('anglerfish', max_pin="x.x") }} requirements: host: - - biopython - - numpy - pip - - python ==3.9.* - - python-levenshtein - - pyyaml + - python >=3.7 run: - biopython - numpy - - python ==3.9.* + - python >=3.7 - python-levenshtein - pyyaml - minimap2 From dffa0118b4f6db632fbeed96d0651cde6c18e7d8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 29 Nov 2023 18:50:48 -0700 Subject: [PATCH 0969/2173] Update lusstr to 0.7 (#44524) * Update lusstr to 0.7 * add run_exports * pin python to <3.12 --------- Co-authored-by: joshuazhuang7 --- recipes/lusstr/meta.yaml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/recipes/lusstr/meta.yaml b/recipes/lusstr/meta.yaml index 3dcccd243cbf3..a0440cbca5b25 100644 --- a/recipes/lusstr/meta.yaml +++ b/recipes/lusstr/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6.4" %} -{% set sha256 = "185da32dd175bd15021c697cbb36da28d64bd6eed0b48846c8002941840414ab" %} +{% set version = "0.7" %} +{% set sha256 = "3a889c33b8c4e39511d761786e1c40842c8732db72e3e6477bca0d77414fca9b" %} package: name: lusstr @@ -12,21 +12,24 @@ source: build: noarch: python entry_points: - - lusstr = lusSTR.__main__:main - script: python -m pip install --no-deps --ignore-installed . + - lusstr = lusSTR.cli:main + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv number: 0 + run_exports: + - {{ pin_subpackage('lusstr', max_pin="x.x") }} requirements: host: - - python >=3 + - python >=3,<3.12 - pip run: - - python >=3 + - python >=3,<3.12 - pandas >=1.0,<2.0 - xlrd >=1.0,<2.0 - openpyxl >=3.0.6 - - snakemake >=7.22.0 + - snakemake-minimal >=7.22.0 - pyyaml >=6.0 + - matplotlib-base >=3.5.3 test: imports: @@ -41,6 +44,7 @@ about: license_family: BSD summary: Tool for converting NGS sequence data of forensic STR loci to various annotation styles dev_url: https://www.github.com/bioforensics/lusSTR + license_file: LICENSE.txt extra: recipe-maintainers: From 3e7405976ed1698603e72d260f75d8dacddf6408 Mon Sep 17 00:00:00 2001 From: hjulienne Date: Thu, 30 Nov 2023 02:52:20 +0100 Subject: [PATCH 0970/2173] added new tag for RAISS (#44502) * added new tag for RAISS * corrected raiss recipe * formatted version constraints * added run export * updated dependancies * corrected sha sum --------- Co-authored-by: hjulienn --- recipes/raiss/meta.yaml | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/recipes/raiss/meta.yaml b/recipes/raiss/meta.yaml index 8408f388cf017..07f2b3b1215de 100644 --- a/recipes/raiss/meta.yaml +++ b/recipes/raiss/meta.yaml @@ -1,5 +1,5 @@ {% set name = "raiss" %} -{% set version = "3.1" %} +{% set version = "4.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.pasteur.fr/statistical-genetics/{{ name }}/-/archive/{{ version }}/{{ name }}-{{ version }}.tar.gz - sha256: fe552f31deab68de2fc0a9086e38f4bfe0339e544733e2a68e84abe2013f06da + sha256: 771a4ec126967daa367daa599178909cd182ed5d564c169b64e0491f1bb19714 build: noarch: python @@ -15,16 +15,23 @@ build: - raiss=raiss.__main__:main number: 0 script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv . + run_exports: + - {{ pin_subpackage('raiss', max_pin="x.x") }} requirements: host: - - python >=3.6 + - python >=3.8 - pip run: - - python >=3.6 - - scipy - - pandas + - python >=3.8 - joblib + - numpy + - pandas + - python-dateutil + - pytz + - scipy + - six + - tzdata test: commands: From 400b99b0d4e743412ecc58a5df1e838f8da0335f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 02:39:51 -0700 Subject: [PATCH 0971/2173] Update treeswift to 1.1.39 (#44535) --- recipes/treeswift/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/treeswift/meta.yaml b/recipes/treeswift/meta.yaml index 1affe755cfa1c..54fd1362581cd 100644 --- a/recipes/treeswift/meta.yaml +++ b/recipes/treeswift/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.38" %} +{% set version = "1.1.39" %} package: name: "treeswift" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/t/treeswift/treeswift-{{ version }}.tar.gz - sha256: 04da31d2fae71f01a8cd6ecd54e77e068b9267d55c0f70f6d4c644f692d3652d + sha256: bdb432acea1fd7c13111e101062f75cf0a7ee721a90d7bc86057ee3cea4edfaa build: noarch: python From fa5dc8d055949940ecb5644f5e81bdd4d93f7d75 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 02:51:58 -0700 Subject: [PATCH 0972/2173] Update mercat2 to 1.3 (#44529) --- recipes/mercat2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mercat2/meta.yaml b/recipes/mercat2/meta.yaml index 3f4f4ce59329c..1808493425f7d 100644 --- a/recipes/mercat2/meta.yaml +++ b/recipes/mercat2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mercat2" %} -{% set version = "1.2" %} +{% set version = "1.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 45c90499dae461ba52e8993359ed04c65c60ed2fa693d417fac9ec274aad3775 + sha256: edcee22e339bdf15ce4709c3192f85c32f576f07eedfd044bad8d3a396cbe0a9 build: number: 0 From b2b03c491ab3f06f0366c1c3359c720260a5a4f4 Mon Sep 17 00:00:00 2001 From: Adam Diehl Date: Thu, 30 Nov 2023 04:53:08 -0500 Subject: [PATCH 0973/2173] Add haplotaglr recipe (#44484) * add recipe for haplotaglr * Fix to description * add run_exports * fix sha256 * add python ranges * Update meta.yaml --------- Co-authored-by: Adam Diehl Co-authored-by: Thanh Lee --- recipes/haplotaglr/meta.yaml | 46 ++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/haplotaglr/meta.yaml diff --git a/recipes/haplotaglr/meta.yaml b/recipes/haplotaglr/meta.yaml new file mode 100644 index 0000000000000..2248cea8c0e91 --- /dev/null +++ b/recipes/haplotaglr/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "HaplotagLR" %} +{% set version = "1.1.4" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: e15dada6a1ee99080e4f1a1b80a80976a2d528f85d41a4e58ed016dff6f4545d + +build: + number: 0 + entry_points: + - HaplotagLR = HaplotagLR.cli:main + script: "{{ PYTHON }} -m pip install . -vv" + noarch: python + run_exports: + - {{ pin_subpackage('haplotaglr', max_pin="x") }} + +requirements: + host: + - python >=3.7,<3.13 + - pip + run: + - python >=3.7,<3.13 + - biopython >=1.78 + - numpy >=1.20.1 + - powerlaw >=1.4.6 + - pyliftover >=0.4 + - pysam >=0.16.0.1 + - powerlaw >=1.4.6 + - requests >=2.26.0 + +test: + imports: + - HaplotagLR + commands: + - HaplotagLR --help + +about: + home: "https://github.com/Boyle-Lab/HaplotagLR.git" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Haplotagging individual long reads using known haplotype information." From 020eda72648ab2a36771ec36bb0a99862ed7ca9e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 02:53:37 -0700 Subject: [PATCH 0974/2173] Update pyrodigal-gv to 0.3.1 (#44537) --- recipes/pyrodigal-gv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyrodigal-gv/meta.yaml b/recipes/pyrodigal-gv/meta.yaml index 40ce691ce8f0e..34996ec3ebe2b 100644 --- a/recipes/pyrodigal-gv/meta.yaml +++ b/recipes/pyrodigal-gv/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrodigal-gv" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pyrodigal_gv-{{ version }}.tar.gz - sha256: f111719d7f4670e5e01cb8e98fd22e48514b035776f7e156aa0dc111b5ec2fc4 + sha256: 287f0507fad25f8c148a1d93a030e1a64b0434beba62f45354526b0eeef4ca97 build: script: {{ PYTHON }} -m pip install . --ignore-installed --use-pep517 --no-deps -vvv From 9ba0c26da41d74477990eaf19f54a1f18d99c7cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Thu, 30 Nov 2023 03:08:56 -0800 Subject: [PATCH 0975/2173] Fix geNomad dependencies (#44528) --- recipes/genomad/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genomad/meta.yaml b/recipes/genomad/meta.yaml index c50a69c57ed96..1ebe7a6072a17 100644 --- a/recipes/genomad/meta.yaml +++ b/recipes/genomad/meta.yaml @@ -10,7 +10,7 @@ source: sha256: fd63b39c47da0fb896ab18dca8138cb1dd37f334c41c04a06b3a3fba6face5be build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . -vv" entry_points: @@ -25,7 +25,7 @@ requirements: - flit-core >=3.2,<4 run: - python >=3.8 - - pyrodigal-gv + - pyrodigal-gv =0.2.0 - mmseqs2 =14.7e284 - aragorn - keras >=2.7 From a65fb386ec9a7cf1f21e6aeaa657f83eb4b0c272 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 04:16:46 -0700 Subject: [PATCH 0976/2173] Update spoa to 4.1.4 (#44542) --- recipes/spoa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/spoa/meta.yaml b/recipes/spoa/meta.yaml index ec3856161cf56..a24aaf1dacb32 100644 --- a/recipes/spoa/meta.yaml +++ b/recipes/spoa/meta.yaml @@ -1,6 +1,6 @@ {% set name = "spoa" %} -{% set version = "4.1.3" %} -{% set sha256 = "3f6c8de40a6163e68cf797d4040348db5f2b9ea067193c7ab78ce2582c10aa21" %} +{% set version = "4.1.4" %} +{% set sha256 = "ea696650460b17881595454c2546a05905f2724927dbbf4d71f4bb8a3f6a99cd" %} package: name: {{ name }} From ade0961c34e433e0ae1c7aded455b47f45cf78a2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 05:57:04 -0700 Subject: [PATCH 0977/2173] Update genomad to 1.7.3 (#44545) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update genomad to 1.7.3 * Set `pyrodigal-gv >=0.3.1` in geNomad --------- Co-authored-by: Antônio Camargo --- recipes/genomad/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/genomad/meta.yaml b/recipes/genomad/meta.yaml index 1ebe7a6072a17..549b081d06dc8 100644 --- a/recipes/genomad/meta.yaml +++ b/recipes/genomad/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genomad" %} -{% set version = "1.7.2" %} +{% set version = "1.7.3" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: fd63b39c47da0fb896ab18dca8138cb1dd37f334c41c04a06b3a3fba6face5be + sha256: a13387992eb1000d84587caed085c01eaaeb875fe6b8bffd3a251af02d2d2a4d build: - number: 1 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install . -vv" entry_points: @@ -25,7 +25,7 @@ requirements: - flit-core >=3.2,<4 run: - python >=3.8 - - pyrodigal-gv =0.2.0 + - pyrodigal-gv >=0.3.1 - mmseqs2 =14.7e284 - aragorn - keras >=2.7 From 669d657634f02077a25fce2eea4ce628ccb688f4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 06:17:38 -0700 Subject: [PATCH 0978/2173] Update nf-test to 0.8.2 (#44544) --- recipes/nf-test/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-test/meta.yaml b/recipes/nf-test/meta.yaml index dc0320369511b..1ad10e7398e1e 100644 --- a/recipes/nf-test/meta.yaml +++ b/recipes/nf-test/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.1" %} +{% set version = "0.8.2" %} package: @@ -13,7 +13,7 @@ build: source: url: https://github.com/askimed/nf-test/releases/download/v{{version}}/nf-test-{{version}}.tar.gz - sha256: fb2e6a098c7bf16e7e849d98838651b95d1bf94ab59766e43d91d19729bcfe9e + sha256: 5d640cea4339da4de50ce3687e9a61bd10488f2cac342eb1f11743414c6a27cd requirements: host: From ea872526938027054e932f598169ff1f81a04016 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 06:59:46 -0700 Subject: [PATCH 0979/2173] Update sage-proteomics to 0.14.5 (#44534) Co-authored-by: Thanh Lee --- recipes/sage-proteomics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sage-proteomics/meta.yaml b/recipes/sage-proteomics/meta.yaml index a06ea0fb9ea15..75e03453a0b0e 100644 --- a/recipes/sage-proteomics/meta.yaml +++ b/recipes/sage-proteomics/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sage-proteomics" %} -{% set version = "0.14.4" %} -{% set sha256 = "a527dce4892cf5b2fb85b56c54b5213e4b25d1ca8864f270eed47f5f223b4e6f" %} +{% set version = "0.14.5" %} +{% set sha256 = "a85b91c6651dfd028d5807163bdb62aa4a8eb222cac03348bd607323af1238c9" %} package: name: {{ name }} From 0d1e09d9812c5b053226cc59c9f5f6a63a6cd1e6 Mon Sep 17 00:00:00 2001 From: andrefaure <39261277+andrefaure@users.noreply.github.com> Date: Thu, 30 Nov 2023 15:01:44 +0100 Subject: [PATCH 0980/2173] Add pymochi recipe (#44479) * pymochi bioconda recipe initial commit * add pin_subpackage to meta.yaml * fix dev_url * fix dependency bugs * updates to meta.yaml * python 3.9 * max_pin=x * deleted run_test.py --- recipes/pymochi/meta.yaml | 43 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 recipes/pymochi/meta.yaml diff --git a/recipes/pymochi/meta.yaml b/recipes/pymochi/meta.yaml new file mode 100644 index 0000000000000..6d20abd0c7781 --- /dev/null +++ b/recipes/pymochi/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "0.9" %} +{% set github = "https://github.com/lehner-lab/MoCHI" %} + +package: + name: pymochi + version: '{{ version }}' + +source: + url: {{ github }}/archive/v{{ version }}.tar.gz + sha256: cec741cc8cda6affc9f4c2fd470afd28ee7c5ec9282bd59a4d4102a6e3afe005 + +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install ./ --ignore-installed --no-deps -vv + run_exports: + - {{ pin_subpackage('pymochi', max_pin="x") }} + +requirements: + host: + - python =3.9 + - pip + run: + - python =3.9 + - pandas >=1.4.2 + - matplotlib-base >=3.5.1 + - numpy >=1.21.2 + - pyreadr >=0.4.4 + - pytorch >=1.10.1 + - scikit-learn >=1.0.2 + - scipy >=1.8.0 + - seaborn >=0.11.2 + +test: + commands: + - run_mochi.py -h + +about: + home: {{ github }} + dev_url: {{ github }} + license: MIT + summary: Neural networks to quantify energies, energetic couplings, epistasis and allostery from deep mutational scanning data + From ee84ca4de7cd1bcbedd2eadf835fb6b101b4df18 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Thu, 30 Nov 2023 15:20:30 +0100 Subject: [PATCH 0981/2173] Update vcfanno to v0.3.5 (#44539) --- recipes/vcfanno/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/vcfanno/meta.yaml b/recipes/vcfanno/meta.yaml index 1696d595df24f..ab4d005b463ac 100644 --- a/recipes/vcfanno/meta.yaml +++ b/recipes/vcfanno/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.3.3' %} +{% set version = '0.3.5' %} package: name: vcfanno @@ -6,12 +6,14 @@ package: source: url: https://github.com/brentp/vcfanno/releases/download/v{{ version }}/vcfanno_osx # [osx] - sha256: 66dfacb03d9915956e0477d51ca460966f6f88a07bd797e5f4bcfc4b8ee42cda # [osx] + sha256: 2f51637c6358fec7e7fcb1dbbfc1b2cbbed6ff47a7c6b7ef386f1152ff74829f # [osx] url: https://github.com/brentp/vcfanno/releases/download/v{{ version }}/vcfanno_linux64 # [linux] - sha256: f8ea2924379a2777b6ae9d4b8da9c6260601febf21a6dab4b3e8c16d4af0f6b3 # [linux] + sha256: a98a9be6dfec32b039b21563659c4ecf0ec884ad3cdfaf0732b44c3857520592 # [linux] build: number: 0 + run_exports: + - {{ pin_subpackage("vcfanno", max_pin="x") }} requirements: From 88310aef91bc8ac2c6ec8edc025d7aab973f5d28 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 07:52:59 -0700 Subject: [PATCH 0982/2173] Update annonars to 0.30.0 (#44549) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 8c824925da4c2..7457d8e28cffb 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.29.4" %} +{% set version = "0.30.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 7394aecf2d9c4f33e63e071c973b4176b6be75db653bb10ebb130acceda5a50c + sha256: ba088a5308d8efdd20d2bc623472d56cb1353b51a5c77b39a3ff378ee2548f0b requirements: build: From 4cfd530625238221f7764155fb15b77f7b34ecdf Mon Sep 17 00:00:00 2001 From: Tobias Baril <46785187+TobyBaril@users.noreply.github.com> Date: Thu, 30 Nov 2023 16:19:55 +0100 Subject: [PATCH 0983/2173] Update earlgrey meta.yaml - add requirement for bedtools (#44541) * Add citation to description in meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/earlgrey/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index 8e70a6bccefe2..7b6cbd4469a23 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('earlgrey', max_pin='x') }} @@ -46,6 +46,7 @@ requirements: - r-optparse - r-tidyverse - r-plyr + - bedtools test: commands: From 7413f1c43d117582ce9504f784f88c1b0ac94002 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 09:09:52 -0700 Subject: [PATCH 0984/2173] Update rbpbench to 0.5 (#44548) --- recipes/rbpbench/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rbpbench/meta.yaml b/recipes/rbpbench/meta.yaml index bcd1e1886d7ed..982469b6dfaf9 100644 --- a/recipes/rbpbench/meta.yaml +++ b/recipes/rbpbench/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RBPBench" %} -{% set version = "0.4" %} -{% set sha256 = "c5fc49bd3801e68170ca624edfc5ab3041d17a5d1814958178ece6e5066aa7b7" %} +{% set version = "0.5" %} +{% set sha256 = "100a592c8b17b3eaf770fd1c986faa81a76d23801deffe9e82642ce206f36d85" %} package: name: {{ name|lower }} From 8cc20de539278b476ca3f19ce606f05b94e01a66 Mon Sep 17 00:00:00 2001 From: Abdallah Meknas <139805477+ameknas-phac@users.noreply.github.com> Date: Thu, 30 Nov 2023 11:30:26 -0500 Subject: [PATCH 0985/2173] First sequenoscope release 0.0.5 (#44508) * sequenoscope release * fixed build number to 0 * fixed v in version * updated summary * added run export * fixed url * changed python version * changed python version to 3.7.12 restricted * changed build to host and unrestricted python version * changed versions of packages and license * updated steup.py for v0.0.5 * updated license --------- Co-authored-by: ameknas --- recipes/sequenoscope/meta.yaml | 48 ++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 recipes/sequenoscope/meta.yaml diff --git a/recipes/sequenoscope/meta.yaml b/recipes/sequenoscope/meta.yaml new file mode 100644 index 0000000000000..2d9184f285845 --- /dev/null +++ b/recipes/sequenoscope/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "0.0.5" %} + +package: + name: sequenoscope + version: {{ version }} + +source: + url: https://github.com/phac-nml/sequenoscope/archive/v{{ version }}.tar.gz + sha256: aac98d2ab286da78c9c4b621e52cac2a16fd6ea3d1200b05861bf82e3fb49701 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage("sequenoscope", max_pin="x.x") }} + script: python -m pip install . + +requirements: + host: + - python + - pip + run: + - python >=3.7.12,<4 + - {{ pin_compatible('pandas') }} + - samtools >=1.6 + - pysam >=0.16.0 + - minimap2 >=2.26 + - mash >=2.3 + - fastp >=0.22.0 + - seqtk >=1.4 + - plotly >=5.16.1 + - biopython >=1.7 + - scipy >=1.7.3 + - six >=1.14.0 + - {{ pin_compatible('numpy') }} +test: + import: + - sequenoscope + commands: + - "sequenoscope --help" + + +about: + license: Apache-2.0 + summary: sequenoscope is a versatile bioinformatic pipeline for the analysis of sequencing data. + author: Abdallah Meknas, James Robertson + home: https://github.com/phac-nml/sequenoscope + dev_url: https://github.com/phac-nml/sequenoscope From 9cd15ac272394e7d7a60f6d8e1dd05a73e0c5926 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 10:36:19 -0700 Subject: [PATCH 0986/2173] Update snakemake-interface-executor-plugins to 8.1.0 (#44554) --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index 3b97d69376c22..7dbc87c76e862 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "8.0.2" %} +{% set version = "8.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: e7838042762b8946cbfae62887ee8ad9b7273e2c3296199c6385c8c2805934c6 + sha256: 5c22d2ada03a7cfe81841488c25ebfc8c392e41fdb6819c1158c7a8cd97c0c37 build: noarch: python From 80159563f726ea06c01e6c3a6315597ab9b6b28c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 10:38:26 -0700 Subject: [PATCH 0987/2173] Update last to 1517 (#44550) --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index d7a542b9ae271..cef8036ec945b 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1513" %} +{% set version = "1517" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: 596d364fa87ba61555645cdaa2dcbe5f2babd38aad0aeb4dfa305a69caf40a07 + sha256: 318e1e3f9e56c906678951f300e559f8765ac29a45ba280b96106e5407a93e63 build: number: 0 From 2b029b6866fd5bfa639bc8857ee38fecca4a51ee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 10:39:59 -0700 Subject: [PATCH 0988/2173] Update ms2rescore to 3.0.0 (#44547) --- recipes/ms2rescore/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ms2rescore/meta.yaml b/recipes/ms2rescore/meta.yaml index abcb896b63201..e6dd1106f161f 100644 --- a/recipes/ms2rescore/meta.yaml +++ b/recipes/ms2rescore/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms2rescore" %} -{% set version = "3.0.0b1" %} +{% set version = "3.0.0" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore-{{ version }}.tar.gz - sha256: d3fa5112038d2e92a916f57b47f634fec5235836260fe0949fd8cc4549cc7410 + sha256: d59b82f3e8543ab6456126f07dd09c0455daf36a6d226042b87e63aa5cc6cee0 build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} From bb7db3cec8c511b98109801ed564702e275f198b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 10:40:24 -0700 Subject: [PATCH 0989/2173] Update geofetch to 0.12.5 (#44525) --- recipes/geofetch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/geofetch/meta.yaml b/recipes/geofetch/meta.yaml index 923b5e0b8e5db..b98bdafa490ec 100644 --- a/recipes/geofetch/meta.yaml +++ b/recipes/geofetch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "geofetch" %} -{% set version = "0.12.4" %} +{% set version = "0.12.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 818aad6cdeacea72854e587bf9babbfbd13dc880e0b031d111d216b68b5f313b + sha256: 350cad0e7117ae76087b229f1ea0191bebb3bff53d90484aa8cea117c16f812f build: number: 0 From 29bd1b3281a4091b1e42fc475daecd9acad9f4f9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 12:18:27 -0700 Subject: [PATCH 0990/2173] Update earlgrey to 4.0.2 (#44538) * Update earlgrey to 4.0.2 * Update earlgrey autobump build number (#44552) --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Tobias Baril <46785187+TobyBaril@users.noreply.github.com> --- recipes/earlgrey/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index 7b6cbd4469a23..99763ef6a5c46 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.1" %} -{% set sha256 = "75910863a12f77ca864eba55e4375ad6dfb1bb548b15324296109eab90c817cd" %} +{% set version = "4.0.2" %} +{% set sha256 = "0873f77dff2dc13c1ab957f301a9a212123258ec0d4a23b660720d66fa12d442" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('earlgrey', max_pin='x') }} From 77938683f9cf4073d037db37d13ca57660590923 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 13:00:29 -0700 Subject: [PATCH 0991/2173] Update mashmap to 3.1.2 (#44555) * Update mashmap to 3.1.2 * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/mashmap/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/mashmap/meta.yaml b/recipes/mashmap/meta.yaml index e447d78bf9921..672f557d6afef 100644 --- a/recipes/mashmap/meta.yaml +++ b/recipes/mashmap/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.1.1" %} +{% set version = "3.1.2" %} {% set github = "https://github.com/marbl/MashMap" %} package: @@ -7,11 +7,13 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: b5794b181f91637940baf0230e8ddc60228bea041dda4588b03d2f8bc908c072 + sha256: cf9bb085cc85b0f1b91f4fc45a907cff536099a4a82031f1e112259e24ba5976 build: number: 0 - + run_exports: + - {{ pin_subpackage("mashmap", max_pin="x.x") }} + # Refer to INSTALL.txt for details. requirements: build: From 8338c65d39bbec23a679abcff4fd30014d64d82f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 13:01:50 -0700 Subject: [PATCH 0992/2173] Update rbpbench to 0.6 (#44557) --- recipes/rbpbench/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rbpbench/meta.yaml b/recipes/rbpbench/meta.yaml index 982469b6dfaf9..17aee16d91f0c 100644 --- a/recipes/rbpbench/meta.yaml +++ b/recipes/rbpbench/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RBPBench" %} -{% set version = "0.5" %} -{% set sha256 = "100a592c8b17b3eaf770fd1c986faa81a76d23801deffe9e82642ce206f36d85" %} +{% set version = "0.6" %} +{% set sha256 = "67f9c8f0bfa53e4602d9083c43beab1edb63e6b0e8619a0ac3cde8c01b29cb0d" %} package: name: {{ name|lower }} From 210bf1cd5517dd41b1d097f2b6f447a300daa894 Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Fri, 1 Dec 2023 07:27:09 +1100 Subject: [PATCH 0993/2173] Add Paragone (#44437) * initial commit. treeshrink not working, see https://github.com/uym2/TreeShrink/pull/40 * test build : * fix test command * tidy build comments * update test command * is this actually failing? * skip macos build? --------- Co-authored-by: Thomas Harrop --- recipes/paragone/build.sh | 9 +++++++ recipes/paragone/meta.yaml | 55 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 recipes/paragone/build.sh create mode 100644 recipes/paragone/meta.yaml diff --git a/recipes/paragone/build.sh b/recipes/paragone/build.sh new file mode 100644 index 0000000000000..0c97c7d01f619 --- /dev/null +++ b/recipes/paragone/build.sh @@ -0,0 +1,9 @@ +# Install paragone +$PYTHON -m pip install --no-deps --ignore-installed . + +# Install HmmCleaner: +${PREFIX}/bin/perl ${PREFIX}/bin/cpanm Bio::MUST::Core --notest +${PREFIX}/bin/perl ${PREFIX}/bin/cpanm Bio::MUST::Drivers --notest +${PREFIX}/bin/perl ${PREFIX}/bin/cpanm --force Bio::MUST::Apps::HmmCleaner --notest + +sed -i 's|#!/opt/miniconda3/miniconda3/bin/env perl|#!/usr/bin/env perl|' ${PREFIX}/bin/HmmCleaner.pl diff --git a/recipes/paragone/meta.yaml b/recipes/paragone/meta.yaml new file mode 100644 index 0000000000000..c35ccddcbb661 --- /dev/null +++ b/recipes/paragone/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "paragone" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: "https://github.com/chrisjackson-pellicle/ParaGone/archive/refs/tags/v{{ version }}.tar.gz" + sha256: 3434714fed0239afdc8c5bd57cb6ee642563cf651fd668150a34f9f2c23981b2 + +build: + number: 0 + skip: True # [win or osx] + run_exports: + - {{ pin_subpackage('paragone', max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - setuptools + host: + - make + - perl >=5.32 + - perl-app-cpanminus + - perl-moose >=2.2202 + - perl-net-ssleay + - python <=3.9.16 + run: + - biopython >=1.79 + - clustalo >=1.2.4 + - ete3 >=3.1.2 + - fasttree + - hmmer >=3.3.2 + - iqtree >=2.2.0.3 + - mafft >=7.245 + - openmp >=8.0.1 + - perl >=5.32 + - perl-moose >=2.2202 + - r-base >=4.0.3 + - treeshrink + - trimal >=1.4.1 + +test: + commands: + - paragone -v + +about: + home: "https://github.com/chrisjackson-pellicle/ParaGone" + license: GPL-3.0-or-later + license_family: GPL + license_file: LICENSE.txt + summary: > + Identify ortholog groups from a set of paralog sequences + from multiple taxa. From 56c77418d3b8b0a55fa5ed83088ce5fa68162e5e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 30 Nov 2023 14:40:52 -0700 Subject: [PATCH 0994/2173] Update pybiolib to 1.1.1566 (#44561) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 6ca4eae58f02b..23d11edf7c44b 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1558" %} +{% set version = "1.1.1566" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: fe8c0f7aa6f6fa45a93956aab198769a4e8ec0dd0a7f330bf52e9f4e9ab87370 + sha256: d7ffb727f4b33a997fce3ca8be6bb5701b662110b3385756a6b17b2b68a07d7f build: noarch: python From 5c8aabd89637d4e4d9fa294cbd627eb77af4c7fd Mon Sep 17 00:00:00 2001 From: Bhavya Papudeshi Date: Fri, 1 Dec 2023 11:37:10 +1030 Subject: [PATCH 0995/2173] add sphae v1.3.1 (#44564) * add sphae v1.3.1 * update meta.yml --- recipes/sphae/meta.yaml | 55 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 recipes/sphae/meta.yaml diff --git a/recipes/sphae/meta.yaml b/recipes/sphae/meta.yaml new file mode 100644 index 0000000000000..8f7644ac4bdf5 --- /dev/null +++ b/recipes/sphae/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "sphae" %} +{% set version = "1.3.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://github.com/linsalrob/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" + sha256: 996a9203c7411422c28860709714f58c4fa3a819738e6a85b92de804c1f81871 + +build: + number: 0 + noarch: python + entry_points: + - sphae=sphae.__main__:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('sphae', max_pin="x") }} + +requirements: + host: + - python <=3.11 + - pip + run: + - python <=3.11 + - snakemake-minimal >=7.14.0 + - pyyaml >=6.0 + - click >=8.1.3 + - jinja2 >=3.0.2 + - mamba <1.4.2 + - metasnek >=0.0.4 + - snaketool-utils >=0.0.4 + - attrmap >=0.0.7 + - biopython >=1.8.1 + - pandas + +test: + commands: + - sphae --help + +about: + home: "https://github.com/linsalrob/sphae/" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Sphae: Assembling and annotating pure culture phages from both Illumina and Nanopore sequencing technology" + description: "Phage toolkit" + doc_url: "https://github.com/linsalrob/sphae" + dev_url: "https://github.com/linsalrob/sphae" + +extra: + recipe-maintainers: + - npbhavya + - linsalrob From d4a58d8ba9b38a13f69d9f427cf1b17b810545a4 Mon Sep 17 00:00:00 2001 From: Michael Uhl Date: Fri, 1 Dec 2023 06:39:46 +0100 Subject: [PATCH 0996/2173] Rbpbench update some dependencies (#44566) * add rbpbench meta yaml * add run exports * updated some dependencies --- recipes/rbpbench/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/rbpbench/meta.yaml b/recipes/rbpbench/meta.yaml index 17aee16d91f0c..7f1e4b8fdb0e6 100644 --- a/recipes/rbpbench/meta.yaml +++ b/recipes/rbpbench/meta.yaml @@ -11,7 +11,7 @@ source: sha256: "{{ sha256 }}" build: - number: 0 + number: 1 noarch: python script: $PYTHON -m pip install . --ignore-installed --no-deps -vv run_exports: @@ -25,7 +25,7 @@ requirements: - python <3.12 - logomaker - markdown - - meme + - meme >=5.0 - scipy - plotly - textdistance @@ -34,6 +34,7 @@ requirements: - infernal - bedtools - upsetplot + - packaging test: commands: From f7e693aac572f66e216e72de349dca84cd4d35ef Mon Sep 17 00:00:00 2001 From: Pooja Strope Date: Fri, 1 Dec 2023 02:46:46 -0500 Subject: [PATCH 0997/2173] update fcs-gx to v0.5.0 (#44556) * v0.5.0 * v0.5.0 * saved 0.4.1 * saved 0.4.1 * 0.5.0 --- recipes/ncbi-fcs-gx/0.4.1/build.sh | 18 +++++++++++++ recipes/ncbi-fcs-gx/0.4.1/meta.yaml | 40 +++++++++++++++++++++++++++++ recipes/ncbi-fcs-gx/build.sh | 1 + recipes/ncbi-fcs-gx/meta.yaml | 14 +++++----- 4 files changed, 67 insertions(+), 6 deletions(-) create mode 100644 recipes/ncbi-fcs-gx/0.4.1/build.sh create mode 100644 recipes/ncbi-fcs-gx/0.4.1/meta.yaml diff --git a/recipes/ncbi-fcs-gx/0.4.1/build.sh b/recipes/ncbi-fcs-gx/0.4.1/build.sh new file mode 100644 index 0000000000000..1597a84f75f1d --- /dev/null +++ b/recipes/ncbi-fcs-gx/0.4.1/build.sh @@ -0,0 +1,18 @@ +#!/bin/bash -e +set -uex + +mkdir -vp ${PREFIX}/bin + +ls -l . + +$GCC --version +$GCC -print-search-dirs + +#cd fcs-gx-0.4.0 +make VERBOSE=1 + +cp $SRC_DIR/build/src/gx ${PREFIX}/bin/ +cp $SRC_DIR/scripts/* ${PREFIX}/bin/ +cp $SRC_DIR/make_gxdb/blast_names_mapping.tsv ${PREFIX}/bin/ +chmod ua+x ${PREFIX}/bin/gx + diff --git a/recipes/ncbi-fcs-gx/0.4.1/meta.yaml b/recipes/ncbi-fcs-gx/0.4.1/meta.yaml new file mode 100644 index 0000000000000..03abf4bee3563 --- /dev/null +++ b/recipes/ncbi-fcs-gx/0.4.1/meta.yaml @@ -0,0 +1,40 @@ +package: + name: ncbi-fcs-gx + version: 0.4.1 + +source: + url: https://github.com/ncbi/fcs-gx/archive/refs/tags/v0.4.1.zip + sha256: 7bedb6a43945df4821d3e23fd1c5c4bf117cd70001cb96b310d177f0fd049a6b + + +requirements: + build: + - {{ compiler('cxx') }} + - make + - cmake + - libstdcxx-ng + - libgcc-ng + run: + - python >=3.9 + - aria2 =1.36.0 + - gzip >=1.5 + - pv >=1.4.6 + - rclone =1.61.1 + - grep >=3.4 + +build: + number: 0 + skip: True # [not linux or not x86_64] + run_exports: + - {{ pin_compatible('nxbi-fcs-gx', max_pin="x.x") }} + +test: + commands: + - gx --help + +about: + home: https://github.com/ncbi/fcs + summary: The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection. + license: NCBI-PD + license_url: https://github.com/ncbi/fcs/blob/main/LICENSE.txt + diff --git a/recipes/ncbi-fcs-gx/build.sh b/recipes/ncbi-fcs-gx/build.sh index 1597a84f75f1d..115d28fa7d971 100644 --- a/recipes/ncbi-fcs-gx/build.sh +++ b/recipes/ncbi-fcs-gx/build.sh @@ -14,5 +14,6 @@ make VERBOSE=1 cp $SRC_DIR/build/src/gx ${PREFIX}/bin/ cp $SRC_DIR/scripts/* ${PREFIX}/bin/ cp $SRC_DIR/make_gxdb/blast_names_mapping.tsv ${PREFIX}/bin/ +echo PREFIX: ${PREFIX} chmod ua+x ${PREFIX}/bin/gx diff --git a/recipes/ncbi-fcs-gx/meta.yaml b/recipes/ncbi-fcs-gx/meta.yaml index 03abf4bee3563..205112082b9a7 100644 --- a/recipes/ncbi-fcs-gx/meta.yaml +++ b/recipes/ncbi-fcs-gx/meta.yaml @@ -1,10 +1,10 @@ package: name: ncbi-fcs-gx - version: 0.4.1 + version: 0.5.0 source: - url: https://github.com/ncbi/fcs-gx/archive/refs/tags/v0.4.1.zip - sha256: 7bedb6a43945df4821d3e23fd1c5c4bf117cd70001cb96b310d177f0fd049a6b + url: https://github.com/ncbi/fcs-gx/archive/refs/tags/v0.5.0.zip + sha256: 2f6b6099584495e1a9115403a5e4cb5f5dac1ddbbc691da9a3158a75391ffe8a requirements: @@ -12,8 +12,8 @@ requirements: - {{ compiler('cxx') }} - make - cmake - - libstdcxx-ng - - libgcc-ng + - libstdcxx-ng <=12.2 + - libgcc-ng <=12.2 run: - python >=3.9 - aria2 =1.36.0 @@ -26,11 +26,13 @@ build: number: 0 skip: True # [not linux or not x86_64] run_exports: - - {{ pin_compatible('nxbi-fcs-gx', max_pin="x.x") }} + - {{ pin_compatible('ncbi-fcs-gx', max_pin="0.5") }} test: commands: - gx --help + - ls -l ${PREFIX}/bin/ + - ${PREFIX}/bin/gx --help about: home: https://github.com/ncbi/fcs From 1c5dacf1154bab39908ebbfecd4a40c3e041916f Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Fri, 1 Dec 2023 05:29:40 -0500 Subject: [PATCH 0998/2173] nrpys - fix license text (#44553) * bump build and fix license text * run_exports * Update meta.yaml * Loosen Python pinning --------- Co-authored-by: Thanh Lee --- recipes/nrpys/LICENSE.txt | 5200 +++++-------------------------------- recipes/nrpys/meta.yaml | 4 +- 2 files changed, 664 insertions(+), 4540 deletions(-) diff --git a/recipes/nrpys/LICENSE.txt b/recipes/nrpys/LICENSE.txt index 006fae0d49aa9..dba13ed2ddf78 100644 --- a/recipes/nrpys/LICENSE.txt +++ b/recipes/nrpys/LICENSE.txt @@ -1,4539 +1,661 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nrpys/LICENSE.txt at main · kblin/nrpys · GitHub - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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GNU AFFERO GENERAL PUBLIC LICENSE
Version 3, 19 November 2007
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Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
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Preamble
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The GNU Affero General Public License is a free, copyleft license for
software and other kinds of works, specifically designed to ensure
cooperation with the community in the case of network server software.
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The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
our General Public Licenses are intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users.
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When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
them if you wish), that you receive source code or can get it if you
want it, that you can change the software or use pieces of it in new
free programs, and that you know you can do these things.
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Developers that use our General Public Licenses protect your rights
with two steps: (1) assert copyright on the software, and (2) offer
you this License which gives you legal permission to copy, distribute
and/or modify the software.
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A secondary benefit of defending all users' freedom is that
improvements made in alternate versions of the program, if they
receive widespread use, become available for other developers to
incorporate. Many developers of free software are heartened and
encouraged by the resulting cooperation. However, in the case of
software used on network servers, this result may fail to come about.
The GNU General Public License permits making a modified version and
letting the public access it on a server without ever releasing its
source code to the public.
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The GNU Affero General Public License is designed specifically to
ensure that, in such cases, the modified source code becomes available
to the community. It requires the operator of a network server to
provide the source code of the modified version running there to the
users of that server. Therefore, public use of a modified version, on
a publicly accessible server, gives the public access to the source
code of the modified version.
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An older license, called the Affero General Public License and
published by Affero, was designed to accomplish similar goals. This is
a different license, not a version of the Affero GPL, but Affero has
released a new version of the Affero GPL which permits relicensing under
this license.
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The precise terms and conditions for copying, distribution and
modification follow.
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TERMS AND CONDITIONS
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0. Definitions.
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"This License" refers to version 3 of the GNU Affero General Public License.
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"Copyright" also means copyright-like laws that apply to other kinds of
works, such as semiconductor masks.
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"The Program" refers to any copyrightable work licensed under this
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A "covered work" means either the unmodified Program or a work based
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To "propagate" a work means to do anything with it that, without
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public, and in some countries other activities as well.
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To "convey" a work means any kind of propagation that enables other
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An interactive user interface displays "Appropriate Legal Notices"
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extent that warranties are provided), that licensees may convey the
work under this License, and how to view a copy of this License. If
the interface presents a list of user commands or options, such as a
menu, a prominent item in the list meets this criterion.
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1. Source Code.
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The "source code" for a work means the preferred form of the work
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A "Standard Interface" means an interface that either is an official
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The "System Libraries" of an executable work include anything, other
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The "Corresponding Source" for a work in object code form means all
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programs which are used unmodified in performing those activities but
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The Corresponding Source for a work in source code form is that
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2. Basic Permissions.
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All rights granted under this License are granted for the term of
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permission to run the unmodified Program. The output from running a
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You may make, run and propagate covered works that you do not
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When you convey a covered work, you waive any legal power to forbid
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You may convey verbatim copies of the Program's source code as you
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keep intact all notices stating that this License and any
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A compilation of a covered work with other separate and independent
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used to limit the access or legal rights of the compilation's users
beyond what the individual works permit. Inclusion of a covered work
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6. Conveying Non-Source Forms.
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You may convey a covered work in object code form under the terms
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in one of these ways:
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a) Convey the object code in, or embodied in, a physical product
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customarily used for software interchange.
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b) Convey the object code in, or embodied in, a physical product
(including a physical distribution medium), accompanied by a
written offer, valid for at least three years and valid for as
long as you offer spare parts or customer support for that product
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copy of the Corresponding Source for all the software in the
product that is covered by this License, on a durable physical
medium customarily used for software interchange, for a price no
more than your reasonable cost of physically performing this
conveying of source, or (2) access to copy the
Corresponding Source from a network server at no charge.
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c) Convey individual copies of the object code with a copy of the
written offer to provide the Corresponding Source. This
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only if you received the object code with such an offer, in accord
with subsection 6b.
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d) Convey the object code by offering access from a designated
place (gratis or for a charge), and offer equivalent access to the
Corresponding Source in the same way through the same place at no
further charge. You need not require recipients to copy the
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may be on a different server (operated by you or a third party)
that supports equivalent copying facilities, provided you maintain
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e) Convey the object code using peer-to-peer transmission, provided
you inform other peers where the object code and Corresponding
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A separable portion of the object code, whose source code is excluded
from the Corresponding Source as a System Library, need not be
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A "User Product" is either (1) a "consumer product", which means any
tangible personal property which is normally used for personal, family,
or household purposes, or (2) anything designed or sold for incorporation
into a dwelling. In determining whether a product is a consumer product,
doubtful cases shall be resolved in favor of coverage. For a particular
product received by a particular user, "normally used" refers to a
typical or common use of that class of product, regardless of the status
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actually uses, or expects or is expected to use, the product. A product
is a consumer product regardless of whether the product has substantial
commercial, industrial or non-consumer uses, unless such uses represent
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"Installation Information" for a User Product means any methods,
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a modified version of its Corresponding Source. The information must
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code is in no case prevented or interfered with solely because
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If you convey an object code work under this section in, or with, or
specifically for use in, a User Product, and the conveying occurs as
part of a transaction in which the right of possession and use of the
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fixed term (regardless of how the transaction is characterized), the
Corresponding Source conveyed under this section must be accompanied
by the Installation Information. But this requirement does not apply
if neither you nor any third party retains the ability to install
modified object code on the User Product (for example, the work has
been installed in ROM).
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The requirement to provide Installation Information does not include a
requirement to continue to provide support service, warranty, or updates
for a work that has been modified or installed by the recipient, or for
the User Product in which it has been modified or installed. Access to a
network may be denied when the modification itself materially and
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Corresponding Source conveyed, and Installation Information provided,
in accord with this section must be in a format that is publicly
documented (and with an implementation available to the public in
source code form), and must require no special password or key for
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7. Additional Terms.
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"Additional permissions" are terms that supplement the terms of this
License by making exceptions from one or more of its conditions.
Additional permissions that are applicable to the entire Program shall
be treated as though they were included in this License, to the extent
that they are valid under applicable law. If additional permissions
apply only to part of the Program, that part may be used separately
under those permissions, but the entire Program remains governed by
this License without regard to the additional permissions.
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When you convey a copy of a covered work, you may at your option
remove any additional permissions from that copy, or from any part of
it. (Additional permissions may be written to require their own
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additional permissions on material, added by you to a covered work,
for which you have or can give appropriate copyright permission.
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Notwithstanding any other provision of this License, for material you
add to a covered work, you may (if authorized by the copyright holders of
that material) supplement the terms of this License with terms:
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a) Disclaiming warranty or limiting liability differently from the
terms of sections 15 and 16 of this License; or
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b) Requiring preservation of specified reasonable legal notices or
author attributions in that material or in the Appropriate Legal
Notices displayed by works containing it; or
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c) Prohibiting misrepresentation of the origin of that material, or
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trade names, trademarks, or service marks; or
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material by anyone who conveys the material (or modified versions of
it) with contractual assumptions of liability to the recipient, for
any liability that these contractual assumptions directly impose on
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All other non-permissive additional terms are considered "further
restrictions" within the meaning of section 10. If the Program as you
received it, or any part of it, contains a notice stating that it is
governed by this License along with a term that is a further
restriction, you may remove that term. If a license document contains
a further restriction but permits relicensing or conveying under this
License, you may add to a covered work material governed by the terms
of that license document, provided that the further restriction does
not survive such relicensing or conveying.
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If you add terms to a covered work in accord with this section, you
must place, in the relevant source files, a statement of the
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where to find the applicable terms.
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Additional terms, permissive or non-permissive, may be stated in the
form of a separately written license, or stated as exceptions;
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8. Termination.
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You may not propagate or modify a covered work except as expressly
provided under this License. Any attempt otherwise to propagate or
modify it is void, and will automatically terminate your rights under
this License (including any patent licenses granted under the third
paragraph of section 11).
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However, if you cease all violation of this License, then your
license from a particular copyright holder is reinstated (a)
provisionally, unless and until the copyright holder explicitly and
finally terminates your license, and (b) permanently, if the copyright
holder fails to notify you of the violation by some reasonable means
prior to 60 days after the cessation.
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Moreover, your license from a particular copyright holder is
reinstated permanently if the copyright holder notifies you of the
violation by some reasonable means, this is the first time you have
received notice of violation of this License (for any work) from that
copyright holder, and you cure the violation prior to 30 days after
your receipt of the notice.
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Termination of your rights under this section does not terminate the
licenses of parties who have received copies or rights from you under
this License. If your rights have been terminated and not permanently
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material under section 10.
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9. Acceptance Not Required for Having Copies.
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You are not required to accept this License in order to receive or
run a copy of the Program. Ancillary propagation of a covered work
occurring solely as a consequence of using peer-to-peer transmission
to receive a copy likewise does not require acceptance. However,
nothing other than this License grants you permission to propagate or
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not accept this License. Therefore, by modifying or propagating a
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10. Automatic Licensing of Downstream Recipients.
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Each time you convey a covered work, the recipient automatically
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propagate that work, subject to this License. You are not responsible
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An "entity transaction" is a transaction transferring control of an
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organization, or merging organizations. If propagation of a covered
work results from an entity transaction, each party to that
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You may not impose any further restrictions on the exercise of the
rights granted or affirmed under this License. For example, you may
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rights granted under this License, and you may not initiate litigation
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any patent claim is infringed by making, using, selling, offering for
sale, or importing the Program or any portion of it.
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11. Patents.
-
A "contributor" is a copyright holder who authorizes use under this
License of the Program or a work on which the Program is based. The
work thus licensed is called the contributor's "contributor version".
-
A contributor's "essential patent claims" are all patent claims
owned or controlled by the contributor, whether already acquired or
hereafter acquired, that would be infringed by some manner, permitted
by this License, of making, using, or selling its contributor version,
but do not include claims that would be infringed only as a
consequence of further modification of the contributor version. For
purposes of this definition, "control" includes the right to grant
patent sublicenses in a manner consistent with the requirements of
this License.
-
Each contributor grants you a non-exclusive, worldwide, royalty-free
patent license under the contributor's essential patent claims, to
make, use, sell, offer for sale, import and otherwise run, modify and
propagate the contents of its contributor version.
-
In the following three paragraphs, a "patent license" is any express
agreement or commitment, however denominated, not to enforce a patent
(such as an express permission to practice a patent or covenant not to
sue for patent infringement). To "grant" such a patent license to a
party means to make such an agreement or commitment not to enforce a
patent against the party.
-
If you convey a covered work, knowingly relying on a patent license,
and the Corresponding Source of the work is not available for anyone
to copy, free of charge and under the terms of this License, through a
publicly available network server or other readily accessible means,
then you must either (1) cause the Corresponding Source to be so
available, or (2) arrange to deprive yourself of the benefit of the
patent license for this particular work, or (3) arrange, in a manner
consistent with the requirements of this License, to extend the patent
license to downstream recipients. "Knowingly relying" means you have
actual knowledge that, but for the patent license, your conveying the
covered work in a country, or your recipient's use of the covered work
in a country, would infringe one or more identifiable patents in that
country that you have reason to believe are valid.
-
If, pursuant to or in connection with a single transaction or
arrangement, you convey, or propagate by procuring conveyance of, a
covered work, and grant a patent license to some of the parties
receiving the covered work authorizing them to use, propagate, modify
or convey a specific copy of the covered work, then the patent license
you grant is automatically extended to all recipients of the covered
work and works based on it.
-
A patent license is "discriminatory" if it does not include within
the scope of its coverage, prohibits the exercise of, or is
conditioned on the non-exercise of one or more of the rights that are
specifically granted under this License. You may not convey a covered
work if you are a party to an arrangement with a third party that is
in the business of distributing software, under which you make payment
to the third party based on the extent of your activity of conveying
the work, and under which the third party grants, to any of the
parties who would receive the covered work from you, a discriminatory
patent license (a) in connection with copies of the covered work
conveyed by you (or copies made from those copies), or (b) primarily
for and in connection with specific products or compilations that
contain the covered work, unless you entered into that arrangement,
or that patent license was granted, prior to 28 March 2007.
-
Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.
-
12. No Surrender of Others' Freedom.
-
If conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot convey a
covered work so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you may
not convey it at all. For example, if you agree to terms that obligate you
to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
-
13. Remote Network Interaction; Use with the GNU General Public License.
-
Notwithstanding any other provision of this License, if you modify the
Program, your modified version must prominently offer all users
interacting with it remotely through a computer network (if your version
supports such interaction) an opportunity to receive the Corresponding
Source of your version by providing access to the Corresponding Source
from a network server at no charge, through some standard or customary
means of facilitating copying of software. This Corresponding Source
shall include the Corresponding Source for any work covered by version 3
of the GNU General Public License that is incorporated pursuant to the
following paragraph.
-
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the work with which it is combined will remain governed by version
3 of the GNU General Public License.
-
14. Revised Versions of this License.
-
The Free Software Foundation may publish revised and/or new versions of
the GNU Affero General Public License from time to time. Such new versions
will be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
-
Each version is given a distinguishing version number. If the
Program specifies that a certain numbered version of the GNU Affero General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
GNU Affero General Public License, you may choose any version ever published
by the Free Software Foundation.
-
If the Program specifies that a proxy can decide which future
versions of the GNU Affero General Public License can be used, that proxy's
public statement of acceptance of a version permanently authorizes you
to choose that version for the Program.
-
Later license versions may give you additional or different
permissions. However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.
-
15. Disclaimer of Warranty.
-
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
16. Limitation of Liability.
-
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
-
17. Interpretation of Sections 15 and 16.
-
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
-
END OF TERMS AND CONDITIONS
-
How to Apply These Terms to Your New Programs
-
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
-
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
-
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
-
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
-
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
-
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
-
Also add information on how to contact you by electronic and paper mail.
-
If your software can interact with users remotely through a computer
network, you should also make sure that it provides a way for users to
get its source. For example, if your program is a web application, its
interface could display a "Source" link that leads users to an archive
of the code. There are many ways you could offer source, and different
solutions will be better for different programs; see section 13 for the
specific requirements.
-
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU AGPL, see
<http://www.gnu.org/licenses/>.
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- - - + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +our General Public Licenses are intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + Developers that use our General Public Licenses protect your rights +with two steps: (1) assert copyright on the software, and (2) offer +you this License which gives you legal permission to copy, distribute +and/or modify the software. + + A secondary benefit of defending all users' freedom is that +improvements made in alternate versions of the program, if they +receive widespread use, become available for other developers to +incorporate. Many developers of free software are heartened and +encouraged by the resulting cooperation. However, in the case of +software used on network servers, this result may fail to come about. +The GNU General Public License permits making a modified version and +letting the public access it on a server without ever releasing its +source code to the public. + + The GNU Affero General Public License is designed specifically to +ensure that, in such cases, the modified source code becomes available +to the community. It requires the operator of a network server to +provide the source code of the modified version running there to the +users of that server. Therefore, public use of a modified version, on +a publicly accessible server, gives the public access to the source +code of the modified version. + + An older license, called the Affero General Public License and +published by Affero, was designed to accomplish similar goals. This is +a different license, not a version of the Affero GPL, but Affero has +released a new version of the Affero GPL which permits relicensing under +this license. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU Affero General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based +on the Program. + + To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + + A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + + The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + + The Corresponding Source for a work in source code form is that +same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + + When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + + A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + + If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + + The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + + All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). 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Remote Network Interaction; Use with the GNU General Public License. + + Notwithstanding any other provision of this License, if you modify the +Program, your modified version must prominently offer all users +interacting with it remotely through a computer network (if your version +supports such interaction) an opportunity to receive the Corresponding +Source of your version by providing access to the Corresponding Source +from a network server at no charge, through some standard or customary +means of facilitating copying of software. This Corresponding Source +shall include the Corresponding Source for any work covered by version 3 +of the GNU General Public License that is incorporated pursuant to the +following paragraph. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU General Public License into a single +combined work, and to convey the resulting work. 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EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff --git a/recipes/nrpys/meta.yaml b/recipes/nrpys/meta.yaml index 587bb75ae1e65..497aba8dd7f46 100644 --- a/recipes/nrpys/meta.yaml +++ b/recipes/nrpys/meta.yaml @@ -7,8 +7,10 @@ package: version: {{ version }} build: - number: 1 + number: 2 noarch: generic + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} source: url: https://github.com/kblin/nrpys/archive/refs/tags/v{{ version }}.tar.gz From a35e6ead6eccea97913b5f9cc4de4ebbd6b4ede0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 05:17:05 -0700 Subject: [PATCH 0999/2173] Update deepfplearn to 2.0 (#42865) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update deepfplearn to 2.0 * add run_exports * add chemprop run dep * add seaborn and umap run deps * remove umap * add umap run dep * add argparse run dep * remove umap and argparse for umap-learn Co-authored-by: M Bernt * test tensorflow and cudatoolkit * revert to tensorflow-base * install fork of chemprop and add chemprop requirements --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: M Bernt Co-authored-by: Björn Grüning --- recipes/deepfplearn/meta.yaml | 35 +++++++++++++++++++++++++++-------- 1 file changed, 27 insertions(+), 8 deletions(-) diff --git a/recipes/deepfplearn/meta.yaml b/recipes/deepfplearn/meta.yaml index 2db5b6fb1b450..e07d4955d6580 100644 --- a/recipes/deepfplearn/meta.yaml +++ b/recipes/deepfplearn/meta.yaml @@ -1,5 +1,5 @@ {% set name = "deepFPlearn" %} -{% set version = "1.2" %} +{% set version = "2.0" %} package: name: {{ name | lower }} @@ -7,21 +7,25 @@ package: source: url: https://github.com/yigbt/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 1f62b049c0ae51631f9eff718c53342fbaf5ccc400ee0f87d2dc1b2304e4e816 + sha256: 858e30e075e64ed49a3db5fcacb9d4a70b3f59bd8841b8f6989a62677107a541 build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + entry_points: + - dfpl=dfpl.__main__:main + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv && {{ PYTHON }} -m pip install git+https://github.com/soulios/chemprop.git@1d73523e49aa28a90b74edc04aaf45d7e124e338 --no-deps --ignore-installed -vv" + run_exports: + - {{ pin_subpackage('deepfplearn', max_pin="x") }} requirements: host: - - python >=3 + - python >=3.6 - pip run: # - cudatoolkit - jsonpickle =2.1 - - matplotlib-base =3.5 + - matplotlib-base =3.5.1 - numpy =1.22 - pandas =1.4 - rdkit =2022.03 @@ -30,6 +34,21 @@ requirements: - tensorflow-base # - tensorflow-gpu =2 - wandb =0.12 + - chemprop + - seaborn =0.12.2 + - umap-learn =0.5.3 + + # additional chemprop requirements + - flask >=1.1.2 + - hyperopt >=0.2.3 + - pandas-flavor >=0.2.0 + - scipy >=1.4.1 + - sphinx >=3.1.2 + - tensorboardx >=2.0 + - pytorch >=1.5.1 + - tqdm >=4.45.0 + - typed-argument-parser >=1.6.1 + - descriptastorus test: # source_files: @@ -39,14 +58,14 @@ test: - dfpl commands: - dfpl --help - - ls # commenting the actual tests due to https://github.com/bioconda/bioconda-utils/issues/897 # - dfpl train -f example/train.json # - dfpl predict -f example/predict.json about: home: https://github.com/yigbt/deepFPlearn - license: GPL + license: GPL-3.0-or-later + license_family: GPL license_file: LICENSE.pdf - summary: Link molecular structures of chemicals (in form of topological fingerprints) with multiple targets. + summary: 'Link molecular structures of chemicals (in form of topological fingerprints) with multiple targets.' From 8b378c3555f50bc018e2b5182b9d8aa61c0be63a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 07:07:06 -0700 Subject: [PATCH 1000/2173] Update galaxy-files to 23.1.3 (#44576) --- recipes/galaxy-files/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml index 54b29aec44cb5..0a61489a554ce 100644 --- a/recipes/galaxy-files/meta.yaml +++ b/recipes/galaxy-files/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.1.2" %} -{% set sha256 = "426a57051264b17dcd1e78c442fd8b09d8548f30ff55baac46eb13bfc6e2e6d5" %} +{% set version = "23.1.3" %} +{% set sha256 = "0facf5bfe8573a6e1a576d4e4b7f0ad7fa7924a1291111b9dfc1714520e1d559" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From 6533f3881a1097ddd837e093f0d179d0ff7a29f4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 07:07:24 -0700 Subject: [PATCH 1001/2173] Update galaxy-objectstore to 23.1.3 (#44575) --- recipes/galaxy-objectstore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml index 589aa6780596d..ac332bc820da2 100644 --- a/recipes/galaxy-objectstore/meta.yaml +++ b/recipes/galaxy-objectstore/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.1.2" %} -{% set sha256 = "0058ee7c17e59d361f92bddad4a3c24e76fb75a43d0ca0a5711a084a01490478" %} +{% set version = "23.1.3" %} +{% set sha256 = "52b9b213e15f1e219a25304f616e44f29f0ac52b61c753a6e89fac9d5c2a0fa2" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From fe1db6b7b6b738c22e7062b9356c5b5b9fcf1cea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 07:11:23 -0700 Subject: [PATCH 1002/2173] Update ncbi-datasets-pylib to 15.31.0 (#44560) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 4d247664fdebd..ca13cfbab4ab9 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.30.0" %} -{% set sha256 = "44a5579bd7122659c0ee8641b1118060d86e5e9e3fba5a220e44b457dbc616ff" %} +{% set version = "15.31.0" %} +{% set sha256 = "bcc99009c2b8b01a95ec95ca5e874e5c3e96d4fdced56635c8d3aaf027650a32" %} package: name: {{ name|lower }} From 2519eda684b319cb945f5d6d946e70677dfc175c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 07:12:00 -0700 Subject: [PATCH 1003/2173] Update bamdash to 0.2.2 (#44574) --- recipes/bamdash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bamdash/meta.yaml b/recipes/bamdash/meta.yaml index 76aee2edec5e6..430d4923962fc 100644 --- a/recipes/bamdash/meta.yaml +++ b/recipes/bamdash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bamdash" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/bamdash-{{ version }}.tar.gz - sha256: 2e3fbd2e4baddf09f64e12168fa77549d1f2fe6bf869883ea4c349180e690980 + sha256: aebd3ea688fac17f9d87ebae87efc33f260a4dedc83d14036c97f2ace08631d6 build: entry_points: From 493fef7f902074013a516746e97b1287f35bf977 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 07:15:24 -0700 Subject: [PATCH 1004/2173] Update sequali to 0.4.0 (#44571) --- recipes/sequali/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index fcc9e14b627a8..425992252db9a 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sequali" %} -{% set version = "0.3.0" %} +{% set version = "0.4.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b194d2d993f61431085b43196d8d829a58cff3ae91cd6cceeefff7dbc1dd5321 + sha256: dc4dd32f652250ff4d2c783f0eb6f99072b9ed14df669e319fa2fa6ab12a558b build: number: 0 From 61db981337249d9c0c88df86fea90a3b2f53c4cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 07:16:56 -0700 Subject: [PATCH 1005/2173] Update oakvar to 2.9.68 (#44562) * Update oakvar to 2.9.66 * Update oakvar to 2.9.67 * Update oakvar to 2.9.68 --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 5dadb2f52affa..5f8944a58a27b 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.64" %} -{% set sha256 = "16395f8aaeb6b79ce30c86be1c7535b91778d0d4941d65fe93a92dbd6db9414b" %} +{% set version = "2.9.68" %} +{% set sha256 = "df2a1ceead63c001bccfdac097c50209bd1ceca913d792fcc5cc689ecaba452c" %} package: name: {{ name|lower }} From 1138941a2668b85121fccedff79d18d04add0547 Mon Sep 17 00:00:00 2001 From: mjohnpayne Date: Sat, 2 Dec 2023 02:12:41 +1100 Subject: [PATCH 1006/2173] Add Campy-AGAINST v0.1.0 (#44536) * Create meta.yml * Add Campy-AGAINST * Update recipes/Campy-AGAINST/meta.yml Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update meta.yml --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/Campy-AGAINST/meta.yml | 35 ++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 recipes/Campy-AGAINST/meta.yml diff --git a/recipes/Campy-AGAINST/meta.yml b/recipes/Campy-AGAINST/meta.yml new file mode 100644 index 0000000000000..c8bb3ca21ab34 --- /dev/null +++ b/recipes/Campy-AGAINST/meta.yml @@ -0,0 +1,35 @@ +{% set version = "0.1.0" %} +{% set name = "Campy-AGAINST" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/LanLab/{{ name }}/archive/v{{ version }}.tar.gz + sha256: 24c42a19498b9519ef32961709938abebaefe1a59f879e02302a61ef659096ec + +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_subpackage('Campy-AGAINST', max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - fastani >=1.3 + +about: + home: https://github.com/LanLab/Campy-AGAINST + license: GPL-3.0-or-later + license_file: LICENSE + summary: Accurate assignment of ANI genomic species to Campylobacter genomes. + +test: + commands: + - campyagainst --help From 37ab6d81947a9a927ef71b74f13ef724b4be2c30 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 08:13:05 -0700 Subject: [PATCH 1007/2173] Update jbrowse2 to 2.9.0 (#44559) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 862d582d90725..fe00dc6c696ba 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.8.0" %} +{% set version = "2.9.0" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 635c6003041251a33c2116bce4f0326e96a1c87b7995a0488a9f67b83ca71df8 + sha256: 3557cea0f7a13c479364de9611f584d5f2e51f70a53c949ee1fc023e3c12db86 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From 323b4d9e30d7acf21813a1e915074388aaf9a5ca Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 08:50:48 -0700 Subject: [PATCH 1008/2173] Update mehari to 0.21.1 (#44578) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index ed61e18bbf4d7..c36b6f1c6475a 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.21.0" %} -{% set sha256 = "ce849731697f834b64da6a6fd1007666c98fb6c21def5a00d57d247dfc91555e" %} +{% set version = "0.21.1" %} +{% set sha256 = "6dcdd453ca44a531e4b4903ebf32921707bebe9d51f389a463dc2df3b3042f12" %} package: name: mehari From 69f21485b48fbe52cb41d2a4fcdbd502652d5be9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 08:52:13 -0700 Subject: [PATCH 1009/2173] Update solvebio to 2.26.0 (#44579) --- recipes/solvebio/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/solvebio/meta.yaml b/recipes/solvebio/meta.yaml index 5db0bbc3a8ebd..81b7235233edb 100644 --- a/recipes/solvebio/meta.yaml +++ b/recipes/solvebio/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.25.0" %} -{% set sha256 = "0cbbdf281e1415385f91b8b2416681207945949ce709cd591505c29fb384fda7" %} +{% set version = "2.26.0" %} +{% set sha256 = "36bba6f199f6f4abca4c5b0aa239692d6c4f2ea83c99ec123009ab1a30770de9" %} package: name: solvebio From 13fa67b33a0c52000fb5a85816139261d503c939 Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Fri, 1 Dec 2023 11:02:37 -0500 Subject: [PATCH 1010/2173] Bot consolidation (#44532) * use BiocondaBot * test on this branch * trigger test * trigger workflow * use builtin token * trigger failure workflow * test without token * trigger wf * revert test changes * revert test change * change to BiocondaBot and remove token to use default --- .github/workflows/Bulk.yml | 15 +++++++-------- .github/workflows/build-failures.yml | 4 ++-- 2 files changed, 9 insertions(+), 10 deletions(-) diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index c6ecd8670d8ae..0ccdf6aa9c9d3 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -15,14 +15,11 @@ jobs: runner: [0, 1, 2, 3, 4, 5] steps: - uses: actions/checkout@v3 - with: - # checkout as bioconda-bot in order to have the permission to push fail logs - token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} - name: set git user run: | - git config user.name bioconda-bot - git config user.email bioconda-bot@users.noreply.github.com + git config user.name BiocondaBot + git config user.email BiocondaBot@users.noreply.github.com - name: set path run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH @@ -85,9 +82,11 @@ jobs: runner: [0, 1, 2, 3] steps: - uses: actions/checkout@v3 - with: - # checkout as bioconda-bot in order to have the permission to push fail logs - token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} + + - name: set git user + run: | + git config user.name BiocondaBot + git config user.email BiocondaBot@users.noreply.github.com - name: set path run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH diff --git a/.github/workflows/build-failures.yml b/.github/workflows/build-failures.yml index 35b23b0eb1aa9..3fcdc275e6547 100644 --- a/.github/workflows/build-failures.yml +++ b/.github/workflows/build-failures.yml @@ -59,8 +59,8 @@ jobs: uses: docker://decathlon/wiki-page-creator-action:latest env: GH_PAT: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} - ACTION_MAIL: bioconda-bot@users.noreply.github.com - ACTION_NAME: bioconda-bot + ACTION_MAIL: BiocondaBot@users.noreply.github.com + ACTION_NAME: BiocondaBot OWNER: bioconda REPO_NAME: bioconda-recipes MD_FOLDER: build-failures From c49fa510f14dc8ef71dda6ff37aa232b459c6197 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 09:21:00 -0700 Subject: [PATCH 1011/2173] Update annonars to 0.30.1 (#44580) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 7457d8e28cffb..0a6f96ee740ea 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.30.0" %} +{% set version = "0.30.1" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: ba088a5308d8efdd20d2bc623472d56cb1353b51a5c77b39a3ff378ee2548f0b + sha256: 17b0116630f06d87c904c5d40666d10e34f6ae3a88c1b9b2b761ea396aa537fb requirements: build: From 6ee28e0f72b67a2e630786bbc0a9c6c578779d9e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 13:04:57 -0700 Subject: [PATCH 1012/2173] Update ncbi-datasets-pylib to 15.31.1 (#44585) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index ca13cfbab4ab9..901b20233d3b5 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.31.0" %} -{% set sha256 = "bcc99009c2b8b01a95ec95ca5e874e5c3e96d4fdced56635c8d3aaf027650a32" %} +{% set version = "15.31.1" %} +{% set sha256 = "f39ac05519485fa14ff01e6cc2057726e52b92947adec9496ebc33314498edc8" %} package: name: {{ name|lower }} From 0ef654a5227a1abbe577b0b37ad94c8ef689f8bb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 13:39:37 -0700 Subject: [PATCH 1013/2173] Update r-acidgenerics to 0.7.4 (#44592) --- recipes/r-acidgenerics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenerics/meta.yaml b/recipes/r-acidgenerics/meta.yaml index 2be4f16d3aa84..014d98f16539e 100644 --- a/recipes/r-acidgenerics/meta.yaml +++ b/recipes/r-acidgenerics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.3" %} +{% set version = "0.7.4" %} {% set github = "https://github.com/acidgenomics/r-acidgenerics" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: e7edbc1c56582b75f3eeb7e360cd91b04ed978e24cb68eb610264ad7845b3d42 + sha256: 495f04e3077d2bc1001d1ba1a1537936f57875791320d4d076b8e571a601a08a build: number: 0 From 06ed45b885bb4c2ea00e31dd264a6e8fb08689fc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 23:03:03 +0100 Subject: [PATCH 1014/2173] Update pbfusion to 0.4.0 (#44563) * Update pbfusion to 0.4.0 * adding pinnings --------- Co-authored-by: Matt Holt --- recipes/pbfusion/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/pbfusion/meta.yaml b/recipes/pbfusion/meta.yaml index dfefc4120c59f..8433b41fcd948 100644 --- a/recipes/pbfusion/meta.yaml +++ b/recipes/pbfusion/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbfusion" %} -{% set version = "0.3.1" %} -{% set pbfusion_sha256 = "fd27b843e0f5e53af54f25ba7e83e0d9c5753d98bd5fb65a701644993935e0fa" %} +{% set version = "0.4.0" %} +{% set pbfusion_sha256 = "bb6c37188288492dbcf5f1e9ddbc02492e86590e5a4567d6ded0d1ab9deb12ec" %} package: name: {{ name }} @@ -24,6 +24,8 @@ extra: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('pbfusion', max_pin="x") }} test: commands: From 06024678c2aa5511cb9940a5d024a0fe8185bc29 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 1 Dec 2023 23:13:30 +0100 Subject: [PATCH 1015/2173] Update elastic-blast to 1.2.0 (#44577) * Update elastic-blast to 1.2.0 --------- Co-authored-by: Thanh Lee Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Greg Boratyn --- recipes/elastic-blast/meta.yaml | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/recipes/elastic-blast/meta.yaml b/recipes/elastic-blast/meta.yaml index fecb3b03eb94d..80e44cda57f33 100644 --- a/recipes/elastic-blast/meta.yaml +++ b/recipes/elastic-blast/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.0" %} +{% set version = "1.2.0" %} package: name: elastic-blast @@ -6,24 +6,22 @@ package: source: url: https://files.pythonhosted.org/packages/source/e/elastic-blast/elastic_blast-{{ version }}.tar.gz - sha256: 2e7fe4c312e43b2990fbe3420fd8a67bf5566ea5ace6d400d3e68058038dfa81 + sha256: 584238fc79befa4e90625752eeca928db4807a0b2e0f8956d1fa9d35c61c083f build: - number: 1 + number: 0 noarch: generic script: {{ PYTHON }} -m pip install . -vv - + run_exports: + - {{ pin_subpackage("elastic-blast", max_pin="x") }} requirements: host: - pip - - python >=3.7 - - google-cloud-sdk - - awscli - - awslimitchecker + - python >=3.7,<3.10 - python-packit - importlib-metadata run: - - python >=3.7 + - python >=3.7,<3.10 - boto3 - awscli - awslimitchecker From ee45301cb43f3e6f37cc3a89b11ae15ba117bbc6 Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Fri, 1 Dec 2023 17:16:21 -0500 Subject: [PATCH 1016/2173] Campy-AGAINST: rename meta.yml to meta.yaml (#44593) * rename meta.yml to meta.yaml * name should be lower case * lowercase package name * rm campy-against, since it cannot be built (and has no package) --------- Co-authored-by: Ryan Dale --- recipes/Campy-AGAINST/meta.yml | 35 ---------------------------------- 1 file changed, 35 deletions(-) delete mode 100644 recipes/Campy-AGAINST/meta.yml diff --git a/recipes/Campy-AGAINST/meta.yml b/recipes/Campy-AGAINST/meta.yml deleted file mode 100644 index c8bb3ca21ab34..0000000000000 --- a/recipes/Campy-AGAINST/meta.yml +++ /dev/null @@ -1,35 +0,0 @@ -{% set version = "0.1.0" %} -{% set name = "Campy-AGAINST" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - url: https://github.com/LanLab/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 24c42a19498b9519ef32961709938abebaefe1a59f879e02302a61ef659096ec - -build: - noarch: python - number: 0 - script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv - run_exports: - - {{ pin_subpackage('Campy-AGAINST', max_pin="x.x") }} - -requirements: - host: - - python >=3.8 - - pip - run: - - python >=3.8 - - fastani >=1.3 - -about: - home: https://github.com/LanLab/Campy-AGAINST - license: GPL-3.0-or-later - license_file: LICENSE - summary: Accurate assignment of ANI genomic species to Campylobacter genomes. - -test: - commands: - - campyagainst --help From 51cd3b7d7da39cf73e5a81f0497c31b2b99e42aa Mon Sep 17 00:00:00 2001 From: Ilya Shlyakhter Date: Sat, 2 Dec 2023 00:39:21 -0500 Subject: [PATCH 1017/2173] Add lrsim (#44558) * WIP adding lrsim * added needed dependencies * wrote build.sh * remove whitespace * fixed pin_subpackage * added cxx build dependency * add patch * add ncurses * add ncurses patch * added missing patch * added LDFLAGS patch * added pthreads * fix copying of files * fixing tests * add cleanup * changes for perl-inline-c * remove compilers for now * added transfer of perl-inline-c compiled results * add aquaskyline * added perl to build env * fix perl location * run test at end * limit to linux; add full test * remove the heavy test at the end --- recipes/lrsim/0002-use-CXX-and-CC.patch | 167 ++++++++++++++++++++++++ recipes/lrsim/0003-use-ncurses.patch | 25 ++++ recipes/lrsim/0004-add-LDFLAGS.patch | 29 ++++ recipes/lrsim/0005-fix-perl-loc.patch | 33 +++++ recipes/lrsim/build.sh | 38 ++++++ recipes/lrsim/meta.yaml | 68 ++++++++++ 6 files changed, 360 insertions(+) create mode 100644 recipes/lrsim/0002-use-CXX-and-CC.patch create mode 100644 recipes/lrsim/0003-use-ncurses.patch create mode 100644 recipes/lrsim/0004-add-LDFLAGS.patch create mode 100644 recipes/lrsim/0005-fix-perl-loc.patch create mode 100755 recipes/lrsim/build.sh create mode 100644 recipes/lrsim/meta.yaml diff --git a/recipes/lrsim/0002-use-CXX-and-CC.patch b/recipes/lrsim/0002-use-CXX-and-CC.patch new file mode 100644 index 0000000000000..9cab56053c9b4 --- /dev/null +++ b/recipes/lrsim/0002-use-CXX-and-CC.patch @@ -0,0 +1,167 @@ +From 406353bf60a7306bc33412a2baa3325ec6a5ef45 Mon Sep 17 00:00:00 2001 +From: Ilya Shlyakhter +Date: Thu, 30 Nov 2023 15:49:26 -0500 +Subject: [PATCH 2/2] use CXX and CC + +--- + DWGSIMSrc/Makefile | 2 -- + DWGSIMSrc/samtools/Makefile | 2 -- + DWGSIMSrc/samtools/bcftools/Makefile | 2 -- + DWGSIMSrc/samtools/misc/Makefile | 4 ---- + SURVIVORSrc/Debug/makefile | 2 +- + SURVIVORSrc/Debug/src/convert/subdir.mk | 2 +- + SURVIVORSrc/Debug/src/merge_vcf/subdir.mk | 2 +- + SURVIVORSrc/Debug/src/simulator/subdir.mk | 2 +- + SURVIVORSrc/Debug/src/subdir.mk | 2 +- + SURVIVORSrc/Debug/src/vcfs/subdir.mk | 2 +- + make.sh | 4 ++-- + 11 files changed, 8 insertions(+), 18 deletions(-) + +diff --git a/DWGSIMSrc/Makefile b/DWGSIMSrc/Makefile +index 0d5b9ec..bbb7047 100644 +--- a/DWGSIMSrc/Makefile ++++ b/DWGSIMSrc/Makefile +@@ -1,6 +1,4 @@ + PACKAGE_VERSION="0.1.11" +-CC= gcc +-CFLAGS= -g -Wall -O3 #-m64 #-arch ppc + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\\\"${PACKAGE_VERSION}\\\" + DWGSIM_AOBJS = src/dwgsim_opt.o src/mut.o src/contigs.o src/regions_bed.o \ + src/mut_txt.o src/mut_bed.o src/mut_vcf.o src/mut_input.o src/dwgsim.o +diff --git a/DWGSIMSrc/samtools/Makefile b/DWGSIMSrc/samtools/Makefile +index a584c7a..37d5345 100644 +--- a/DWGSIMSrc/samtools/Makefile ++++ b/DWGSIMSrc/samtools/Makefile +@@ -4,8 +4,6 @@ + # make git-stamp + VERSION= + +-CC= gcc +-CFLAGS= -g -Wall $(VERSION) -O2 + #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 + KNETFILE_O= knetfile.o +diff --git a/DWGSIMSrc/samtools/bcftools/Makefile b/DWGSIMSrc/samtools/bcftools/Makefile +index be831de..df67d1d 100644 +--- a/DWGSIMSrc/samtools/bcftools/Makefile ++++ b/DWGSIMSrc/samtools/bcftools/Makefile +@@ -1,5 +1,3 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE + LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o + OMISC= .. +diff --git a/DWGSIMSrc/samtools/misc/Makefile b/DWGSIMSrc/samtools/misc/Makefile +index d36e7ac..388bfb7 100644 +--- a/DWGSIMSrc/samtools/misc/Makefile ++++ b/DWGSIMSrc/samtools/misc/Makefile +@@ -1,7 +1,3 @@ +-CC= gcc +-CXX= g++ +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc +-CXXFLAGS= $(CFLAGS) + DFLAGS= -D_FILE_OFFSET_BITS=64 + OBJS= + PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck +diff --git a/SURVIVORSrc/Debug/makefile b/SURVIVORSrc/Debug/makefile +index fb44537..e1fdd42 100644 +--- a/SURVIVORSrc/Debug/makefile ++++ b/SURVIVORSrc/Debug/makefile +@@ -48,7 +48,7 @@ all: SURVIVOR + SURVIVOR: $(OBJS) $(USER_OBJS) + @echo 'Building target: $@' + @echo 'Invoking: Cross G++ Linker' +- g++ -o "SURVIVOR" $(OBJS) $(USER_OBJS) $(LIBS) ++ ${CXX} ${CXXFLAGS} -o "SURVIVOR" $(OBJS) $(USER_OBJS) $(LIBS) + @echo 'Finished building target: $@' + @echo ' ' + +diff --git a/SURVIVORSrc/Debug/src/convert/subdir.mk b/SURVIVORSrc/Debug/src/convert/subdir.mk +index b4e47c9..dccb68f 100644 +--- a/SURVIVORSrc/Debug/src/convert/subdir.mk ++++ b/SURVIVORSrc/Debug/src/convert/subdir.mk +@@ -35,7 +35,7 @@ CPP_DEPS += \ + src/convert/%.o: ../src/convert/%.cpp + @echo 'Building file: $<' + @echo 'Invoking: Cross G++ Compiler' +- g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" ++ ${CXX} ${CXXFLAGS} -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" + @echo 'Finished building: $<' + @echo ' ' + +diff --git a/SURVIVORSrc/Debug/src/merge_vcf/subdir.mk b/SURVIVORSrc/Debug/src/merge_vcf/subdir.mk +index f4d793d..fd27596 100644 +--- a/SURVIVORSrc/Debug/src/merge_vcf/subdir.mk ++++ b/SURVIVORSrc/Debug/src/merge_vcf/subdir.mk +@@ -20,7 +20,7 @@ CPP_DEPS += \ + src/merge_vcf/%.o: ../src/merge_vcf/%.cpp + @echo 'Building file: $<' + @echo 'Invoking: Cross G++ Compiler' +- g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" ++ ${CXX} ${CXXFLAGS} -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" + @echo 'Finished building: $<' + @echo ' ' + +diff --git a/SURVIVORSrc/Debug/src/simulator/subdir.mk b/SURVIVORSrc/Debug/src/simulator/subdir.mk +index 8ffd9ec..7f15f88 100644 +--- a/SURVIVORSrc/Debug/src/simulator/subdir.mk ++++ b/SURVIVORSrc/Debug/src/simulator/subdir.mk +@@ -23,7 +23,7 @@ CPP_DEPS += \ + src/simulator/%.o: ../src/simulator/%.cpp + @echo 'Building file: $<' + @echo 'Invoking: Cross G++ Compiler' +- g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" ++ ${CXX} ${CXXFLAGS} -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" + @echo 'Finished building: $<' + @echo ' ' + +diff --git a/SURVIVORSrc/Debug/src/subdir.mk b/SURVIVORSrc/Debug/src/subdir.mk +index 24863c4..5a4bdf2 100644 +--- a/SURVIVORSrc/Debug/src/subdir.mk ++++ b/SURVIVORSrc/Debug/src/subdir.mk +@@ -29,7 +29,7 @@ CPP_DEPS += \ + src/%.o: ../src/%.cpp + @echo 'Building file: $<' + @echo 'Invoking: Cross G++ Compiler' +- g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" ++ ${CXX} ${CXXFLAGS} -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" + @echo 'Finished building: $<' + @echo ' ' + +diff --git a/SURVIVORSrc/Debug/src/vcfs/subdir.mk b/SURVIVORSrc/Debug/src/vcfs/subdir.mk +index 6d434f7..d76422f 100644 +--- a/SURVIVORSrc/Debug/src/vcfs/subdir.mk ++++ b/SURVIVORSrc/Debug/src/vcfs/subdir.mk +@@ -29,7 +29,7 @@ CPP_DEPS += \ + src/vcfs/%.o: ../src/vcfs/%.cpp + @echo 'Building file: $<' + @echo 'Invoking: Cross G++ Compiler' +- g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" ++ ${CXX} -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<" + @echo 'Finished building: $<' + @echo ' ' + +diff --git a/make.sh b/make.sh +index eff30bb..186da1f 100755 +--- a/make.sh ++++ b/make.sh +@@ -1,6 +1,6 @@ + set -e + +-g++ extractReads.cpp -O3 -o extractReads ++${CXX} extractReads.cpp -O3 -o extractReads + + cd DWGSIMSrc + make -j +@@ -9,7 +9,7 @@ cp -f ./samtools/samtools ../ + cd ../ + + cd msortSrc +-g++ msort.c sort_funs.c stdhashc.cc -lm -m64 -fpermissive -o msort ++${CXX} msort.c sort_funs.c stdhashc.cc -lm -m64 -fpermissive -o msort + cp -f msort ../ + cd ../ + +-- +2.43.0 + diff --git a/recipes/lrsim/0003-use-ncurses.patch b/recipes/lrsim/0003-use-ncurses.patch new file mode 100644 index 0000000000000..514d891af8edc --- /dev/null +++ b/recipes/lrsim/0003-use-ncurses.patch @@ -0,0 +1,25 @@ +From 76b05cabbfda30cfcc81f07081cc1a091127b393 Mon Sep 17 00:00:00 2001 +From: Ilya Shlyakhter +Date: Thu, 30 Nov 2023 16:34:22 -0500 +Subject: [PATCH 3/3] use ncurses + +--- + DWGSIMSrc/samtools/Makefile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/DWGSIMSrc/samtools/Makefile b/DWGSIMSrc/samtools/Makefile +index 37d5345..5143709 100644 +--- a/DWGSIMSrc/samtools/Makefile ++++ b/DWGSIMSrc/samtools/Makefile +@@ -19,7 +19,7 @@ PROG= samtools + INCLUDES= -I. + SUBDIRS= . bcftools misc + LIBPATH= +-LIBCURSES= -lcurses # -lXCurses ++LIBCURSES= -lncurses # -lXCurses + + + .SUFFIXES:.c .o +-- +2.43.0 + diff --git a/recipes/lrsim/0004-add-LDFLAGS.patch b/recipes/lrsim/0004-add-LDFLAGS.patch new file mode 100644 index 0000000000000..557fc7f2ce861 --- /dev/null +++ b/recipes/lrsim/0004-add-LDFLAGS.patch @@ -0,0 +1,29 @@ +From 3de5f1769e5fca938ef0479bf0f7a670ad737540 Mon Sep 17 00:00:00 2001 +From: Ilya Shlyakhter +Date: Thu, 30 Nov 2023 17:16:53 -0500 +Subject: [PATCH 4/4] add LDFLAGS + +--- + DWGSIMSrc/Makefile | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/DWGSIMSrc/Makefile b/DWGSIMSrc/Makefile +index bbb7047..3aea51f 100644 +--- a/DWGSIMSrc/Makefile ++++ b/DWGSIMSrc/Makefile +@@ -35,10 +35,10 @@ all:$(PROG) + .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur + + dwgsim:lib-recur $(DWGSIM_AOBJS) +- $(CC) $(CFLAGS) -o $@ $(DWGSIM_AOBJS) -lm -lz -lpthread ++ $(CC) $(CFLAGS) -o $@ $(DWGSIM_AOBJS) $(LDFLAGS) -lm -lz -lpthread + + dwgsim_eval:lib-recur $(DWGSIM_EVAL_AOBJS) +- $(CC) $(CFLAGS) -o $@ $(DWGSIM_EVAL_AOBJS) -Lsamtools -lm -lz -lpthread ++ $(CC) $(CFLAGS) -o $@ $(DWGSIM_EVAL_AOBJS) $(LDFLAGS) -Lsamtools -lm -lz -lpthread + + cleanlocal: + rm -vfr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib; \ +-- +2.43.0 + diff --git a/recipes/lrsim/0005-fix-perl-loc.patch b/recipes/lrsim/0005-fix-perl-loc.patch new file mode 100644 index 0000000000000..1450fafc8b8bb --- /dev/null +++ b/recipes/lrsim/0005-fix-perl-loc.patch @@ -0,0 +1,33 @@ +From ba85d6222226cc95ff0bbcc33d29806467e3d774 Mon Sep 17 00:00:00 2001 +From: Ilya Shlyakhter +Date: Thu, 30 Nov 2023 21:28:16 -0500 +Subject: [PATCH 5/5] fix perl loc + +--- + faFilter.pl | 2 +- + simulateLinkedReads.pl | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/faFilter.pl b/faFilter.pl +index d1faa2f..7c11208 100755 +--- a/faFilter.pl ++++ b/faFilter.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + use strict; + use warnings; +diff --git a/simulateLinkedReads.pl b/simulateLinkedReads.pl +index 302748a..bb8a0c0 100755 +--- a/simulateLinkedReads.pl ++++ b/simulateLinkedReads.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + # The MIT License (MIT) + # Copyright (c) 2016 Ruibang Luo +-- +2.43.0 + diff --git a/recipes/lrsim/build.sh b/recipes/lrsim/build.sh new file mode 100755 index 0000000000000..9d83fb7218ba2 --- /dev/null +++ b/recipes/lrsim/build.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +set -eux -o pipefail + +rm -f DWGSIMSrc/samtools/bcftools/*.[oa] +bash make.sh + +mkdir -p $PREFIX/share/lrsim +for LRSIM_PROG in simulateLinkedReads.pl dwgsim SURVIVOR msort extractReads samtools faFilter.pl +do + cp ${LRSIM_PROG} $PREFIX/share/lrsim/ + chmod u+x $PREFIX/share/lrsim/${LRSIM_PROG} +done +cp 4M-with-alts-february-2016.txt $PREFIX/share/lrsim/ +#cp simulateLinkedReads.pl_*.so $PREFIX/share/lrsim/ +#cp simulateLinkedReads.pl_*.inl $PREFIX/share/lrsim/ + +mkdir -p $PREFIX/share/lrsim/_Inline +export PERL_INLINE_DIRECTORY=$PREFIX/share/lrsim/_Inline + +mkdir -p $PREFIX/bin +echo "#! /usr/bin/env bash" >> $PREFIX/bin/lrsim +echo "set -eux -o pipefail" >> $PREFIX/bin/lrsim +echo "export PERL_INLINE_DIRECTORY=$PREFIX/share/lrsim/_Inline" +echo "perl $PREFIX/share/lrsim/simulateLinkedReads.pl \"\$@\"" >> $PREFIX/bin/lrsim +chmod +x $PREFIX/bin/lrsim + +cat $PREFIX/bin/lrsim +./lrsim || true + +# Run the test to ensure that perl-inline-c compile the C code +# snippets and stores the compiled results under $PREFIX/share/lrsim/_Inline +pushd test +bash -x test.sh +popd + +chmod -R u+w $PREFIX/share/lrsim/_Inline +bash -x clean.sh diff --git a/recipes/lrsim/meta.yaml b/recipes/lrsim/meta.yaml new file mode 100644 index 0000000000000..eb97739dad760 --- /dev/null +++ b/recipes/lrsim/meta.yaml @@ -0,0 +1,68 @@ +{% set name = "LRSIM" %} +{% set version = "1.0" %} +{% set sha256 = "89623fba2ce624da4e2c8ce8a99b1a46eb3bc03a8c38044c64f4b8a0d0d9721e" %} + +package: + name: {{ name | lower }} + version: {{ version }} + +source: + url: https://github.com/aquaskyline/{{ name }}/archive/refs/tags/{{ version }}.tar.gz + sha256: {{ sha256 }} + patches: + - 0002-use-CXX-and-CC.patch + - 0003-use-ncurses.patch + - 0004-add-LDFLAGS.patch + - 0005-fix-perl-loc.patch + +build: + number: 0 + skip: True # [not linux] + run_exports: + - {{ pin_subpackage(name | lower, max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - autoconf + - automake + - perl + - perl-inline + - perl-inline-c + - perl-math-random + host: + - gsl + - htslib + - ncurses + - perl + - perl-inline + - perl-inline-c + - perl-math-random + - pthread-stubs + - zlib + run: + - perl + - perl-inline + - perl-inline-c + - perl-math-random + +test: + commands: + - "lrsim 2>&1 | grep 'Usage'" + - "lrsim 2>&1 | grep 'simulateLinkedReads.pl'" + +about: + home: https://github.com/aquaskyline/{{ name }} + license: MIT + license_file: LICENSE + summary: "Simulator for 10X Genomics Linked Reads" + +extra: + recipe-maintainers: + - notestaff + - aquaskyline + identifiers: + - doi:10.1016/j.csbj.2017.10.002 + - doi:10.5281/zenodo.808913 From 62e47b81a9fbc59f365a198129351cc8274fc252 Mon Sep 17 00:00:00 2001 From: hjulienne Date: Sat, 2 Dec 2023 06:43:39 +0100 Subject: [PATCH 1018/2173] Jass 2.3 (#44531) * added sha256 * added dependancies * fixed dependency circle and matplotlib * fixed dependencies * fixed mgspack dependency * keep pydantic version 1 --------- Co-authored-by: hjulienn --- recipes/jass/meta.yaml | 87 +++++++++++++++++++++++++++++++++++++----- 1 file changed, 77 insertions(+), 10 deletions(-) diff --git a/recipes/jass/meta.yaml b/recipes/jass/meta.yaml index 32f687595af23..a9d420781c8d8 100644 --- a/recipes/jass/meta.yaml +++ b/recipes/jass/meta.yaml @@ -1,7 +1,7 @@ {% set name = "jass" %} -{% set version = "2.2" %} +{% set version = "2.3" %} {% set owner = "statistical-genetics" %} -{% set sha256 = "06fa6b4decf210da91f7d6eaa60e436983843203bdeb04bb40581f9464325936" %} +{% set sha256 = "799731c3de8301f610402af17ed0dfda54e6cdd18e59cd8ce16ee26d5a9b9f22" %} package: name: {{ name }} @@ -17,10 +17,12 @@ build: - jass=jass.__main__:main number: 0 script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv . + run_exports: + - {{ pin_subpackage('jass', max_pin="x.x") }} requirements: host: - - python >=3 + - python >=3.10 - setuptools - flask-smorest - aiohttp @@ -36,17 +38,82 @@ requirements: - pytest-runner - setuptools run: - - python >=3 - - flask-smorest + - python >=3.10 - aiohttp - - python-dateutil + - aiosignal + - amqp + - anyio + - apispec + - async-timeout + - attrs + - billiard + - blinker + - blosc + - celery + - certifi + - charset-normalizer + - click + - click-didyoumean + - click-plugins + - click-repl + - contourpy + - cycler + - exceptiongroup + - fastapi + - Flask + - Flask-Cors + - flask-smorest + - fonttools + - frozenlist + - h11 + - httpcore + - httptools + - httpx + - idna + - importlib-metadata + - itsdangerous + - Jinja2 + - kiwisolver + - kombu + - MarkupSafe + - marshmallow + - matplotlib-base + - msgpack-python + - multidict + - ndindex + - numexpr - numpy + - packaging - pandas - - pytables - - h5py + - Pillow + - prompt-toolkit + - py-cpuinfo + - pydantic <2.0 + - pyparsing + - python-dateutil + - python-dotenv + - pytz + - PyYAML + - requests - scipy - - matplotlib-base - - celery + - seaborn + - six + - sniffio + - starlette + - tables + - typing_extensions + - tzdata + - urllib3 + - uvicorn + - uvloop + - vine + - watchfiles + - wcwidth + - webargs + - websockets + - Werkzeug + - yarl + - zipp test: commands: From a1a803c3a8bfcbb53c114551ab8a9e53011e4f50 Mon Sep 17 00:00:00 2001 From: benzoid Date: Sat, 2 Dec 2023 05:44:40 +0000 Subject: [PATCH 1019/2173] Update Jalview to 2.11.3.2 (#44572) --- recipes/jalview/jalview.sh | 26 +++++++++++++++++++++++--- recipes/jalview/meta.yaml | 4 ++-- 2 files changed, 25 insertions(+), 5 deletions(-) diff --git a/recipes/jalview/jalview.sh b/recipes/jalview/jalview.sh index 1f35b44d829af..9ac28075bc3ce 100755 --- a/recipes/jalview/jalview.sh +++ b/recipes/jalview/jalview.sh @@ -107,8 +107,14 @@ else fi if [ "${HEADLESS}" = 1 ]; then - # this suppresses the Java icon appearing in the macOS Dock and maybe other things in other OSes - JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" ) + # not setting java.awt.headless in java invocation of running jalview due to problem with Jmol + if [ "${HELP}" = 1 ]; then + JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" ) + fi + # this suppresses the Java icon appearing in the macOS Dock + if [ "${ISMACOS}" = 1 ]; then + JVMARGS=( "${JVMARGS[@]}" "-Dapple.awt.UIElement=true" ) + fi fi JAVA=java @@ -172,8 +178,22 @@ elif command -v resize 2>&1 >/dev/null; then fi JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" ) +function quotearray() { + QUOTEDVALS="" + for VAL in "${@}"; do + if [ \! "$QUOTEDVALS" = "" ]; then + QUOTEDVALS="${QUOTEDVALS} " + fi + QUOTEDVALS="${QUOTEDVALS}\"${VAL}\"" + done + echo $QUOTEDVALS +} + +JVMARGSSTR=$(quotearray "${JVMARGS[@]}") +ARGSSTR=$(quotearray "${ARGS[@]}") + if [ "${DEBUG}" = 1 ]; then - echo Shell running: \""${JAVA}"\" \""${JVMARGS[@]}"\" -jar \""${JARPATH}"\" "${ARGS[@]}" + echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -jar \""${JARPATH}"\" ${ARGSSTR} fi "${JAVA}" "${JVMARGS[@]}" -jar "${JARPATH}" "${ARGS[@]}" diff --git a/recipes/jalview/meta.yaml b/recipes/jalview/meta.yaml index 5701dd1f676e1..c31c03b7edb7b 100644 --- a/recipes/jalview/meta.yaml +++ b/recipes/jalview/meta.yaml @@ -1,5 +1,5 @@ {% set name = "jalview" %} -{% set version = "2.11.3.1" %} +{% set version = "2.11.3.2" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ build: source: url: https://www.jalview.org/source/jalview_{{ version|replace(".", "_") }}.tar.gz - sha256: "d70338e1f8f0aca01c26484c1cbc9693067b3858c326c1de360a24a0fe5c7078" + sha256: "c6dfa17b70695939b66d1036f94bcf030b4db7031037cc91e1e0e5494f10001c" requirements: build: From 356ccd0e16ea16d54696e4a00594d218ca89eba5 Mon Sep 17 00:00:00 2001 From: John Harting Date: Fri, 1 Dec 2023 22:11:45 -0800 Subject: [PATCH 1020/2173] Add hifihla recipe (#44595) * initial creation of hifihla recipe * fix run_exports --- recipes/hifihla/build.sh | 5 +++++ recipes/hifihla/meta.yaml | 30 ++++++++++++++++++++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 recipes/hifihla/build.sh create mode 100644 recipes/hifihla/meta.yaml diff --git a/recipes/hifihla/build.sh b/recipes/hifihla/build.sh new file mode 100644 index 0000000000000..0f329aac0ed0b --- /dev/null +++ b/recipes/hifihla/build.sh @@ -0,0 +1,5 @@ +#!/usr/bin/env bash + +mkdir -p "${PREFIX}"/bin +cp hifihla "${PREFIX}"/bin/ +chmod +x "${PREFIX}"/bin/hifihla diff --git a/recipes/hifihla/meta.yaml b/recipes/hifihla/meta.yaml new file mode 100644 index 0000000000000..c0eedd01c0050 --- /dev/null +++ b/recipes/hifihla/meta.yaml @@ -0,0 +1,30 @@ +{% set name = "hifihla" %} +{% set version = "0.2.2" %} +{% set hifihla_sha256 = "3de4f6166f7a253571a6feeeed17fc38a53f274881757c883204c7c3963de5cc" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + - url: https://github.com/PacificBiosciences/hifihla/releases/download/v{{ version }}/hifihla + sha256: {{ hifihla_sha256 }} + +about: + home: https://github.com/PacificBiosciences/hifihla + license: BSD-3-Clause-Clear + summary: An HLA star-calling tool for PacBio HiFi data types + +extra: + recipe-maintainers: + - jrharting + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('hifihla', max_pin="x") }} + +test: + commands: + - hifihla -h From 8a62c3ab9858a622e8ad06946a84032fc9a63fd5 Mon Sep 17 00:00:00 2001 From: Moray Smith <65286772+SwiftSeal@users.noreply.github.com> Date: Sat, 2 Dec 2023 06:16:10 +0000 Subject: [PATCH 1021/2173] Add Resistify (#44498) * add resistify * pin * tests to test * update name field * fix name --- recipes/resistify/meta.yaml | 42 +++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 recipes/resistify/meta.yaml diff --git a/recipes/resistify/meta.yaml b/recipes/resistify/meta.yaml new file mode 100644 index 0000000000000..ad45a542f97be --- /dev/null +++ b/recipes/resistify/meta.yaml @@ -0,0 +1,42 @@ +{% set name = "resistify" %} +{% set version = "0.1.0" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 4fb7a11d524bf740c0832368ca8f5724e29e94f945b81c50062f85c6c719612e + +build: + noarch: python + number: 0 + entry_points: + - resistify = resistify.main:main + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - pip + - python >=3.9 + - hatchling + run: + - python >=3.9 + - scikit-learn ==0.24.2 + - biopython + - numpy + - hmmer + +test: + imports: + - resistify + commands: + - resistify --help + +about: + home: https://github.com/swiftseal/resistify + license: MIT + summary: A resistance gene annotation tool From efa26eb131d3d1195d99b0344c82634b5b4e2229 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 07:18:55 +0100 Subject: [PATCH 1022/2173] Update bioconda-utils to 2.11.0 (#44598) --- recipes/bioconda-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index 709431ae41c1f..e106e87104a89 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.10.0" %} -{% set sha256 = "06c0560de53105c08b1ac2fad15c828980002ba3b5a19ca61fd2520227fe614b" %} +{% set version = "2.11.0" %} +{% set sha256 = "d30e9e0fff49d36f7e480672468e4355a2bf77bc82c9fbaa539edc0c9ac6def0" %} package: name: bioconda-utils From 01eae18c7a93f1e604fa7c5f7b36057e04a062d0 Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Fri, 1 Dec 2023 22:20:26 -0800 Subject: [PATCH 1023/2173] Update AmpliconSuite to version 1.1.1 (#44597) * Add ampliconsuite * Fix ampliconsuite meta.yaml Fix ampliconsuite meta.yaml Fix ampliconsuite meta.yaml add "noarch: python" * Fix ampliconsuite meta.yaml * adjust recipe based on reviewer feedback * bugfix for ampliconarchitectlib src pathing * bump ampsuite version * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml include python in host section of requirements * Update meta.yaml * Update meta.yaml * Update build.sh expose amplicon_classifier.py and feature_similarity.py * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml add run_exports * Update meta.yaml typo * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml --- recipes/ampliconsuite/build.sh | 1 + recipes/ampliconsuite/meta.yaml | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/ampliconsuite/build.sh b/recipes/ampliconsuite/build.sh index cf34795dc10cd..c2e5e3f353cc0 100644 --- a/recipes/ampliconsuite/build.sh +++ b/recipes/ampliconsuite/build.sh @@ -18,6 +18,7 @@ cp GroupedAnalysisAmpSuite.py ${PREFIX}/bin/GroupedAnalysisAmpSuite.py cp amplicon_classifier.py ${PREFIX}/bin/amplicon_classifier.py cp feature_similarity.py ${PREFIX}/bin/feature_similarity.py cp make_results_table.py ${PREFIX}/bin/make_results_table.py +cp make_input.sh ${PREFIX}/bin/make_input.sh # Python command to install the package. $PYTHON setup.py install --install-data aa_data_repo/ --single-version-externally-managed --record=record.txt diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml index e7a4ba1f85188..844ce741edb94 100644 --- a/recipes/ampliconsuite/meta.yaml +++ b/recipes/ampliconsuite/meta.yaml @@ -1,5 +1,5 @@ {% set name="ampliconsuite" %} -{% set AS_version="1.1.0" %} +{% set AS_version="1.1.1" %} {% set AA_version="1.3.r6" %} {% set AC_version="1.0.0" %} @@ -11,7 +11,7 @@ source: # the sha256 sum is generated by doing # $ wget -O- [URL] | shasum -a 256 - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz - sha256: 9fd2d0f5bbdc0c60dd60ec38cef7cac1fd2253ce9b644360dbdefadd2c8af29b + sha256: 0a874698ae3468d6ca02c3a3e1542d945e9940c703cf24c409eeb6e70e3bf3a7 - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz sha256: cc21a52d9853cd5e0b5b9374773a6ea24191241b9b9cf1d71e2a928ab3d97f01 folder: ampliconarchitectlib From ec6ed4c5665a85a6d781002f72b64054e66d29b3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 10:47:21 +0100 Subject: [PATCH 1024/2173] Update last to 1518 (#44602) --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index cef8036ec945b..92ee402755a58 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1517" %} +{% set version = "1518" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: 318e1e3f9e56c906678951f300e559f8765ac29a45ba280b96106e5407a93e63 + sha256: 9b41bd90a786a4538ca79d0f4b03cfb353423e929ae537f6d953c57e11b8dd04 build: number: 0 From a07ada445ec09c7ba608d47c62182dc2ae0ca03c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 12:18:19 +0100 Subject: [PATCH 1025/2173] Update ont-modkit to 0.2.3 (#44601) --- recipes/ont-modkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml index b9c9b8d249964..f7e04c144049a 100644 --- a/recipes/ont-modkit/meta.yaml +++ b/recipes/ont-modkit/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.2" %} -{% set sha256 = "3271c54a34d2b9a413169079ed357ead056b60c54a3ade1dcac71350899555ac" %} +{% set version = "0.2.3" %} +{% set sha256 = "24f53d3725a5d54524c80698cbae017b7ff9f4158507ac8052e273cac0d22373" %} package: name: ont-modkit From e2d91ae78c0b3705ce67949bc574bed35330763e Mon Sep 17 00:00:00 2001 From: Bhavya Papudeshi Date: Sat, 2 Dec 2023 23:53:32 +1030 Subject: [PATCH 1026/2173] Update sphae to v1.3.1b (#44603) * add sphae v1.3.1 * update meta.yml * update sphae meta.yaml * update sphae meta.yaml * update sphae meta.yaml sphae version * update sphae meta.yaml sphae version --- recipes/sphae/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/sphae/meta.yaml b/recipes/sphae/meta.yaml index 8f7644ac4bdf5..8942e6a5f5937 100644 --- a/recipes/sphae/meta.yaml +++ b/recipes/sphae/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sphae" %} -{% set version = "1.3.1" %} +{% set version = "1.3.1b" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/linsalrob/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 996a9203c7411422c28860709714f58c4fa3a819738e6a85b92de804c1f81871 + sha256: ffdb5ae19858f8c7642d580c156cd3da9bb97731e90f2eb9549d34c4a788d754 build: number: 0 @@ -28,7 +28,7 @@ requirements: - pyyaml >=6.0 - click >=8.1.3 - jinja2 >=3.0.2 - - mamba <1.4.2 + - mamba <1.5.3 - metasnek >=0.0.4 - snaketool-utils >=0.0.4 - attrmap >=0.0.7 @@ -44,8 +44,8 @@ about: license: MIT license_family: MIT license_file: LICENSE - summary: "Sphae: Assembling and annotating pure culture phages from both Illumina and Nanopore sequencing technology" - description: "Phage toolkit" + summary: "Phage toolkit" + description: "Assembling and annotating pure culture phages from both Illumina and Nanopore sequencing technology" doc_url: "https://github.com/linsalrob/sphae" dev_url: "https://github.com/linsalrob/sphae" From 212019d6c30518dc2d82aacbfd7b958eff230213 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 14:24:00 +0100 Subject: [PATCH 1027/2173] Update dxpy to 0.366.0 (#44586) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index ce62cf169e98b..7c42041c642d4 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.365.0" %} +{% set version = "0.366.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 234efe289c71da5069cb7e42f569c9dbff922e270267365d8b36798fd541240c + sha256: 4f00cc2611d8def8ffc0a996a53e8019fcdc658f827ea9cf56999be7d334ed32 build: number: 0 From 545a30929d2dc343a11d0dfc285907d5e7b986e4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 14:24:24 +0100 Subject: [PATCH 1028/2173] Update sequali to 0.4.1 (#44587) --- recipes/sequali/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index 425992252db9a..8aeec56e9acfe 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sequali" %} -{% set version = "0.4.0" %} +{% set version = "0.4.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: dc4dd32f652250ff4d2c783f0eb6f99072b9ed14df669e319fa2fa6ab12a558b + sha256: cc62e1641d85fc14eaa70418f0e32cac2b0639374d8b1eba9e9d95388daab369 build: number: 0 From 9d20f6e8a8857cb108f18c8a1ef3afc7b968c270 Mon Sep 17 00:00:00 2001 From: Tatsumi Mizubayashi <112037683+TatsumiMizubayashi@users.noreply.github.com> Date: Sat, 2 Dec 2023 22:25:38 +0900 Subject: [PATCH 1029/2173] Add poly-qtlseq (#44488) * Add poly-qtlseq * Update meta.yaml * Update meta.yaml. Add run_exports --- recipes/poly-qtlseq/build.sh | 12 ++++++++++ recipes/poly-qtlseq/meta.yaml | 37 +++++++++++++++++++++++++++++++ recipes/poly-qtlseq/polyQtlseq.sh | 6 +++++ 3 files changed, 55 insertions(+) create mode 100644 recipes/poly-qtlseq/build.sh create mode 100644 recipes/poly-qtlseq/meta.yaml create mode 100644 recipes/poly-qtlseq/polyQtlseq.sh diff --git a/recipes/poly-qtlseq/build.sh b/recipes/poly-qtlseq/build.sh new file mode 100644 index 0000000000000..249f40c8f7515 --- /dev/null +++ b/recipes/poly-qtlseq/build.sh @@ -0,0 +1,12 @@ +#!/usr/bin/env bash + +BINARY_HOME=$PREFIX/bin +PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM + +mkdir -p $BINARY_HOME +mkdir -p $PACKAGE_HOME + +cp -r $SRC_DIR/* $PACKAGE_HOME +cp $RECIPE_DIR/polyQtlseq.sh $PACKAGE_HOME/polyQtlseq.sh +chmod +x $PACKAGE_HOME/polyQtlseq.sh +ln -s $PACKAGE_HOME/polyQtlseq.sh $BINARY_HOME/polyQtlseq diff --git a/recipes/poly-qtlseq/meta.yaml b/recipes/poly-qtlseq/meta.yaml new file mode 100644 index 0000000000000..b08bcc23379d1 --- /dev/null +++ b/recipes/poly-qtlseq/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "polyQtlseq" %} +{% set version = "1.0.0" %} +{% set sha256 = "800b669bdd89c89d2cc2218f842b419ff5aac29747b8f1dfd32ecba5f961543e" %} + +package: + name: poly-qtlseq + version: {{ version }} + +source: + url: https://github.com/TatsumiMizubayashi/PolyploidQtlSeq/releases/download/v1.0.0/polyQtlseq-1.0.0.zip + sha256: {{ sha256 }} + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('poly-qtlseq', max_pin="x") }} + +requirements: + build: + run: + - dotnet-runtime >=6,<7 + - fastp >=0.23 + - bwa + - bcftools >=1.16 + - samtools >=1.16 + - snpeff + +test: + commands: + - polyQtlseq -h + +about: + home: https://github.com/TatsumiMizubayashi/PolyploidQtlSeq + license: MIT License + summary: PolyploidQtlSeq is a program that extends QTL-seq for polyploid F1 populations. + diff --git a/recipes/poly-qtlseq/polyQtlseq.sh b/recipes/poly-qtlseq/polyQtlseq.sh new file mode 100644 index 0000000000000..0b6d6ada0abdf --- /dev/null +++ b/recipes/poly-qtlseq/polyQtlseq.sh @@ -0,0 +1,6 @@ +#!/usr/bin/env bash + +SCRIPT_PATH=$(readlink -f $0) +SCRIPT_DIR=$(dirname $SCRIPT_PATH) + +dotnet $SCRIPT_DIR/PolyploidQtlSeq.dll $@ From 30b5060d81dcc9d49044493bbd03d1ed8e1285d4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 17:31:00 +0100 Subject: [PATCH 1030/2173] Update varvamp to 1.0 (#44583) --- recipes/varvamp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varvamp/meta.yaml b/recipes/varvamp/meta.yaml index 9d6ea2b324986..62528f05909fb 100644 --- a/recipes/varvamp/meta.yaml +++ b/recipes/varvamp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varvamp" %} -{% set version = "0.9.5" %} +{% set version = "1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/varvamp-{{ version }}.tar.gz - sha256: 9d6d0d5dc6095aab8920089fd730595ec33bdd43a7de6309bdce84e7870dca4b + sha256: 6cc45e06b19f3e74c70dc6df3fee6db6a02ed1d967f9cb286dfb00eeb1f72ab8 build: entry_points: From c15e6395dc7ec1b2b5c5d9ea617d49590656624f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 17:32:37 +0100 Subject: [PATCH 1031/2173] Update dnaapler to 0.5.0 (#44606) --- recipes/dnaapler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnaapler/meta.yaml b/recipes/dnaapler/meta.yaml index 029be166a23d9..e483b65cb9b96 100644 --- a/recipes/dnaapler/meta.yaml +++ b/recipes/dnaapler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dnaapler" %} -{% set version = "0.4.0" %} +{% set version = "0.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: d6940a0fda068d67ee8c45353761188544b5504b6a7642d87775476d51918d9b + sha256: 19bc7c140b9047be5a094ad65c71f042b438cc1bb1a9c03a2c11ea8b54c3d506 build: number: 0 From 71163abcf096a534cc2cd638097d512efdeba1d9 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sat, 2 Dec 2023 17:40:30 +0100 Subject: [PATCH 1032/2173] Update nextstrain-cli recipe (not version) (#44590) Remove skip lint now that bug is fixed Remove Python 3.6 and 3.7 specific run requirements as bioconda no longer supports them (https://github.com/bioconda/bioconda-utils/pull/878) Raise host requirement to 3.8 and above Python 3.7 can no longer be installed, see: ``` micromamba create -n py37 -c conda-forge -c bioconda nextstrain-cli python=3.7 ``` which errors --- recipes/nextstrain-cli/meta.yaml | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml index fbd4f02908b8b..cdd7f714d9895 100644 --- a/recipes/nextstrain-cli/meta.yaml +++ b/recipes/nextstrain-cli/meta.yaml @@ -9,7 +9,7 @@ source: sha256: bc678d817dac6351466728122dff1ce37d7e8f3f8b8402fd2cef5822287b7de4 build: - number: 0 + number: 1 noarch: python entry_points: - nextstrain = nextstrain.cli.__main__:main @@ -19,15 +19,13 @@ build: requirements: host: - - python >=3.6 + - python >=3.8 - pip run: - - python >=3.6 - - dataclasses # [py<37] + - python >=3.8 - docutils - fasteners - - importlib_metadata # [py<38] - importlib_resources >=5.3.0 # [py<311] - packaging >=3.0.0 - pyjwt >=2.0.0 @@ -73,6 +71,3 @@ extra: recipe-maintainers: - tsibley - corneliusroemer - skip-lints: - # False positive, can be removed once bioconda/bioconda-utils#919 is merged - - version_constraints_missing_whitespace From 5264cfe6c9283a0ff69b87804f59e3920c0802fa Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sat, 2 Dec 2023 17:46:31 +0100 Subject: [PATCH 1033/2173] Update: add nextclade2 symlink to nextclade (#44588) * Add nextclade2 binary symlinked to nextclade * Correct pin --- recipes/nextclade/build.sh | 5 +++++ recipes/nextclade/meta.yaml | 4 +++- recipes/nextclade/run_test.sh | 25 +++++++++++++++++-------- 3 files changed, 25 insertions(+), 9 deletions(-) diff --git a/recipes/nextclade/build.sh b/recipes/nextclade/build.sh index 2de4b8e90b81a..8af0b63eb3b7c 100644 --- a/recipes/nextclade/build.sh +++ b/recipes/nextclade/build.sh @@ -4,3 +4,8 @@ ls "${SRC_DIR}" chmod +x "${SRC_DIR}"/nextclade* mkdir -p "${PREFIX}/bin" mv "${SRC_DIR}"/nextclade* "${PREFIX}"/bin/nextclade + +# Allow nextclade to be called as nextclade$MAJOR_VERSION +# $PKG_VERSION is in the form of MAJOR.MINOR.PATCH +MAJOR_VERSION=$(echo "$PKG_VERSION" | cut -d. -f1) +ln -s "${PREFIX}"/bin/nextclade "${PREFIX}"/bin/nextclade"$MAJOR_VERSION" \ No newline at end of file diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index e0240b83896cb..9b1edcb0d60bf 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -14,8 +14,10 @@ source: sha256: aaac669618d953381428eac3674fe6cb22bef66e7c1ae55552f6a1567f3d3030 # [arm64] build: - number: 1 + number: 2 binary_relocation: False + run_exports: + - {{ pin_compatible(name, max_pin='x') }} requirements: diff --git a/recipes/nextclade/run_test.sh b/recipes/nextclade/run_test.sh index fab365bd0ad62..7fe8383073ee4 100644 --- a/recipes/nextclade/run_test.sh +++ b/recipes/nextclade/run_test.sh @@ -3,11 +3,20 @@ set -x set -e -nextclade dataset get --name 'sars-cov-2' --output-dir 'data/sars-cov-2' - -nextclade run \ ---input-dataset 'data/sars-cov-2' \ -'data/sars-cov-2/sequences.fasta' \ ---output-tsv 'output/nextclade.tsv' \ ---output-tree 'output/tree.json' \ ---output-all 'output/' +MAJOR_VERSION=$(echo "$PKG_VERSION" | cut -d. -f1) + +for BIN in nextclade nextclade$MAJOR_VERSION; do + "$BIN" --version + + "$BIN" dataset get --name 'sars-cov-2' --output-dir 'data/sars-cov-2' + + "$BIN" run \ + --input-dataset 'data/sars-cov-2' \ + 'data/sars-cov-2/sequences.fasta' \ + --output-tsv 'output/nextclade.tsv' \ + --output-tree 'output/tree.json' \ + --output-all 'output/' + + rm -rf data output + +done From 1dd9592f93f1a917c046b44578e8f8287a5ecc65 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 17:47:47 +0100 Subject: [PATCH 1034/2173] Update psims to 1.3.2 (#44609) --- recipes/psims/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psims/meta.yaml b/recipes/psims/meta.yaml index b3012cb90ed31..92f026d771450 100644 --- a/recipes/psims/meta.yaml +++ b/recipes/psims/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.3.1" %} -{% set sha256 = "a6da07168737bdae3fdf0ee9e422be86990e004081c27027d50acecb3be8c248" %} +{% set version = "1.3.2" %} +{% set sha256 = "53efaa9cbd8ae8eec263f39d69e4fcd02cbf2f25b359badf7c38e81fa812a273" %} package: name: "psims" From e7e240dcaa345c53bfed45095f2788880e00bc57 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 18:02:25 +0100 Subject: [PATCH 1035/2173] Update rbpbench to 0.7 (#44608) --- recipes/rbpbench/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/rbpbench/meta.yaml b/recipes/rbpbench/meta.yaml index 7f1e4b8fdb0e6..e41251f1110c9 100644 --- a/recipes/rbpbench/meta.yaml +++ b/recipes/rbpbench/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RBPBench" %} -{% set version = "0.6" %} -{% set sha256 = "67f9c8f0bfa53e4602d9083c43beab1edb63e6b0e8619a0ac3cde8c01b29cb0d" %} +{% set version = "0.7" %} +{% set sha256 = "227846d23b4ee3b52da6069ae18d1265d337d7fca460eb768e9e5087d5431f15" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: "{{ sha256 }}" build: - number: 1 + number: 0 noarch: python script: $PYTHON -m pip install . --ignore-installed --no-deps -vv run_exports: From 9ce5bd4ef7483fa009974b0c425881d0e9c2281c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 16:18:02 -0500 Subject: [PATCH 1036/2173] Update perl-math-bigint to 2.002000 (#44604) --- recipes/perl-math-bigint/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-math-bigint/meta.yaml b/recipes/perl-math-bigint/meta.yaml index f9e6c046f450d..40db7208bbadc 100644 --- a/recipes/perl-math-bigint/meta.yaml +++ b/recipes/perl-math-bigint/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-math-bigint" %} -{% set version = "2.001001" %} -{% set sha256 = "d9ce4697c40ac59f4b6fc3a474a69aa40f9e7ccc35eb7053d8d9aa69ac2fa9ba" %} +{% set version = "2.002000" %} +{% set sha256 = "517c3f36adeb0669a8dfb76b0ac812eedf785e1635e890ee184b2a1c5517fb8d" %} package: name: {{ name }} From 33596dbee08beaa23fdd2e64c6dc7960a210e85f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 17:08:29 -0500 Subject: [PATCH 1037/2173] Update tissuumaps to 3.2.0.1 (#44605) --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index 8763cabd920d0..48a2ffb917bd6 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2" %} +{% set version = "3.2.0.1" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: 82ecde593a748ac7e0a438d6322e026405b6a758dbdcb83b1fc81d2c7b13a1e2 + sha256: 5f4db54ba8bb63e92f556d3a4802a6ba949692350189439c87aa8bcca6a61a4e build: number: 0 From e9f84f0502222572e4dd1a4c1d1b657499964906 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sun, 3 Dec 2023 02:08:00 +0100 Subject: [PATCH 1038/2173] Add nextclade2 to allow nextclade 3 and nextclade 2 to exist in same environment (#44589) * Add nextclade2 to allow nextclade 3 and nextclade 2 to exist in same environment * fix: download path --- recipes/nextclade2/build.sh | 6 +++++ recipes/nextclade2/meta.yaml | 41 ++++++++++++++++++++++++++++++++++ recipes/nextclade2/run_test.sh | 17 ++++++++++++++ 3 files changed, 64 insertions(+) create mode 100644 recipes/nextclade2/build.sh create mode 100644 recipes/nextclade2/meta.yaml create mode 100644 recipes/nextclade2/run_test.sh diff --git a/recipes/nextclade2/build.sh b/recipes/nextclade2/build.sh new file mode 100644 index 0000000000000..53cd234503763 --- /dev/null +++ b/recipes/nextclade2/build.sh @@ -0,0 +1,6 @@ +#!/usr/bin/env bash + +ls "${SRC_DIR}" +chmod +x "${SRC_DIR}"/nextclade* +mkdir -p "${PREFIX}/bin" +mv "${SRC_DIR}"/nextclade* "${PREFIX}"/bin/nextclade2 diff --git a/recipes/nextclade2/meta.yaml b/recipes/nextclade2/meta.yaml new file mode 100644 index 0000000000000..6c32c4579b5ae --- /dev/null +++ b/recipes/nextclade2/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "nextclade2" %} +{% set version = "2.14.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/nextclade-x86_64-unknown-linux-gnu # [linux64] + sha256: 1a9a82655830243ffd01937ebb895744ff46ec49f725ef6feff9a3f0e37d90d1 # [linux64] + - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/nextclade-x86_64-apple-darwin # [osx and x86_64] + sha256: 432f56d2152edda49b8c4a2c3f81d9a5da7419a6cc7c4a3d5205d17d5f834cf6 # [osx and x86_64] + - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/nextclade-aarch64-apple-darwin # [arm64] + sha256: aaac669618d953381428eac3674fe6cb22bef66e7c1ae55552f6a1567f3d3030 # [arm64] + +build: + number: 0 + binary_relocation: False + run_exports: + - {{ pin_compatible(name, max_pin='x') }} + +requirements: + +test: + commands: + - nextclade2 --help + +about: + home: https://github.com/nextstrain/nextclade + license: MIT + license_family: MIT + summary: "Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement" + doc_url: https://docs.nextstrain.org/projects/nextclade/en/stable/ + dev_url: https://github.com/nextstrain/nextclade + +extra: + recipe-maintainers: + - corneliusroemer + skip-lints: + # repackaged binary + - should_be_noarch_generic diff --git a/recipes/nextclade2/run_test.sh b/recipes/nextclade2/run_test.sh new file mode 100644 index 0000000000000..62e0808d80930 --- /dev/null +++ b/recipes/nextclade2/run_test.sh @@ -0,0 +1,17 @@ +#!/usr/bin/env bash + +set -x +set -e + +nextclade2 --version + +nextclade2 dataset get --name 'sars-cov-2' --output-dir 'data/sars-cov-2' + +nextclade2 run \ +--input-dataset 'data/sars-cov-2' \ +'data/sars-cov-2/sequences.fasta' \ +--output-tsv 'output/nextclade.tsv' \ +--output-tree 'output/tree.json' \ +--output-all 'output/' + +rm -rf data output From f7abd818f4108679e7c8287e18735b6ff798a7e8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 2 Dec 2023 21:09:43 -0500 Subject: [PATCH 1039/2173] Update zol to 1.3.16 (#44613) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index c290db062ef25..c1af50a0bcea9 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.15" %} +{% set version = "1.3.16" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: a745b5e02fd5cb7516b284622fab8181c70b56f4067ddce7ff282b66a2799e79 + sha256: 1b881771eac51bfcf0b58ea13b090514e3f0ed1e1d4d0a252709881ffc46730f build: number: 0 From 8e5da8672676463396b7623b34561e2855f1d17c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 3 Dec 2023 04:00:55 -0500 Subject: [PATCH 1040/2173] Update r-biomartr to 1.0.7 (#44611) --- recipes/r-biomartr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-biomartr/meta.yaml b/recipes/r-biomartr/meta.yaml index 8f656c787839f..350413e5b3959 100644 --- a/recipes/r-biomartr/meta.yaml +++ b/recipes/r-biomartr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.0.6' %} +{% set version = '1.0.7' %} package: name: r-biomartr @@ -8,7 +8,7 @@ source: url: - {{ cran_mirror }}/src/contrib/biomartr_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/biomartr/biomartr_{{ version }}.tar.gz - sha256: 35fe0d6090a71c68df989932cb98cffd321f0f73e880966e47856bcd84468d1b + sha256: 9d1d5c51b61ee67ce7ca18afdb0a136ef5709d92d077d80163f9d52ee6c28645 build: noarch: generic From dad2c6ced0f7ac222a66e83313a25fbe440dbc6d Mon Sep 17 00:00:00 2001 From: Julian Uszkoreit Date: Sun, 3 Dec 2023 10:02:56 +0100 Subject: [PATCH 1041/2173] Update PIA - make build and wrapper update save (#44582) * initial commit for PIA recipe * adding run_exports * edit license * making pia recipe update save * Update recipes/pia/meta.yaml Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --------- Co-authored-by: Julian Uszkoreit Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Robert A. Petit III --- recipes/pia/build.sh | 3 +++ recipes/pia/meta.yaml | 6 +++--- recipes/pia/pia.sh | 2 +- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/pia/build.sh b/recipes/pia/build.sh index 028f72640e218..1414b0b5646e7 100644 --- a/recipes/pia/build.sh +++ b/recipes/pia/build.sh @@ -5,6 +5,9 @@ outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $outdir mkdir -p $PREFIX/bin cp -R * $outdir/ + +ln -s $outdir/pia-$PKG_VERSION.jar $outdir/pia.jar + cp $RECIPE_DIR/pia.sh $outdir/pia ln -s $outdir/pia $PREFIX/bin chmod 0755 "${PREFIX}/bin/pia" diff --git a/recipes/pia/meta.yaml b/recipes/pia/meta.yaml index 7c280d8360500..f9a15a29de112 100644 --- a/recipes/pia/meta.yaml +++ b/recipes/pia/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pia" %} -{% set version = "1.4.8" %} -{% set sha256 = "2eb9b17dc2834ceb1264edbf2825a8d97af0867b057d53751dabf13a5aa302d4" %} +{% set version = "1.4.9" %} +{% set sha256 = "9759c0c5d7a6bbd310d67e35043a3d87106e05be2102ca6159ea3c7eea645fad" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ build: - {{ pin_subpackage('pia', max_pin="x") }} source: - url: https://github.com/medbioinf/pia/releases/download/1.4.8/pia-1.4.8.zip + url: https://github.com/medbioinf/pia/releases/download/{{ version }}/pia-{{ version }}.zip sha256: {{ sha256 }} requirements: diff --git a/recipes/pia/pia.sh b/recipes/pia/pia.sh index 2adef565a148f..dfee7ec12a982 100644 --- a/recipes/pia/pia.sh +++ b/recipes/pia/pia.sh @@ -2,7 +2,7 @@ # Wraps pia.jar set -o pipefail -jar_file="pia-1.4.8.jar" +jar_file="pia.jar" # Find original directory of bash script, resovling symlinks # http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 From ab66e13b56656cae19b3537192023aafe4d1db77 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 3 Dec 2023 08:58:21 -0500 Subject: [PATCH 1042/2173] Update pybiolib to 1.1.1571 (#44612) * Update pybiolib to 1.1.1569 * Update pybiolib to 1.1.1571 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 23d11edf7c44b..b40ea91070407 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1566" %} +{% set version = "1.1.1571" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: d7ffb727f4b33a997fce3ca8be6bb5701b662110b3385756a6b17b2b68a07d7f + sha256: bec8cc60aa02c934f0a3a40ed8831cc2708ab507504788d77345069436a7de89 build: noarch: python From 5f39e9fb55f9bd7514faf38814bf718f02a14aa4 Mon Sep 17 00:00:00 2001 From: AlexTate <0xalextate@gmail.com> Date: Sun, 3 Dec 2023 07:22:01 -0800 Subject: [PATCH 1043/2173] Add ShortSeq (#44600) * Adding ShortSeq recipe * Adding run_exports entry --- recipes/shortseq/meta.yaml | 44 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 recipes/shortseq/meta.yaml diff --git a/recipes/shortseq/meta.yaml b/recipes/shortseq/meta.yaml new file mode 100644 index 0000000000000..5a2f1a7355ad6 --- /dev/null +++ b/recipes/shortseq/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "0.0.1" %} +{% set sha256 = "99fa125603dbf5f55d80c0e42430e6a79b535ec40de51905b4b4117897022dd4" %} + +package: + name: shortseq + version: {{ version }} + +source: + url: https://github.com/AlexTate/ShortSeq/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + skip: True # [not unix] + number: 0 + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('shortseq', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('cxx') }} + host: + - python 3.10.* + - setuptools + - cython + - numpy + run: + - python 3.10.* + +test: + imports: + - ShortSeq + - numpy + commands: + - python -m unittest ShortSeq.tests.unit_tests_main + +about: + home: https://github.com/AlexTate/ShortSeq + license: MIT + summary: \ + ShortSeqs are compact and efficient Python objects that hold short sequences + while using up to 73% less memory compared to built-in types. They have a + pre-computed hash value, can be compared for equality, and are + easily converted back to the original sequence string. From 3baec72de33fb8ef65044187b67e326652933434 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 3 Dec 2023 18:50:00 -0500 Subject: [PATCH 1044/2173] Update oakvar to 2.9.69 (#44614) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 5f8944a58a27b..6f044b414760b 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.68" %} -{% set sha256 = "df2a1ceead63c001bccfdac097c50209bd1ceca913d792fcc5cc689ecaba452c" %} +{% set version = "2.9.69" %} +{% set sha256 = "7e6f8dd20c236c40f39db5017ba503498ad5309528a47ad918c9e8db4a154eb6" %} package: name: {{ name|lower }} From 6706898669c06589bf5ac8d59c12f45ed32c76fb Mon Sep 17 00:00:00 2001 From: Ilya Shlyakhter Date: Sun, 3 Dec 2023 20:12:39 -0500 Subject: [PATCH 1045/2173] Added insilicoSV (#44594) * Added insilicoSV * add run_exports and use matplotlib-base * add python dependency in host --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/insilicosv/meta.yaml | 55 ++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 recipes/insilicosv/meta.yaml diff --git a/recipes/insilicosv/meta.yaml b/recipes/insilicosv/meta.yaml new file mode 100644 index 0000000000000..a94d415129ccd --- /dev/null +++ b/recipes/insilicosv/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "insilicosv" %} +{% set version = "0.0.4" %} +{% set sha256 = "2e12d42d43d6bb50c2f7b987d52717d9dbc1cba0b1959fde2dc28fcb8a6e6525" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: "{{ sha256 }}" + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + noarch: python + entry_points: + - insilicosv=insilicosv.simulate:run_insilicosv + script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + +requirements: + host: + - pip + - python =>3.8 + run: + - cycler + - kiwisolver + - matplotlib-base + - numpy + - pillow + - pyparsing + - pysam + - python >=3.8 + - python-dateutil + - pyyaml + - six + +test: + imports: + - insilicosv + commands: + - insilicosv --help + +about: + home: "https://github.com/PopicLab/insilicoSV" + license: MIT + license_family: MIT + summary: "Simulator for complex structural variants" + +extra: + recipe-maintainers: + - notestaff + - crohlicek + - viq854 From c3f9328755c946b0285b30a1b67846aa80d30dfb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 3 Dec 2023 20:12:59 -0500 Subject: [PATCH 1046/2173] Update fastlin to 0.2.2.1 (#44573) * Update fastlin to 0.2.2 * Update fastlin to 0.2.2.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fastlin/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/fastlin/meta.yaml b/recipes/fastlin/meta.yaml index 98070f5a6218e..adfd8a2ba286c 100644 --- a/recipes/fastlin/meta.yaml +++ b/recipes/fastlin/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fastlin" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2.1" %} package: name: {{ name|lower}} @@ -7,11 +7,13 @@ package: source: url: https://github.com/rderelle/fastlin/archive/v{{ version }}.tar.gz - sha256: 765820a4c68018a4c8caab76b522eff6a6dca80111721acc38a75840dc94a51b + sha256: 0e2773ead72ae17fdd0a41965f97bb6282170cead24cfe3d80ab1c46317777fc build: number: 0 script: "cargo install --no-track --locked --verbose --root \"${PREFIX}\" --path ." + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: @@ -24,5 +26,6 @@ test: about: home: https://github.com/rderelle/fastlin license: MIT + license_family: MIT license_file: LICENSE summary: fastlin, ultra-fast MTBC lineage typing From 1cf2127c1d8f0e2769bf91e60c8c51beadb3a5d3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Dec 2023 02:25:55 -0500 Subject: [PATCH 1047/2173] Update insilicosv to 0.0.5 (#44617) --- recipes/insilicosv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/insilicosv/meta.yaml b/recipes/insilicosv/meta.yaml index a94d415129ccd..b988bd62ad270 100644 --- a/recipes/insilicosv/meta.yaml +++ b/recipes/insilicosv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "insilicosv" %} -{% set version = "0.0.4" %} -{% set sha256 = "2e12d42d43d6bb50c2f7b987d52717d9dbc1cba0b1959fde2dc28fcb8a6e6525" %} +{% set version = "0.0.5" %} +{% set sha256 = "47417a0c421a4eadd959a1c353e8f50c3634e4c3d1497008610e85c5a1b84667" %} package: name: "{{ name|lower }}" From 7258918849fa471e2cb5aa823680e3313121c524 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Mon, 4 Dec 2023 10:37:55 +0100 Subject: [PATCH 1048/2173] =?UTF-8?q?Correct=20license=20for=20deeptoolsin?= =?UTF-8?q?tervals,=20it's=20MIT,=20not=20sure=20why=20it's=20l=E2=80=A6?= =?UTF-8?q?=20(#44618)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Correct license for deeptoolsintervals, it's MIT, not sure why it's listed as GPL3 * lint * LOL * lint * lint * lint --------- Co-authored-by: Devon Ryan --- recipes/deeptoolsintervals/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/deeptoolsintervals/meta.yaml b/recipes/deeptoolsintervals/meta.yaml index 8aac5d66478b9..592130b2c9fbe 100644 --- a/recipes/deeptoolsintervals/meta.yaml +++ b/recipes/deeptoolsintervals/meta.yaml @@ -10,11 +10,13 @@ source: sha256: 7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6 build: - number: 5 + number: 6 + run_exports: + - {{ pin_subpackage("deeptoolsintervals", max_pin="x.x") }} requirements: build: - - "{{ compiler('c') }}" + - {{ compiler('c') }} host: - python - setuptools @@ -29,5 +31,5 @@ test: about: home: https://github.com/deeptools/deeptools_intervals - license: GPL3 + license: MIT summary: A python module creating/accessing GTF-based interval trees with associated meta-data From 3c78ad83f92f91c0c9a8abc4c123f112ac780d15 Mon Sep 17 00:00:00 2001 From: aguus8 <139561482+aguus8@users.noreply.github.com> Date: Mon, 4 Dec 2023 13:04:20 +0100 Subject: [PATCH 1049/2173] [v4.1.0] update 2023.4 (#44621) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [v4.1.0] update 2023.4 * [v4.1.0] update 2023.4 --------- Co-authored-by: Agustín García Doñate --- recipes/biobb_pdb_tools/meta.yaml | 52 +++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/biobb_pdb_tools/meta.yaml diff --git a/recipes/biobb_pdb_tools/meta.yaml b/recipes/biobb_pdb_tools/meta.yaml new file mode 100644 index 0000000000000..2de77d46048e3 --- /dev/null +++ b/recipes/biobb_pdb_tools/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "biobb_pdb_tools" %} +{% set version = "4.1.0" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: a956ceb461219df25154a59c8b319c79802f0f7975095837aef40d6b057c0744 + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.8 + - setuptools + - biobb_common ==4.1.0 + - pdb-tools + run: + - python >=3.8 + - biobb_common ==4.1.0 + - pdb-tools +test: + imports: + - biobb_pdb_tools + - biobb_pdb_tools.pdb_tools + +about: + home: https://github.com/bioexcel/biobb_pdb_tools + license: Apache Software License + license_family: APACHE + license_file: '' + summary: Biobb_pdb_tools is a swiss army knife for manipulating and editing PDB files. + description: "# biobb_pdb_tools\n\n### Introduction\biobb_pdb_tools is a swiss army knife for manipulating and editing PDB files.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\ + \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](https://biobb-pdb-tools.readthedocs.io/en/latest/).\n\ + \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\ + \n\n* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\ + Licensed under the\n\ + [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\ + \n\ + ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n" + doc_url: '' + dev_url: '' + +extra: + recipe-maintainers: '' From bb1a895d81cff6a2a1bced749111e805a1ce0149 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Dec 2023 15:10:05 -0500 Subject: [PATCH 1050/2173] Update hiphase to 1.1.0 (#44623) --- recipes/hiphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index 448e441c918b4..e6d8bad778424 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "1.0.0" %} -{% set hiphase_sha256 = "7aee796e83263a8158b0f5b3ed21ca701cf8fc3e7db275fec05f974a859c2510" %} +{% set version = "1.1.0" %} +{% set hiphase_sha256 = "b5034e3adc53c0314ac9b8b5b205553830e43c65f77169e91635f18559c5be3b" %} package: name: {{ name }} From adc50b731008a476c4604da3b4935298f59e46d3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Dec 2023 15:12:52 -0500 Subject: [PATCH 1051/2173] Update clinvar-this to 0.13.1 (#44622) --- recipes/clinvar-this/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clinvar-this/meta.yaml b/recipes/clinvar-this/meta.yaml index c2c2405ee7076..671020435cb2b 100644 --- a/recipes/clinvar-this/meta.yaml +++ b/recipes/clinvar-this/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.12.0" %} -{% set sha256 = "af2bc01c9b5a761e0e26ee6d4fcea80692943dc790cb52f2e60ba1db644ecc49" %} +{% set version = "0.13.1" %} +{% set sha256 = "0e2fb9200f5150a423173839f635cbf95e069413174be56fc732d27be19335ca" %} package: name: clinvar-this From a388a75d09fedf6a78ca2ed321f53231f7bc946e Mon Sep 17 00:00:00 2001 From: Joe Wirth <71667025+dr-joe-wirth@users.noreply.github.com> Date: Mon, 4 Dec 2023 18:12:11 -0500 Subject: [PATCH 1052/2173] PHANTASM recipe (#44051) * added recipe for phantasm-xenogi * added sha256 * add run_exports and test * got test passing * updated the sha256 to the current release * updated xenoGI version, sha256, and python3 version * add spdx * added recipe for phantasm (test passing; unpolished) * test passing * added R dependencies * updated version to 1.1.3 * fixed statement * trying a new strategy for providing a phantasm executable * attempt to fix permissions issues * small edit to circumvent permissions issues * fixed typo to circumvent permissions issues * added a test cmd for debugging * attempt to fix permissions issue * another attempt to fix permissions issue * fixed typo in debug command * trying a new way to specify python3 in executable * revised activate script; might be working * attempting to fix duplicated code issue * fixed duplicated code issue * fixed problems with * fixed xenoGI import issue * fixed xenoGI import issue --------- Co-authored-by: Robert A. Petit III --- recipes/phantasm/build.sh | 100 +++++++++++++++++++++++++++++++++++++ recipes/phantasm/meta.yaml | 52 +++++++++++++++++++ 2 files changed, 152 insertions(+) create mode 100644 recipes/phantasm/build.sh create mode 100644 recipes/phantasm/meta.yaml diff --git a/recipes/phantasm/build.sh b/recipes/phantasm/build.sh new file mode 100644 index 0000000000000..4eddc5cd3108d --- /dev/null +++ b/recipes/phantasm/build.sh @@ -0,0 +1,100 @@ +#!/bin/bash + +# create variables for this build script +export PYVER=$(python3 --version|sed -E "s/^\S+ ([0-9]+\.[0-9]+)\..+$/\1/g") +export TEMP_FN=".tmp" +export BIN_DIR=$PREFIX/bin +export ACTIVATE_DIR=$PREFIX/etc/conda/activate.d +export PHANTASM_EXE=$BIN_DIR/phantasm +export PHANTASM_DIR=$PREFIX/lib/python$PYVER/site-packages/phantasm +export PARAM_FN=$PHANTASM_DIR/param.py + +# move phantasm files to the directory +mkdir -p $PHANTASM_DIR +cp -rf ./ $PHANTASM_DIR + +# define global variables that point at the executables +echo "BLASTPLUS_DIR:str = '$BIN_DIR'" > $TEMP_FN +echo "MUSCLE_EXE:str = '$BIN_DIR/muscle'" >> $TEMP_FN +echo "FASTTREE_EXE:str = '$BIN_DIR/FastTreeMP'" >> $TEMP_FN +echo "IQTREE_EXE:str = '$BIN_DIR/iqtree'" >> $TEMP_FN + +# define global variables that point at phantasm and xenogi directories +echo "PHANTASM_DIR:str = '$PHANTASM_DIR'" >> $TEMP_FN +echo "XENOGI_DIR:str = '$PREFIX/lib/python$PYVER/site-packages/'" >> $TEMP_FN + +# add the last five lines of param.py (LPSN csv files) +tail -n 5 $PARAM_FN >> $TEMP_FN + +# overwrite param.py with the new file +mv $TEMP_FN $PARAM_FN + +# modify PHANTASM_PY variable so it prints the correct usage +sed -E "s/^(PHANTASM_PY = ).+$/\1'phantasm'/g" $PHANTASM_DIR/phantasm.py > $TEMP_FN +mv $TEMP_FN $PHANTASM_DIR/phantasm.py + +# make the phantasm executable +touch $PHANTASM_EXE +chmod a+x $PHANTASM_EXE + +# make an activate script +mkdir -p $ACTIVATE_DIR + +# export variables for the activate script +cat < $ACTIVATE_DIR/phantasm.sh +export BIN_DIR=$BIN_DIR +export LIB_DIR=$PREFIX/lib/python +export PHANTASM_EXE=$PHANTASM_EXE +export BUILD_PYVER=$PYVER +End + +# PYVER and PHANTASM_DIR need to be defined upon activation +cat <<\End >> $ACTIVATE_DIR/phantasm.sh +export PYVER=$(python3 --version|sed -E "s/^\S+ ([0-9]+\.[0-9]+)\..+$/\1/g") +export PHANTASM_DIR=$LIB_DIR$PYVER/site-packages/phantasm +End + +# replace the build pyver with the current pyver +cat <<\End >> $ACTIVATE_DIR/phantasm.sh +cat $PHANTASM_DIR/param.py | sed -E "s/python$BUILD_PYVER/python$PYVER/g" > .tmp +mv .tmp $PHANTASM_DIR/param.py +End + +# start building the python executable +cat <> $ACTIVATE_DIR/phantasm.sh +echo "#!/usr/bin/env python3" > $PHANTASM_EXE +echo "import os, sys, subprocess" >> $PHANTASM_EXE +End + +# $PHANTASM_DIR needs to be evaluated as string literal +cat <<\End >> $ACTIVATE_DIR/phantasm.sh +echo "sys.path.append('$PHANTASM_DIR')" >> $PHANTASM_EXE +End + +# continue building python executable +cat <> $ACTIVATE_DIR/phantasm.sh +echo "if __name__ == '__main__'": >> $PHANTASM_EXE +End + +# PHANTASM_DIR needs to be evalutated as a string literal +cat <<\End >> $ACTIVATE_DIR/phantasm.sh +echo " cmd = ['python3', os.path.join('$PHANTASM_DIR', 'phantasm.py')]" >> $PHANTASM_EXE +End + +# finish building python executable and unset variables +cat <> $ACTIVATE_DIR/phantasm.sh +echo " cmd.extend(sys.argv[1:])" >> $PHANTASM_EXE +echo " try:" >> $PHANTASM_EXE +echo " subprocess.run(cmd, check=True)" >> $PHANTASM_EXE +echo " except subprocess.CalledProcessError as e:" >> $PHANTASM_EXE +echo " raise RuntimeError(e.stderr)" >> $PHANTASM_EXE +unset BIN_DIR +unset LIB_DIR +unset BUILD_PYVER +unset PYVER +unset PHANTASM_DIR +unset PHANTASM_EXE +End + +# make activate script executable +chmod a+x $ACTIVATE_DIR/phantasm.sh diff --git a/recipes/phantasm/meta.yaml b/recipes/phantasm/meta.yaml new file mode 100644 index 0000000000000..eada44f5c7663 --- /dev/null +++ b/recipes/phantasm/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "PHANTASM" %} +{% set version = "1.1.3" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/dr-joe-wirth/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 6aa9e00a325750ba3299ffe61a4937fd5df237d4efa9f2bfd78bc2b2dae31939 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('phantasm', max_pin="x") }} + +requirements: + host: + - python >=3.9 + - pip + run: + - bioconductor-decipher + - biopython + - blast + - fasttree + - iqtree >=1.6.12 + - muscle >=5 + - numpy + - parasail-python + - phantasm-xenogi + - pyani + - python >=3.9 + - r-ape + - r-base + - r-dendextend + - r-gplots + - rpy2 + - scipy + - semver + - textdistance + +test: + commands: + - phantasm check + +about: + home: https://github.com/dr-joe-wirth/{{ name|lower }} + license: MIT + license_family: GPL3 + license_file: LICENSE.md + summary: "PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes" From 720789601db79f47bc71da571c8270c66661a083 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Dec 2023 19:13:33 -0500 Subject: [PATCH 1053/2173] Update r-goalie to 0.7.7 (#44628) --- recipes/r-goalie/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-goalie/meta.yaml b/recipes/r-goalie/meta.yaml index 92a46d939565b..ad0ccf22a5c52 100644 --- a/recipes/r-goalie/meta.yaml +++ b/recipes/r-goalie/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.6" %} +{% set version = "0.7.7" %} {% set github = "https://github.com/acidgenomics/r-goalie" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: c2894758e58c994813deaa3767916bdd4ca0ffac111fc88159cc766f54cd4a1b + sha256: 58e751134e5b0431a3a8fee58eefdef2b169e782f1a6eea623c6c9e7fadcd937 build: number: 0 From e9b8861a0d2375a69f40d00d92b6902c2095e819 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Dec 2023 20:01:55 -0500 Subject: [PATCH 1054/2173] Update rosella to 0.5.2 (#44634) --- recipes/rosella/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rosella/meta.yaml b/recipes/rosella/meta.yaml index 792250cabb4fe..bcc70f4e4c7a5 100644 --- a/recipes/rosella/meta.yaml +++ b/recipes/rosella/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.5.1" %} +{% set version = "0.5.2" %} {% set name = "rosella" %} -{% set hash = "6fa50c3c82a0e792ad9e44abb814992753732d169e99f74b228a834d822f1a8c" %} +{% set hash = "7f0851bbeef7e694983b3002a06c4cc1346544818a532373ca63dab14fa0245a" %} package: name: rosella From 0289842569a8a6241c6de9a86123203fa69c3062 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Dec 2023 21:15:16 -0500 Subject: [PATCH 1055/2173] Update r-acidgenomes to 0.7.0 (#44636) --- recipes/r-acidgenomes/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenomes/meta.yaml b/recipes/r-acidgenomes/meta.yaml index c3c299fe4266e..6190500f2f729 100644 --- a/recipes/r-acidgenomes/meta.yaml +++ b/recipes/r-acidgenomes/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.1" %} +{% set version = "0.7.0" %} {% set github = "https://github.com/acidgenomics/r-acidgenomes" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: c69cd608fcab47ef5360bc2dd5a87b09eae5aa0a38e1689a21ae97f03958f32d + sha256: 312e93794d0712fe348cd5d211d380a3c345f385f2de9af60139637c543caf37 build: number: 0 From bdaafc0b5464e09a9e2cac4e368062a53ab6687f Mon Sep 17 00:00:00 2001 From: Mikko Rautiainen Date: Tue, 5 Dec 2023 04:21:55 +0200 Subject: [PATCH 1056/2173] Update ribotin v1.2 build 1 (#44619) * Update ribotin v1.2 build number 1 * pin specific liftoff version to make sure version change doesn't lead to index incompatibility * space --- recipes/ribotin/build.sh | 2 ++ recipes/ribotin/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ribotin/build.sh b/recipes/ribotin/build.sh index 21514ab5ec912..3b102e3f455cb 100644 --- a/recipes/ribotin/build.sh +++ b/recipes/ribotin/build.sh @@ -7,5 +7,7 @@ cp bin/ribotin-verkko $PREFIX/bin mkdir -p $PREFIX/share/${PKG_NAME}-${PKG_VERSION} cp template_seqs/rDNA_one_unit.fasta $PREFIX/share/${PKG_NAME}-${PKG_VERSION}/rDNA_one_unit.fasta +cp template_seqs/rDNA_one_unit.fasta.fai $PREFIX/share/${PKG_NAME}-${PKG_VERSION}/rDNA_one_unit.fasta.fai cp template_seqs/chm13_rDNAs.fa $PREFIX/share/${PKG_NAME}-${PKG_VERSION}/chm13_rDNAs.fa cp template_seqs/rDNA_annotation.gff3 $PREFIX/share/${PKG_NAME}-${PKG_VERSION}/rDNA_annotation.gff3 +cp template_seqs/rDNA_annotation.gff3_db $PREFIX/share/${PKG_NAME}-${PKG_VERSION}/rDNA_annotation.gff3_db diff --git a/recipes/ribotin/meta.yaml b/recipes/ribotin/meta.yaml index 360feb7cd003d..a362932854381 100644 --- a/recipes/ribotin/meta.yaml +++ b/recipes/ribotin/meta.yaml @@ -12,7 +12,7 @@ source: - makefile.patch build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('ribotin', max_pin="x.x") }} @@ -27,7 +27,7 @@ requirements: run: - graphaligner - mbg - - liftoff + - liftoff =1.6.3 # Use a specific version to make sure the annotation index files are compatible test: commands: From b177dc19b4422f39be814d58501d97628fda4827 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Dec 2023 22:12:21 -0500 Subject: [PATCH 1057/2173] Update vg to 1.53.0 (#44629) --- recipes/vg/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml index c8e20fce3bf63..8549c995de117 100644 --- a/recipes/vg/meta.yaml +++ b/recipes/vg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vg" %} -{% set version = "1.52.0" %} +{% set version = "1.53.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg - sha256: 07776b51aa6494b45982e4134eb84005ddc743e81c67e61fa52bff211d81777c + sha256: a86dfc47c143af9f9a89c5e4595ed32b493384aac2b067f97d0684ec2d9a413b build: number: 0 From 09cb7a81c94b400bc4158565deb3400ac4598e42 Mon Sep 17 00:00:00 2001 From: leoisl Date: Tue, 5 Dec 2023 03:15:14 +0000 Subject: [PATCH 1058/2173] Update kissplice to 2.6.2 (#44624) --- recipes/kissplice/build.sh | 3 +-- recipes/kissplice/meta.yaml | 32 +++++++++++++++++++++----------- 2 files changed, 22 insertions(+), 13 deletions(-) diff --git a/recipes/kissplice/build.sh b/recipes/kissplice/build.sh index 77c03585743f9..47fa0a33dd8fe 100644 --- a/recipes/kissplice/build.sh +++ b/recipes/kissplice/build.sh @@ -6,8 +6,7 @@ export CXXFLAGS="$CXXFLAGS -fcommon -I$PREFIX/include" export CFLAGS="$CFLAGS -fcommon -I$PREFIX/include" # Unfortunately this is not written to pass on appropriate flags -sed -i.bak "s#fopenmp#fopenmp -I$PREFIX/include#g" CMakeLists.txt -cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_LIBRARY_PATH=$PREFIX/lib $DCMAKE_INCLUDE_PATH=$PREFIX/include . +cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_LIBRARY_PATH=$PREFIX/lib $DCMAKE_INCLUDE_PATH=$PREFIX/include -DUSER_GUIDE=OFF . # make commands make -j1 VERBOSE=1 diff --git a/recipes/kissplice/meta.yaml b/recipes/kissplice/meta.yaml index efa85956ffe0b..cde5ecc202fa0 100644 --- a/recipes/kissplice/meta.yaml +++ b/recipes/kissplice/meta.yaml @@ -1,27 +1,32 @@ +{% set name = "kissplice" %} +{% set version = "2.6.2" %} + package: - name: kissplice - version: '2.5.5' + name: {{ name|lower }} + version: {{ version }} source: - url: "ftp://pbil.univ-lyon1.fr/pub/logiciel/kissplice/download/kissplice-2.5.5.tar.gz" - sha256: "d75d17393938d94b98811a7ef602e07d7c936d84c4ba2531bfd0830e9bf2a261" + url: "https://gitlab.inria.fr/erable/{{ name }}/-/archive/{{ version }}/{{ name }}-{{ version }}.tar.gz" + sha256: "e2a4f8108c7668a8e50263d105889004f9f18b24f7a20f13ddb7dc903389f3e6" build: - number: 2 -# skip: True # [py2k] + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: build: - - make - - {{ compiler('c') }} - {{ compiler('cxx') }} - - cmake + - libgomp # [linux] - llvm-openmp # [osx] - - libgomp # [linux] + - cmake + - make + - bcalm >=2.2.3 host: - zlib run: - - python >=3 + - python >=3.8 + - bcalm >=2.2.3 test: commands: @@ -31,3 +36,8 @@ about: home: http://kissplice.prabi.fr license: CeCILL license summary: A local transcriptome assembler for SNPs, indels and AS events + +extra: + recipe-maintainers: + - MONJEAUD Cyril + - leoisl From b29364b87969b04bc28471dae252a69a27d42f76 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Dec 2023 22:41:12 -0500 Subject: [PATCH 1059/2173] Update nda-tools to 0.2.26 (#44626) * Update nda-tools to 0.2.26 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/nda-tools/meta.yaml | 34 ++++++++++++++++------------------ 1 file changed, 16 insertions(+), 18 deletions(-) diff --git a/recipes/nda-tools/meta.yaml b/recipes/nda-tools/meta.yaml index 2aac727631ed9..1884495f78db8 100644 --- a/recipes/nda-tools/meta.yaml +++ b/recipes/nda-tools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nda-tools" %} -{% set version = "0.2.25" %} -{% set sha256 = "2b3b5d27a7884124eb990378d1fc9a38cba555ff7b49764f42ae1b97d1cf0580" %} +{% set version = "0.2.26" %} +{% set sha256 = "863bbbf6399aa38bcec6cf8159aca90d3afcb1221eb26b20243f4f41e7eec2fe" %} package: name: {{ name }} @@ -13,29 +13,27 @@ source: build: noarch: python number: 0 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps -vvv + entry_points: + - vtcmd = NDATools.clientscripts.vtcmd:main + - downloadcmd = NDATools.clientscripts.downloadcmd:main + - unit_tests = tests.run_unit_tests:main + - integration_tests = tests.run_integration_tests:main + run_exports: + - {{ pin_subpackage('nda-tools', max_pin="x.x") }} requirements: host: - python - pip - - keyring - - pyyaml - - packaging - - mock - - requests - - tqdm - - botocore - - boto3 run: - python - - keyring - - pyyaml - - packaging - - mock - - requests - - tqdm - - botocore + - keyring + - pyyaml + - packaging + - mock + - requests + - tqdm - boto3 - pandas From 9cf5b63585f5a00d30b7579a1db937fb884fad15 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Dec 2023 22:43:18 -0500 Subject: [PATCH 1060/2173] Update oakvar to 2.9.71 (#44631) * Update oakvar to 2.9.70 * Update oakvar to 2.9.71 --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 6f044b414760b..2f45d4aedd2ee 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.69" %} -{% set sha256 = "7e6f8dd20c236c40f39db5017ba503498ad5309528a47ad918c9e8db4a154eb6" %} +{% set version = "2.9.71" %} +{% set sha256 = "764174068a918f25715dab3359176e261867a5cf7dac4986c3a0002d92877fe0" %} package: name: {{ name|lower }} From 21b964fc14bb8a04193b5c3ea4d6be89511c9fce Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Dec 2023 22:45:56 -0500 Subject: [PATCH 1061/2173] Update ncbi-datasets-pylib to 15.31.2 (#44630) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 901b20233d3b5..342fc03a5d0a6 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.31.1" %} -{% set sha256 = "f39ac05519485fa14ff01e6cc2057726e52b92947adec9496ebc33314498edc8" %} +{% set version = "15.31.2" %} +{% set sha256 = "a4e88dd0bf0ad2a4169283863b771c7e0013d9c3398f551c4dda600c62b3dfd7" %} package: name: {{ name|lower }} From c4355a3c7595215536c986943f66ade779a1803e Mon Sep 17 00:00:00 2001 From: Pavel Vazquez Faci <79310152+pavelvazquez@users.noreply.github.com> Date: Tue, 5 Dec 2023 04:47:17 +0100 Subject: [PATCH 1062/2173] Add OLGA 1.2.4 recipe to Bioconda (#44442) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Add OLGA 1.2.4 recipe to Bioconda * Fix linter errors: add noarch and missing run_exports in OLGA recipe * Fix error in name * Fix syntax error * Update recipes/olga/meta.yaml Co-authored-by: Björn Grüning * Update OLGA recipe, SPDX license identifier and license file --------- Co-authored-by: Björn Grüning --- recipes/olga/meta.yaml | 48 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 recipes/olga/meta.yaml diff --git a/recipes/olga/meta.yaml b/recipes/olga/meta.yaml new file mode 100644 index 0000000000000..db0f8ab2d47a9 --- /dev/null +++ b/recipes/olga/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "olga" %} +{% set version = "1.2.4" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 66b537a5c53aa840466c27fc51d22c24d57eb0124eeaf2cd2dfb6bbe53b38dda + +build: + number: 0 + noarch: python + entry_points: + - olga-compute_pgen=olga.compute_pgen:main + - olga-generate_sequences=olga.generate_sequences:main + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('olga', max_pin="x") }} + +requirements: + host: + - pip + - python + run: + - python + - numpy >=1.20 + +test: + imports: + - olga + commands: + - olga-compute_pgen --help + - olga-generate_sequences --help + +about: + home: "https://github.com/zsethna/OLGA" + license: "GPL-3.0-only" + license_family: GPL3 + license_file: LICENSE + summary: "OLGA (Optimized Likelihood estimate of immunoGlobulin Amino-acid sequences) is a python 2.7/3.6 software + developed to compute the generation probability of amino acid and in-frame nucleotide CDR3 sequences from a + generative model of V(D)J recombination." + +extra: + recipe-maintainers: + - pavelvazquez From f00ea68244790322d321de34d1faef886c3f4a17 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 4 Dec 2023 22:47:42 -0500 Subject: [PATCH 1063/2173] Update recentrifuge to 1.12.2 (#44632) * Update recentrifuge to 1.12.2 * add run_exports * edit license_family --------- Co-authored-by: joshuazhuang7 --- recipes/recentrifuge/meta.yaml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/recipes/recentrifuge/meta.yaml b/recipes/recentrifuge/meta.yaml index d5b01399af34f..b22789af9d4a7 100644 --- a/recipes/recentrifuge/meta.yaml +++ b/recipes/recentrifuge/meta.yaml @@ -1,5 +1,5 @@ -{% set name="recentrifuge" %} -{% set version="1.12.1" %} +{% set name = "recentrifuge" %} +{% set version = "1.12.2" %} package: name: {{ name }} @@ -8,18 +8,20 @@ package: build: noarch: python number: 0 - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv + run_exports: + - {{ pin_subpackage('recentrifuge', max_pin="x") }} source: url: https://github.com/khyox/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 076dedf54f5d465580e6c2792335c4b0a42853c1eabb891c362479c21ba7e491 + sha256: b2dc96faf702d32d98bc178e283bf64934a6628a783644c8338dd50cf9227c3a requirements: host: - - python >=3 + - python >=3.6 - pip run: - - python >=3 + - python >=3.6 - biopython 1.79 - numpy >=1.19.5 - matplotlib-base >=3.3.4 @@ -32,9 +34,11 @@ test: about: home: https://github.com/khyox/recentrifuge - license: 'AGPLv3' + license: 'AGPL-3.0-or-later' + license_family: AGPL license_file: LICENSE.txt summary: 'Robust comparative analysis and contamination removal for metagenomics' + doc_url: https://github.com/khyox/recentrifuge/wiki extra: recipe-maintainers: From 50043d171b63659aa87f1a48db2e21b32bd0da59 Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Mon, 4 Dec 2023 19:48:39 -0800 Subject: [PATCH 1064/2173] Update Ampliconsuite to v1.1.2 (#44637) * Add ampliconsuite * Fix ampliconsuite meta.yaml Fix ampliconsuite meta.yaml Fix ampliconsuite meta.yaml add "noarch: python" * Fix ampliconsuite meta.yaml * adjust recipe based on reviewer feedback * bugfix for ampliconarchitectlib src pathing * bump ampsuite version * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml include python in host section of requirements * Update meta.yaml * Update meta.yaml * Update build.sh expose amplicon_classifier.py and feature_similarity.py * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml add run_exports * Update meta.yaml typo * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml --- recipes/ampliconsuite/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml index 844ce741edb94..1a8bf1a1d8a33 100644 --- a/recipes/ampliconsuite/meta.yaml +++ b/recipes/ampliconsuite/meta.yaml @@ -1,5 +1,5 @@ {% set name="ampliconsuite" %} -{% set AS_version="1.1.1" %} +{% set AS_version="1.1.2" %} {% set AA_version="1.3.r6" %} {% set AC_version="1.0.0" %} @@ -11,7 +11,7 @@ source: # the sha256 sum is generated by doing # $ wget -O- [URL] | shasum -a 256 - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz - sha256: 0a874698ae3468d6ca02c3a3e1542d945e9940c703cf24c409eeb6e70e3bf3a7 + sha256: 4483b38a89dfde309bc82e589c334df010de9315e34115790dd5c664f9f80bde - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz sha256: cc21a52d9853cd5e0b5b9374773a6ea24191241b9b9cf1d71e2a928ab3d97f01 folder: ampliconarchitectlib From 1fbe63f46597812ac65a9c795be093755051afc9 Mon Sep 17 00:00:00 2001 From: santiago-es Date: Mon, 4 Dec 2023 21:04:04 -0800 Subject: [PATCH 1065/2173] add telometer v0.5 (#44616) * Create setup.sh * Create meta.yaml * Add files via upload * Add recipe for telometer * x x * telometer try2 * add telometer fixing meta yaml * add telometer2 * add telometer3 * add telometer4 * Update meta.yaml * Update recipes/telometer/meta.yaml Co-authored-by: Florian Wuennemann * Update meta.yaml license file * Update recipes/telometer/meta.yaml Co-authored-by: Florian Wuennemann * adding LICENSE * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Florian Wuennemann --- recipes/telometer/LICENSE.txt | 21 +++++++++++++++ recipes/telometer/meta.yaml | 48 +++++++++++++++++++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 recipes/telometer/LICENSE.txt create mode 100644 recipes/telometer/meta.yaml diff --git a/recipes/telometer/LICENSE.txt b/recipes/telometer/LICENSE.txt new file mode 100644 index 0000000000000..84e9e4c0a691f --- /dev/null +++ b/recipes/telometer/LICENSE.txt @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2023 santiago-es + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/recipes/telometer/meta.yaml b/recipes/telometer/meta.yaml new file mode 100644 index 0000000000000..9635ae5603af9 --- /dev/null +++ b/recipes/telometer/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "telometer" %} +{% set version = "0.5" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://test.pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 6225b28342a8120ed2dc138cfc30c07f2c887b1ac996d27eeddee62544a37572 + +build: + number: 0 + noarch: python + entry_points: + - telometer=telometer:calculate_telomere_length + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + + +requirements: + host: + - pip + - python + run: + - python + - pysam + - pandas + +test: + imports: + - telometer + commands: + - telometer --help + +about: + home: https://github.com/santiago-es/Telometer + license: MIT + license_file: LICENSE.txt + summary: "Tool for measuring telomeres from long-read data." + dev_url: https://github.com/santiago-es + + + +extra: + recipe-maintainers: + - santiago-es From 52126e7b3e4f137af5fa85406288df1af292b133 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Dec 2023 00:22:43 -0500 Subject: [PATCH 1066/2173] Update macrel to 1.3.0 (#44638) * Update macrel to 1.3.0 * macrel: relax version bounds Macrel 1.3 added compatibility with newer Python/Pyrodigal --------- Co-authored-by: Luis Pedro Coelho --- recipes/macrel/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/macrel/meta.yaml b/recipes/macrel/meta.yaml index af7a36f07f3a7..67f0e499b2867 100644 --- a/recipes/macrel/meta.yaml +++ b/recipes/macrel/meta.yaml @@ -1,6 +1,6 @@ {% set name = "macrel" %} -{% set version = "1.2.0" %} -{% set sha256 = "7d506748a68c163478426c0fa8183b1fec4c31acf47a1cddf677104aca029cd8" %} +{% set version = "1.3.0" %} +{% set sha256 = "c4cdd8cc186135b78bc8da4d40b71f0a62ecf622107a0c9c64c29b8000cfbda9" %} package: name: {{ name }} @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 0 entry_points: - macrel= macrel.main:main script: python -m pip install --disable-pip-version-check --no-cache-dir --ignore-installed --no-deps -vv . @@ -21,10 +21,10 @@ build: requirements: host: - - python <3.11 + - python - pip run: - - python <3.11 + - python - atomicwrites - ngless - megahit @@ -33,7 +33,7 @@ requirements: - scikit-learn <1.3.0 - joblib <1.3.0 - tzlocal - - pyrodigal >=0.7.3,<3.0.0 + - pyrodigal >=0.7.3 test: imports: From 12b0c43d1329787eb58169f6a39d111b31239b39 Mon Sep 17 00:00:00 2001 From: Sam W Date: Tue, 5 Dec 2023 12:10:15 +0000 Subject: [PATCH 1067/2173] Update artic to 1.2.4 (#42605) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update artic to 1.2.4 * Update meta.yaml Actually update version and hash, oops * Fix bwa def typo * CONDA_OVERRIDE_CUDA env var * No quotes around conda_override_cuda * Update meta.yaml Added run_exports * Update meta.yaml Try adding cudatoolkit to trigger downloading cuda rather than using tensorflow * bump medaka version * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Relaxing requirements * Re-pin muscle --------- Co-authored-by: Thanh Lee Co-authored-by: Robert A. Petit III Co-authored-by: Andreas Sjödin --- recipes/artic/meta.yaml | 48 ++++++++++++++++++++++------------------- 1 file changed, 26 insertions(+), 22 deletions(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index 447e7d20a3806..7d81c8941ea34 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -1,6 +1,6 @@ {% set name = "artic" %} -{% set version = "1.2.3" %} -{% set sha256 = "92ddaf38c46681299b22ac91b4b64ec57c6d2965ea3886620fa9348398204506" %} +{% set version = "1.2.4" %} +{% set sha256 = "981219a49cec01dc82a9375b16f844278e797ad4034efa1eaa410ccb1849c617" %} package: name: {{ name|lower }} @@ -12,6 +12,8 @@ source: build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage('artic', max_pin='x.x') }} script: python -m pip install --ignore-installed . entry_points: - artic=artic.pipeline:main @@ -32,29 +34,31 @@ requirements: - python >=3 - pip run: - - artic-porechop =0.3.2pre - - artic-tools =0.2.6 - - longshot =0.4.5 - - bcftools =1.15.1 - - biopython =1.79 - - bwa =0.7.17 - - clint =0.5.1 - - htslib =1.15.1 - - medaka >=1.6.1 - - minimap2 =2.24 - - multiqc =1.13 + - python + - artic-porechop >=0.3.2pre + - artic-tools + - longshot + - bcftools + - biopython + - bwa + - clint + - htslib + - medaka >=1.10.0 + - minimap2 >=2.26 + - multiqc - muscle =3.8 - - nanopolish =0.14.0 - - pandas =1.4.4 + - nanopolish >=0.14.0 + - pandas - pip - pysam - - pytest =7.1.3 - - python =3.8.13 - - pyvcf =0.6.8 - - pyfaidx =0.6.0 - - requests =2.28 - - samtools =1.15 - - tqdm =4.64 + - pytest + - pyvcf + - pyfaidx + - requests + - samtools + - tqdm + - keras-preprocessing >=1.1.2 + test: commands: From 8b341b50464b00e369979e3e0e5aab18ff606ebd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Dec 2023 08:49:37 -0500 Subject: [PATCH 1068/2173] Update r-acidplyr to 0.5.2 (#44591) Co-authored-by: Michael Steinbaugh --- recipes/r-acidplyr/meta.yaml | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/recipes/r-acidplyr/meta.yaml b/recipes/r-acidplyr/meta.yaml index 52af371705552..28d18de30e631 100644 --- a/recipes/r-acidplyr/meta.yaml +++ b/recipes/r-acidplyr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.1" %} +{% set version = "0.5.2" %} {% set github = "https://github.com/acidgenomics/r-acidplyr" %} package: @@ -7,8 +7,8 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 80c9722f0c254fd7619989b8cfe06aff11e545b6598de3e73f0255c7252b04ec - + sha256: 76e4bead1439a5586b32977427294080b360760908933386e5780697963f8c2b + build: number: 0 noarch: generic @@ -21,17 +21,19 @@ requirements: - r-base # Imports: - bioconductor-biocgenerics >=0.46.0 + - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidgenerics >=0.7.0 - - r-goalie >=0.7.0 + - r-acidgenerics >=0.7.4 + - r-goalie >=0.7.6 run: # Depends: - r-base # Imports: - bioconductor-biocgenerics >=0.46.0 + - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidgenerics >=0.7.0 - - r-goalie >=0.7.0 + - r-acidgenerics >=0.7.4 + - r-goalie >=0.7.6 test: commands: From c1b13ab46de70aae002a7cdfcf466d3b8d027a4a Mon Sep 17 00:00:00 2001 From: Alexandra Valeanu <57878719+alexandra-valeanu@users.noreply.github.com> Date: Tue, 5 Dec 2023 17:00:20 +0200 Subject: [PATCH 1069/2173] Add kinex 1.0.1 (#44615) * Add kinex 1.0.1 * fixup! Add kinex 1.0.1 * fixup! Add kinex 1.0.1 * Pin the python version in host, use spdx license identifier --- recipes/kinex/meta.yaml | 50 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 recipes/kinex/meta.yaml diff --git a/recipes/kinex/meta.yaml b/recipes/kinex/meta.yaml new file mode 100644 index 0000000000000..b22d57e489243 --- /dev/null +++ b/recipes/kinex/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "kinex" %} +{% set version = "1.0.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://github.com/bedapub/{{ name }}/archive/v{{ version }}.tar.gz" + sha256: 8f153d85657e16f0bae58df8d5a6cb52f8ba28ff992203e7762d81e04a448e0d + +build: + number: 0 + noarch: python + script: + - {{ PYTHON }} -m pip install . --no-deps -vv + run_exports: + - {{ pin_subpackage("kinex", max_pin="x") }} + +requirements: + host: + - pip + - python >=3.8,<=3.11 + run: + - python >=3.8,<=3.11 + - scipy >=1.10.0 + - numpy >=1.19.5 + - nbformat >=4.2.0 + - pandas + - statsmodels + - plotly + - scikit-learn + - umap-learn + - importlib-resources + +test: + imports: + - kinex + +about: + home: "https://github.com/bedapub/kinex" + license: GPL-3.0-only + license_file: LICENSE + summary: "Kinex infers causal kinases from phosphoproteomics data" + doc_url: "https://kinex.readthedocs.io/en/latest/" + dev_url: "https://github.com/bedapub/kinex" + +extra: + identifiers: + - doi:10.1101/2023.11.23.568445 \ No newline at end of file From 29ec4e1cd396157e14442206b47be7e950b70381 Mon Sep 17 00:00:00 2001 From: Kerim Heber <122597229+kheber@users.noreply.github.com> Date: Tue, 5 Dec 2023 10:02:53 -0500 Subject: [PATCH 1070/2173] Add StrainR2 Recipe (#44485) * initial commit * Rename meta.yml to meta.yaml * Update meta.yaml * Update meta.yaml with test commands * add run_exports to meta.yaml and use short identifier for MIT License * replace gcc with $CC in build.sh * update subcontig test command in meta.yaml (--help long option invalid, had to use -h) * Added r-optparse to run requirements. --- recipes/strainr2/build.sh | 16 ++++++++++++++ recipes/strainr2/meta.yaml | 45 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 recipes/strainr2/build.sh create mode 100644 recipes/strainr2/meta.yaml diff --git a/recipes/strainr2/build.sh b/recipes/strainr2/build.sh new file mode 100644 index 0000000000000..9e30d76742542 --- /dev/null +++ b/recipes/strainr2/build.sh @@ -0,0 +1,16 @@ +#! /bin/bash +mkdir -p ${PREFIX}/bin + +$CC $SRC_DIR/subcontig.c -o subcontig + +chmod +x $SRC_DIR/PreProcessR +chmod +x $SRC_DIR/subcontig +chmod +x $SRC_DIR/hashcounter.py +chmod +x $SRC_DIR/Plot.R +chmod +x $SRC_DIR/StrainR + +cp $SRC_DIR/PreProcessR ${PREFIX}/bin/ +cp $SRC_DIR/subcontig ${PREFIX}/bin/ +cp $SRC_DIR/hashcounter.py ${PREFIX}/bin/ +cp $SRC_DIR/Plot.R ${PREFIX}/bin/ +cp $SRC_DIR/StrainR ${PREFIX}/bin/ diff --git a/recipes/strainr2/meta.yaml b/recipes/strainr2/meta.yaml new file mode 100644 index 0000000000000..d0e50a9dcfb66 --- /dev/null +++ b/recipes/strainr2/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.0" %} + +package: + name: strainr2 + version: {{ version }} + +source: + url: https://github.com/BisanzLab/StrainR2/archive/v{{ version }}.tar.gz + sha256: 6ed9671c875ec6388960dbac02a73629d58ad20adad1fe297d905d8969ec0489 + +build: + number: 0 + run_exports: + - {{ pin_subpackage("strainr2", max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - python >=3.12.0 + - r-base >=4.3.2 + run: + - bbmap >=39.01 + - fastp >=0.23.4 + - python >=3.12.0 + - samtools >=1.18 + - sourmash >=4.8.4 + - r-base >=4.3.2 + - r-optparse >=1.7.3 + - r-tidyverse >=2.0.0 + +test: + commands: + - PreProcessR --help + - subcontig -h + - hashcounter.py --help + - StrainR --help + - Plot.R --help + +about: + home: https://github.com/BisanzLab/StrainR2 + license: MIT + summary: 'strainr2: get high accuracy metagenomic strain abundance.' + license_family: MIT + license_file: LICENSE From b8d91bbb3633b2675303ee3d49ada6965fcd9ca3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Dec 2023 10:31:27 -0500 Subject: [PATCH 1071/2173] Update r-acidexperiment to 0.5.4 (#44635) Co-authored-by: Michael Steinbaugh --- recipes/r-acidexperiment/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidexperiment/meta.yaml b/recipes/r-acidexperiment/meta.yaml index 91b75662280e9..7b252486f45e8 100644 --- a/recipes/r-acidexperiment/meta.yaml +++ b/recipes/r-acidexperiment/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.3" %} +{% set version = "0.5.4" %} {% set github = "https://github.com/acidgenomics/r-acidexperiment" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 9124f900518566cd1555ec439411b7b3f4c59736f92ed0a3d784583697f661b1 + sha256: 4b8d093269e15d11a7565e4144d17caeac59e0491043bb3639713a9b769b5918 build: number: 0 From 4b5577505a33b2930759dabe05c2d695afa6345b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Dec 2023 10:31:59 -0500 Subject: [PATCH 1072/2173] Update r-bcbiosinglecell to 0.7.1 (#44643) --- recipes/r-bcbiosinglecell/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-bcbiosinglecell/meta.yaml b/recipes/r-bcbiosinglecell/meta.yaml index 822cb5d07aea9..f0d67d0cfeb51 100644 --- a/recipes/r-bcbiosinglecell/meta.yaml +++ b/recipes/r-bcbiosinglecell/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} {% set github = "https://github.com/hbc/bcbioSingleCell" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 60e4aaf76db0b307d0fec376db7d533faffce465c14e20fbbbeb981603ae8603 + sha256: 42a7272709a65cda9b45b79aa172226839342578049a9841b73ee92a5e76e3f5 build: number: 0 From 63626a1ffa582a13c05c7c26604001ee865f1391 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Dec 2023 10:43:55 -0500 Subject: [PATCH 1073/2173] Update r-acidgenomes to 0.7.1 (#44646) --- recipes/r-acidgenomes/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenomes/meta.yaml b/recipes/r-acidgenomes/meta.yaml index 6190500f2f729..64d06436b565f 100644 --- a/recipes/r-acidgenomes/meta.yaml +++ b/recipes/r-acidgenomes/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} {% set github = "https://github.com/acidgenomics/r-acidgenomes" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 312e93794d0712fe348cd5d211d380a3c345f385f2de9af60139637c543caf37 + sha256: 2f44e07480840db87e38eca989f5387a98350c49d57daf1eb9bf1b3448e6e662 build: number: 0 From 8f72fa09b27e845f06e1aaa665e7c5193262f211 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Ligeti?= Date: Tue, 5 Dec 2023 17:11:07 +0100 Subject: [PATCH 1074/2173] prokBERT conda recipe (#44263) * prokBERT conda recipe * reformat meta.yaml * add noarch:python and fix doi --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/prokbert/meta.yaml | 52 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/prokbert/meta.yaml diff --git a/recipes/prokbert/meta.yaml b/recipes/prokbert/meta.yaml new file mode 100644 index 0000000000000..aad92e9121840 --- /dev/null +++ b/recipes/prokbert/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "prokbert" %} +{% set version = "0.0.40" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/prokbert-{{ version }}.tar.gz + sha256: 8705d47d1d22ecd1e9c1b67345661b298f116b7c2ec65b167a01c25645ec4a03 + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('prokbert', max_pin="x.x") }} + +requirements: + host: + - python >=3.10 + - pip + run: + - python >=3.10 + - pytorch + - torchvision + - biopython + - pandas >=2.0.0 + - datasets >=2.0.1 + - scikit-learn >=1.2.2 + - scipy >=1.10.0 + - transformers >=4.23 + - tables >=3.8.0 + - h5py >=3.7.0 + +test: + imports: + - prokbert + +about: + home: https://github.com/nbrg-ppcu/prokbert + license: MIT + license_family: MIT + license_file: LICENSE + summary: 'ProkBERT is a genomic language model specifically designed for microbiome applications. It leverages the power of machine learning to decipher complex microbial interactions, predict functionalities, and uncover novel patterns in extensive datasets. The ProkBERT model family, built on transfer learning and self-supervised methodologies, capitalizes on the abundant genomic data available.' + doc_url: https://prokbert.readthedocs.io/en/latest/ + +extra: + recipe-maintainers: + - obalasz + identifiers: + - doi:10.1101/2023.11.09.566411 From 1a18a6f005f847fe5be2984293adff230cfaa5d9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Dec 2023 12:32:24 -0500 Subject: [PATCH 1075/2173] Update r-acidplots to 0.7.2 (#44627) Co-authored-by: Michael Steinbaugh --- recipes/r-acidplots/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidplots/meta.yaml b/recipes/r-acidplots/meta.yaml index a4217ce91b0fa..c34dc6a9b5aa5 100644 --- a/recipes/r-acidplots/meta.yaml +++ b/recipes/r-acidplots/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.1" %} +{% set version = "0.7.2" %} {% set github = "https://github.com/acidgenomics/r-acidplots" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: bda01fadcb22b2978d4aa7965e246de94e9f51b5673fdd6e5e59fe5a2a76c87f + sha256: 29edee3a481384cb4b3593e07f87cde2c7313f6d3318c7747ec3bfa1c933376a build: noarch: generic From 59cdde4eaa435da5c48c8ceb127468f9b9dddd55 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Dec 2023 13:11:31 -0500 Subject: [PATCH 1076/2173] Update lotus2 to 2.30 (#44648) --- recipes/lotus2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/lotus2/meta.yaml b/recipes/lotus2/meta.yaml index ec89fad4686f5..5ba5d2a771b3a 100644 --- a/recipes/lotus2/meta.yaml +++ b/recipes/lotus2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "lotus2" %} -{% set version = "2.28.1" %} -{% set sha256 = "0e7ed1f816db8d8e6946a101bc22924323e772484e0dc4bde319a36451d22186" %} +{% set version = "2.30" %} +{% set sha256 = "6bd815324f409c188d9d7533583a9d4a642ee2add4ed9aaef63cbb3bdac1d5de" %} package: name: {{ name }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin='x') }} From c77a3cb4997bff83600d6b89c2099690fcc8fa27 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Dec 2023 14:11:29 -0500 Subject: [PATCH 1077/2173] Update r-bcbiornaseq to 0.6.1 (#44649) Co-authored-by: Michael Steinbaugh --- recipes/r-bcbiornaseq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-bcbiornaseq/meta.yaml b/recipes/r-bcbiornaseq/meta.yaml index 24cd7740aadd0..bcf9df357c9d3 100644 --- a/recipes/r-bcbiornaseq/meta.yaml +++ b/recipes/r-bcbiornaseq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.0" %} +{% set version = "0.6.1" %} {% set github = "https://github.com/hbc/bcbioRNASeq" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 317f907519a0242892f461eb10d4cd3cd5421eedc765ffddb6435cd2186e5541 + sha256: 75399d753cd0fbef5f644e43fc1e30b7ccd3a56b754b999b5ce9086de0259596 build: number: 0 From 89dd5a26e2a11aac5095c146b694717363c19316 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 5 Dec 2023 22:28:52 -0500 Subject: [PATCH 1078/2173] Update gfftk to 23.12.5 (#44651) --- recipes/gfftk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gfftk/meta.yaml b/recipes/gfftk/meta.yaml index 6951a1651e927..0e92ea547b684 100644 --- a/recipes/gfftk/meta.yaml +++ b/recipes/gfftk/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gfftk" %} -{% set version = "23.9.6" %} +{% set version = "23.12.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/gfftk-{{ version }}.tar.gz - sha256: ee6b9aeef9923bea566bf3cb60fc4de0fec1c73dd157990d50cb26ecd8b6c495 + sha256: 447280eee990625ea84eab899400ff1be7c38ef818172dc7f4f2a0bebb6cb5e4 build: number: 0 From 0564ce49a821e4d096f3672d1dcaa42416ca1a90 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 03:48:02 -0500 Subject: [PATCH 1079/2173] Update lamassemble to 1.7.0 (#44653) --- recipes/lamassemble/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/lamassemble/meta.yaml b/recipes/lamassemble/meta.yaml index bba6f006b581d..1c0464b1f1233 100644 --- a/recipes/lamassemble/meta.yaml +++ b/recipes/lamassemble/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.6.2" %} +{% set version = "1.7.0" %} package: name: lamassemble @@ -6,7 +6,7 @@ package: source: url: https://gitlab.com/mcfrith/lamassemble/-/archive/{{ version }}/lamassemble-{{ version }}.tar.gz - sha256: 4d578d829f7d65a8e227fe6a4c5bb906d1423a15967ac209423acfcf7d2eed8c + sha256: e30c1450fb2d17e9203ff702971e100a2e9e842c4fa06d6c605105d1b895957f build: number: 0 From b83472db41112acaf83540470401bb708c1d4ce5 Mon Sep 17 00:00:00 2001 From: mjohnpayne Date: Wed, 6 Dec 2023 23:30:00 +1100 Subject: [PATCH 1080/2173] Add campy-against (#44640) --- recipes/campyagainst/meta.yaml | 35 ++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 recipes/campyagainst/meta.yaml diff --git a/recipes/campyagainst/meta.yaml b/recipes/campyagainst/meta.yaml new file mode 100644 index 0000000000000..d239e6bbe61fa --- /dev/null +++ b/recipes/campyagainst/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.1.0" %} +{% set name = "campyagainst" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/LanLab/{{ name }}/archive/v{{ version }}.tar.gz + sha256: aaa8434bc5cc06b7d8c567a8b1c7dc2ea926ffbfdebb0196a89559c4bdd92b74 + +build: + noarch: python + number: 0 + script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_subpackage('campyagainst', max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - fastani >=1.3 + +about: + home: https://github.com/LanLab/campyagainst + license: GPL-3.0-or-later + license_file: LICENSE + summary: Accurate assignment of ANI genomic species to Campylobacter genomes. + +test: + commands: + - campyagainst --help From 71b22ceb2348ef80171c8797031b4bb0f1696687 Mon Sep 17 00:00:00 2001 From: akrinos Date: Wed, 6 Dec 2023 07:30:58 -0500 Subject: [PATCH 1081/2173] Update EUKulele to version 2.0.7 (#44639) --- recipes/eukulele/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/eukulele/meta.yaml b/recipes/eukulele/meta.yaml index 7a16a1f0ad8ba..23dce68e05f3c 100644 --- a/recipes/eukulele/meta.yaml +++ b/recipes/eukulele/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "2.0.6" %} -{% set sha256 = "6d3026124b27dd55d627f6728493ee088bfb81aded1e4c7e0dec621bbddd14d1" %} +{% set version = "2.0.7" %} +{% set sha256 = "e52ca613c92ef99a6f01e503674b1c35ee26de6c03c4cb58338278e3a348a394" %} package: name: eukulele - version: 2.0.6 + version: 2.0.7 build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps" + run_exports: + - {{ pin_subpackage('eukulele', max_pin="2.0.7") }} source: - url: https://github.com/AlexanderLabWHOI/EUKulele/archive/refs/tags/v2.0.6-2.tar.gz + url: https://github.com/AlexanderLabWHOI/EUKulele/archive/refs/tags/v2.0.7_3.tar.gz sha256: {{ sha256 }} test: From 898de3b51ce9978edabdb97a9663a2a4cbc5a7a3 Mon Sep 17 00:00:00 2001 From: Katherine Eaton Date: Wed, 6 Dec 2023 05:33:04 -0700 Subject: [PATCH 1082/2173] Create new recipe for rebar (#44625) --- recipes/rebar/LICENSE | 201 ++++++++++++++++++++++++++++++++++++++ recipes/rebar/build.sh | 6 ++ recipes/rebar/meta.yaml | 40 ++++++++ recipes/rebar/run_test.sh | 16 +++ 4 files changed, 263 insertions(+) create mode 100644 recipes/rebar/LICENSE create mode 100644 recipes/rebar/build.sh create mode 100644 recipes/rebar/meta.yaml create mode 100644 recipes/rebar/run_test.sh diff --git a/recipes/rebar/LICENSE b/recipes/rebar/LICENSE new file mode 100644 index 0000000000000..56b1b473c89f8 --- /dev/null +++ b/recipes/rebar/LICENSE @@ -0,0 +1,201 @@ +Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright 2023 Public Health Agency of Canada + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/recipes/rebar/build.sh b/recipes/rebar/build.sh new file mode 100644 index 0000000000000..2136c1ec32aa2 --- /dev/null +++ b/recipes/rebar/build.sh @@ -0,0 +1,6 @@ +#!/usr/bin/env bash + +ls "${SRC_DIR}" +chmod +x "${SRC_DIR}"/rebar* +mkdir -p "${PREFIX}/bin" +mv "${SRC_DIR}"/rebar* "${PREFIX}"/bin/rebar diff --git a/recipes/rebar/meta.yaml b/recipes/rebar/meta.yaml new file mode 100644 index 0000000000000..57c99e47b7c34 --- /dev/null +++ b/recipes/rebar/meta.yaml @@ -0,0 +1,40 @@ +{% set name = "rebar" %} +{% set version = "0.2.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + - url: https://github.com/phac-nml/rebar/releases/download/v{{ version }}/{{ name }}-x86_64-unknown-linux-musl # [linux64] + sha256: 7b5648b353552662c66aab8347657dfebe92ee2d83e4a4f0b7a9526c58502b28 # [linux64] + - url: https://github.com/phac-nml/rebar/releases/download/v{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] + sha256: b3577c5ea7965133fc5b934a9c4f9b5e1ba41603d5f9ce47fff79d6ee11adaa7 # [osx and x86_64] + +build: + binary_relocation: False + number: 0 + # If the software version starts with a 0 (e.g. 0.3.2) semantic versioning allows breaking changes in minor releases. + # https://bioconda.github.io/contributor/linting.html#missing-run-exports + run_exports: + - {{ pin_compatible(name, max_pin="x.x") }} + +test: + commands: + - rebar --help + +about: + home: https://github.com/phac-nml/rebar + license: Apache-2.0 + license_family: APACHE + license_file: LICENSE + summary: "Genomic recombination detection using mutational barcodes." + +extra: + maintainers: + - ktmeaton + recipe-maintainers: + - ktmeaton + skip-lints: + - should_be_noarch_generic + diff --git a/recipes/rebar/run_test.sh b/recipes/rebar/run_test.sh new file mode 100644 index 0000000000000..8fab8c1320d57 --- /dev/null +++ b/recipes/rebar/run_test.sh @@ -0,0 +1,16 @@ +#!/usr/bin/env bash + +set -x +set -e + +rebar --version + +# Dataset: Toy1 +rebar dataset download --name toy1 --tag custom --output-dir dataset/toy1 +rebar run --dataset-dir dataset/toy1 --populations "*" --mask 0,0 --min-length 3 --output-dir output/toy1 +rebar plot --run-dir output/toy1 --annotations dataset/toy1/annotations.tsv + +# Dataset: SARS-CoV-2 +rebar dataset download --name sars-cov-2 --tag 2023-11-30 --output-dir dataset/sars-cov-2/2023-11-30 +rebar run --dataset-dir dataset/sars-cov-2/2023-11-30 --populations "AY.4.2*,BA.5.2,XBC.1.6*,XBB.1.5.1,XBL" --output-dir output/sars-cov-2 +rebar plot --run-dir output/sars-cov-2 --annotations dataset/sars-cov-2/2023-11-30/annotations.tsv From 171a2706a5e648e35c7cc9982b253d6bd36fa704 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 07:51:07 -0500 Subject: [PATCH 1083/2173] Update snakemake-interface-common to 1.14.5 (#44658) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index b99011ecde299..49a7a6b45e002 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.14.4" %} +{% set version = "1.14.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 9a5ab67dcb5298dccb5b19c60c61b80071358700be1b506515b87820e4d1d916 + sha256: e21f9566b2bd04e50f3f73557f2a72e0eb1829f27192c3f8bc00bd240857a689 build: noarch: python From a9fe285dea84d15a80335f7930b44527b049e7b6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 08:00:51 -0500 Subject: [PATCH 1084/2173] Update r-acidgenomes to 0.7.2 (#44659) --- recipes/r-acidgenomes/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenomes/meta.yaml b/recipes/r-acidgenomes/meta.yaml index 64d06436b565f..ef00b8d102371 100644 --- a/recipes/r-acidgenomes/meta.yaml +++ b/recipes/r-acidgenomes/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.1" %} +{% set version = "0.7.2" %} {% set github = "https://github.com/acidgenomics/r-acidgenomes" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 2f44e07480840db87e38eca989f5387a98350c49d57daf1eb9bf1b3448e6e662 + sha256: 7305aeaadbb0507c49b59f3b12971fd6d0f3504473f196f68ac20f59e751d131 build: number: 0 From 4b3de1b13fde795b917134787c7088142fe789df Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 10:30:43 -0500 Subject: [PATCH 1085/2173] Update bionumpy to 1.0.0 (#44663) --- recipes/bionumpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index 6e09348526ff0..0747df16db339 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.31" %} +{% set version = "1.0.0" %} package: name: bionumpy @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5216b0bb72fedae87cfe35a06e189b803b39e5051bcdb347886762a4aaea956d + sha256: 25b2d8baed6705ef8f242f7d755c4fe927d6609232dca338bd485c295ed6b3a7 build: noarch: python From c44eb49f4d983c82838bda1a4479046fe2351c2c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 10:31:03 -0500 Subject: [PATCH 1086/2173] Update npstructures to 0.2.15 (#44664) --- recipes/npstructures/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/npstructures/meta.yaml b/recipes/npstructures/meta.yaml index c83ef94138932..aabf2fa368189 100644 --- a/recipes/npstructures/meta.yaml +++ b/recipes/npstructures/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.14" %} +{% set version = "0.2.15" %} {% set name = "npstructures" %} package: name: {{ name }} @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 2b9b8aab8b9209f3a96e783b2c773dd98be70ef171865b53cc0fbb283b11fee6 + sha256: 6266b74fae8f58d1cdc8967e5a85f557610df4956fae28e6b3eb39ddebb46aae build: From 304e06227fa5dd6402c8fdddeca7601ef99e6a81 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 11:53:46 -0500 Subject: [PATCH 1087/2173] Update cutadapt to 4.6 (#44665) --- recipes/cutadapt/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/cutadapt/meta.yaml b/recipes/cutadapt/meta.yaml index 2d2947af1bfe4..e2d0085e40488 100644 --- a/recipes/cutadapt/meta.yaml +++ b/recipes/cutadapt/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "4.5" %} +{% set version = "4.6" %} package: name: cutadapt version: {{ version }} source: - url: https://files.pythonhosted.org/packages/36/f6/3e040d24a2a475aae2afc193957abe9bc90139b8b72b8a5317198201f2fb/cutadapt-4.5.tar.gz - sha256: 33e56678bb3ba90fd7045d03184b83e135f61e8a6b9f29aa3db8c63611a08e94 + url: https://files.pythonhosted.org/packages/35/b4/f1a7401c3503c17998fb9547b04353217a18323d5d85a3b957f1049ab800/cutadapt-4.6.tar.gz + sha256: 924116f34569248035b16f58e73458ed4c0004e44823b80b07f4ab419272f591 build: number: 0 From bc8e333e9bafda0ddeec7a8ad3f9403c7f80cfda Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 21:12:45 -0500 Subject: [PATCH 1088/2173] Update planemo to 0.75.19 (#44667) --- recipes/planemo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 1d659535dbf15..344b78da1932e 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "planemo" %} -{% set version = "0.75.18" %} -{% set sha256 = "a38c7edef459fd6daaba1f9d63da6ad5b3e39b7a6d62aecd0f71395ae56e6629" %} +{% set version = "0.75.19" %} +{% set sha256 = "4e935cc359071c0aea4a65c965eb96cb5330a33e3dcf66e1a7ad937d72a36083" %} package: name: {{ name|lower }} From 876b3b1e99920276282102360306352d99693416 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 21:13:00 -0500 Subject: [PATCH 1089/2173] Update cptac to 1.5.10 (#44652) * Update cptac to 1.5.9 * Update cptac to 1.5.10 --- recipes/cptac/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cptac/meta.yaml b/recipes/cptac/meta.yaml index bb81951f69797..8a64077d86dde 100644 --- a/recipes/cptac/meta.yaml +++ b/recipes/cptac/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cptac" %} -{% set version = "1.5.8" %} +{% set version = "1.5.10" %} package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: c30d3faf666454c208a103620a094bdb6fea607953305ad48ee069bb7e6e6783 + sha256: 85176554062e73dd0226027baa876357056acd4c81e233082403817252e4fa1e build: number: 0 From e237ceb79aa2876fcfec152273b25d70f18ae06d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 21:14:35 -0500 Subject: [PATCH 1090/2173] Update dnarrange to 1.6.0 (#44657) * Update dnarrange to 1.6.0 * run_exports --------- Co-authored-by: Thanh Lee <247862+thanhleviet@users.noreply.github.com> --- recipes/dnarrange/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/dnarrange/meta.yaml b/recipes/dnarrange/meta.yaml index e62072dfbf40f..750e644ec4904 100644 --- a/recipes/dnarrange/meta.yaml +++ b/recipes/dnarrange/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.5.3" %} +{% set version = "1.6.0" %} package: name: dnarrange @@ -6,13 +6,14 @@ package: source: url: https://github.com/mcfrith/dnarrange/archive/{{ version }}.tar.gz - sha256: 5a1b1b4e3aec6d808fe2811c078af2137eecef7668f9a3dbb0037fe4aebd9b6f + sha256: 2d5622382473586bda425f1873a72bc7413c044d4f993a5e3ead80e12ebdf9d5 build: number: 0 noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv - + run_exports: + - {{ pin_subpackage("dnarrange", max_pin="x.x") }} requirements: host: - python From f04afd0c5a07a6e5e17cadf59e00e348123a2d07 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 21:15:03 -0500 Subject: [PATCH 1091/2173] Update oakvar to 2.9.72 (#44655) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 2f45d4aedd2ee..8691ae13c8cb3 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.71" %} -{% set sha256 = "764174068a918f25715dab3359176e261867a5cf7dac4986c3a0002d92877fe0" %} +{% set version = "2.9.72" %} +{% set sha256 = "4a08936251845c51fedb8bea812ab1f3f8dc71e0652ffa96b794449ebb6ea986" %} package: name: {{ name|lower }} From 3f275fd310807267340954141051888d44eddce9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 22:16:06 -0500 Subject: [PATCH 1092/2173] Update fairease-source to 1.4.4 (#44641) * Update fairease-source to 1.4.2 * Update fairease-source to 1.4.3 * Update fairease-source to 1.4.4 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fairease-source/build.sh | 2 +- recipes/fairease-source/meta.yaml | 15 ++++++++------- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/recipes/fairease-source/build.sh b/recipes/fairease-source/build.sh index 777614692a236..d954115446cb3 100644 --- a/recipes/fairease-source/build.sh +++ b/recipes/fairease-source/build.sh @@ -1,6 +1,6 @@ #!/bin/bash -e -$PYTHON -m pip install --no-deps . +$PYTHON -m pip install --no-deps --no-build-isolation . -vvv # Copy/link executables somewhere on the path python_path=$(find $PREFIX -name SOURCE) diff --git a/recipes/fairease-source/meta.yaml b/recipes/fairease-source/meta.yaml index e1fbf1b345aff..d6ecda35e3cbe 100644 --- a/recipes/fairease-source/meta.yaml +++ b/recipes/fairease-source/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fairease-source" %} -{% set version = "1.4.1" %} +{% set version = "1.4.4" %} package: name: "{{ name|lower }}" @@ -7,21 +7,23 @@ package: source: url: https://github.com/fair-ease/Source/archive/refs/tags/v{{ version }}.tar.gz - sha256: b92fd32f80d6f894da9f130b792fddb3a6f0e1b56aca4d01baa653ed7bcbc1ff + sha256: 2c29f71fe34c6ea6bf45d1bf10340a5dc901bbcf4830d5f892d7bee5ad4f0178 build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage('fairease-source', max_pin="x") }} requirements: host: - - python + - python >=3.6 - pip run: - netCDF4 - numpy - pandas - - python + - python >=3.6 - pykml - scipy - seawater @@ -37,7 +39,7 @@ test: - create_probes_earth_map.py - duplicated_records_remover.py - find_variable_name.py - - insitu_evaluation.py + - insitu_evaluation.py - pointwise_datasets_concatenator.py - ptmp_to_temp.py - real_time_concatenator.py @@ -68,5 +70,4 @@ about: license: CC-BY-NC-4.0 license_family: CC summary: "SOURCE: Sea Observations Utility for Reprocessing, Calibration and Evaluation" - dev_url: https://github.com/fair-ease/Source - + dev_url: https://github.com/fair-ease/Source From e88de66570821b4ae2b1061fef7eb16d1433f493 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 22:22:08 -0500 Subject: [PATCH 1093/2173] Update fastobo to 0.12.3 (#44661) * Update fastobo to 0.12.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fastobo/build.sh | 2 +- recipes/fastobo/meta.yaml | 16 +++++++++------- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/recipes/fastobo/build.sh b/recipes/fastobo/build.sh index 9c8d67584dbb7..fa59a1bd38ab5 100644 --- a/recipes/fastobo/build.sh +++ b/recipes/fastobo/build.sh @@ -19,7 +19,7 @@ sh rustup.sh -y --default-toolchain nightly export PATH="$CARGO_HOME/bin:$PATH" # build statically linked binary with Rust -RUSTFLAGS="-C linker=$CC" C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib $PYTHON -m pip install . --no-deps --ignore-installed -vv +RUSTFLAGS="-C linker=$CC" C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib $PYTHON -m pip install . --no-deps --no-build-isolation -vvv # remove rustup and cargo rm -rf "$RUSTUP_HOME" diff --git a/recipes/fastobo/meta.yaml b/recipes/fastobo/meta.yaml index 917836b262f84..a7722fbb82b30 100644 --- a/recipes/fastobo/meta.yaml +++ b/recipes/fastobo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fastobo" %} -{% set version = "0.12.2" %} +{% set version = "0.12.3" %} package: name: "{{ name | lower }}" @@ -7,28 +7,30 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "2f2779f70ac54874329dddc74cabd86fea88abe56c544c2238076c1d27fe045e" + sha256: "f375932a24b078706797eb9296740f2d2e6987a34309bda7c9f235aba1d74217" build: - number: 2 + number: 0 skip: True # [osx or py27 or py36] + run_exports: + - {{ pin_subpackage('fastobo', max_pin="x.x") }} requirements: build: - wget - {{ compiler('c') }} # [not osx] - {{ compiler('cxx') }} # [not osx] - - clang_osx-64 # [osx] - - clangxx_osx-64 # [osx] + - clang_osx-64 # [osx] + - clangxx_osx-64 # [osx] - pkg-config # [osx] host: - pip - setuptools-rust - python - - libiconv #[osx] + - libiconv # [osx] run: - python - - libiconv #[osx] + - libiconv # [osx] test: imports: From 4367b9274ebed68bd29592adc3cdc23af6618619 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 6 Dec 2023 22:23:55 -0500 Subject: [PATCH 1094/2173] Update hicmatrix to 17.1 (#44670) * Update hicmatrix to 17.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/hicmatrix/build.sh | 3 --- recipes/hicmatrix/meta.yaml | 18 ++++++++++++------ 2 files changed, 12 insertions(+), 9 deletions(-) delete mode 100644 recipes/hicmatrix/build.sh diff --git a/recipes/hicmatrix/build.sh b/recipes/hicmatrix/build.sh deleted file mode 100644 index 3786386a73c83..0000000000000 --- a/recipes/hicmatrix/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/hicmatrix/meta.yaml b/recipes/hicmatrix/meta.yaml index 7014531be701c..6d8a5deba2f6a 100644 --- a/recipes/hicmatrix/meta.yaml +++ b/recipes/hicmatrix/meta.yaml @@ -1,19 +1,24 @@ +{% set name = "hicmatrix" %} +{% set version = "17.1" %} + package: - name: hicmatrix - version: 17 + name: {{ name }} + version: {{ version }} source: - url: https://github.com/deeptools/HiCMatrix/archive/refs/tags/17.tar.gz - sha256: 40d0d0ed670ca8084bd67ec1fe9eb7aff6c180ca0e0fca277f5ad76d25ed97bb + url: https://github.com/deeptools/HiCMatrix/archive/refs/tags/{{ version }}.tar.gz + sha256: 8f431725f7aa548c9774c18e052dabfab10da72e0f0edf0f9dc512b66a4d9df4 build: number: 0 noarch: python + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('hicmatrix', max_pin="x") }} requirements: host: - python >=3.7 - - setuptools - numpy >=1.20 - scipy >=1.2.* - intervaltree >=3.0.* @@ -35,5 +40,6 @@ test: about: home: https://github.com/deeptools/HiCMatrix - license: GPL3 + license: GPL-3.0-or-later + license_family: GPL3 summary: Library to manage Hi-C matrices for HiCExplorer and pyGenomeTracks From 07edfe26baa3ccfe62dce1b23e7482ffb0ca9b41 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Dec 2023 10:05:47 -0500 Subject: [PATCH 1095/2173] Update arcs to 1.2.6 (#44669) * Update arcs to 1.2.6 * add run_exports * add make back to run deps --------- Co-authored-by: joshuazhuang7 --- recipes/arcs/meta.yaml | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/recipes/arcs/meta.yaml b/recipes/arcs/meta.yaml index e7a813f95e16c..e32cd8699d69f 100644 --- a/recipes/arcs/meta.yaml +++ b/recipes/arcs/meta.yaml @@ -1,15 +1,17 @@ -{% set version = "1.2.5" %} +{% set version = "1.2.6" %} package: name: arcs version: {{ version }} build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('arcs', max_pin="x") }} source: url: https://github.com/bcgsc/arcs/releases/download/v{{ version }}/arcs-{{ version }}.tar.gz - sha256: 9bf0fc0f2da748356339ce3a89edbffc5b63804cb3680829391365bb7de8ca39 + sha256: 6efc120d55212bfb0483a262731827318ec0a5f037d4984da8445cc3788ba297 requirements: build: @@ -19,11 +21,10 @@ requirements: - boost-cpp - sparsehash - zlib - - llvm-openmp # [osx] + - llvm-openmp # [osx] - btllib run: - - zlib - - llvm-openmp # [osx] + - llvm-openmp # [osx] - make test: @@ -33,6 +34,7 @@ test: about: home: https://github.com/bcgsc/arcs - license: GPL-3.0 + license: GPL-3.0-or-later + license_family: GPL3 license_file: '{{ environ["RECIPE_DIR"] }}/LICENSE' - summary: Scaffolding genome sequence assemblies using linked or long reads + summary: Scaffolding genome sequence assemblies using linked or long reads From cc2d249958164c2bb99a7e67fbf32a2ef01e9837 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Dec 2023 10:06:03 -0500 Subject: [PATCH 1096/2173] Update last to 1519 (#44672) --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 92ee402755a58..22cfbe700d846 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1518" %} +{% set version = "1519" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: 9b41bd90a786a4538ca79d0f4b03cfb353423e929ae537f6d953c57e11b8dd04 + sha256: 2c1ab2d5671fbe96f47e94c6f5d77805cdb36c1afda3906e07e18fb6bb77d013 build: number: 0 From b55dc6b86715266d2e406da1ddf54957241f5a30 Mon Sep 17 00:00:00 2001 From: Matt Holt Date: Thu, 7 Dec 2023 09:07:14 -0600 Subject: [PATCH 1097/2173] initial copy-modify from hiphase recipe (#44668) --- recipes/pbstarphase/build.sh | 7 +++++++ recipes/pbstarphase/meta.yaml | 35 +++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 recipes/pbstarphase/build.sh create mode 100644 recipes/pbstarphase/meta.yaml diff --git a/recipes/pbstarphase/build.sh b/recipes/pbstarphase/build.sh new file mode 100644 index 0000000000000..9ea2f67d671bb --- /dev/null +++ b/recipes/pbstarphase/build.sh @@ -0,0 +1,7 @@ +#!/usr/bin/env bash + +mkdir -p "${PREFIX}"/bin +# bioconda auto-extract for us apparently +# tar -xzf pbstarphase-*.tar.gz +md5sum -c pbstarphase.md5 +cp pbstarphase "${PREFIX}"/bin/ diff --git a/recipes/pbstarphase/meta.yaml b/recipes/pbstarphase/meta.yaml new file mode 100644 index 0000000000000..91eed38e8b5fc --- /dev/null +++ b/recipes/pbstarphase/meta.yaml @@ -0,0 +1,35 @@ +{% set name = "pbstarphase" %} +{% set version = "0.7.2" %} +{% set sha256 = "a10a1d4e9e7aaa3fc18c207ab0483cd39ac2624ef96730903aa5aac970fb4e7c" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/PacificBiosciences/pb-StarPhase/releases/download/v{{ version }}/pbstarphase-v{{ version }}-x86_64-unknown-linux-gnu.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('pbstarphase', max_pin="x") }} + +test: + commands: + - pbstarphase --version + +about: + home: https://github.com/PacificBiosciences/pb-StarPhase + license: BSD-3-Clause-Clear + summary: A phase-aware pharmacogenomic diplotyper for PacBio sequencing data + +extra: + recipe-maintainers: + - holtjma + - ctsa + - zeeev + skip-lints: + - should_use_compilers + - should_be_noarch_generic From cedb73b0dfa649bf0f96803dcea9e093989ae20e Mon Sep 17 00:00:00 2001 From: Bhavya Papudeshi Date: Fri, 8 Dec 2023 01:48:49 +1030 Subject: [PATCH 1098/2173] update to sphae v1.3.2 (#44673) * add sphae v1.3.1 * update meta.yml * update sphae meta.yaml * update sphae meta.yaml * update sphae meta.yaml sphae version * update sphae meta.yaml sphae version * updating to sphae v1.3.2 * add sphae v1.3.2 --- recipes/sphae/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/sphae/meta.yaml b/recipes/sphae/meta.yaml index 8942e6a5f5937..2f20b1f849694 100644 --- a/recipes/sphae/meta.yaml +++ b/recipes/sphae/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sphae" %} -{% set version = "1.3.1b" %} +{% set version = "1.3.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/linsalrob/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: ffdb5ae19858f8c7642d580c156cd3da9bb97731e90f2eb9549d34c4a788d754 + sha256: 922cb7bb85eb310bca57996a5165c17199b1b8a5722d890f9f2a88c271532619 build: number: 0 @@ -28,7 +28,6 @@ requirements: - pyyaml >=6.0 - click >=8.1.3 - jinja2 >=3.0.2 - - mamba <1.5.3 - metasnek >=0.0.4 - snaketool-utils >=0.0.4 - attrmap >=0.0.7 From 145de1c29f6d90d1f43b5e63877732f23920b15d Mon Sep 17 00:00:00 2001 From: kowallus Date: Thu, 7 Dec 2023 16:21:21 +0100 Subject: [PATCH 1099/2173] Update mbgc to 2.0.1 (#44660) * Update mbgc to 2.0.1 * modified test for osx * resigned from avx for osx build * reverted test command * updated sha256 * trigger * sha256 update --- recipes/mbgc/build.sh | 7 ++++++- recipes/mbgc/meta.yaml | 10 +++++++--- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/recipes/mbgc/build.sh b/recipes/mbgc/build.sh index 241cc53ea2f60..5ba02c5655448 100644 --- a/recipes/mbgc/build.sh +++ b/recipes/mbgc/build.sh @@ -9,5 +9,10 @@ export CFLAGS="$CFLAGS -I$BUILD_PREFIX/include" export CXXFLAGS="$CFLAGS -I$BUILD_PREFIX/include" export LDFLAGS="$LDFLAGS -L$BUILD_PREFIX/lib" cmake .. -make mbgc +if [[ "$(uname)" == "Linux" ]]; then + make mbgc +else + make mbgc-noavx + mv mbgc-noavx mbgc +fi cp mbgc $PREFIX/bin diff --git a/recipes/mbgc/meta.yaml b/recipes/mbgc/meta.yaml index cc8deff5207e3..12643af3c5da8 100644 --- a/recipes/mbgc/meta.yaml +++ b/recipes/mbgc/meta.yaml @@ -1,24 +1,27 @@ -{% set version = "2.0" %} +{% set version = "2.0.1" %} package: name: mbgc version: {{ version }} build: - skip: True # [osx] number: 0 run_exports: - {{ pin_subpackage('mbgc', max_pin="x") }} source: url: https://github.com/kowallus/mbgc/archive/refs/tags/v{{ version }}.tar.gz - sha256: 58620079cd813cd7bc8c5362af514fb92bf166a71f7f5f978923e36dd5bd655d + sha256: fb422fc89aa95d82dab0b1431b7f220d5f4cdab2dfc1141218e74668461fa530 requirements: build: - {{ compiler('cxx') }} - cmake >=3.5 - make + host: + - llvm-openmp # [osx] + run: + - llvm-openmp # [osx] test: commands: @@ -34,3 +37,4 @@ about: extra: maintainers: - kowallus + From 5d291000656cfb69e9b393f003e0f341ca0cac0e Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Thu, 7 Dec 2023 17:32:15 +0000 Subject: [PATCH 1100/2173] Fix lotus2 2.30 updated requirements (#44676) --- recipes/lotus2/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/lotus2/meta.yaml b/recipes/lotus2/meta.yaml index 5ba5d2a771b3a..17d78892937f9 100644 --- a/recipes/lotus2/meta.yaml +++ b/recipes/lotus2/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -25,15 +25,17 @@ requirements: - cd-hit - clustalo - fasttree + - hmmer >=3.1 - infernal - iqtree - itsx - - lambda <2 + - lambda >=3,<4 - lca >=0.25 - mafft - minimap2 - perl - perl-getopt-long + - pigz - r-dplyr - rdp_classifier - rtk From 97a59722bae09cd11b1124ae12bb53a00b914f9c Mon Sep 17 00:00:00 2001 From: Mohsen Taheri Date: Thu, 7 Dec 2023 16:02:29 -0500 Subject: [PATCH 1101/2173] Add YACHT to bioconda (#44326) * add meta.yaml file * version1.0 * resolving comments * delete license file in about section * resolve test issue * delete tests * new release * adding tests * build with post-link.sh on bioconda * add hash * set build number to 0 * delete build field * ignore lint error * delete env variable * add rust and cargo in host section * remove cargo as dependencies in host section * add compiler c * delete noarch * add llvm and clang to dependencies * add libclang-dev in host * add maturin * add libclang to host section * add cmake * add # [unix] to libclang * release just for unix base systems * small correction * exact same meta.yaml that sourmash team used to deploy branchwater in conda-forge * add build.sh * small change * delete marturin line * add libclang path to post-link.sh * added branchwater dependency * add noarch: python * delete noarch * skip noarch check * add skip lints * using env variable for python * remove should use compiler skip lint * add should use compiler skip lint * remove unnecessary runtime dependencies --- recipes/yacht/meta.yaml | 67 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 recipes/yacht/meta.yaml diff --git a/recipes/yacht/meta.yaml b/recipes/yacht/meta.yaml new file mode 100644 index 0000000000000..3155b743cd2d6 --- /dev/null +++ b/recipes/yacht/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.0" %} + +package: + name: yacht + version: {{ version }} + +source: + url: https://github.com/KoslickiLab/YACHT/releases/download/v{{ version }}/yacht-{{ version }}.tar.gz + sha256: 93b8584774ecc0b72e9778566a348e3649d7e418699e3c27bad68c14d3f15384 + +build: + number: 0 + noarch: python + skip: True # [win or osx] + script: "{{ PYTHON }} -m pip install . --ignore-installed --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('yacht', max_pin="x") }} + +requirements: + host: + - python >3.6 + - pip + run: + - python >3.6 + - sourmash >=4.8.3,<5 + - scipy + - numpy + - pandas + - scikit-learn + - codecov + - pytest + - pytest-cov + - loguru + - tqdm + - biom-format + - pytaxonkit + - openpyxl + - sourmash_plugin_branchwater + +test: + commands: + - yacht --help + +about: + home: https://github.com/KoslickiLab/YACHT + summary: 'YACHT is a mathematically rigorous hypothesis test for the presence or absence of organisms in a metagenomic sample, based on average nucleotide identity (ANI).' + license: MIT + dev_url: https://github.com/KoslickiLab/YACHT + doc_url: https://github.com/KoslickiLab/YACHT/wiki + +extra: + skip-lints: + - should_not_be_noarch_skip + - should_use_compilers + identifiers: + - doi:10.1101/2023.04.18.537298 + recipe-maintainers: + - dkoslicki + authors: + - dkoslicki + - chunyuma + - sew347 + - mlupei + - mfl15 + - ShaopengLiu1 + - raquellewei + - mohsenht From 02a999be171d9633a0c835a2460fa4fd8e9d1bae Mon Sep 17 00:00:00 2001 From: Leandro Lima Date: Thu, 7 Dec 2023 21:05:43 +0000 Subject: [PATCH 1102/2173] Update COBS to v0.3.0 (#44685) * fix: updating COBS to v0.3.0 * fix: small fix to build.run_exports.max_pin --- recipes/cobs/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/cobs/meta.yaml b/recipes/cobs/meta.yaml index ae42225155e83..76cb1c7eca1d7 100644 --- a/recipes/cobs/meta.yaml +++ b/recipes/cobs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.1" %} +{% set version = "0.3.0" %} {% set name = "cobs" %} package: @@ -7,10 +7,12 @@ package: source: url: https://github.com/iqbal-lab-org/{{ name }}/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.gz - sha256: ce2ab77ffb17327250244f47481e100df5191a3e8c218e9725cb5e9c80e24ee2 + sha256: 5597f0c366be3acc6fe3b59d2c49ef46696bb7676fe72fb99dd74deb4c8c192e build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} requirements: build: From 7be5a271cad03086947f9927e511781959b40376 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Dec 2023 16:20:57 -0500 Subject: [PATCH 1103/2173] Update pybiolib to 1.1.1598 (#44674) * Update pybiolib to 1.1.1583 * Update pybiolib to 1.1.1596 * Update pybiolib to 1.1.1598 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index b40ea91070407..8dfe6c8c95ffc 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1571" %} +{% set version = "1.1.1598" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: bec8cc60aa02c934f0a3a40ed8831cc2708ab507504788d77345069436a7de89 + sha256: 206d44c2e2606d785750ad2b3811622f272ffdc4a8fee6528c3ba853200f2a22 build: noarch: python From 9217392a1da8355f730fb10dcbb4ad2c0469ae1a Mon Sep 17 00:00:00 2001 From: Rhys Newell Date: Fri, 8 Dec 2023 11:01:58 +1100 Subject: [PATCH 1104/2173] Update lorikeet-genome version v0.8.2 (#44654) * chore: update lorikeet version and recipe * fix: fix linting issues by removing pip section * fix: remove lorikeet from blacklist as associated error is fixed * fix: pinned subpackage error * fix: package name and folder matching * fix: sha256 correction * fix: change install path * fix: python version must be the same at runtime * fix: python version must be compatible with scikit-allel --------- Co-authored-by: Thanh Lee <247862+thanhleviet@users.noreply.github.com> --- build-fail-blacklist | 3 -- recipes/lorikeet-genome/build.sh | 2 +- recipes/lorikeet-genome/meta.yaml | 57 ++++++++++++++----------------- 3 files changed, 27 insertions(+), 35 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 67c1df1136542..8b4c49af4f690 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -357,9 +357,6 @@ recipes/conduit-assembler recipes/metabat2 recipes/bcftools-snvphyl-plugin -# error: no matching package named `bird_tool_utils` found location searched: https://github.com/wwood/galah#8440eeb8 required by package `galah v0.3.1 (https://github.com/wwood/galah#8440eeb8)` ... which satisfies git dependency `galah` of package `lorikeet-genome v0.7.3 -recipes/lorikeet-genome - # rnamoves.c:(.text.RNA2_move_noLP_bpshift+0x1f): undefined reference to `close_bp' recipes/kinsimriboswitch diff --git a/recipes/lorikeet-genome/build.sh b/recipes/lorikeet-genome/build.sh index d527f13682240..d7a50654b5c60 100644 --- a/recipes/lorikeet-genome/build.sh +++ b/recipes/lorikeet-genome/build.sh @@ -12,4 +12,4 @@ C_INCLUDE_PATH=$PREFIX/include \ LIBRARY_PATH=$PREFIX/lib \ LIBCLANG_PATH=$PREFIX/lib/libclang.so \ OPENSSL_DIR=$PREFIX \ -cargo install --force --root $PREFIX +cargo install --path ./ --force --root $PREFIX diff --git a/recipes/lorikeet-genome/meta.yaml b/recipes/lorikeet-genome/meta.yaml index cce4b74e27507..74cd2f2cb9905 100644 --- a/recipes/lorikeet-genome/meta.yaml +++ b/recipes/lorikeet-genome/meta.yaml @@ -1,62 +1,57 @@ -{% set version = "0.7.3" %} -{% set name = "lorikeet" %} -{% set sha256 = "663e53c2451e06af3334b612a7518180fa528e2d12ebe869f74f78996e2a82a5" %} +{% set version = "0.8.2" %} +{% set name = "lorikeet-genome" %} +{% set sha256 = "125fb87f7aa586aa92183ed2c11721477d0b2ba2481f80a1e047ab581e3ff50b" %} package: - name: lorikeet-genome + name: {{ name }} version: {{ version }} build: - number: 2 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} source: - url: https://github.com/rhysnewell/{{ name }}/archive/v{{ version }}.tar.gz + url: https://github.com/rhysnewell/lorikeet/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: build: - - rust >=1.40 - - python >=3.9 + - rust >=1.70 + - python ==3.10 - {{ compiler('c') }} - {{ compiler('cxx') }} - - perl - pkg-config - make - cmake host: - zlib - - gsl + - blis - libblas + - openblas - openssl - - htslib + - clangdev run: - - python >=3.9 - - htslib - - parallel - - numpy - - matplotlib-base + - samtools >=1.9 + - coreutils + - python ==3.10 - prodigal + - minimap2 >=2.24 + - bwa >=0.7.17 + - bwa-mem2 + - numpy + - scikit-allel >=1.3.6 - svim - - samtools >=1.9 - bcftools - - vt - - zlib - - gsl - - starcode - - bwa >=0.7.17 - - bwa-mem2 >=2.2.1 - - minimap2 - - fastani - - dashing - - ngmlr - - scikit-allel - - polars - - scipy + - pip + - polars >=0.18 + - scipy >=1.11 + - cmake >=3.21 test: commands: - - {{ name }} --version | grep '{{ version }}' + - lorikeet --version | grep '{{ version }}' about: home: https://github.com/rhysnewell/Lorikeet From 7b71b1b957fd840fd28de3f9d4a7ab8a66de95f3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Dec 2023 20:05:37 -0500 Subject: [PATCH 1105/2173] Update sequana to 0.16.3 (#44633) * Update sequana to 0.16.2 * Update sequana to 0.16.3 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/sequana/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequana/meta.yaml b/recipes/sequana/meta.yaml index 7e25a04a05c6a..d96325a4a17b5 100644 --- a/recipes/sequana/meta.yaml +++ b/recipes/sequana/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.16.1" %} -{% set sha256 = "5a519ca7156109c044cce41b6414e750dd5a257c11f78fc443abf8c2f6652b48" %} +{% set version = "0.16.3" %} +{% set sha256 = "4a9f0c8dbbd23fad6517d601b835319d6942337a670ded685a412ba06180e546" %} {% set name = "sequana" %} package: From 5a285634567e685e5414bd182c5c4fabd1a1faec Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Dec 2023 20:05:53 -0500 Subject: [PATCH 1106/2173] Update pegs to 0.6.6 (#44678) * Update pegs to 0.6.6 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/pegs/meta.yaml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/pegs/meta.yaml b/recipes/pegs/meta.yaml index 4b6a293b1df68..7aad68b4c5830 100644 --- a/recipes/pegs/meta.yaml +++ b/recipes/pegs/meta.yaml @@ -1,21 +1,23 @@ {% set name = "pegs" %} -{% set version = "0.6.5" %} +{% set version = "0.6.6" %} package: - name: "{{ name|lower }}" + name: "{{ name|lower }}" version: "{{ version }}" source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 33bbb01db501edba4081bb0970297f9abfd130623e5a11e821bb0369ee1f978c + sha256: b19059cb2de25ec3c9cbeafb333ffbac417fcd28ccf64680e7bb42ecacb4d467 build: number: 0 entry_points: - pegs = pegs.cli:pegs - mk_pegs_intervals = pegs.cli:mk_pegs_intervals - script: "{{ PYTHON }} -m pip install . -vv" - noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + noarch: python + run_exports: + - {{ pin_subpackage('pegs', max_pin="x.x") }} requirements: host: @@ -42,7 +44,7 @@ test: about: home: "https://github.com/fls-bioinformatics-core/pegs" - license: BSD + license: BSD-3-Clause license_family: BSD license_file: LICENSE summary: "Peak-set Enrichment of Gene-Sets (PEGS)" From 5e1648f4966e849654671a77d4624696fd5689ca Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 7 Dec 2023 19:38:00 -0600 Subject: [PATCH 1107/2173] Update peptide-shaker to 3.0.3 (#44690) --- recipes/peptide-shaker/meta.yaml | 8 ++++---- recipes/peptide-shaker/peptide-shaker.py | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/peptide-shaker/meta.yaml b/recipes/peptide-shaker/meta.yaml index 31071e2cc8831..4185fdcc4869e 100644 --- a/recipes/peptide-shaker/meta.yaml +++ b/recipes/peptide-shaker/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the peptide-shaker.py file {% set name = "PeptideShaker" %} -{% set version = "3.0.1" %} -{% set sha256 = "3f3f34c9b3f5640e39dbb5b4fd83549701353d0c2884c6742c5e40b54ba859f3"%} +{% set version = "3.0.3" %} +{% set sha256 = "528a526595317c033534bf7bb5fbca3368139df6c3123d11e2397182c4f0007e" %} package: name: peptide-shaker @@ -10,7 +10,7 @@ package: build: number: 0 noarch: generic - # Due to backend changes in v3.0.0, older PeptideShaker projects can not be opened in this new version. + # Due to backend changes in v3.0.0, older PeptideShaker projects can not be opened in newer versions (v3.0.0+). run_exports: - {{ pin_subpackage('peptide-shaker', max_pin="x.x") }} @@ -31,7 +31,7 @@ test: about: home: "https://compomics.github.io/projects/peptide-shaker.html" dev_url: "https://github.com/compomics/peptide-shaker" - license: Apache License 2.0 + license: Apache-2.0 license_family: APACHE summary: Independent platform for interpretation of proteomics identification results description: diff --git a/recipes/peptide-shaker/peptide-shaker.py b/recipes/peptide-shaker/peptide-shaker.py index ddca31961a444..cf551f496a7de 100755 --- a/recipes/peptide-shaker/peptide-shaker.py +++ b/recipes/peptide-shaker/peptide-shaker.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'PeptideShaker-3.0.1.jar' +jar_file = 'PeptideShaker-3.0.3.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] From 3928ca97abdc3560f6fdb69cdeaf762ceea7f2d3 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 7 Dec 2023 19:47:06 -0600 Subject: [PATCH 1108/2173] Update searchgui to 4.3.3 (#44691) --- recipes/searchgui/meta.yaml | 4 ++-- recipes/searchgui/searchgui.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index 3b30556a6c98f..a3ab75e2274aa 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the searchgui.py file {% set name = "SearchGUI" %} -{% set version = "4.3.1" %} -{% set sha256 = "ef21ea768d5f67f4c4c6c1d592bfc68f2aa62ce1f0f69f7966918a2442918c18" %} +{% set version = "4.3.3" %} +{% set sha256 = "503331735883d6ebbc7b3f77bc5ebaf9e609833d475b69920c69b05bad6d35b8" %} {% set build = "0" %} package: diff --git a/recipes/searchgui/searchgui.py b/recipes/searchgui/searchgui.py index 7c365e0a1105d..298cb9a26bcf3 100755 --- a/recipes/searchgui/searchgui.py +++ b/recipes/searchgui/searchgui.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'SearchGUI-4.3.1.jar' +jar_file = 'SearchGUI-4.3.3.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] From 94f94e6cfb4860d31687079c9164222d37b02c61 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 7 Dec 2023 19:51:26 -0600 Subject: [PATCH 1109/2173] Update iqtree to 2.2.6 (#44689) --- recipes/iqtree/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/iqtree/meta.yaml b/recipes/iqtree/meta.yaml index f4d9d77c0de13..546ddf58b9357 100644 --- a/recipes/iqtree/meta.yaml +++ b/recipes/iqtree/meta.yaml @@ -1,6 +1,6 @@ {% set name = "IQTREE" %} -{% set version = "2.2.5" %} -{% set sha256 = "e7b34c1fb73b21a7af337ef05685b96d4791585815faccbccd8221179486ed9b" %} +{% set version = "2.2.6" %} +{% set sha256 = "8026bf089a135f4586ebca43fff9af6d4718a936f262b5ea11648b8947782c42" %} package: name: {{ name|lower }} @@ -39,6 +39,7 @@ about: home: "http://www.iqtree.org/" dev_url: "https://github.com/iqtree/iqtree2" license: GPL-2.0-or-later + license_family: GPL2 license_file: LICENSE summary: "Efficient phylogenomic software by maximum likelihood." From 3cdf9936bb0f7c1661b03725be78d98b4dba3fbe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Dec 2023 20:59:15 -0500 Subject: [PATCH 1110/2173] Update atropos to 1.1.32 (#44682) * Update atropos to 1.1.32 * add run_exports * add run_exports * try removing patch --------- Co-authored-by: joshuazhuang7 --- recipes/atropos/meta.yaml | 18 ++++++------ recipes/atropos/python310.patch | 49 --------------------------------- 2 files changed, 9 insertions(+), 58 deletions(-) delete mode 100644 recipes/atropos/python310.patch diff --git a/recipes/atropos/meta.yaml b/recipes/atropos/meta.yaml index 407d86835a930..88e84a06fad27 100644 --- a/recipes/atropos/meta.yaml +++ b/recipes/atropos/meta.yaml @@ -1,6 +1,6 @@ {% set name = "atropos" %} -{% set version = "1.1.31" %} -{% set hash = "5219575de12334d4b6a365ff682d6271d54fb01568ae52cc27522e33684789c6" %} +{% set version = "1.1.32" %} +{% set sha256 = "17e9dc3d76d7a2ca607a12da191a6d7ba1cfbd1a8c924215870417f85858fd83" %} package: name: {{ name }} @@ -8,15 +8,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: {{ hash }} - patches: - - python310.patch + sha256: {{ sha256 }} build: - number: 3 + number: 0 # Ensure Cython is rerun by removing *.c output files and PKG-INFO (checked for by setup.py) - script: find . "(" -name "*.c" -o -name PKG-INFO ")" -exec rm {} ";" && python -m pip install --no-deps --ignore-installed . - skip: True # [py27] + script: find . "(" -name "*.c" -o -name PKG-INFO ")" -exec rm {} ";" && {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv + run_exports: + - {{ pin_subpackage('atropos', max_pin="x") }} requirements: build: @@ -36,6 +35,7 @@ test: - atropos | grep "Atropos version" about: - home: https://atropos.readthedocs.io/ + home: https://github.com/jdidion/atropos license: CC0 and partly MIT summary: 'trim adapters from high-throughput sequencing reads' + doc_url: https://atropos.readthedocs.io diff --git a/recipes/atropos/python310.patch b/recipes/atropos/python310.patch deleted file mode 100644 index cb8c9ba8952c8..0000000000000 --- a/recipes/atropos/python310.patch +++ /dev/null @@ -1,49 +0,0 @@ -commit 740d337e89320dbd1ba5c011333193cbb5eb952a -Author: John Marshall -Date: Sun Sep 11 17:45:11 2022 +0100 - - Import ABCs from collections.abc (Python 3.10 compatibility) - - These classes are no longer available in collections in 3.10. - The collections.abc module was introduced in 3.3, and atropos - supports only Python >= 3.3, so fortunately there is no need - to make this conditional. - -diff --git a/atropos/commands/base.py b/atropos/commands/base.py -index 2a05b6c..0a5cd9e 100644 ---- a/atropos/commands/base.py -+++ b/atropos/commands/base.py -@@ -1,6 +1,6 @@ - """Common classes/functions used in commands. - """ --from collections import Sequence -+from collections.abc import Sequence - import copy - import platform - import sys -diff --git a/atropos/commands/trim/__init__.py b/atropos/commands/trim/__init__.py -index c8d6cb8..536c2a5 100644 ---- a/atropos/commands/trim/__init__.py -+++ b/atropos/commands/trim/__init__.py -@@ -1,6 +1,7 @@ - """Implementation of the 'trim' command. - """ --from collections import Sequence, defaultdict -+from collections import defaultdict -+from collections.abc import Sequence - import logging - import os - import sys -diff --git a/atropos/util/__init__.py b/atropos/util/__init__.py -index d5d9bf3..68af7a2 100644 ---- a/atropos/util/__init__.py -+++ b/atropos/util/__init__.py -@@ -1,6 +1,7 @@ - """Widely useful utility methods. - """ --from collections import OrderedDict, Iterable, Sequence -+from collections import OrderedDict -+from collections.abc import Iterable, Sequence - from datetime import datetime - import errno - import functools From 808fd96e091f565256cc44da43fa5ff4320e60c4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Dec 2023 21:38:46 -0500 Subject: [PATCH 1111/2173] Update genoboo to 0.4.12 (#44679) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/genoboo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genoboo/meta.yaml b/recipes/genoboo/meta.yaml index c7ad9fc8ac572..1ea6112da89ba 100644 --- a/recipes/genoboo/meta.yaml +++ b/recipes/genoboo/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'genoboo' %} -{% set version = '0.4.11' %} -{% set sha256 = '3511b73acccacd07cf15dc30f70fbb8907f65cefeb7caa82e63a9dda2dab664a' %} +{% set version = '0.4.12' %} +{% set sha256 = 'd8c280a174360c03ad4be4292e628ccf416a170771a369aa4bf32a5cebf1085e' %} package: name: {{ name|lower }} From d8a849b65ace81a014d4cc6aa01c95715c159249 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Dec 2023 21:39:21 -0500 Subject: [PATCH 1112/2173] Update kinex to 1.0.2 (#44683) --- recipes/kinex/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/kinex/meta.yaml b/recipes/kinex/meta.yaml index b22d57e489243..80ebad9c3037b 100644 --- a/recipes/kinex/meta.yaml +++ b/recipes/kinex/meta.yaml @@ -1,5 +1,5 @@ {% set name = "kinex" %} -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/bedapub/{{ name }}/archive/v{{ version }}.tar.gz" - sha256: 8f153d85657e16f0bae58df8d5a6cb52f8ba28ff992203e7762d81e04a448e0d + sha256: ec9809bf7f401a064824d4883ef2877d945e65b7eb1e6f10b160590b515f4553 build: number: 0 @@ -47,4 +47,4 @@ about: extra: identifiers: - - doi:10.1101/2023.11.23.568445 \ No newline at end of file + - doi:10.1101/2023.11.23.568445 From 144713adb725e26d3d82abbea525754046c00fe0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Dec 2023 21:39:32 -0500 Subject: [PATCH 1113/2173] Update oakvar to 2.9.75 (#44686) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 8691ae13c8cb3..2f9dfadd88054 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.72" %} -{% set sha256 = "4a08936251845c51fedb8bea812ab1f3f8dc71e0652ffa96b794449ebb6ea986" %} +{% set version = "2.9.75" %} +{% set sha256 = "d81393e19ca016dff38f3daa69ee58cc1801fb36794bccfbecd51a1037f523fe" %} package: name: {{ name|lower }} From 741f4eceb22f1af23c7cc3089622d9df8702a7f7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Dec 2023 21:39:42 -0500 Subject: [PATCH 1114/2173] Update el_gato to 1.15.0 (#44687) --- recipes/el_gato/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/el_gato/meta.yaml b/recipes/el_gato/meta.yaml index c4ddd980219d7..657700715c719 100644 --- a/recipes/el_gato/meta.yaml +++ b/recipes/el_gato/meta.yaml @@ -1,6 +1,6 @@ {% set name = "el_gato" %} -{% set version = "1.14.4" %} -{% set hash = "120b294baa58d833d9973da2d203eb88090a4ecc9538a34b0c5d6c8382cac1a4" %} +{% set version = "1.15.0" %} +{% set hash = "2f2b8942c8327531ad69fe178eb0b1a050402d31f647e6a03e01f6dd3a9db510" %} {% set user = "appliedbinf" %} package: From f0fdba1bd4bb5fe504a127f41613f3d75a26c490 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 7 Dec 2023 21:39:51 -0500 Subject: [PATCH 1115/2173] Update haplotaglr to 1.1.5 (#44688) --- recipes/haplotaglr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/haplotaglr/meta.yaml b/recipes/haplotaglr/meta.yaml index 2248cea8c0e91..474b17810f67c 100644 --- a/recipes/haplotaglr/meta.yaml +++ b/recipes/haplotaglr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "HaplotagLR" %} -{% set version = "1.1.4" %} +{% set version = "1.1.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e15dada6a1ee99080e4f1a1b80a80976a2d528f85d41a4e58ed016dff6f4545d + sha256: 5cbaa37b817a40f4b06ff3437f24e5364d516477df3abd550e3b00382be7b7f8 build: number: 0 From c32dffbedf2e84777d1751ea5d6050aa5198bd93 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Dec 2023 08:20:01 -0500 Subject: [PATCH 1116/2173] Update vembrane to 1.0.4 (#44680) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update vembrane to 1.0.4 * add run_exports * Update meta.yaml --------- Co-authored-by: joshuazhuang7 Co-authored-by: Felix Mölder --- recipes/vembrane/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/vembrane/meta.yaml b/recipes/vembrane/meta.yaml index 31bd417db94f3..753f85df6c5f3 100644 --- a/recipes/vembrane/meta.yaml +++ b/recipes/vembrane/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.3" %} +{% set version = "1.0.4" %} package: name: vembrane @@ -6,26 +6,28 @@ package: source: url: https://pypi.io/packages/source/v/vembrane/vembrane-{{ version }}.tar.gz - sha256: c788e7077a10b388f5fb2f78f79a99025d1d5871af1bc1655e98d3b6a21c97d7 + sha256: 8d0892c61e4172440390f89cbda16ba2fccd0c519a3e763a0e3950479869673c build: number: 0 entry_points: - vembrane = vembrane.cli:main noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('vembrane', max_pin="x") }} requirements: host: - pip - - poetry >=0.12 + - poetry >=1.5.1 - python >=3.8 run: - asttokens >=2.0,<3.0 - intervaltree >=3.0,<4.0 - numpy >=1.23,<2.0 - pysam >=0.20,<0.21 - - python >=3.8,<4 + - python >=3.8 - pyyaml >=6.0,<7 test: @@ -38,6 +40,7 @@ test: about: home: https://github.com/vembrane/vembrane license: MIT + license_family: MIT license_file: LICENSE summary: Filter VCF/BCF files with Python expressions. From 1815e52f0e8855b64e6b7a0bde993ba9c2588140 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Dec 2023 10:05:52 -0500 Subject: [PATCH 1117/2173] Update dnarrange to 1.6.1 (#44695) --- recipes/dnarrange/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnarrange/meta.yaml b/recipes/dnarrange/meta.yaml index 750e644ec4904..5bf8821eb06a2 100644 --- a/recipes/dnarrange/meta.yaml +++ b/recipes/dnarrange/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.6.0" %} +{% set version = "1.6.1" %} package: name: dnarrange @@ -6,7 +6,7 @@ package: source: url: https://github.com/mcfrith/dnarrange/archive/{{ version }}.tar.gz - sha256: 2d5622382473586bda425f1873a72bc7413c044d4f993a5e3ead80e12ebdf9d5 + sha256: e5046acb96e561b3dc12c4685eb0acf3170b812577a32655c08c21b8eb5a957d build: number: 0 From d329b8814767239d9cd9891cbc8884186d4074bc Mon Sep 17 00:00:00 2001 From: M Bernt Date: Fri, 8 Dec 2023 16:06:14 +0100 Subject: [PATCH 1118/2173] ezomero: initial commit (#44675) * ezomero: initial commit * Add python to run dependencies Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ezomero/meta.yaml | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 recipes/ezomero/meta.yaml diff --git a/recipes/ezomero/meta.yaml b/recipes/ezomero/meta.yaml new file mode 100644 index 0000000000000..c7c97d63bc839 --- /dev/null +++ b/recipes/ezomero/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.1.0" %} +{% set name = "ezomero" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 729db284c27067b8accb127c6501b2205f63e639045339e6939f7c991f0759c7 + +build: + noarch: python + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + run_exports: + - {{ pin_subpackage("ezomero", max_pin="x.x") }} +requirements: + host: + - pip + - python >=3.8 + run: + - python >=3.8 + - omero-py =5.16 + - numpy >=1.22,<2.0 + +test: + imports: + - ezomero + +about: + home: https://github.com/TheJacksonLaboratory/ezomero + license: GPL-2.0-only + license_file: LICENSE + summary: A module with convenience functions for writing Python code that interacts with OMERO From 382f876d68af5a2e74be26ffa1bd95b287107faf Mon Sep 17 00:00:00 2001 From: llegregam <75795040+llegregam@users.noreply.github.com> Date: Fri, 8 Dec 2023 16:42:03 +0100 Subject: [PATCH 1119/2173] Add influx data manager v0.1.2 (#44677) * Add influx-si-data-manager v0.1.1 * meta.yml fix * Removed unnecessary pin_subpackage step * fixed pin_subpackage step * Removed whitespaces * Removed typo in LICENCE file name * Fixed license not in tarball * Fixed home link not in recipe * Changed license short id --- recipes/influx-si-data-manager/meta.yaml | 46 ++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/influx-si-data-manager/meta.yaml diff --git a/recipes/influx-si-data-manager/meta.yaml b/recipes/influx-si-data-manager/meta.yaml new file mode 100644 index 0000000000000..c98a7312b3168 --- /dev/null +++ b/recipes/influx-si-data-manager/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "influx-si-data-manager" %} +{% set version = "0.1.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/influx_si_data_manager-{{ version }}.tar.gz + sha256: ca0ef718ce69a23aaba28fda5b6584161620096165c39a96bceb30ebec35ea92 + +build: + entry_points: + - influx_si_data_manager = influx_si_data_manager.main:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('influx-si-data-manager', max_pin="x") }} + +requirements: + host: + - python >=3.9,<4.0 + - poetry-core + - pip + run: + - python >=3.9.0,<4.0.0 + - pandas >=2.0.1,<3.0.0 + +test: + imports: + - influx_si_data_manager + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/llegregam/influx_data_manager + summary: Data manager for handling influx_si inputs on Workflow4Metabolomics (usegalaxy.org) + license: GPL-3.0-or-later + license_file: LICENSE + +extra: + recipe-maintainers: + - llegregam From e199498885aad8f58e530f6f3cfad85bf8012978 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Dec 2023 11:00:52 -0500 Subject: [PATCH 1120/2173] Update genomad to 1.7.4 (#44699) --- recipes/genomad/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genomad/meta.yaml b/recipes/genomad/meta.yaml index 549b081d06dc8..e52a7e786a2c5 100644 --- a/recipes/genomad/meta.yaml +++ b/recipes/genomad/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genomad" %} -{% set version = "1.7.3" %} +{% set version = "1.7.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a13387992eb1000d84587caed085c01eaaeb875fe6b8bffd3a251af02d2d2a4d + sha256: 3f7395ef18652c8f4ef1809d7bc97d7c3a7ae59fc86012cbf1ed35b7986ecad2 build: number: 0 From 921186557b4c234f4e7cf14967299ace111fd74a Mon Sep 17 00:00:00 2001 From: Lightning Auriga <8940921+lightning-auriga@users.noreply.github.com> Date: Fri, 8 Dec 2023 11:18:59 -0500 Subject: [PATCH 1121/2173] Update bcftools-gtc2vcf-plugin to (bcftools) 1.18 (#44666) * feat: update bcftools-gtc2vcf-plugin to 1.18 * fix: add pin_subpackage * try using PKG_VERSION variable in build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- .../1.9/affy2vcf.c.patch | 119 ----- recipes/bcftools-gtc2vcf-plugin/1.9/build.sh | 35 -- .../1.9/conda_build_config.yaml | 2 - .../1.9/fixref.c.patch | 107 ----- .../1.9/gtc2vcf.c.patch | 410 ------------------ recipes/bcftools-gtc2vcf-plugin/1.9/meta.yaml | 40 -- recipes/bcftools-gtc2vcf-plugin/build.sh | 2 +- .../conda_build_config.yaml | 4 +- recipes/bcftools-gtc2vcf-plugin/meta.yaml | 11 +- 9 files changed, 10 insertions(+), 720 deletions(-) delete mode 100644 recipes/bcftools-gtc2vcf-plugin/1.9/affy2vcf.c.patch delete mode 100644 recipes/bcftools-gtc2vcf-plugin/1.9/build.sh delete mode 100644 recipes/bcftools-gtc2vcf-plugin/1.9/conda_build_config.yaml delete mode 100644 recipes/bcftools-gtc2vcf-plugin/1.9/fixref.c.patch delete mode 100644 recipes/bcftools-gtc2vcf-plugin/1.9/gtc2vcf.c.patch delete mode 100644 recipes/bcftools-gtc2vcf-plugin/1.9/meta.yaml diff --git a/recipes/bcftools-gtc2vcf-plugin/1.9/affy2vcf.c.patch b/recipes/bcftools-gtc2vcf-plugin/1.9/affy2vcf.c.patch deleted file mode 100644 index ec89a7b984274..0000000000000 --- a/recipes/bcftools-gtc2vcf-plugin/1.9/affy2vcf.c.patch +++ /dev/null @@ -1,119 +0,0 @@ ---- gtc2vcf-b890909/affy2vcf.c.orig 2018-10-11 10:20:20.163766095 -0400 -+++ gtc2vcf-b890909/affy2vcf.c 2018-10-11 10:22:47.924639141 -0400 -@@ -192,7 +192,8 @@ - - int moff = 0, *off = NULL; - int ncols = ksplit_core(str.s, ',', &moff, &off); -- for (int i=0; iprobeset_id); -- for (int i=0; in_records; i++) -+ int i; -+ for (i=0; in_records; i++) - { - free(annot->records[i].probe_set); - free(annot->records[i].dbsnp); -@@ -297,7 +299,8 @@ - - static void report_destroy(report_t *report) - { -- for (int i=0; in_samples; i++) free(report->cel_files[i]); -+ int i; -+ for (i=0; in_samples; i++) free(report->cel_files[i]); - free(report->genders); - } - -@@ -309,7 +312,8 @@ - { - bcf_hdr_t *hdr = bcf_hdr_init("w"); - int n = faidx_nseq(fai); -- for (int i=0; iab_delta ) - { -@@ -393,7 +398,8 @@ - ncols = ksplit_core(str.s, '\t', &moff, &off); - if ( strcmp(&str.s[off[0]], "probeset_id") ) error("Malformed first line from summary file: %s\n%s\n", summary_fn, str.s); - -- for (int i=1; in_samples; i++) fprintf(sex_fh, "%s\t%d\n", report->cel_files[i], report->genders[i]); -+ int i; -+ for (i=0; in_samples; i++) fprintf(sex_fh, "%s\t%d\n", report->cel_files[i], report->genders[i]); - fclose(sex_fh); - report_destroy(report); - } -@@ -650,4 +658,4 @@ - bcf_hdr_destroy(hdr); - hts_close(out_fh); - return 0; --} -\ No newline at end of file -+} diff --git a/recipes/bcftools-gtc2vcf-plugin/1.9/build.sh b/recipes/bcftools-gtc2vcf-plugin/1.9/build.sh deleted file mode 100644 index 207209d5626c3..0000000000000 --- a/recipes/bcftools-gtc2vcf-plugin/1.9/build.sh +++ /dev/null @@ -1,35 +0,0 @@ -#!/bin/sh - -export VERSION=1.9 -export C_INCLUDE_PATH=${PREFIX}/include -export CPP_INCLUDE_PATH=${PREFIX}/include -export CXX_INCLUDE_PATH=${PREFIX}/include -export CPLUS_INCLUDE_PATH=${PREFIX}/include -export LIBRARY_PATH=${PREFIX}/lib -export CPPFLAGS="$CPPFLAGS -I$PREFIX/include" -export LDFLAGS="$LDFLAGS -L$PREFIX/lib" -export CFLAGS="$CFLAGS -I$PREFIX/include" - -mkdir -p $PREFIX/bin -mkdir -p $PREFIX/libexec/bcftools - -# Copy plugin source to the bcftools plugin directory. -cp gtc2vcf-b890909/affy2vcf.c bcftools-$VERSION/plugins/ -cp gtc2vcf-b890909/gtc2vcf.c bcftools-$VERSION/plugins/ - -# Compile htslib and bcftools with affy2vcf and gtc2vcf plugins. -pushd htslib-$VERSION -autoheader -(autoconf || autoconf) -./configure --disable-bz2 --disable-lzma --prefix=$PREFIX -make CC=$CC -popd - -pushd bcftools-$VERSION -make -popd - -# Move custom bcftools plugins to the ~/libexec/bcftools directory. -mv bcftools-$VERSION/plugins/affy2vcf.so $PREFIX/libexec/bcftools/ -mv bcftools-$VERSION/plugins/fixref.so $PREFIX/libexec/bcftools/ -mv bcftools-$VERSION/plugins/gtc2vcf.so $PREFIX/libexec/bcftools/ diff --git a/recipes/bcftools-gtc2vcf-plugin/1.9/conda_build_config.yaml b/recipes/bcftools-gtc2vcf-plugin/1.9/conda_build_config.yaml deleted file mode 100644 index 96ee63743f28a..0000000000000 --- a/recipes/bcftools-gtc2vcf-plugin/1.9/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -htslib: - - 1.9 diff --git a/recipes/bcftools-gtc2vcf-plugin/1.9/fixref.c.patch b/recipes/bcftools-gtc2vcf-plugin/1.9/fixref.c.patch deleted file mode 100644 index 473e19023a8c0..0000000000000 --- a/recipes/bcftools-gtc2vcf-plugin/1.9/fixref.c.patch +++ /dev/null @@ -1,107 +0,0 @@ ---- bcftools-1.9/plugins/fixref.c.orig 2018-06-30 03:48:02.000000000 -0400 -+++ bcftools-1.9/plugins/fixref.c 2018-10-03 09:03:07.270160080 -0400 -@@ -90,6 +90,7 @@ - #define MODE_TOP2FWD 2 - #define MODE_FLIP2FWD 3 - #define MODE_USE_ID 4 -+#define MODE_SWAP 6 - - typedef struct - { -@@ -104,12 +105,14 @@ - typedef struct - { - char *dbsnp_fname; -- int mode, discard; -+ int mode, discard, flip_baf; - bcf_hdr_t *hdr; - faidx_t *fai; - int rid, skip_rid; - i2m_t *i2m; - int32_t *gts, ngts, pos; -+ float *bafs; -+ int32_t nbafs; - uint32_t nsite,nok,nflip,nunresolved,nswap,nflip_swap,nonSNP,nonACGT,nonbiallelic; - uint32_t count[4][4], npos_err, unsorted; - } -@@ -130,6 +133,7 @@ - " Currently the following modes are recognised:\n" - " flip .. flips non-ambiguous SNPs and ignores the rest\n" - " id .. swap REF/ALT and GTs using the ID column to determine the REF allele\n" -+ " swap .. swap REF/ALT columns and GTs and ignore the rest\n" - " stats .. collect and print stats\n" - " top .. converts from Illumina TOP strand to fwd\n" - "\n" -@@ -148,7 +152,8 @@ - " -i, --use-id Swap REF/ALT using the ID column to determine the REF allele, implies -m id.\n" - " Download the dbSNP file from\n" - " https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf\n" -- " -m, --mode Collect stats (\"stats\") or convert (\"flip\", \"id\", \"top\") [stats]\n" -+ " -m, --mode Collect stats (\"stats\") or convert (\"flip\", \"id\", \"swap\", \"top\") [stats]\n" -+ " -b --flip-baf Flip BAF when swapping genotypes\n" - "\n" - "Examples:\n" - " # run stats\n" -@@ -178,10 +183,11 @@ - {"discard",no_argument,NULL,'d'}, - {"fasta-ref",required_argument,NULL,'f'}, - {"use-id",required_argument,NULL,'i'}, -+ {"flip-baf",no_argument,NULL,'b'}, - {NULL,0,NULL,0} - }; - int c; -- while ((c = getopt_long(argc, argv, "?hf:m:di:",loptions,NULL)) >= 0) -+ while ((c = getopt_long(argc, argv, "?hf:m:di:b:",loptions,NULL)) >= 0) - { - switch (c) - { -@@ -190,11 +196,13 @@ - else if ( !strcasecmp(optarg,"flip") ) args.mode = MODE_FLIP2FWD; - else if ( !strcasecmp(optarg,"id") ) args.mode = MODE_USE_ID; - else if ( !strcasecmp(optarg,"stats") ) args.mode = MODE_STATS; -+ else if ( !strcasecmp(optarg,"swap") ) args.mode = MODE_SWAP; - else error("The source strand convention not recognised: %s\n", optarg); - break; - case 'i': args.dbsnp_fname = optarg; args.mode = MODE_USE_ID; break; - case 'd': args.discard = 1; break; - case 'f': ref_fname = optarg; break; -+ case 'b': args.flip_baf = 1; break; - case 'h': - case '?': - default: error("%s", usage()); break; -@@ -231,6 +239,13 @@ - } - } - bcf_update_genotypes(args->hdr,rec,args->gts,args->ngts); -+ -+ if (args->flip_baf && bcf_get_format_float(args->hdr, rec, "BAF", &args->bafs, &args->nbafs) >= 0) -+ { -+ float *ptr = args->bafs; -+ for (i=0; inbafs; i++, ptr++) *ptr = 1 - *ptr; -+ bcf_update_format_float(args->hdr, rec, "BAF", args->bafs, args->nbafs); -+ } - - return rec; - } -@@ -430,6 +445,13 @@ - if ( ir==revint(ib) ) { args.nflip_swap++; return set_ref_alt(&args,rec,int2nt(revint(ib)),int2nt(revint(ia)),1); } - error("FIXME: this should not happen %s:%d\n", bcf_seqname(args.hdr,rec),rec->pos+1); - } -+ else if ( args.mode==MODE_SWAP ) -+ { -+ if ( ir==ia ) return ret; -+ if ( ir==ib ) { args.nswap++; return set_ref_alt(&args,rec,int2nt(ib),int2nt(ia),1); } -+ args.nunresolved++; -+ return args.discard ? NULL : ret; -+ } - else if ( args.mode==MODE_TOP2FWD ) - { - int pair = 1 << ia | 1 << ib; -@@ -567,6 +589,7 @@ - fprintf(stderr,"NS\tnon-biallelic\t%u\n", args.nonbiallelic); - - free(args.gts); -+ free(args.bafs); - if ( args.fai ) fai_destroy(args.fai); - if ( args.i2m ) kh_destroy(i2m, args.i2m); - } diff --git a/recipes/bcftools-gtc2vcf-plugin/1.9/gtc2vcf.c.patch b/recipes/bcftools-gtc2vcf-plugin/1.9/gtc2vcf.c.patch deleted file mode 100644 index fd43df0fc62b6..0000000000000 --- a/recipes/bcftools-gtc2vcf-plugin/1.9/gtc2vcf.c.patch +++ /dev/null @@ -1,410 +0,0 @@ ---- gtc2vcf-b890909/gtc2vcf.c.orig 2018-10-11 10:31:54.875895471 -0400 -+++ gtc2vcf-b890909/gtc2vcf.c 2018-10-11 10:55:39.935944745 -0400 -@@ -66,7 +66,8 @@ - else - { - int c = 0; -- for (int i=0; ifp, (void *)&idat->m_run_infos, sizeof(int32_t)); - idat->run_infos = (RunInfo *)malloc(idat->m_run_infos * sizeof(RunInfo)); -- for (int i=0; im_run_infos; i++) -+ for (i=0; im_run_infos; i++) - { - read_pfx_string(idat->fp, &idat->run_infos[i].run_time, NULL); - read_pfx_string(idat->fp, &idat->run_infos[i].block_type, NULL); -@@ -329,13 +331,14 @@ - read_bytes(idat->fp, (void *)&idat->number_toc_entries, sizeof(int32_t)); - idat->id = (uint16_t *)malloc(idat->number_toc_entries * sizeof(uint16_t)); - idat->toc = (int64_t *)malloc(idat->number_toc_entries * sizeof(int64_t)); -- for (int i=0; inumber_toc_entries; i++) -+ int i; -+ for (i=0; inumber_toc_entries; i++) - { - read_bytes(idat->fp, (void *)&idat->id[i], sizeof(uint16_t)); - read_bytes(idat->fp, (void *)&idat->toc[i], sizeof(int64_t)); - } - -- for (int i=0; inumber_toc_entries; i++) idat_read(idat, idat->id[i]); -+ for (i=0; inumber_toc_entries; i++) idat_read(idat, idat->id[i]); - - return idat; - } -@@ -358,7 +361,8 @@ - free(idat->unknown5); - free(idat->unknown6); - free(idat->unknown7); -- for (int i=0; im_run_infos; i++) -+ int i; -+ for (i=0; im_run_infos; i++) - { - free(idat->run_infos[i].run_time); - free(idat->run_infos[i].block_type); -@@ -402,7 +406,8 @@ - fprintf(stream, "Mid Blocks Count ,%d\n", idat->mid_block->item_num); - fprintf(stream, "[Assay]\n"); - fprintf(stream, "IlmnID,Sd,Mean,Nbeads\n"); -- for (int i=0; inum_snps; i++) -+ int i; -+ for (i=0; inum_snps; i++) - { - int32_t ilmn_id; - get_element(idat->ilmn_id, (void *)&ilmn_id, i); -@@ -415,14 +420,14 @@ - fprintf(stream, "%d,%d,%d,%d\n", ilmn_id, sd, mean, nbeads); - } - fprintf(stream, "[Mid Blocks]\n"); -- for (int i=0; imid_block->item_num; i++) -+ for (i=0; imid_block->item_num; i++) - { - int8_t mid_block; - get_element(idat->mid_block, (void *)&mid_block, i); - fprintf(stream, "%d\n", mid_block); - } - fprintf(stream, "[Run Infos]\n"); -- for (int i=0; im_run_infos; i++) -+ for (i=0; im_run_infos; i++) - { - fprintf(stream, "%s\t%s\t%s\t%s\t%s\n", idat->run_infos[i].run_time, idat->run_infos[i].block_type, - idat->run_infos[i].block_pars, idat->run_infos[i].block_code, idat->run_infos[i].code_version); -@@ -546,17 +551,18 @@ - static uint8_t *bpm_norm_lookups(bpm_t *bpm) - { - uint8_t sorted_norm_ids[256]; -- for (int i=0; i<256; i++) sorted_norm_ids[i] = 0xFF; -- for (int i=0; inum_loci; i++) -+ int i; -+ for (i=0; i<256; i++) sorted_norm_ids[i] = 0xFF; -+ for (i=0; inum_loci; i++) - { - int norm_id = bpm->locus_entries[i].norm_id; - sorted_norm_ids[norm_id] = norm_id; - } - int j=0; -- for (int i=0; i<256; i++) if ( sorted_norm_ids[i] != 0xFF ) sorted_norm_ids[j++] = sorted_norm_ids[i]; -+ for (i=0; i<256; i++) if ( sorted_norm_ids[i] != 0xFF ) sorted_norm_ids[j++] = sorted_norm_ids[i]; - uint8_t *norm_lookups = (uint8_t *)malloc(256 * sizeof(uint8_t *)); - memset((void *)norm_lookups, 0xFF, 256 * sizeof(uint8_t *)); -- for (int i=0; ifp, (void *)&bpm->num_loci, sizeof(int32_t)); - read_array(bpm->fp, (void **)&bpm->indexes, NULL, bpm->num_loci, sizeof(int32_t), 0); - bpm->names = (char **)malloc(bpm->num_loci * sizeof(char *)); -- for (int i=0; inum_loci; i++) read_pfx_string(bpm->fp, &bpm->names[i], NULL); -+ int i; -+ for (i=0; inum_loci; i++) read_pfx_string(bpm->fp, &bpm->names[i], NULL); - read_array(bpm->fp, (void **)&bpm->norm_ids, NULL, bpm->num_loci, sizeof(uint8_t), 0); - - bpm->locus_entries = (LocusEntry *)malloc(bpm->num_loci * sizeof(LocusEntry)); - LocusEntry locus_entry; -- for (int i=0; inum_loci; i++) -+ for (i=0; inum_loci; i++) - { - memset(&locus_entry, 0, sizeof(LocusEntry)); - locusentry_read(&locus_entry, bpm->fp); -@@ -599,14 +606,14 @@ - memcpy(&bpm->locus_entries[ idx ], &locus_entry, sizeof(LocusEntry)); - } - bpm->norm_lookups = bpm_norm_lookups(bpm); -- for (int i=0; inum_loci; i++) -+ for (i=0; inum_loci; i++) - { - if ( i != bpm->locus_entries[i].index - 1 ) error("Manifest format error: read invalid number of assay entries\n"); - } - - read_bytes(bpm->fp, (void *)&bpm->m_header, sizeof(int32_t)); - bpm->header = (char **)malloc(bpm->m_header * sizeof(char *)); -- for (int i=0; im_header; i++) read_pfx_string(bpm->fp, &bpm->header[i], NULL); -+ for (i=0; im_header; i++) read_pfx_string(bpm->fp, &bpm->header[i], NULL); - - if ( !heof(bpm->fp) ) error("BPM reader did not reach the end of file %s at position %ld\n", bpm->fn, htell(bpm->fp)); - -@@ -621,13 +628,14 @@ - free(bpm->manifest_name); - free(bpm->control_config); - free(bpm->indexes); -+ int i; - if ( bpm->names ) - { -- for (int i=0; inum_loci; i++) free(bpm->names[i]); -+ for (i=0; inum_loci; i++) free(bpm->names[i]); - free(bpm->names); - } - free(bpm->norm_ids); -- for (int i=0; inum_loci; i++) -+ for (i=0; inum_loci; i++) - { - free(bpm->locus_entries[i].ilmn_id); - free(bpm->locus_entries[i].name); -@@ -650,7 +658,7 @@ - } - free(bpm->locus_entries); - free(bpm->norm_lookups); -- for (int i=0; im_header; i++) free(bpm->header[i]); -+ for (i=0; im_header; i++) free(bpm->header[i]); - free(bpm->header); - free(bpm); - } -@@ -664,9 +672,10 @@ - - static void bpm_to_csv(const bpm_t *bpm, FILE *stream) - { -- for (int i=0; im_header; i++) fprintf(stream, "%s\n", bpm->header[i]); -+ int i; -+ for (i=0; im_header; i++) fprintf(stream, "%s\n", bpm->header[i]); - fprintf(stream, "Index,NormID,IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_ProbeSeq,GenomeBuild,Chr,MapInfo,Ploidy,Species,Source,SourceVersion,SourceStrand,SourceSeq,TopGenomicSeq,BeadSetID,Exp_Clusters,Intensity_Only,Assay_Type,Frac A,Frac C,Frac G,Frac T,RefStrand\n"); -- for (int i=0; inum_loci; i++) -+ for (i=0; inum_loci; i++) - { - LocusEntry *locus_entry = &bpm->locus_entries[i]; - fprintf(stream, "%d,%d,%s,%s,%s,%s,%010d,,%010d,,%s,%s,%s,%s,%s,%s,,%s,,,,%d,%d,%d,%f,%f,%f,%f,%s\n", -@@ -813,7 +822,8 @@ - int moff = 0, *off = NULL; - bpm->m_header = ksplit_core(str.s, '\n', &moff, &off); - bpm->header = (char **)malloc(bpm->m_header * sizeof(char *)); -- for (int i=0; im_header; i++) bpm->header[i] = strdup(&str.s[off[i]]); -+ int i; -+ for (i=0; im_header; i++) bpm->header[i] = strdup(&str.s[off[i]]); - free(off); - - str.l = 0; -@@ -851,7 +861,7 @@ - tsv_register(tsv, "RefStrand", tsv_read_string, &locus_entry.ref_strand); - - bpm->locus_entries = (LocusEntry *)malloc(bpm->num_loci * sizeof(LocusEntry)); -- for (int i=0; inum_loci; i++) -+ for (i=0; inum_loci; i++) - { - memset(&locus_entry, 0, sizeof(LocusEntry)); - locus_entry.norm_id = 0xFF; -@@ -959,6 +969,7 @@ - egt_t *egt = (egt_t *)calloc(1, sizeof(egt_t)); - egt->fn = strdup(fn); - egt->fp = hopen(egt->fn, "rb"); -+ int i; - if ( egt->fp == NULL ) error("Could not open %s\n", egt->fn); - if ( is_gzip(egt->fp) ) error("File %s is gzip compressed and currently cannot be seeked\n", egt->fn); - -@@ -982,21 +993,21 @@ - - read_bytes(egt->fp, (void *)&egt->num_records, sizeof(int32_t)); - egt->cluster_records = (ClusterRecord *)malloc(egt->num_records * sizeof(ClusterRecord)); -- for (int i=0; inum_records; i++) clusterrecord_read(&egt->cluster_records[i], egt->fp); -- for (int i=0; inum_records; i++) clusterscore_read(&egt->cluster_records[i].cluster_score, egt->fp); -+ for (i=0; inum_records; i++) clusterrecord_read(&egt->cluster_records[i], egt->fp); -+ for (i=0; inum_records; i++) clusterscore_read(&egt->cluster_records[i].cluster_score, egt->fp); - - // toss useless strings such as aa_ab_bb/aa_ab/aa_bb/ab_bb -- for (int i=0; inum_records; i++) read_pfx_string(egt->fp, NULL, NULL); -+ for (i=0; inum_records; i++) read_pfx_string(egt->fp, NULL, NULL); - - egt->loci_names = (char **)malloc(egt->num_records * sizeof(char *)); -- for (int i=0; inum_records; i++) -+ for (i=0; inum_records; i++) - { - read_pfx_string(egt->fp, &egt->loci_names[i], NULL); - } -- for (int i=0; inum_records; i++) read_bytes(egt->fp, (void *)&egt->cluster_records[i].address, sizeof(int32_t)); -+ for (i=0; inum_records; i++) read_bytes(egt->fp, (void *)&egt->cluster_records[i].address, sizeof(int32_t)); - - int32_t aa_n, ab_n, bb_n; -- for (int i=0; inum_records; i++) -+ for (i=0; inum_records; i++) - { - read_bytes(egt->fp, (void *)&aa_n, sizeof(int32_t)); - read_bytes(egt->fp, (void *)&ab_n, sizeof(int32_t)); -@@ -1025,7 +1036,8 @@ - free(egt->date_created); - free(egt->manifest_name); - free(egt->cluster_records); -- for (int i=0; inum_records; i++) free(egt->loci_names[i]); -+ int i; -+ for (i=0; inum_records; i++) free(egt->loci_names[i]); - free(egt->loci_names); - free(egt); - } -@@ -1056,7 +1068,8 @@ - fprintf(stream, "Records Count ,%d\n", egt->num_records); - fprintf(stream, "[Assay]\n"); - fprintf(stream, "Name,AA.N,AA.R_dev,AA.R_mean,AA.Theta_dev,AA.Theta_mean,AB.N,AB.R_dev,AB.R_mean,AB.Theta_dev,AB.Theta_mean,BB.N,BB.R_dev,BB.R_mean,BB.Theta_dev,BB.Theta_mean,Intensity Threshold,Cluster Separation,GenTrain Score,Original Score,Edited,Address\n"); -- for (int i=0; inum_records; i++) -+ int i; -+ for (i=0; inum_records; i++) - { - ClusterRecord *cluster_record = &egt->cluster_records[i]; - fprintf(stream, "%s,%d,%f,%f,%f,%f,%d,%f,%f,%f,%f,%d,%f,%f,%f,%f,%f,%f,%f,%f,%d,%d\n", -@@ -1341,17 +1354,18 @@ - read_bytes(gtc->fp, (void *)>c->number_toc_entries, sizeof(int32_t)); - gtc->id = (uint16_t *)malloc(gtc->number_toc_entries * sizeof(uint16_t)); - gtc->toc = (int32_t *)malloc(gtc->number_toc_entries * sizeof(int32_t)); -- for (int i=0; inumber_toc_entries; i++) -+ int i; -+ for (i=0; inumber_toc_entries; i++) - { - read_bytes(gtc->fp, (void *)>c->id[i], sizeof(uint16_t)); - read_bytes(gtc->fp, (void *)>c->toc[i], sizeof(int32_t)); - } - -- for (int i=0; inumber_toc_entries; i++) gtc_read(gtc, gtc->id[i]); -+ for (i=0; inumber_toc_entries; i++) gtc_read(gtc, gtc->id[i]); - - gtc->sin_theta = (float *)malloc(gtc->m_normalization_transforms * sizeof(float)); - gtc->cos_theta = (float *)malloc(gtc->m_normalization_transforms * sizeof(float)); -- for (int i=0; im_normalization_transforms; i++) -+ for (i=0; im_normalization_transforms; i++) - { - gtc->sin_theta[i] = sinf(gtc->normalization_transforms[i].theta); - gtc->cos_theta[i] = cosf(gtc->normalization_transforms[i].theta); -@@ -1450,7 +1464,8 @@ - fprintf(stream, "SNP Count ,%d\n", gtc->num_snps); - fprintf(stream, "[Assay]\n"); - fprintf(stream, "Raw X,Raw Y,GType,Top Alleles,Score,B Allele Freq,Log R Ratio\n"); -- for (int i=0; inum_snps; i++) -+ int i; -+ for (i=0; inum_snps; i++) - { - uint16_t raw_x = 0, raw_y = 0; - get_element(gtc->raw_x, (void *)&raw_x, i); -@@ -1468,7 +1483,7 @@ - } - fprintf(stream, "[Normalization Transforms]\n"); - fprintf(stream, "Version,Offset X,Offset Y,Scale X,Scale Y,Shear,Theta\n"); -- for (int i=0; im_normalization_transforms; i++) -+ for (i=0; im_normalization_transforms; i++) - { - fprintf(stream, "%d,%f,%f,%f,%f,%f,%f\n", - gtc->normalization_transforms[i].version, -@@ -1595,11 +1610,13 @@ - { - // print header - fprintf(stream, "Index\tName\tAddress\tChr\tPosition\tGenTrain Score\tFrac A\tFrac C\tFrac G\tFrac T"); -- for (int i=0; isample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name); -+ int i; -+ for (i=0; isample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name, gtc[i]->sample_name); - fprintf(stream, "\n"); - - // print loci -- for (int j=0; jnum_loci; j++) -+ int j; -+ for (j=0; jnum_loci; j++) - { - fprintf(stream, "%d\t%s\t%d\t%s\t%s\t%f\t%f\t%f\t%f\t%f", bpm->indexes[j], - bpm->names[j], -@@ -1611,7 +1628,7 @@ - bpm->locus_entries[j].frac_c, - bpm->locus_entries[j].frac_g, - bpm->locus_entries[j].frac_t); -- for (int i=0; igenotypes, (void *)&genotype, j); -@@ -1663,7 +1680,8 @@ - { - bcf_hdr_t *hdr = bcf_hdr_init("w"); - int n = faidx_nseq(fai); -- for (int i=0; inum_loci; j++) -+ int j; -+ for (j=0; jnum_loci; j++) - { - bcf_clear(rec); - rec->rid = bcf_hdr_name2id_flexible(hdr, bpm->locus_entries[j].chrom); -@@ -1721,7 +1740,8 @@ - b_top[0] = revnt(b_top[0]); - } - bcf_update_alleles(hdr, rec, alleles, 2); -- for (int i=0; igenotypes, (void *)&genotype, j); -@@ -1927,7 +1947,8 @@ - int moff = 0, *off = NULL, ncols = ksplit_core(line.s, '\t', &moff, &off); - kstring_t str = {0, 0, NULL}; - int *col2sample = (int *) malloc(sizeof(int)*ncols); -- for (int i=0; i0 ) ksprintf(&str, ","); -@@ -2144,7 +2165,8 @@ - { - int flags = 0, n; - char **tags = hts_readlist(str, 0, &n); -- for (int i=0; ifn, '/'); - char *str = ptr ? ptr+1 : gtc[i]->fn; -@@ -2376,10 +2399,10 @@ - bpm_destroy(bpm); - if ( gtc_list ) - { -- for (int i=0; i Date: Fri, 8 Dec 2023 17:47:44 +0100 Subject: [PATCH 1122/2173] Update pasta (#44543) * using latest release of upstream * use recent gapc update with hopes to compile on OSX * add subrecipe for older version 4.3.10 (pinned in qiime2) which shall additionally expose upp.config * trigger py38 build * clean sepp * remove pasta from blacklist * adding run_exports * since pasta upstream has no releases, we will source from git_url. Software was updated to 1.9.0 * adding license info; adding hash; adding lint exception * instead of pulling clustalw2 from Siavash's tool repo, we use a bioconda package * hmpf, had to fix OS dependent dirname * complete rewrite to avoid pulling old binaries from github repo, use conda dependencies instead * cp instead of ln * pasta is arch dependent! * patch python code instead of setting env variable to define pasta's tool dir * no /bin suffix * move to proper location * append /bin suffix * applying patch to fix multiprocess start method to "fork" * defer raxml renaming until pasta's setup.py was executed (as it might overwrite raxml files) * more debug info for test * omitting raxml test execution for now ... help from upstream seems necessary * use SPDX identifier for GPL-3.0 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- build-fail-blacklist | 1 - recipes/pasta/build.sh | 57 ++++++++++++--------------------- recipes/pasta/fix_tooldir.patch | 28 ++++++++++++++++ recipes/pasta/meta.yaml | 55 +++++++++++++++++++++++-------- recipes/pasta/mpstart.patch | 12 +++++++ 5 files changed, 103 insertions(+), 50 deletions(-) create mode 100644 recipes/pasta/fix_tooldir.patch create mode 100644 recipes/pasta/mpstart.patch diff --git a/build-fail-blacklist b/build-fail-blacklist index 8b4c49af4f690..941f4c5e5352c 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -304,7 +304,6 @@ recipes/rsat-core recipes/ig-checkflowtypes recipes/bufet recipes/mapsplice -recipes/pasta recipes/halla recipes/qtip recipes/tagger diff --git a/recipes/pasta/build.sh b/recipes/pasta/build.sh index 3ef8da204e5fe..ef32e2c5760ad 100644 --- a/recipes/pasta/build.sh +++ b/recipes/pasta/build.sh @@ -2,46 +2,31 @@ set -eu -o pipefail -work_dir=$PREFIX/pasta-build -install_dir=$PREFIX/bin - -mkdir -p $work_dir -mkdir -p $work_dir/pasta - -cp -R ./* $work_dir/pasta -cd $work_dir - +# obtain opal.jar from Siavash's extra repo unamestr=`uname` if [ $unamestr == 'Linux' ]; then - wget --no-check-certificate https://github.com/smirarab/sate-tools-linux/archive/a3e6f56.tar.gz - tar -xzf a3e6f56.tar.gz - mv sate-tools-linux-a3e6f56372599ffacf1bd43adb2d67cf361228e2 sate-tools-linux - cd pasta - $PYTHON setup.py install --single-version-externally-managed --record=/tmp/record.txt - mkdir $install_dir/sate-tools-linux - cp -R $work_dir/sate-tools-linux/* $install_dir/sate-tools-linux/ - # Handle a PASTA bug. - cp $install_dir/sate-tools-linux/hmmalign $install_dir/sate-tools-linux/hmmeralign - cp $install_dir/sate-tools-linux/hmmbuild $install_dir/sate-tools-linux/hmmerbuild - # So tools are available in the bin directory. - ln -s $install_dir/sate-tools-linux/* $install_dir/ + wget --no-check-certificate https://github.com/smirarab/sate-tools-linux/raw/master/opal.jar -O $PREFIX/bin/opal.jar + mkdir -p ../sate-tools-linux/mafftdir/bin ../sate-tools-linux/mafftdir/libexec # fake existens of tool collection elif [ $unamestr == 'Darwin' ]; then - export DYLD_LIBRARY_PATH=$PREFIX/lib - wget --no-check-certificate https://github.com/smirarab/sate-tools-mac/archive/0712214.tar.gz - tar -xzf 0712214.tar.gz - mv sate-tools-mac-0712214e20152b2ec989fc102602afa53d3a7b1a sate-tools-mac - cd pasta - $PYTHON setup.py install --single-version-externally-managed --record=/tmp/record.txt - mkdir $install_dir/sate-tools-mac - cp -R $work_dir/sate-tools-mac/* $install_dir/sate-tools-mac/ - # Handle a PASTA bug. - cp $install_dir/sate-tools-mac/hmmalign $install_dir/sate-tools-mac/hmmeralign - cp $install_dir/sate-tools-mac/hmmbuild $install_dir/sate-tools-mac/hmmerbuild - # So tools are available in the bin directory. - ln -s $install_dir/sate-tools-mac/* $install_dir/ + wget --no-check-certificate https://github.com/smirarab/sate-tools-mac/raw/master/opal.jar -O $PREFIX/bin/opal.jar + mkdir -p ../sate-tools-mac/mafftdir/bin ../sate-tools-mac/mafftdir/libexec # fake existens of tool collection fi -mkdir $install_dir/pasta -cp -R $work_dir/pasta/* $install_dir/pasta/ +# Handle a PASTA bug. +ln -s $PREFIX/bin/hmmalign $PREFIX/bin/hmmeralign +ln -s $PREFIX/bin/hmmbuild $PREFIX/bin/hmmerbuild + +# copy files for tests to shared conda directory +mkdir -p $PREFIX/share/pasta/data/ +cp -v data/small.fasta $PREFIX/share/pasta/data/ + +# install pasta itself +$PYTHON setup.py install --single-version-externally-managed --record=record.txt +cp bin/treeshrink $PREFIX/bin/treeshrink + +# "rename" raxml binaries, after pasta's setup.py did copy bundled raxml versions into bin/ +rm -f -v $PREFIX/bin/raxml $PREFIX/bin/raxmlp +ln -s $PREFIX/bin/raxmlHPC $PREFIX/bin/raxml +ln -s $PREFIX/bin/raxmlHPC-PTHREADS $PREFIX/bin/raxmlp diff --git a/recipes/pasta/fix_tooldir.patch b/recipes/pasta/fix_tooldir.patch new file mode 100644 index 0000000000000..8a8d25024fb09 --- /dev/null +++ b/recipes/pasta/fix_tooldir.patch @@ -0,0 +1,28 @@ +--- pasta/__init__.py 2023-12-04 08:02:14.754964843 +0100 ++++ pasta/__init__.condafixed.py 2023-12-04 09:36:40.981661306 +0100 +@@ -20,7 +20,7 @@ + PROGRAM_LONG_DESCRIPTION = """ + PASTA performs iterative realignment and tree inference, similar to SATe, but uses a very different merge algorithm which improves running time, memory usage, and accuracy. The current code is heavily based on SATe, with lots of modifications, many related to algorithmic differences between PASTA and SATe, but also many scalability improvements (parallelization, tree parsing, defaults, etc.) + +-Minimally you must provide a sequence file (with the '--input' option); a starting tree is optional. By default, important algorithmic parameters are set based on automatic rules. ++Minimally you must provide a sequence file (with the '--input' option); a starting tree is optional. By default, important algorithmic parameters are set based on automatic rules. + + The command line allows you to alter the behavior of the algorithm (termination criteria, when the algorithm switches to "Blind" acceptance of new alignments, how the tree is decomposed to find subproblems to be used, and the external tools to use). + +@@ -251,8 +251,9 @@ + if "PASTA_TOOLS_RUNDIR" in os.environ: + bin_path = os.path.expanduser(os.path.expandvars(os.environ["PASTA_TOOLS_RUNDIR"])) + else: +- home_path = pasta_home_dir() +- bin_path = os.path.join(home_path, pasta_tools_deploy_subpath()) ++ bin_path = os.path.join(os.path.abspath(os.environ['CONDA_PREFIX']), 'bin') # injected via conda patching process ++ # home_path = pasta_home_dir() ++ # bin_path = os.path.join(home_path, pasta_tools_deploy_subpath()) + if os.path.exists(bin_path) or not default_to_dev_dir: + return bin_path + try: +@@ -288,4 +289,3 @@ + raise ToolsDirNotFoundError(paths_tried=[bin_path], + env_var_name="PASTA_TOOLS_DEVDIR") + return bin_path +- diff --git a/recipes/pasta/meta.yaml b/recipes/pasta/meta.yaml index d3cedf63e6eb0..e98629dfcff09 100644 --- a/recipes/pasta/meta.yaml +++ b/recipes/pasta/meta.yaml @@ -1,33 +1,52 @@ +{% set version = "1.9.0" %} +{% set sha256 = "6f816aebe00b7b6bb78a250ad45f5aa2aa8eff0f9719736f05b0597dd3b1f9a1" %} + package: name: pasta - version: "1.7.8" + version: '{{version}}' source: - url: https://github.com/smirarab/pasta/archive/43076b8.tar.gz - sha256: 5eecec1710790df642696d1a52ecf723e5f02dd94e971427117344342a7c2a42 + - url: https://github.com/smirarab/pasta/archive/v{{version}}.tar.gz + sha256: '{{sha256}}' + patches: + - fix_tooldir.patch # ensure PASTA "knows" where to find third party tools + - mpstart.patch # issue in OSX py38 (not in Linux nor OSX py37): RuntimeError: An attempt has been made to start a new process before the current process has finished its bootstrapping phase. build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage('pasta', max_pin="x") }} requirements: - build: - - {{ compiler('c') }} - host: - python - setuptools - - dendropy >=4.1.0 + - dendropy <=4.5.1 - wget - openjdk - pcre - pymongo >=3.3.0 + - clustalw + - fasttree + - raxml + - muscle <4 # later versions expects other cmd argument names + - mafft + - hmmer ==3.1b2 + - prank run: - python - - dendropy >=4.1.0 + - dendropy <=4.5.1 # later version do not expose _convert_node_to_root_polytomy - openjdk - pcre - pymongo >=3.3.0 + - clustalw + - fasttree + - raxml + - muscle <4 # later versions expects other cmd argument names + - mafft + - hmmer ==3.1b2 + - prank test: imports: @@ -37,12 +56,22 @@ test: - clustalw2 -help | grep OPTIONS - hmmalign -h | grep HMMER - hmmbuild -h | grep HMMER - - muscle -version | grep MUSCLE + - muscle -version | grep -i MUSCLE - prank -help | grep prank - - raxml -h | grep raxmlHPC - - raxmlp -h | grep raxmlHPC + - raxml -h | grep -i raxml + - raxmlp -h | grep -i raxml + - export PASTA_LOGGING_LEVEL=DEBUG; export PASTA_LOGGING_FORMAT=RICH; run_pasta.py -i $PREFIX/share/pasta/data/small.fasta + # we need support from upstream to fix this special execution for OSX specific - export PASTA_LOGGING_LEVEL=DEBUG; export PASTA_LOGGING_FORMAT=RICH; run_pasta.py -i $PREFIX/share/pasta/data/small.fasta --tree-estimator raxml about: home: https://github.com/smirarab/pasta - license: GNU General Public License v3 or later (GPLv3+) + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE summary: 'An implementation of the PASTA (Practical Alignment using Sate and TrAnsitivity) algorithm' + +extra: + skip-lints: + # necessary, because pasta is NOT platform independent: + # during build time, platform specific binaries for mafft/raxml/muscle/... are copied into the PREFIX/bin dir + - should_be_noarch_generic diff --git a/recipes/pasta/mpstart.patch b/recipes/pasta/mpstart.patch new file mode 100644 index 0000000000000..4766807f0094d --- /dev/null +++ b/recipes/pasta/mpstart.patch @@ -0,0 +1,12 @@ +--- run_pasta.py 2023-12-04 14:25:42.341227081 +0100 ++++ run_pasta.mpstart.py 2023-12-04 14:25:34.944972464 +0100 +@@ -22,6 +22,9 @@ + # Jiaye Yu and Mark Holder, University of Kansas + + if __name__ == "__main__": ++ import multiprocessing as mp ++ mp.set_start_method('fork') # how to create child processes. Does not work with default in OSX py38 ++ + import os + import sys + import pasta From a3da6241f019a2af6b8ce39ed6c0c5eb8c6840ad Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 8 Dec 2023 11:36:38 -0600 Subject: [PATCH 1123/2173] Add narfmap recipe (#44706) * feat: Add narfmap recipe * fix: Add run_exports * fix: Remove fancy repo --- recipes/narfmap/build.sh | 8 ++++++++ recipes/narfmap/meta.yaml | 41 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 recipes/narfmap/build.sh create mode 100644 recipes/narfmap/meta.yaml diff --git a/recipes/narfmap/build.sh b/recipes/narfmap/build.sh new file mode 100644 index 0000000000000..a61afaac5bc31 --- /dev/null +++ b/recipes/narfmap/build.sh @@ -0,0 +1,8 @@ +export HAS_GTEST=0 + +# fix build number in config +sed -i.bak 's/VERSION_STRING.*/VERSION_STRING="${PKG_VERSION}"/' config.mk + +make CXX=$CXX CC=$CC CXXFLAGS="$CXXFLAGS" CFLAGS="$CFLAGS" +mkdir -p "${PREFIX}/bin" +mv build/release/dragen-os ${PREFIX}/bin/ diff --git a/recipes/narfmap/meta.yaml b/recipes/narfmap/meta.yaml new file mode 100644 index 0000000000000..97b860bfd5c12 --- /dev/null +++ b/recipes/narfmap/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "narfmap" %} +{% set version = "1.4.0" %} +{% set sha256 = "86dc55dcad1fd83b6d486ec18aa5e212412e65546ce8c9e59134c827128aff71" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/Emiller88/NARFMAP/archive/refs/tags/{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage("narfmap", max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - zlib + - boost + - boost-cpp + run: + - zlib + - boost + - boost-cpp + +test: + commands: + - dragen-os -h + +about: + home: https://github.com/Emiller88/NARFMAP + license: GPL-3 + licence_file: COPYRIGHT + summary: "NARFMAP is a fork of the Dragen mapper/aligner Open Source Software." From a0f80a2fbaee7de9fe61ad66d31cd0483f5ac77e Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Fri, 8 Dec 2023 19:23:55 +0000 Subject: [PATCH 1124/2173] Add me-PCR v1.0.6 (#43751) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Package me-PCR v1.0.6 * C compiler too? * Update build.sh * Update meta.yaml * debugging test * Update build.sh * Update build.sh * Update meta.yaml --------- Co-authored-by: Andreas Sjödin Co-authored-by: Robert A. Petit III --- recipes/me-pcr/build.sh | 10 ++++++++ recipes/me-pcr/meta.yaml | 50 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 recipes/me-pcr/build.sh create mode 100644 recipes/me-pcr/meta.yaml diff --git a/recipes/me-pcr/build.sh b/recipes/me-pcr/build.sh new file mode 100644 index 0000000000000..eb50a1af2b62b --- /dev/null +++ b/recipes/me-pcr/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +make CC=$CC CPP=$CXX -C src/ -f makefile + +mkdir -p $PREFIX/share/me-pcr/ +cp README.txt $PREFIX/share/me-pcr/ + +mkdir -p $PREFIX/bin +chmod +x src/me-PCR +cp src/me-PCR $PREFIX/bin/ diff --git a/recipes/me-pcr/meta.yaml b/recipes/me-pcr/meta.yaml new file mode 100644 index 0000000000000..76450d25ec72c --- /dev/null +++ b/recipes/me-pcr/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "me-pcr" %} +{% set version = "1.0.6" %} +{% set sha256 = "61e84af827ef99de245a7a711746e0b0b905e40f5adaf5e34da936a486c8b0e7" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://web.archive.org/web/20100708193215/http://genome.chop.edu/mePCR/me-PCR-{{ version }}.zip + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} + +test: + commands: + - me-PCR 2>&1 | grep "Multithreaded Electronic PCR" + # - me-PCR test/test.sts test/test.fa + +about: + home: https://web.archive.org/web/20100708193215/http://genome.chop.edu/mePCR/ + license: Public Domain + summary: Multithreaded Electronic PCR (in-silico PCR) based on NCBI e-PCR. + description: | + Multithreaded Electronic PCR (me-PCR) was developed by Kevin Murphy at + Children's Hospital of Philadelphia. It is described in Murphy et al + (2004) https://doi.org/10.1093/bioinformatics/btg466 and was originally + available from http://genome.chop.edu/mePCR (defunct). It was based on the + public domain NCBI tool e-PCR by Gregory D. Schuler, described in Schuler + (1997) https://doi.org/10.1101/gr.7.5.541 which was origially availble + from ftp://ncbi.nlm.nih.gov/pub/schuler/e-PCR/ (defunct). The final + release of me-PCR was v1.0.6 (2008-02-18), and the author wrote that in + general NCBI e-PCR should be used instead having been improved greatly + over the years. The NCBI retired and withdrew the e-PCR webservice and + command line tool on 2017-06-28, suggesting the online-only tool + Primer-BLAST instead. However, this is not suitable for offline high + throughput usage. See also Jim Kent's isPCR (aslo available in BioConda). + +extra: + identifiers: + - biotools:{{ name }} From f8c92680dbf5ae74662a4f978d592b8bbfb31c9f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Dec 2023 15:30:06 -0500 Subject: [PATCH 1125/2173] Update pybiolib to 1.1.1608 (#44697) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 8dfe6c8c95ffc..4226a108463ae 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1598" %} +{% set version = "1.1.1608" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 206d44c2e2606d785750ad2b3811622f272ffdc4a8fee6528c3ba853200f2a22 + sha256: aec0b5b2ef10435d457939c800e88c07be113b49c99d5d3b014da1858b491351 build: noarch: python From ef94bfbc5aa49fad0fc7b71e95a32e712437c580 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 8 Dec 2023 16:25:44 -0500 Subject: [PATCH 1126/2173] Update insilicosv to 0.0.6 (#44713) --- recipes/insilicosv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/insilicosv/meta.yaml b/recipes/insilicosv/meta.yaml index b988bd62ad270..2000d8906237d 100644 --- a/recipes/insilicosv/meta.yaml +++ b/recipes/insilicosv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "insilicosv" %} -{% set version = "0.0.5" %} -{% set sha256 = "47417a0c421a4eadd959a1c353e8f50c3634e4c3d1497008610e85c5a1b84667" %} +{% set version = "0.0.6" %} +{% set sha256 = "be14fc77d5d53563686328e38657ce84dc34ba46e2e44eb67e4df4e44a4474eb" %} package: name: "{{ name|lower }}" From 65a156f353793b067cbd5cc0ef6fc92e83631dca Mon Sep 17 00:00:00 2001 From: boukn Date: Fri, 8 Dec 2023 18:45:49 -0500 Subject: [PATCH 1127/2173] ncbi-fcs-gx : Add a patch to improve AWS download times (#44712) * add aria_split_16.patch to improve AWS downloads * add aria_split_16.patch to improve AWS downloads * update build number for linter --- recipes/ncbi-fcs-gx/0.4.1/aria_split_16.patch | 26 +++++++++++++++++++ recipes/ncbi-fcs-gx/0.4.1/meta.yaml | 5 ++-- recipes/ncbi-fcs-gx/aria_split_16.patch | 26 +++++++++++++++++++ recipes/ncbi-fcs-gx/meta.yaml | 4 ++- 4 files changed, 58 insertions(+), 3 deletions(-) create mode 100755 recipes/ncbi-fcs-gx/0.4.1/aria_split_16.patch create mode 100755 recipes/ncbi-fcs-gx/aria_split_16.patch diff --git a/recipes/ncbi-fcs-gx/0.4.1/aria_split_16.patch b/recipes/ncbi-fcs-gx/0.4.1/aria_split_16.patch new file mode 100755 index 0000000000000..dbc30ef59b262 --- /dev/null +++ b/recipes/ncbi-fcs-gx/0.4.1/aria_split_16.patch @@ -0,0 +1,26 @@ +diff --git a/scripts/sync_files.py b/scripts/sync_files.py +index 3c404d37..2d87a87e 100755 +--- a/scripts/sync_files.py ++++ b/scripts/sync_files.py +@@ -360,16 +360,18 @@ def check_space(mft, dir): + def download_file_with_aria(url, file_path): + + aria_config = file_path.with_suffix(".aria2_config") ++ num_connections = 4 if "ncbi.nlm.nih.gov" in url else 16 ++ + with open(aria_config, "w", encoding="ascii") as f: +- f.write(""" ++ f.write(f""" + file-allocation=none + check-certificate=false + allow-overwrite=true + auto-file-renaming=false + max-tries=5 +- max-connection-per-server=5 +- max-concurrent-downloads=5 +- split=5 ++ max-concurrent-downloads=2 ++ max-connection-per-server={num_connections} ++ split={num_connections} + console-log-level=warn + """) diff --git a/recipes/ncbi-fcs-gx/0.4.1/meta.yaml b/recipes/ncbi-fcs-gx/0.4.1/meta.yaml index 03abf4bee3563..b4503a798fb23 100644 --- a/recipes/ncbi-fcs-gx/0.4.1/meta.yaml +++ b/recipes/ncbi-fcs-gx/0.4.1/meta.yaml @@ -5,7 +5,8 @@ package: source: url: https://github.com/ncbi/fcs-gx/archive/refs/tags/v0.4.1.zip sha256: 7bedb6a43945df4821d3e23fd1c5c4bf117cd70001cb96b310d177f0fd049a6b - + patches: + - aria_split_16.patch requirements: build: @@ -23,7 +24,7 @@ requirements: - grep >=3.4 build: - number: 0 + number: 1 skip: True # [not linux or not x86_64] run_exports: - {{ pin_compatible('nxbi-fcs-gx', max_pin="x.x") }} diff --git a/recipes/ncbi-fcs-gx/aria_split_16.patch b/recipes/ncbi-fcs-gx/aria_split_16.patch new file mode 100755 index 0000000000000..dbc30ef59b262 --- /dev/null +++ b/recipes/ncbi-fcs-gx/aria_split_16.patch @@ -0,0 +1,26 @@ +diff --git a/scripts/sync_files.py b/scripts/sync_files.py +index 3c404d37..2d87a87e 100755 +--- a/scripts/sync_files.py ++++ b/scripts/sync_files.py +@@ -360,16 +360,18 @@ def check_space(mft, dir): + def download_file_with_aria(url, file_path): + + aria_config = file_path.with_suffix(".aria2_config") ++ num_connections = 4 if "ncbi.nlm.nih.gov" in url else 16 ++ + with open(aria_config, "w", encoding="ascii") as f: +- f.write(""" ++ f.write(f""" + file-allocation=none + check-certificate=false + allow-overwrite=true + auto-file-renaming=false + max-tries=5 +- max-connection-per-server=5 +- max-concurrent-downloads=5 +- split=5 ++ max-concurrent-downloads=2 ++ max-connection-per-server={num_connections} ++ split={num_connections} + console-log-level=warn + """) diff --git a/recipes/ncbi-fcs-gx/meta.yaml b/recipes/ncbi-fcs-gx/meta.yaml index 205112082b9a7..8f25c0282f3b9 100644 --- a/recipes/ncbi-fcs-gx/meta.yaml +++ b/recipes/ncbi-fcs-gx/meta.yaml @@ -5,6 +5,8 @@ package: source: url: https://github.com/ncbi/fcs-gx/archive/refs/tags/v0.5.0.zip sha256: 2f6b6099584495e1a9115403a5e4cb5f5dac1ddbbc691da9a3158a75391ffe8a + patches: + - aria_split_16.patch requirements: @@ -23,7 +25,7 @@ requirements: - grep >=3.4 build: - number: 0 + number: 1 skip: True # [not linux or not x86_64] run_exports: - {{ pin_compatible('ncbi-fcs-gx', max_pin="0.5") }} From 0c9972604059ef0caa4efe291d2157959c060256 Mon Sep 17 00:00:00 2001 From: Mohsen Taheri Date: Sat, 9 Dec 2023 04:50:53 -0500 Subject: [PATCH 1128/2173] Update version (#44715) * add meta.yaml file * version1.0 * resolving comments * delete license file in about section * resolve test issue * delete tests * new release * adding tests * build with post-link.sh on bioconda * add hash * set build number to 0 * delete build field * ignore lint error * delete env variable * add rust and cargo in host section * remove cargo as dependencies in host section * add compiler c * delete noarch * add llvm and clang to dependencies * add libclang-dev in host * add maturin * add libclang to host section * add cmake * add # [unix] to libclang * release just for unix base systems * small correction * exact same meta.yaml that sourmash team used to deploy branchwater in conda-forge * add build.sh * small change * delete marturin line * add libclang path to post-link.sh * added branchwater dependency * add noarch: python * delete noarch * skip noarch check * add skip lints * using env variable for python * remove should use compiler skip lint * add should use compiler skip lint * remove unnecessary runtime dependencies * new version * new version1.1.0 * add setuptools to build * add setuptools to host * new sha with new release package * minor bug --- recipes/yacht/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/yacht/meta.yaml b/recipes/yacht/meta.yaml index 3155b743cd2d6..c7f12473b7254 100644 --- a/recipes/yacht/meta.yaml +++ b/recipes/yacht/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "1.0" %} +{% set version = "1.1.0" %} package: name: yacht version: {{ version }} source: - url: https://github.com/KoslickiLab/YACHT/releases/download/v{{ version }}/yacht-{{ version }}.tar.gz - sha256: 93b8584774ecc0b72e9778566a348e3649d7e418699e3c27bad68c14d3f15384 + url: https://github.com/KoslickiLab/YACHT/releases/download/v{{ version }}/yacht-{{ version }}.tar.gz + sha256: 0655301d2ecb949fe75799b8ee67b4032e8a778a03f2edc3572b48066d0e4007 build: number: 0 @@ -20,6 +20,7 @@ requirements: host: - python >3.6 - pip + - setuptools run: - python >3.6 - sourmash >=4.8.3,<5 From 9691a6b2d4c4454e99d3477b05bac5473cf18fec Mon Sep 17 00:00:00 2001 From: Dirk-Jan <72025902+dirkjanvw@users.noreply.github.com> Date: Sat, 9 Dec 2023 10:51:33 +0100 Subject: [PATCH 1129/2173] update pantools to v4.3.1 (#44718) --- recipes/pantools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pantools/meta.yaml b/recipes/pantools/meta.yaml index 49c0210b7a1cb..cb74b8616ead8 100644 --- a/recipes/pantools/meta.yaml +++ b/recipes/pantools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PanTools" %} -{% set version = "4.3.0" %} -{% set sha256 = "8cef87de8aadf2555e97dc78d32bee92cc2ca069bdd4637d4cb7c1b41681cbf1" %} +{% set version = "4.3.1" %} +{% set sha256 = "e9472d7283b1f64e54318f06b8ac6de63cd9338b54ea5153a24e1a081ea930a2" %} package: name: {{ name|lower }} From fc677b5ef0e3342a0d225fefa81a45c22e53fb69 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 04:53:53 -0500 Subject: [PATCH 1130/2173] Update oakvar to 2.9.77 (#44708) * Update oakvar to 2.9.76 * Update oakvar to 2.9.77 --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 2f9dfadd88054..b3d296345a27a 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.75" %} -{% set sha256 = "d81393e19ca016dff38f3daa69ee58cc1801fb36794bccfbecd51a1037f523fe" %} +{% set version = "2.9.77" %} +{% set sha256 = "1ea3ef7d6e0a677daab3f9031fd296f9657a5ca548578e7b08d04086e0d59646" %} package: name: {{ name|lower }} From 2a64e53923dc9895dc1c15b973b7eafb0a3f314f Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Sat, 9 Dec 2023 01:54:34 -0800 Subject: [PATCH 1131/2173] Update ntlink build (#44707) * Update ntlink build * Add run_exports section * Fix run_exports section * Add second test --- recipes/ntlink/build.sh | 4 ++-- recipes/ntlink/meta.yaml | 5 ++++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/ntlink/build.sh b/recipes/ntlink/build.sh index 2d7d0044c363e..6b4436d0ed2b0 100644 --- a/recipes/ntlink/build.sh +++ b/recipes/ntlink/build.sh @@ -8,6 +8,6 @@ cp ntLink* ${PREFIX}/bin/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM cp bin/*py ${PREFIX}/bin/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/bin echo "#!/bin/bash" > ${PREFIX}/bin/ntLink -echo "make -f $(command -v ${PREFIX}/bin/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/ntLink) \$@" >> ${PREFIX}/bin/ntLink +echo "make -f $(command -v ${PREFIX}/bin/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/ntLink) \"\$@\"" >> ${PREFIX}/bin/ntLink echo "#!/bin/bash" > ${PREFIX}/bin/ntLink_rounds -echo "make -f $(command -v ${PREFIX}/bin/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/ntLink_rounds) \$@" >> ${PREFIX}/bin/ntLink_rounds +echo "make -f $(command -v ${PREFIX}/bin/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/ntLink_rounds) \"\$@\"" >> ${PREFIX}/bin/ntLink_rounds diff --git a/recipes/ntlink/meta.yaml b/recipes/ntlink/meta.yaml index 308aee04aaa73..609bc60ac8087 100644 --- a/recipes/ntlink/meta.yaml +++ b/recipes/ntlink/meta.yaml @@ -9,8 +9,10 @@ source: sha256: 3a6fe7ca9c7a0226cf51b7e55804e235ac2b959e82a30f9bce55b9caea5bb03b build: - number: 1 + number: 2 skip: True # [py<38 or py > 39] + run_exports: + - {{ pin_subpackage('ntlink', max_pin="x") }} requirements: build: @@ -34,6 +36,7 @@ requirements: test: commands: - ntLink help + - ntLink_rounds help about: home: https://github.com/bcgsc/ntLink From a5940b7fd28944c9374d9d172db0839b51daf05a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 04:55:46 -0500 Subject: [PATCH 1132/2173] Update syngap to 1.1.1 (#44711) --- recipes/syngap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/syngap/meta.yaml b/recipes/syngap/meta.yaml index 62014cd0a04d1..c53f862549b9a 100644 --- a/recipes/syngap/meta.yaml +++ b/recipes/syngap/meta.yaml @@ -1,5 +1,5 @@ {% set name = "syngap" %} -{% set version = "1.1.0" %} +{% set version = "1.1.1" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/yanyew/SynGAP/releases/download/v{{ version }}/{{ name }}_v{{ version }}.tar.gz - sha256: a6b58dcf7c650e0be290352c4cec5889fb79fd610a666d7754f670e8ea8b14b3 + sha256: 4756cba6ede6cef4d7784a46bc2add4dd5eabf2136b39fc982592d031b55e064 build: number: 0 From f0faf2e9fd2d398ef1b2ff77f69189467f72104d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 04:59:30 -0500 Subject: [PATCH 1133/2173] Update tissuumaps to 3.2.0.2 (#44698) --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index 48a2ffb917bd6..a8cc66ef61471 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.0.1" %} +{% set version = "3.2.0.2" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: 5f4db54ba8bb63e92f556d3a4802a6ba949692350189439c87aa8bcca6a61a4e + sha256: d47443e5cda7c1f8dd63879feeb799a1874638026d15c7ce1f190004d87fd384 build: number: 0 From 481dd9577edeb7810361847863c4ba086595cd8d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 04:59:50 -0500 Subject: [PATCH 1134/2173] Update sam2lca to 1.1.4 (#44702) * Update sam2lca to 1.1.4 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/sam2lca/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/sam2lca/meta.yaml b/recipes/sam2lca/meta.yaml index 721c30ad9f321..1a23c3b4a533d 100644 --- a/recipes/sam2lca/meta.yaml +++ b/recipes/sam2lca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sam2lca" %} -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sam2lca-{{ version }}.tar.gz - sha256: d1789f06a0ea15949e45b9cb61ad32249663481750d5082d523d615b5d0e8c5f + sha256: c1d26f67458c2ad3ff8541b4ecf672c97c81fd65c91092beefab10cdea6f945b build: entry_points: @@ -15,6 +15,8 @@ build: noarch: python script: {{ PYTHON }} -m pip install . -vv number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: From 4f20dd2ee19b30431eb03dc2aa6f530c160fae4a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 05:03:26 -0500 Subject: [PATCH 1135/2173] Update snakemake-interface-common to 1.15.0 (#44705) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 49a7a6b45e002..b428c3de168a4 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.14.5" %} +{% set version = "1.15.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: e21f9566b2bd04e50f3f73557f2a72e0eb1829f27192c3f8bc00bd240857a689 + sha256: 58eb3c02d0e34fa1fd28c87218964d3ab65df6de3a0dab0f51fdce2c9179d8d0 build: noarch: python From 6c75a794bc47474333d8d694575f789f28a9f1f4 Mon Sep 17 00:00:00 2001 From: Leandro Lima Date: Sat, 9 Dec 2023 10:03:59 +0000 Subject: [PATCH 1136/2173] fix: bumping build number to trigger rebuild as the cobs release has been amended (#44709) --- recipes/cobs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cobs/meta.yaml b/recipes/cobs/meta.yaml index 76cb1c7eca1d7..5bc5a476470e7 100644 --- a/recipes/cobs/meta.yaml +++ b/recipes/cobs/meta.yaml @@ -7,10 +7,10 @@ package: source: url: https://github.com/iqbal-lab-org/{{ name }}/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.gz - sha256: 5597f0c366be3acc6fe3b59d2c49ef46696bb7676fe72fb99dd74deb4c8c192e + sha256: cbbb9039ac0077f139d1ba2841f88d75efc351296e48ac9d388822d1f95063c1 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} From db66abc529e5e474d796ac36f5e616beb746906c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 05:22:04 -0500 Subject: [PATCH 1137/2173] Update snakemake-interface-executor-plugins to 8.1.1 (#44704) --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index 7dbc87c76e862..5b7ed68c2217a 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "8.1.0" %} +{% set version = "8.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: 5c22d2ada03a7cfe81841488c25ebfc8c392e41fdb6819c1158c7a8cd97c0c37 + sha256: f695c27fae5c750c7a2b3e628ea057d2a941ead592e219e37d14d57eb895f047 build: noarch: python From 51cfcff49fd921d3f2e518a10e4eaf7f6f17b3f4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 05:22:29 -0500 Subject: [PATCH 1138/2173] Update xengsort to 2.0.3 (#44701) --- recipes/xengsort/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/xengsort/meta.yaml b/recipes/xengsort/meta.yaml index 0950c1283bbf4..0c8ea25b50318 100644 --- a/recipes/xengsort/meta.yaml +++ b/recipes/xengsort/meta.yaml @@ -1,5 +1,5 @@ {% set name = "xengsort" %} -{% set version = "2.0.2" %} +{% set version = "2.0.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 58540e42d86b943dc00e0d4b3b3131fb2dd26286b03228bf8a08553911a18052 + sha256: 4783b53d4641b053f928994c9c316962b6cb1604ed7de0853aa3aa3e339e7e76 build: number: 0 From baec8f1bc38320e1e3cb8fb39d6aab895fa861cd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 05:22:48 -0500 Subject: [PATCH 1139/2173] Update pydeseq2 to 0.4.4 (#44700) --- recipes/pydeseq2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pydeseq2/meta.yaml b/recipes/pydeseq2/meta.yaml index a15262ff69be7..5086ace06d91f 100644 --- a/recipes/pydeseq2/meta.yaml +++ b/recipes/pydeseq2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pydeseq2" %} -{% set version = "0.4.3" %} +{% set version = "0.4.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pydeseq2-{{ version }}.tar.gz - sha256: 694f4fa1d390304488cd55b317204b21cb1d724a60ebb167a6973138d0f05faf + sha256: ebd978d51d4d66b40e6dce8826029d9551fec9946c2a75793e75eb748cc3b207 build: noarch: python From 718ba1e96963cdd9edd72af7c6b4ce2282c0d1f3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 08:01:17 -0500 Subject: [PATCH 1140/2173] Update perl-math-bigint to 2.002001 (#44722) --- recipes/perl-math-bigint/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-math-bigint/meta.yaml b/recipes/perl-math-bigint/meta.yaml index 40db7208bbadc..ac8101ef2f026 100644 --- a/recipes/perl-math-bigint/meta.yaml +++ b/recipes/perl-math-bigint/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-math-bigint" %} -{% set version = "2.002000" %} -{% set sha256 = "517c3f36adeb0669a8dfb76b0ac812eedf785e1635e890ee184b2a1c5517fb8d" %} +{% set version = "2.002001" %} +{% set sha256 = "21a2874639a5830d9215ed2f1645b700069cb914d8bb92edac1ca27e0db5e60f" %} package: name: {{ name }} From 404859b9394ac723def10a72cad9de2b206de21e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 12:17:37 -0500 Subject: [PATCH 1141/2173] Update oakvar to 2.9.78 (#44723) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index b3d296345a27a..f03193cbfd07e 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.77" %} -{% set sha256 = "1ea3ef7d6e0a677daab3f9031fd296f9657a5ca548578e7b08d04086e0d59646" %} +{% set version = "2.9.78" %} +{% set sha256 = "5531a1c1bced07011bcc3a8c94426b443ef96d2f05bf17e72709c22d6c412eee" %} package: name: {{ name|lower }} From f576a7e5711706fb3f9c05a1e3c6467c7f997cdf Mon Sep 17 00:00:00 2001 From: Jaebeom Kim <68528165+jaebeom-kim@users.noreply.github.com> Date: Sun, 10 Dec 2023 04:53:48 +0900 Subject: [PATCH 1142/2173] Update metabuli1.0.2 (#44725) * from 1.0.1 to 1.0.2 * pin_subpackage('myrecipe', max_pin=x) --- recipes/metabuli/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/metabuli/meta.yaml b/recipes/metabuli/meta.yaml index 20d813fdcfed8..3c74fd689a9fd 100644 --- a/recipes/metabuli/meta.yaml +++ b/recipes/metabuli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.0.1" %} -{% set sha256 = "544926b73e7e0ed7c34d5f4f76e78e483261e5b13db6a6bb45217551bce1fae0" %} +{% set version = "1.0.2" %} +{% set sha256 = "cf5c74a7aa585457c0014614e59cf850aaacfab03f326e6113466fa2b436d2c2" %} package: name: metabuli @@ -7,6 +7,8 @@ package: build: number: 0 + run_exports: + - {{ pin_subpackage('metabuli', max_pin="x") }} source: url: https://github.com/steineggerlab/metabuli/archive/{{ version }}.tar.gz @@ -45,3 +47,4 @@ about: extra: recipe-maintainers: - milot-mirdita + - jaebeom-kim From 8e03aeb11269dae97bd9c2604aa82212f13d6c65 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 15:30:16 -0500 Subject: [PATCH 1143/2173] Update fgbio to 2.2.0 (#44720) * Update fgbio to 2.2.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fgbio/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/fgbio/meta.yaml b/recipes/fgbio/meta.yaml index 1478e00d13907..e48a484303a73 100644 --- a/recipes/fgbio/meta.yaml +++ b/recipes/fgbio/meta.yaml @@ -1,4 +1,4 @@ -{% set version="2.1.0" %} +{% set version = "2.2.0" %} package: name: fgbio @@ -6,11 +6,13 @@ package: source: url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar - sha256: 7a07d86b1263a89375c5796fec51ecc4bf31b3850ec205df8ae8c9ccba7ca314 + sha256: e3907b0edf525f9becc69472f843fa3bf5a5fd6e2e03b88532d6622aa264ed3d build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('fgbio', max_pin="x") }} requirements: run: @@ -28,4 +30,5 @@ test: about: home: https://github.com/fulcrumgenomics/fgbio license: MIT + license_family: MIT summary: A set of tools for working with genomic and high throughput sequencing data, including UMIs From 576f7a2a94bb1ce794f39682d9bd68723381b5aa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 9 Dec 2023 15:31:45 -0500 Subject: [PATCH 1144/2173] Update fgbio-minimal to 2.2.0 (#44719) * Update fgbio-minimal to 2.2.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/fgbio-minimal/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/fgbio-minimal/meta.yaml b/recipes/fgbio-minimal/meta.yaml index e4961234d0447..c1588facf506d 100644 --- a/recipes/fgbio-minimal/meta.yaml +++ b/recipes/fgbio-minimal/meta.yaml @@ -1,4 +1,4 @@ -{% set version="2.1.0" %} +{% set version = "2.2.0" %} package: name: fgbio-minimal @@ -6,11 +6,13 @@ package: source: url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar - sha256: 7a07d86b1263a89375c5796fec51ecc4bf31b3850ec205df8ae8c9ccba7ca314 + sha256: e3907b0edf525f9becc69472f843fa3bf5a5fd6e2e03b88532d6622aa264ed3d build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('fgbio-minimal', max_pin="x") }} requirements: run: @@ -25,6 +27,7 @@ test: about: home: https://github.com/fulcrumgenomics/fgbio license: MIT + license_family: MIT summary: A set of tools for working with genomic and high throughput sequencing data, including UMIs description: A set of tools for working with genomic and high throughput sequencing data, including UMIs. The 'fgbio-minimal' package offers an installation of fgbio without the 'r-base' dependency. From 8953d530cfac68f583094966f87bba0b63265529 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Dec 2023 02:17:52 -0500 Subject: [PATCH 1145/2173] Update kalign3 to 3.4.0 (#44728) --- recipes/kalign3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kalign3/meta.yaml b/recipes/kalign3/meta.yaml index 56b22956d1687..c9be17442a1a0 100644 --- a/recipes/kalign3/meta.yaml +++ b/recipes/kalign3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "kalign3" %} -{% set version = "3.3.5" %} +{% set version = "3.4.0" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ build: source: url: https://github.com/TimoLassmann/kalign/archive/refs/tags/v{{ version }}.tar.gz - sha256: 75f3a127d2a9eef1eafd931fb0785736eb3f82826be506e7edd00daf1ba26212 + sha256: 67d1a562d54b3b7622cc3164588c05b9e2bf8f1a5140bb48a4e816c61a87d4a8 requirements: build: From b645935c3e1a3cb306897003e758d29a3996181c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Dec 2023 12:00:03 -0500 Subject: [PATCH 1146/2173] Update rbpbench to 0.8 (#44731) --- recipes/rbpbench/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rbpbench/meta.yaml b/recipes/rbpbench/meta.yaml index e41251f1110c9..9feea28617aac 100644 --- a/recipes/rbpbench/meta.yaml +++ b/recipes/rbpbench/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RBPBench" %} -{% set version = "0.7" %} -{% set sha256 = "227846d23b4ee3b52da6069ae18d1265d337d7fca460eb768e9e5087d5431f15" %} +{% set version = "0.8" %} +{% set sha256 = "05bdc4cb76c81337615dbc4125c42e2d27bd25376f8dc520d1d06bc0257fcf0c" %} package: name: {{ name|lower }} From d0e913b084651430905b88880e7d331d44a718de Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Dec 2023 16:31:02 -0500 Subject: [PATCH 1147/2173] Update b2b-utils to 0.019 (#44729) * Update b2b-utils to 0.019 * add run_exports --------- Co-authored-by: mencian --- recipes/b2b-utils/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/b2b-utils/meta.yaml b/recipes/b2b-utils/meta.yaml index 4c3cffdd7e2ac..3005bb5005855 100755 --- a/recipes/b2b-utils/meta.yaml +++ b/recipes/b2b-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "b2b-utils" %} -{% set version = "0.018" %} -{% set sha256 = "4629fb8b16c1198737684168aa75af8a25937e7c7e758b9ec9e52e9114b137c8" %} +{% set version = "0.019" %} +{% set sha256 = "91bc2b5cb1f093f42b51e218c398e5fffdbd7bda36a6281b3e30fa2c1c784e83" %} package: name: "{{ name|lower }}" @@ -12,6 +12,8 @@ source: build: number: 0 + run_exports: + - {{ pin_subpackage('b2b-utils', max_pin="x.x") }} requirements: host: @@ -66,8 +68,8 @@ test: about: home: https://github.com/jvolkening/b2b-utils dev_url: https://github.com/jvolkening/b2b-utils - license: GPLv3 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Genomics tools from BASE2BIO description: | From edc31885801aa747017713c73009ffebd556eee5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Dec 2023 17:07:19 -0500 Subject: [PATCH 1148/2173] Update callingcardstools to 1.3.0 (#44737) * Update callingcardstools to 1.3.0 * add scipy --------- Co-authored-by: mencian --- recipes/callingcardstools/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/callingcardstools/meta.yaml b/recipes/callingcardstools/meta.yaml index cda0d39800ab3..23f0b4d081e5b 100644 --- a/recipes/callingcardstools/meta.yaml +++ b/recipes/callingcardstools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "callingcardstools" %} -{% set version = "1.2.0" %} +{% set version = "1.3.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 5a6b70800c91ed52c61edfd87b2fd773a660b77c01a81a554de1718146bfe7be + sha256: db96c71fed2622a23a57b6700637cdda3ec70c4890378b8441944ad76b531b3d build: noarch: python @@ -30,6 +30,7 @@ requirements: - pandas - pysam - python >=3.8 + - scipy >=1.11.4 test: imports: From a3d87b1847f95687cd4ba3daa8f2d8e8a033bfe4 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sun, 10 Dec 2023 16:35:52 -0600 Subject: [PATCH 1149/2173] Update medaka to 1.11.3 (#44734) --- recipes/medaka/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 130e59ae53756..39da07aeeb982 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -1,6 +1,6 @@ {% set name = "Medaka" %} -{% set version = "1.11.2" %} -{% set sha256 = "8dcb9941ead369b0a8715db80a3375b50a1ad8b58ea12009222b1d70f39cfb07" %} +{% set version = "1.11.3" %} +{% set sha256 = "940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9" %} # Bot PRs - Always review requirements.txt for new release package: @@ -8,7 +8,7 @@ package: version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/medaka-{{ version }}.tar.gz + url: https://github.com/nanoporetech/medaka/releases/download/v{{ version }}/medaka-{{ version }}.tar.gz sha256: {{ sha256 }} patches: - patch From 5f2951871ea7bbb84fa50f0a56ab3ec949ac90bf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 10 Dec 2023 22:23:47 -0500 Subject: [PATCH 1150/2173] Update pypgx to 0.22.0 (#44738) --- recipes/pypgx/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pypgx/meta.yaml b/recipes/pypgx/meta.yaml index f288b340e2fb8..8f066487f74da 100644 --- a/recipes/pypgx/meta.yaml +++ b/recipes/pypgx/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pypgx" %} -{% set version = "0.21.0" %} +{% set version = "0.22.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 9152f9a6c9e90cc98aad94cd89bc4371fa833583bd40d3b82182329b5ab969ea + sha256: 522f9dcba319ecef08af026a134a45bc6267c9b482d615e774a7f877dcc6462e build: number: 0 From 3004e78785a5e3d3a3cc90bb52d4a0c9d21fa8cb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Dec 2023 08:56:19 -0500 Subject: [PATCH 1151/2173] Update earlgrey to 4.0.3 (#44741) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index 99763ef6a5c46..caa4eddb4e6a7 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.2" %} -{% set sha256 = "0873f77dff2dc13c1ab957f301a9a212123258ec0d4a23b660720d66fa12d442" %} +{% set version = "4.0.3" %} +{% set sha256 = "5715301151d7d6609aa703c9c174f00e1bde61c6d2f0493f5c01831d95152fb0" %} package: name: {{ name|lower }} From e2c20f2b34c4af1be995c6f6445866f46d721a8d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Dec 2023 09:43:35 -0500 Subject: [PATCH 1152/2173] Update clinvar-this to 0.14.0 (#44747) --- recipes/clinvar-this/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clinvar-this/meta.yaml b/recipes/clinvar-this/meta.yaml index 671020435cb2b..acafecd533715 100644 --- a/recipes/clinvar-this/meta.yaml +++ b/recipes/clinvar-this/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.13.1" %} -{% set sha256 = "0e2fb9200f5150a423173839f635cbf95e069413174be56fc732d27be19335ca" %} +{% set version = "0.14.0" %} +{% set sha256 = "cbefeb541767da2725e3c9c29481483b404bc8d8b3261b157c0013514c5ef402" %} package: name: clinvar-this From d5e4c61a67e69a293473a7c9d86227b6b61a0d9f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Dec 2023 10:04:06 -0500 Subject: [PATCH 1153/2173] Update dnaio to 1.2.0 (#44746) --- recipes/dnaio/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/dnaio/meta.yaml b/recipes/dnaio/meta.yaml index d98d56e78497e..6b39d3c44a898 100644 --- a/recipes/dnaio/meta.yaml +++ b/recipes/dnaio/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "1.1.0" %} +{% set version = "1.2.0" %} package: name: dnaio version: {{ version }} source: - url: https://files.pythonhosted.org/packages/c6/67/d07ada36ad76198197cee7deea862ee568aa255adc8b6f93535f5bf00da8/dnaio-1.1.0.tar.gz - sha256: 7ecdfb3de3fd82c69b9750ba66202edc095610646d0720961ca7308af4ee8c45 + url: https://files.pythonhosted.org/packages/5b/45/fe12f29d76add9e63290535f0397adc761ceea11e84f995d006b1cb911fe/dnaio-1.2.0.tar.gz + sha256: d0528c23516fe4e947970bdef33c423f0a30ab3b083bd4f6f049fd66d8cef803 build: number: 0 From 45a1d4582b91b1832d6597104169d33000c4edb5 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Mon, 11 Dec 2023 16:26:16 +0100 Subject: [PATCH 1154/2173] Update - add long description, dev_url and run_export (#44744) * Update - add long description, dev_url and run_export --------- Co-authored-by: Jacques Dainat --- recipes/proovframe/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/proovframe/meta.yaml b/recipes/proovframe/meta.yaml index 049b39ce3d5e0..d625a9037982e 100644 --- a/recipes/proovframe/meta.yaml +++ b/recipes/proovframe/meta.yaml @@ -12,8 +12,10 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 noarch: generic + run_exports: + - {{ pin_subpackage('proovframe', max_pin='x') }} requirements: run: @@ -41,6 +43,10 @@ about: license_family: MIT license_file: LICENSE summary: frame-shift correction for long read (meta)genomics + description: | + Gene prediction on long reads, aka PacBio and Nanopore, is often impaired by indels causing frameshift. + Proovframe detects and corrects frameshifts in coding sequences from raw long reads or long-read derived assemblies. + dev_url: https://github.com/{{ user }}/{{ name }} maintainers: - thanhleviet From ab454dffe37cb4b55b9eb6798a5657cb6b27280a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Dec 2023 14:36:31 -0500 Subject: [PATCH 1155/2173] Update clinvar-this to 0.14.1 (#44754) --- recipes/clinvar-this/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clinvar-this/meta.yaml b/recipes/clinvar-this/meta.yaml index acafecd533715..19c9e877a8bed 100644 --- a/recipes/clinvar-this/meta.yaml +++ b/recipes/clinvar-this/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.14.0" %} -{% set sha256 = "cbefeb541767da2725e3c9c29481483b404bc8d8b3261b157c0013514c5ef402" %} +{% set version = "0.14.1" %} +{% set sha256 = "02c41c81915459bedb4656ea688de5e43f8f11e54b1786929550f9d7e3ff4480" %} package: name: clinvar-this From f39a17eebf724cc0d607c58cbe8fd4d451b429cc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Dec 2023 16:35:17 -0500 Subject: [PATCH 1156/2173] Update ncbi-datasets-pylib to 15.31.3 (#44750) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 342fc03a5d0a6..378ed99474464 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.31.2" %} -{% set sha256 = "a4e88dd0bf0ad2a4169283863b771c7e0013d9c3398f551c4dda600c62b3dfd7" %} +{% set version = "15.31.3" %} +{% set sha256 = "b99552d4a5a2167c15cd51674085a23cf16aedc3988870a27ebe02495fb582ce" %} package: name: {{ name|lower }} From b8df35204e01485d8694b173e5e95180235b14ed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Dec 2023 16:39:31 -0500 Subject: [PATCH 1157/2173] Update influx-si-data-manager to 0.1.4 (#44745) * Update influx-si-data-manager to 0.1.3 * Update influx-si-data-manager to 0.1.4 --- recipes/influx-si-data-manager/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/influx-si-data-manager/meta.yaml b/recipes/influx-si-data-manager/meta.yaml index c98a7312b3168..ca2b9010333ef 100644 --- a/recipes/influx-si-data-manager/meta.yaml +++ b/recipes/influx-si-data-manager/meta.yaml @@ -1,5 +1,5 @@ {% set name = "influx-si-data-manager" %} -{% set version = "0.1.2" %} +{% set version = "0.1.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/influx_si_data_manager-{{ version }}.tar.gz - sha256: ca0ef718ce69a23aaba28fda5b6584161620096165c39a96bceb30ebec35ea92 + sha256: 3d5e224166d4c85995a56e1f906548630e54066413f59651c9c6874800999c38 build: entry_points: From 8bdf38a88cd855ce49e08e2004df98dfdca4fcfd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 03:05:54 -0500 Subject: [PATCH 1158/2173] Update phables to 1.2.2 (#44760) --- recipes/phables/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phables/meta.yaml b/recipes/phables/meta.yaml index 8e5ccfddad8c5..a021fa80dec1f 100644 --- a/recipes/phables/meta.yaml +++ b/recipes/phables/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phables" %} -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/Vini2/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: a533c9d841f3fb3e4eb4d7faf9b734047317806f50ab1d0568291fd60bd2d464 + sha256: 316b6f3c9c2a0267745b0ebbaf2f8e82084f3863695274a4c0c6c58d248b4842 build: number: 0 From 69031b628090d2ba508bec2f92e48619dfedf403 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 03:09:14 -0500 Subject: [PATCH 1159/2173] Update freyja to 1.4.8 (#44758) --- recipes/freyja/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/freyja/meta.yaml b/recipes/freyja/meta.yaml index 42a9d309a8566..41ae8a92a8758 100644 --- a/recipes/freyja/meta.yaml +++ b/recipes/freyja/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.7" %} +{% set version = "1.4.8" %} {% set name = "Freyja" %} package: @@ -16,7 +16,7 @@ build: source: url: https://github.com/andersen-lab/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 3eca6731d817c10c6fcda327a763180909a0da3ce151a9e67a88efea734c02ce + sha256: 4534bf227fc58317c535c2c5d0d031816c8a5b1ae0968175a97cd02cb3530672 requirements: host: From 222ebbdfdb3ea6fb5a40fcad1ab296cb9bf93d9f Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 12 Dec 2023 10:42:21 +0100 Subject: [PATCH 1160/2173] cutadapt: require dnaio 1.2 (#44763) https://github.com/marcelm/cutadapt/issues/746 --- recipes/cutadapt/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cutadapt/meta.yaml b/recipes/cutadapt/meta.yaml index e2d0085e40488..a6b4c6ec5aa58 100644 --- a/recipes/cutadapt/meta.yaml +++ b/recipes/cutadapt/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 924116f34569248035b16f58e73458ed4c0004e44823b80b07f4ab419272f591 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps -vv" skip: True # [py27 or py36] run_exports: @@ -26,7 +26,7 @@ requirements: run: - python - xopen >=1.6.0 - - dnaio >=0.10.0 + - dnaio >=1.2.0 test: imports: From 2cda84606f1a75a3340300838ca5b43e1c03ad66 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 06:05:28 -0500 Subject: [PATCH 1161/2173] Update phykit to 1.12.2 (#44756) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index 0f98b1f2d4dda..e3c4a4c7bfc73 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.12.0" %} +{% set version = "1.12.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8dfc084780ce4c9a37ee49952ef9d86c617359d8cec5ef97b98ff63b0b95a486 + sha256: 9a99977e74146904eb65d392c0ed33ad2fb1c8a73fb4f15088e82fdd76139cef build: noarch: python From 623e12b90e43ab48222c819b54d7c2dbf7f03f72 Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Tue, 12 Dec 2023 06:07:19 -0500 Subject: [PATCH 1162/2173] mob_suite v3.1.8 manual recipe submit (#44755) * mob_suite v3.1.8 manual recipe submit * added version pin * added numpy pin * added pin_compatible scipy and pycurl * ete3 pin at 3.1.3 * pandas and numpy pin_compatible * pandas==1.0.5 restricted * pandas<2 --- recipes/mob_suite/meta.yaml | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/recipes/mob_suite/meta.yaml b/recipes/mob_suite/meta.yaml index 56cc01e2c4663..b16baa7188321 100644 --- a/recipes/mob_suite/meta.yaml +++ b/recipes/mob_suite/meta.yaml @@ -1,6 +1,6 @@ {% set name = "mob_suite" %} -{% set version = "3.1.7" %} -{% set sha256 = "1e9e5be166c4d7e2478b4b65f5a42d252f5d476b558e6501ce6feed2da679de4" %} +{% set version = "3.1.8" %} +{% set sha256 = "aa20c989b6d6dc624612a4e9821afac00b170168ca4d860dd00e104c5881b3f3" %} package: name: {{ name|lower }} @@ -15,8 +15,7 @@ build: number: 0 noarch: python run_exports: - - python - - pip + - {{ pin_subpackage(name, max_pin="x") }} script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vvv entry_points: - mob_init=mob_suite.mob_init:main @@ -31,13 +30,13 @@ requirements: - pytest-runner run: - python >=3.7 - - numpy >=1.11.1,<1.23.5 + - {{ pin_compatible('numpy', max_pin="x") }} - pytables - - pandas >=0.22.0,<=1.0.5 + - pandas >=0.22.0,<2 - biopython >=1.8,<2 - - pycurl - - scipy - - ete3 + - {{ pin_compatible('pycurl') }} + - {{ pin_compatible('scipy') }} + - ete3 >=3.1.3 - six - blast >=2.9.0 - mash >=2.0 From 2d3bcbc40ad6a0ba4e2c452a35df61f76eb5a8ce Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 06:36:27 -0500 Subject: [PATCH 1163/2173] Update clinvar-this to 0.14.2 (#44766) --- recipes/clinvar-this/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clinvar-this/meta.yaml b/recipes/clinvar-this/meta.yaml index 19c9e877a8bed..66021b37b0638 100644 --- a/recipes/clinvar-this/meta.yaml +++ b/recipes/clinvar-this/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.14.1" %} -{% set sha256 = "02c41c81915459bedb4656ea688de5e43f8f11e54b1786929550f9d7e3ff4480" %} +{% set version = "0.14.2" %} +{% set sha256 = "e651bd63ca9bd9ba71e133e48c34868c6d72d095e102df6a82b660f44f90cf3b" %} package: name: clinvar-this From 021a75d57d6ca2d4850d6fa4919d495f681254b3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 10:06:53 -0500 Subject: [PATCH 1164/2173] Update bionumpy to 1.0.1 (#44770) --- recipes/bionumpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index 0747df16db339..30519b96389e1 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: bionumpy @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: 25b2d8baed6705ef8f242f7d755c4fe927d6609232dca338bd485c295ed6b3a7 + sha256: 9e00254dc1c2ee2669048b7fd0bb6309e6caa218f8a330b00e3929f1dfeee58c build: noarch: python From d9780f62252daac9f813aff2b409a8685370111d Mon Sep 17 00:00:00 2001 From: Akihiro Kuno Date: Wed, 13 Dec 2023 00:14:44 +0900 Subject: [PATCH 1165/2173] Update DAJIN2 (#44761) --- recipes/dajin2/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index 9d98f0440c51c..cd35c58305925 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "DAJIN2" %} -{% set version = "0.3.3" %} +{% set version = "0.3.4" %} package: name: {{ name|lower }} @@ -7,14 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: 1fe0f42e3dd79cf9e21f2c93706004c668440edd385ef112214fdfa8e9396a9f + sha256: 0165301f801242d3fd9e09064d78e5ca162cf1e6b55fec5100efebd35a3e8243 build: entry_points: - DAJIN2=DAJIN2.main:execute noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 1 + number: 0 run_exports: - {{ pin_subpackage('dajin2', max_pin="x.x") }} @@ -38,7 +38,7 @@ requirements: - jinja2 >=3.1.0 - plotly >=5.0.0 - python-kaleido >=0.2.0 - - cstag >=0.4.1 + - cstag >=1.0.0 - midsv >=0.10.1 - wslpath >=0.3.0 From 219c398a30c5a8cfc90e545065b4d8998993e27b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 12:19:52 -0500 Subject: [PATCH 1166/2173] Update cyvcf2 to 0.30.25 (#44751) * Update cyvcf2 to 0.30.25 * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/cyvcf2/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/cyvcf2/meta.yaml b/recipes/cyvcf2/meta.yaml index a9a4ca590cbb9..c90af45fe4553 100644 --- a/recipes/cyvcf2/meta.yaml +++ b/recipes/cyvcf2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cyvcf2" %} -{% set version = "0.30.22" %} -{% set sha256 = "324613c41f9bbb322533f351fd8d33a4454b391d76841da0a28a7075a0e15d84" %} +{% set version = "0.30.25" %} +{% set sha256 = "40f1fda66e3bad9873bba08fe3c0839f590089137b2aa7070247561e77ce0d8d" %} package: name: {{ name }} @@ -19,6 +19,8 @@ build: script: {{ PYTHON }} -m pip install . --use-pep517 -vv entry_points: - cyvcf2 = cyvcf2.__main__:cli + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: From cc485fb55197a80a1aac62298d4ecfeb35ab5887 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 12:51:33 -0500 Subject: [PATCH 1167/2173] Update ccmetagen to 1.4.2 (#44742) * Update ccmetagen to 1.4.2 * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/ccmetagen/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ccmetagen/meta.yaml b/recipes/ccmetagen/meta.yaml index 5661e6a3706f7..9a724a9a6a7d6 100644 --- a/recipes/ccmetagen/meta.yaml +++ b/recipes/ccmetagen/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ccmetagen" %} -{% set version = "1.4.1" %} +{% set version = "1.4.2" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://github.com/vrmarcelino/CCMetagen/archive/v{{ version }}.tar.gz" - sha256: "38f6535296a8c9ce173cbc859368f8ddcec2d7612bc52bd8ea38d21f67e4d67f" + sha256: "9e01a3e123e6fb2d30ac0f17f452bc5262c938821def867cfaea705e4f327940" build: noarch: python number: 0 script: "python -m pip install --no-deps --ignore-installed . " + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: From cb90c2035b4657a1d1199496bb792276b7c45201 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 12:51:58 -0500 Subject: [PATCH 1168/2173] Update trgt to 0.7.0 (#44752) --- recipes/trgt/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/trgt/meta.yaml b/recipes/trgt/meta.yaml index 883dff1c8071c..e56dd01517b57 100644 --- a/recipes/trgt/meta.yaml +++ b/recipes/trgt/meta.yaml @@ -1,7 +1,7 @@ {% set name = "trgt" %} -{% set version = "0.5.0" %} -{% set trgt_sha256 = "d16deb99be8cdd3bc29fee5539fa270642ed2018cdd35f3228e7061938eb923a" %} -{% set trvz_sha256 = "51c18e1bdd1221c225e477c2f2938e1269f7cbfe3d0e92681c1db34226780311" %} +{% set version = "0.7.0" %} +{% set trgt_sha256 = "09ea997ffd90e1c9aba0a25a38eaa70a95d0d4c365518003b6f340b6f6b9e186" %} +{% set trvz_sha256 = "4b7a642dc69093d68eb8d68a10c49749c382f0db8f71131ce703687438b69b13" %} package: name: {{ name }} From b368aba96d1fa1ac3e39b2cb9ebd7e2c077335ea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 12:52:42 -0500 Subject: [PATCH 1169/2173] Update el_gato to 1.15.2 (#44748) * Update el_gato to 1.15.1 * Update el_gato to 1.15.2 --- recipes/el_gato/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/el_gato/meta.yaml b/recipes/el_gato/meta.yaml index 657700715c719..7d299d85a9136 100644 --- a/recipes/el_gato/meta.yaml +++ b/recipes/el_gato/meta.yaml @@ -1,6 +1,6 @@ {% set name = "el_gato" %} -{% set version = "1.15.0" %} -{% set hash = "2f2b8942c8327531ad69fe178eb0b1a050402d31f647e6a03e01f6dd3a9db510" %} +{% set version = "1.15.2" %} +{% set hash = "ef930f7e0e2940f7d28820fbfc19b2262d1898c82d8699ca47dbc4c851eb11ad" %} {% set user = "appliedbinf" %} package: From 061066dc6fe91e4fcc96c37cf8b9302105056479 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 12:53:05 -0500 Subject: [PATCH 1170/2173] Update dxpy to 0.367.0 (#44757) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 7c42041c642d4..cd113ae146441 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.366.0" %} +{% set version = "0.367.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4f00cc2611d8def8ffc0a996a53e8019fcdc658f827ea9cf56999be7d334ed32 + sha256: 21491f943b3cd1aeb5d0ad33b8f5e269653c43f23ce796b129c93599204d7caa build: number: 0 From f5839c7f8129a30437bb149dde1ad8e887400310 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 12:53:40 -0500 Subject: [PATCH 1171/2173] Update hyphy to 2.5.58 (#44773) --- recipes/hyphy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hyphy/meta.yaml b/recipes/hyphy/meta.yaml index a22a1c4664913..66f4c7839bcdf 100644 --- a/recipes/hyphy/meta.yaml +++ b/recipes/hyphy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.5.57" %} -{% set sha256 = "5412331ff40b58fa69f34ad67f3431e662e9c2002f5d035f47225f26b8e3533c" %} +{% set version = "2.5.58" %} +{% set sha256 = "f448d4a95bdb356eb6b1384b0c507a79f152511ad76bb67170ab5b8eb2798231" %} package: name: hyphy From ffbcfdc6bc14ee2e9612ef66cc2812e99ba2e1bc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 14:40:48 -0500 Subject: [PATCH 1172/2173] Update r-acidgenerics to 0.7.5 (#44779) --- recipes/r-acidgenerics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenerics/meta.yaml b/recipes/r-acidgenerics/meta.yaml index 014d98f16539e..0b0349f1f6021 100644 --- a/recipes/r-acidgenerics/meta.yaml +++ b/recipes/r-acidgenerics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.4" %} +{% set version = "0.7.5" %} {% set github = "https://github.com/acidgenomics/r-acidgenerics" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 495f04e3077d2bc1001d1ba1a1537936f57875791320d4d076b8e571a601a08a + sha256: cc992d9e5b1c3245dd7334a63815c66d58e6085b9e587cb6f192b20c2b536c97 build: number: 0 From bea8a10f2a9f75311a9445bd4cc09df21cd75654 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 15:14:53 -0500 Subject: [PATCH 1173/2173] Update clinvar-this to 0.14.3 (#44780) --- recipes/clinvar-this/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clinvar-this/meta.yaml b/recipes/clinvar-this/meta.yaml index 66021b37b0638..3b342202c2fa9 100644 --- a/recipes/clinvar-this/meta.yaml +++ b/recipes/clinvar-this/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.14.2" %} -{% set sha256 = "e651bd63ca9bd9ba71e133e48c34868c6d72d095e102df6a82b660f44f90cf3b" %} +{% set version = "0.14.3" %} +{% set sha256 = "d9212dc6e6a6bb178028dd358eac3bd92395cb62d94bc0ffc1929c2d27fae342" %} package: name: clinvar-this From 3cf9c9ce7be930f21c45e2a751df0c2cd867a914 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 17:12:26 -0500 Subject: [PATCH 1174/2173] Update htslib to 1.19 (#44774) * Update htslib to 1.19 * Remove run requirements for shared libraries [JM] These will be inferred from the library dependencies, as appropriate. In particular, this will omit the spurious zlib package dependency: only libzlib is required. --------- Co-authored-by: John Marshall --- recipes/htslib/meta.yaml | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml index 3890a36b3c80d..de1440505082b 100644 --- a/recipes/htslib/meta.yaml +++ b/recipes/htslib/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.18" %} +{% set version = "1.19" %} package: name: htslib @@ -11,7 +11,7 @@ build: source: url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2 - sha256: f1ab53a593a2320a1bfadf4ef915dae784006c5b5c922c8a8174d7530a9af18f + sha256: 8751c40c4fa7d1f23a6864c5b20a73744f8be68239535ae7729c5f7d394d0736 requirements: build: @@ -24,13 +24,6 @@ requirements: - zlib - libdeflate - openssl # [not osx] - run: - - libcurl - - bzip2 - - xz - - zlib - - libdeflate - - openssl # [not osx] test: files: From 127c81a2818a7eb795f5173cbf42c599eb0159e4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 12 Dec 2023 20:52:59 -0500 Subject: [PATCH 1175/2173] Update samtools to 1.19 (#44788) --- recipes/samtools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index 80c070b43d5c7..b17cf299e837e 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "1.18" %} +{% set version = "1.19" %} package: name: samtools version: {{ version }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage("samtools", max_pin="x") }} source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - sha256: d686ffa621023ba61822a2a50b70e85d0b18e79371de5adb07828519d3fc06e1 + sha256: fa6b3b18e20851b6f3cb55afaf3205d02fcb79dae3b849fcf52e8fc10ff08b83 requirements: build: From b1b9df6892912e0e89c604a9e20667e11e2832a5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 05:36:10 -0500 Subject: [PATCH 1176/2173] Update bcftools to 1.19 (#44793) * Update bcftools to 1.19 * Remove library `run` dependencies These libraries will add appropriate dependencies themselves via their run_exports, and in particular zlib will add libzlib so we should not over-depend on zlib as well. --------- Co-authored-by: John Marshall --- recipes/bcftools/meta.yaml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/recipes/bcftools/meta.yaml b/recipes/bcftools/meta.yaml index 0fade8e8dac4e..cbe333349ad2f 100644 --- a/recipes/bcftools/meta.yaml +++ b/recipes/bcftools/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.18" %} +{% set version="1.19" %} package: name: bcftools @@ -11,7 +11,7 @@ build: source: url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 - sha256: d9b9d36293e4cc62ab7473aa2539389d4e1de79b1a927d483f6e91f3c3ceac7e + sha256: 782b5f1bc690415192231e82213b3493b047f45e630dc8ef6f154d6126ab3e68 requirements: build: @@ -22,12 +22,9 @@ requirements: - zlib - gsl run: - - gsl - - htslib # Currently removed due to size and dependency issues #- matplotlib # for plot-vcfstats #- tectonic # for plot-vcfstats - - zlib - perl test: From f2ce03bb4b0808302aa2862baee78718ebdd360f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 06:22:52 -0500 Subject: [PATCH 1177/2173] Update t1k to 1.0.5 (#44792) --- recipes/t1k/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/t1k/meta.yaml b/recipes/t1k/meta.yaml index 24f2102ec5b3a..8a80c8f20c3f9 100644 --- a/recipes/t1k/meta.yaml +++ b/recipes/t1k/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.4" %} +{% set version = "1.0.5" %} package: name: t1k @@ -11,7 +11,7 @@ build: source: url: https://github.com/mourisl/T1K/archive/v{{ version }}.tar.gz - sha256: 1ace975b9e6ab07a10d801ab783dceab534c3754c3f25805c536f34413d63ca0 + sha256: 8230d732ec92f66ca7dedb5786e8823d5def8c00dd020d9b99a889de8ed849e3 requirements: build: From cf3579c996e8997631213dad5586a7377e8889bf Mon Sep 17 00:00:00 2001 From: Kristy Horan Date: Wed, 13 Dec 2023 22:32:20 +1100 Subject: [PATCH 1178/2173] Add tbtamr 2 (#44671) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * added in tbtamr * added in tbtamr * added in tbtamr * added in tbtamr * added in tbtamr * added in tbtamr * Update recipes/tbtamr/meta.yaml Co-authored-by: Björn Grüning * addressed issues with licence * adding licence file * added max_pin x.x --------- Co-authored-by: Björn Grüning --- recipes/tbtamr/LICENSE | 674 +++++++++++++++++++++++++++++++++++++++ recipes/tbtamr/meta.yaml | 55 ++++ 2 files changed, 729 insertions(+) create mode 100644 recipes/tbtamr/LICENSE create mode 100644 recipes/tbtamr/meta.yaml diff --git a/recipes/tbtamr/LICENSE b/recipes/tbtamr/LICENSE new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/tbtamr/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/tbtamr/meta.yaml b/recipes/tbtamr/meta.yaml new file mode 100644 index 0000000000000..435271ec684fd --- /dev/null +++ b/recipes/tbtamr/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "tbtamr" %} +{% set version = "0.0.4" %} +{% set sha256 = "72db1eb835574f02b0d7768e6b04e310bd2229d0f684100004b20a133eecd882" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: "{{ sha256 }}" + +build: + noarch: python + number: 0 + entry_points: + - tbtamr=tbtamr.tbtamr:main + run_exports: + - {{ pin_subpackage('tbtamr', max_pin="x.x") }} + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + +requirements: + host: + - python >=3.8 + - pip + run: + - python >=3.8 + - psutil + - pandas + - csvtk + - bwa + - samtools =1.12 + - snpeff =5.0 + - samclip + - freebayes + - bcftools + - bedtools + - delly + +test: + imports: + - tbtamr + commands: + - tbtamr --help + +about: + home: "https://github.com/MDU-PHL/tbtamr" + license: GPL-3.0-or-later + license_file: LICENSE + license_family: "GPL3" + summary: "A tool implementing TB-Profiler for reporting of genomic DST for M. tuberculosis in a CPHL" + +extra: + recipe-maintainers: + - kristyhoran From e78f816350f03f747eeb292acddd1e03e38f781b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 08:38:11 -0500 Subject: [PATCH 1179/2173] Update r-acidplyr to 0.5.3 (#44798) --- recipes/r-acidplyr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidplyr/meta.yaml b/recipes/r-acidplyr/meta.yaml index 28d18de30e631..39281769fbecc 100644 --- a/recipes/r-acidplyr/meta.yaml +++ b/recipes/r-acidplyr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.2" %} +{% set version = "0.5.3" %} {% set github = "https://github.com/acidgenomics/r-acidplyr" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 76e4bead1439a5586b32977427294080b360760908933386e5780697963f8c2b + sha256: d7667aa3ec534fbe13667a30ede0fc2f7bc25f0ea63a7b4708a28e1ed999ebf5 build: number: 0 From c2c448fec5e0b627dcca695994023b6dfd4912f7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 09:25:47 -0500 Subject: [PATCH 1180/2173] Update pyabpoa to 1.4.2 (#44795) * Update pyabpoa to 1.4.2 * Update meta.yaml --------- Co-authored-by: Thanh Lee --- recipes/pyabpoa/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/pyabpoa/meta.yaml b/recipes/pyabpoa/meta.yaml index 373ebc270b2c3..11bab9a30140e 100644 --- a/recipes/pyabpoa/meta.yaml +++ b/recipes/pyabpoa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyabpoa" %} -{% set version = "1.4.1" %} +{% set version = "1.4.2" %} package: name: {{ name|lower }} @@ -7,12 +7,13 @@ package: source: url: https://github.com/yangao07/abPOA/releases/download/v{{ version }}/abPOA-v{{ version }}.tar.gz - sha256: 54b1f5cfd94fb5894e189d9e099f8158051411bcbcc9ba2d77478cfb9221dde1 + sha256: 955109ee28ccdef60c371f7ad113e380d1a6d42b658243eafc00239b9e58a087 build: number: 0 script: {{ PYTHON }} -m pip install . -vvv - + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: - {{ compiler('c') }} From a7928ba80682e981dd98a59ead823274f320f95d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 10:23:42 -0500 Subject: [PATCH 1181/2173] Update abpoa to 1.4.2 (#44794) * Update abpoa to 1.4.2 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Yan Gao --- recipes/abpoa/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/abpoa/meta.yaml b/recipes/abpoa/meta.yaml index 8f056ed0430dc..4bd663c59d297 100644 --- a/recipes/abpoa/meta.yaml +++ b/recipes/abpoa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.1" %} +{% set version = "1.4.2" %} {% set program = "abpoa" %} {% set PROGRAM = "abPOA" %} @@ -8,10 +8,12 @@ package: source: url: https://github.com/yangao07/{{ PROGRAM }}/releases/download/v{{ version }}/{{ PROGRAM }}-v{{ version }}.tar.gz - sha256: 54b1f5cfd94fb5894e189d9e099f8158051411bcbcc9ba2d77478cfb9221dde1 + sha256: 955109ee28ccdef60c371f7ad113e380d1a6d42b658243eafc00239b9e58a087 build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(program, max_pin="x.x") }} requirements: build: From ad1345f6f29df83f3aa745f9e8b3695cfe993e7b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 12:56:50 -0500 Subject: [PATCH 1182/2173] Update phykit to 1.12.3 (#44778) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index e3c4a4c7bfc73..fa7d43baddc88 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.12.2" %} +{% set version = "1.12.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 9a99977e74146904eb65d392c0ed33ad2fb1c8a73fb4f15088e82fdd76139cef + sha256: 36001777df73aed39b4e41dc35d774d089439005aa45358de22db71b51130b63 build: noarch: python From 25770bcb775ad69abcb23f4c9528581f703bcbb3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 12:56:59 -0500 Subject: [PATCH 1183/2173] Update arvados-python-client to 2.7.1 (#44781) --- recipes/arvados-python-client/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml index 1459e6302377b..8c8e710950c0a 100644 --- a/recipes/arvados-python-client/meta.yaml +++ b/recipes/arvados-python-client/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.7.0" %} +{% set version = "2.7.1" %} package: name: arvados-python-client @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/a/arvados-python-client/arvados-python-client-{{ version }}.tar.gz - sha256: da948a17fcc8146175f17b37e14dc7ab12dfc96bb8b5e481e16568ea78918723 + sha256: c973be949dbb35959d5eeda1d2bad31813484756e8367573e7b2f0149190039e build: noarch: python From 9ab0ebc2ea739f26ab44ff4fd590b81230b0f24f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 12:57:10 -0500 Subject: [PATCH 1184/2173] Update flashlfq to 1.2.6 (#44783) --- recipes/flashlfq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/flashlfq/meta.yaml b/recipes/flashlfq/meta.yaml index 55483f0779d06..f2e8c55ecec23 100644 --- a/recipes/flashlfq/meta.yaml +++ b/recipes/flashlfq/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.2.5" %} -{% set sha256 = "a86e3153bc6833317a68eba1156a88bb84c37b247da55df94e57650a77034567" %} +{% set version = "1.2.6" %} +{% set sha256 = "4b5bede68303d3073c9884280c9e4215be0b08a1c7f6c2e90dd726845a41cec0" %} source: url: https://github.com/smith-chem-wisc/FlashLFQ/releases/download/{{version}}/FlashLFQ.zip From 88d5dec9f5f6b6ea4a23bd6af8cf50f7de4ef8ef Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Wed, 13 Dec 2023 19:01:47 +0100 Subject: [PATCH 1185/2173] add Craq recipe (#44743) --- recipes/craq/build.sh | 13 +++++++++++++ recipes/craq/meta.yaml | 43 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 recipes/craq/build.sh create mode 100755 recipes/craq/meta.yaml diff --git a/recipes/craq/build.sh b/recipes/craq/build.sh new file mode 100644 index 0000000000000..9becccee47f38 --- /dev/null +++ b/recipes/craq/build.sh @@ -0,0 +1,13 @@ +#!/bin/sh +set -x -e + +# As CRAQ does not use standard packaging approach (Makefile.PL, Build.PL, ...), we need to keep CRAQ and its modules all together at the same place. +# So CRAQ is copied in the share folder with all related modules (copy of the repo) +CRAQ_DIR=${PREFIX}/share/CRAQ +mkdir -p ${CRAQ_DIR} +cp -r * ${CRAQ_DIR} +chmod +x ${CRAQ_DIR}/bin/craq + +# Add the craq executable in the bin by softlinking the tool located in share. +mkdir -p ${PREFIX}/bin +ln -s ${CRAQ_DIR}/bin/craq ${PREFIX}/bin/craq diff --git a/recipes/craq/meta.yaml b/recipes/craq/meta.yaml new file mode 100755 index 0000000000000..1646266d28952 --- /dev/null +++ b/recipes/craq/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "CRAQ" %} +{% set version = "1.0.9" %} +{% set sha256 = "83eaa8964fe62241caef334986bdeda0d45d3c4be2416351257c9599264d664d" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/JiaoLaboratory/CRAQ/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('craq', max_pin="x") }} + +requirements: + run: + - perl >=5 + - python >=3.7 + - minimap2 >=2.17 + - python_circos + +test: + commands: + - craq -h | grep Usage + +about: + home: https://github.com/JiaoLaboratory/CRAQ + license: MIT + license_family: MIT + license_file: LICENSE + summary: Pinpoint assembly errors for genomic assessing and correcting. + description: | + CRAQ (Clipping Reveals Assembly Quality) is a reference-free genome assembly evaluator that can assess the accuracy of assembled genomic sequences and provide detailed assembly quality assessment from multiple perspectives. It can report precise locations of small-scale Clip-based Regional Errors (CREs), large-scale Clip-based Structural Errors (CSEs), as well as regional and overall AQI metrics (R-AQI & S-AQI) for assembly evaluation. Through evaluating a large set of genome assemblies with different qualities, we classified genomes as following: AQI > 90, reference quality; AQI from 80-90, high quality; AQI from 60-80, draft quality; and AQI < 60, low quality. CRAQ also considered haplotype features which is important for identifying true misassembly. It can output coordinates of regional heterozygous variants (CRHs) and coordinates of structural heterozygous variants (CSHs) based on the ratio of clipped alignments and mapping coverage. Moreover, CRAQ detects potential chimeric contigs and break them at conflict breakpoints for assembly correction. This document has the information on how to run CRAQ. + doc_url: https://github.com/JiaoLaboratory/CRAQ + dev_url: https://github.com/JiaoLaboratory/CRAQ + +extra: + recipe-maintainers: + - juke34 From 509e341db4c24937b4b9da40492a90e9e581a2bb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 13:26:28 -0500 Subject: [PATCH 1186/2173] Update ncbi-datasets-pylib to 15.32.0 (#44787) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 378ed99474464..00edc6fe33a31 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.31.3" %} -{% set sha256 = "b99552d4a5a2167c15cd51674085a23cf16aedc3988870a27ebe02495fb582ce" %} +{% set version = "15.32.0" %} +{% set sha256 = "ab31148412f56be34b6ae2879f847139484a1be2b9b58298cb5c9ae88f245bfa" %} package: name: {{ name|lower }} From dcdce95abdff111c8166f97eef902c6c8e262586 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 13:26:55 -0500 Subject: [PATCH 1187/2173] Update sequana to 0.16.4 (#44803) --- recipes/sequana/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequana/meta.yaml b/recipes/sequana/meta.yaml index d96325a4a17b5..8d67e0ad64f7a 100644 --- a/recipes/sequana/meta.yaml +++ b/recipes/sequana/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.16.3" %} -{% set sha256 = "4a9f0c8dbbd23fad6517d601b835319d6942337a670ded685a412ba06180e546" %} +{% set version = "0.16.4" %} +{% set sha256 = "d2624dd09dd04a7d27a38bbfb90e8ae5bf554bdc2e0b1e6a9484ab979a56e1ea" %} {% set name = "sequana" %} package: From 73c18395b23785f647c7673d31c077526cc89412 Mon Sep 17 00:00:00 2001 From: pmjklemm Date: Wed, 13 Dec 2023 19:27:42 +0100 Subject: [PATCH 1188/2173] Update meta.yaml, added doi (#44800) * Update meta.yaml, added doi added doi * maxpin --------- Co-authored-by: Paul Klemm --- recipes/proteinortho/meta.yaml | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/recipes/proteinortho/meta.yaml b/recipes/proteinortho/meta.yaml index af04c4ecd31fe..3f378b3862338 100755 --- a/recipes/proteinortho/meta.yaml +++ b/recipes/proteinortho/meta.yaml @@ -1,6 +1,6 @@ {% set name = "proteinortho" %} -{% set version = "6.3.0" %} -{% set sha256 = "9b0142d29d22a35732b17be2ce125ccbc7d711edc4bb8caf1ffc808eb16975f1" %} +{% set version = "6.3.1" %} +{% set sha256 = "9b3f5eb946a4f0f85c362db550163534d7687b8c88906b2eaf81f519de844b08" %} package: name: {{ name }} @@ -12,6 +12,9 @@ source: build: number: 0 + run_exports: + - {{ pin_subpackage('proteinortho', max_pin="x.x.x") }} + requirements: build: @@ -44,3 +47,8 @@ about: license_family: GPL license_file: LICENSE summary: "Proteinortho is a tool to detect orthologous genes within different species." + +extra: + identifiers: + - biotools:proteinortho + - doi:10.3389/fbinf.2023.1322477 From 6bd1b4b8207413fa091ce31354acd7801bf66ee2 Mon Sep 17 00:00:00 2001 From: Krzysztof Polanski Date: Wed, 13 Dec 2023 19:28:33 +0100 Subject: [PATCH 1189/2173] Update bbknn to 1.6.0 (#44786) * update bbknn to 1.6.0 * try to follow linter suggestions * remove bbknn from blacklist * add flit-core to host --- build-fail-blacklist | 4 ---- recipes/bbknn/meta.yaml | 22 ++++++++++++---------- 2 files changed, 12 insertions(+), 14 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 941f4c5e5352c..774aa42cd376e 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1061,10 +1061,6 @@ recipes/d4binding # maturin build fails recipes/taxonomy -# from numba.np.ufunc import _internal -# SystemError: initialization of _internal failed without raising an exception -recipes/bbknn - # no matching package named `quickersort` found recipes/mudskipper diff --git a/recipes/bbknn/meta.yaml b/recipes/bbknn/meta.yaml index 64871ea31723a..55e9dcda0c2c7 100644 --- a/recipes/bbknn/meta.yaml +++ b/recipes/bbknn/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bbknn" %} -{% set version = "1.5.1" %} +{% set version = "1.6.0" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 16da9c778ddfe363f8a3fa0d72707694d2217f94d3a87482336e8a2c6beb2160 + sha256: 1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b build: - number: 3 - skip: true # [py2k or py == 310] + number: 0 + skip: true # [py2k] script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + run_exports: + - {{ pin_subpackage('bbknn', max_pin="x") }} requirements: build: @@ -24,19 +26,19 @@ requirements: - numpy >=1.13 - pip - python - - scipy - - scikit-learn + - flit-core >=3.2,<4 + - scipy >=1.6.0 + - scikit-learn >=1.0.2 - umap-learn - - packaging + - pandas run: - python - python-annoy - pynndescent - numpy >=1.13 - - scipy - - scikit-learn + - scipy >=1.6.0 + - scikit-learn >=1.0.2 - umap-learn - - packaging - pandas test: From 6e7f8afb500ccc66c8c4b7835262d0d23a8aa984 Mon Sep 17 00:00:00 2001 From: Tobias Rausch Date: Wed, 13 Dec 2023 19:29:17 +0100 Subject: [PATCH 1190/2173] dicey v0.2.8 (#44797) --- recipes/dicey/meta.yaml | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/recipes/dicey/meta.yaml b/recipes/dicey/meta.yaml index 5ab8983cfd535..c5ceeb4d70007 100644 --- a/recipes/dicey/meta.yaml +++ b/recipes/dicey/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.6" %} -{% set sha256 = "7bfbf0e6f548b6a29215f417befe541d5a839fdf1e12db0f704f519692c45515" %} +{% set version = "0.2.8" %} +{% set sha256 = "63ca4bc5579023de12a0495fe0989ed3ddf7e0eb06bfde15c7bbaa2894c6844e" %} package: name: dicey @@ -15,11 +15,8 @@ source: build: number: 0 - -extra: - skip-lints: - - uses_vcs_url - - missing_hash + run_exports: + - {{ pin_subpackage("dicey", max_pin="x.x") }} requirements: build: @@ -34,6 +31,7 @@ requirements: host: - zlib - bzip2 + - libdeflate - boost-cpp - htslib - clangdev @@ -41,6 +39,7 @@ requirements: run: - zlib - bzip2 + - libdeflate - boost-cpp - htslib @@ -54,3 +53,10 @@ about: license_family: GPL license_file: LICENSE summary: In-silico PCR and variant primer design + +extra: + skip-lints: + - uses_vcs_url + - missing_hash + identifiers: + - biotools:Gear-Genomics From 6e86f44402b29c3c898728f3be31021e9f9e2c7d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 13:30:55 -0500 Subject: [PATCH 1191/2173] Update clinvar-this to 0.14.5 (#44796) --- recipes/clinvar-this/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clinvar-this/meta.yaml b/recipes/clinvar-this/meta.yaml index 3b342202c2fa9..7fb142d5b12fe 100644 --- a/recipes/clinvar-this/meta.yaml +++ b/recipes/clinvar-this/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.14.3" %} -{% set sha256 = "d9212dc6e6a6bb178028dd358eac3bd92395cb62d94bc0ffc1929c2d27fae342" %} +{% set version = "0.14.5" %} +{% set sha256 = "88be8458f10043b7dec266395204e17332fe0a05ba1776f7586f50d36722aa6c" %} package: name: clinvar-this From ef70e3e5b4c3627cb30056594e44db5b9d78f470 Mon Sep 17 00:00:00 2001 From: Xi Chen <38089207+xinehc@users.noreply.github.com> Date: Thu, 14 Dec 2023 02:31:31 +0800 Subject: [PATCH 1192/2173] update melon recipe (#44805) --- recipes/melon/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/melon/meta.yaml b/recipes/melon/meta.yaml index ce8a8b5bd87cd..abb0bd264262a 100644 --- a/recipes/melon/meta.yaml +++ b/recipes/melon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "melon" %} -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/xinehc/melon/archive/refs/tags/v{{ version }}.tar.gz - sha256: 4532d2a618e72adc235fde46945983cc7581f1917c8ceb82a1b65d6c1df9cc70 + sha256: 2f2aefe5fa99064dc7f1cdbafbf1bfaf98907ce3487c75cee4758c79c827f6d2 build: noarch: python @@ -27,6 +27,7 @@ requirements: - kraken2 - seqkit - numpy + - scipy test: imports: @@ -38,7 +39,7 @@ about: home: https://github.com/xinehc/melon license: MIT license_family: MIT - summary: 'Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes' + summary: 'Melon: metagenomic long-read-based taxonomic identification and quantification' extra: recipe-maintainers: From 9013cf38021c7815b83719ef5746842f9be4706b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 14:57:10 -0500 Subject: [PATCH 1193/2173] Update pia to 1.4.10 (#44809) --- recipes/pia/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pia/meta.yaml b/recipes/pia/meta.yaml index f9a15a29de112..1fe65791e2b82 100644 --- a/recipes/pia/meta.yaml +++ b/recipes/pia/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pia" %} -{% set version = "1.4.9" %} -{% set sha256 = "9759c0c5d7a6bbd310d67e35043a3d87106e05be2102ca6159ea3c7eea645fad" %} +{% set version = "1.4.10" %} +{% set sha256 = "f42550b51ea244f38d351205b1d1b7fda5aff1341ff451ef9530f67e1e73a017" %} package: name: {{ name|lower }} From 7d566f14c1b35f580887c606ced966115df93fd8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 18:55:44 -0500 Subject: [PATCH 1194/2173] Update bioconda-utils to 2.11.1 (#44811) --- recipes/bioconda-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index e106e87104a89..223a443b5d610 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.11.0" %} -{% set sha256 = "d30e9e0fff49d36f7e480672468e4355a2bf77bc82c9fbaa539edc0c9ac6def0" %} +{% set version = "2.11.1" %} +{% set sha256 = "7ed52d449b19beecf9461a998aeb8194b5930538ec6468996448bf28f1bab2f5" %} package: name: bioconda-utils From 8384647a32ddfd9e45820d6ae4839f68295f5c09 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 13 Dec 2023 21:08:40 -0600 Subject: [PATCH 1195/2173] Update methylpy to 1.4.7 (#44735) * Update methylpy to 1.4.7 * edit python variable in build.sh * bump version and edit sha256 * try CPLUS_INCLUDE_PATH * use SP_DIR instead --- build-fail-blacklist | 1 - recipes/methylpy/build.sh | 8 ++++---- recipes/methylpy/meta.yaml | 11 +++++++---- 3 files changed, 11 insertions(+), 9 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 774aa42cd376e..5406b11e29630 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -309,7 +309,6 @@ recipes/qtip recipes/tagger recipes/compare-reads recipes/strainest -recipes/methylpy recipes/t_coffee recipes/shannon_cpp recipes/ecopy diff --git a/recipes/methylpy/build.sh b/recipes/methylpy/build.sh index 9527695cadb4a..6f124e68e5e57 100644 --- a/recipes/methylpy/build.sh +++ b/recipes/methylpy/build.sh @@ -1,12 +1,12 @@ #!/bin/bash # Install methylpy -python -m pip install . --no-deps --ignore-installed -vv +${PYTHON} -m pip install . --no-deps --no-build-isolation -vvv # Install RMS -export CPATH=${PREFIX}/include +export CPLUS_INCLUDE_PATH=${PREFIX}/include cd methylpy -$CXX -O3 -L${PREFIX}/lib -lgsl -lgslcblas -o run_rms_tests.out rms.cpp +${CXX} -O3 -L${PREFIX}/lib -lgsl -lgslcblas -o run_rms_tests.out rms.cpp # run_rms_tests.out needs to be copied to the directory where methylpy is installed -cp run_rms_tests.out ${PREFIX}/lib/python*/site-packages/methylpy/ +cp run_rms_tests.out ${SP_DIR}/methylpy/ cd .. diff --git a/recipes/methylpy/meta.yaml b/recipes/methylpy/meta.yaml index 2d3559812ed78..3fe58629ca9d4 100644 --- a/recipes/methylpy/meta.yaml +++ b/recipes/methylpy/meta.yaml @@ -1,6 +1,6 @@ {% set name = "methylpy" %} -{% set version = "1.4.3" %} -{% set sha256 = "3ad7ea3093dc3751544936bbbcdc55b16e8b3b39600f86c75219360e2a1437d7" %} +{% set version = "1.4.7" %} +{% set sha256 = "bbd9ab01cd7b6bba9b96b94aed2e1deee5af405d743eef4f031eb8b846ae8156" %} package: name: {{ name|lower }} @@ -11,7 +11,9 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('methylpy', max_pin="x") }} requirements: build: @@ -43,10 +45,11 @@ test: about: home: https://github.com/yupenghe/methylpy - license: Apache 2.0 + license: Apache-2.0 license_family: APACHE license_file: LICENSE.txt summary: "Bisulfite sequencing data processing and differential methylation analysis" + doc_url: "https://github.com/yupenghe/methylpy/blob/methylpy/tutorial/tutorial.md" extra: identifiers: From a455fab65fc344af57d7c9335826864f8247306d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 22:09:25 -0500 Subject: [PATCH 1196/2173] Update tobias to 0.16.1 (#44749) * Update tobias to 0.16.1 * Update meta.yaml * edit run_exports --------- Co-authored-by: Thanh Lee Co-authored-by: joshuazhuang7 --- recipes/tobias/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/tobias/meta.yaml b/recipes/tobias/meta.yaml index ed930427d0581..f2c9e5143b87b 100644 --- a/recipes/tobias/meta.yaml +++ b/recipes/tobias/meta.yaml @@ -1,6 +1,6 @@ {% set name = "TOBIAS" %} -{% set version = "0.16.0" %} -{% set sha256 = "db44f1b06d733882ca8bef1dcc8fcb374230ce2ab720f534811915452e05d25c" %} +{% set version = "0.16.1" %} +{% set sha256 = "c46267c01287be06201b3e6f7a36daad1ad86d6c578f96e878501be7da7fd109" %} package: name: {{ name|lower }} @@ -13,9 +13,11 @@ source: build: number: 0 skip: True # [py < 37] - script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vv + script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps --no-build-isolation -vvv entry_points: - TOBIAS=tobias.TOBIAS:main + run_exports: + - {{ pin_subpackage('tobias', max_pin="x.x") }} requirements: build: @@ -58,6 +60,7 @@ about: home: 'https://github.com/loosolab/TOBIAS' summary: 'Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal' license: MIT + license_family: MIT license_file: LICENSE doc_url: 'https://github.com/loosolab/TOBIAS/wiki' dev_url: 'https://pypi.org/project/tobias/' From 56297a64e2ed33375a96cb0af2ba179ecebbcf4b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 22:09:47 -0500 Subject: [PATCH 1197/2173] Update r-sigminer to 2.3.0 (#44771) * Update r-sigminer to 2.3.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/r-sigminer/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/r-sigminer/meta.yaml b/recipes/r-sigminer/meta.yaml index ac8f8bd265d54..778fd2f37ba4d 100644 --- a/recipes/r-sigminer/meta.yaml +++ b/recipes/r-sigminer/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '2.2.2' %} +{% set version = '2.3.0' %} package: name: r-sigminer @@ -8,13 +8,15 @@ source: url: - {{ cran_mirror }}/src/contrib/sigminer_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/sigminer/sigminer_{{ version }}.tar.gz - sha256: 57c75c7ad5991b10ee95b2b1b51ef952e6d6cfdfa05e4f8115fc3d19eb2e89ac + sha256: 8ba213927f1f0edad7e9dc8fb2b18053bb5c369b385efaf529283e545e71d8c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-sigminer', max_pin="x") }} requirements: build: From b85ab051a7f4dcc265a335e60a0fa198ead0c7e4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 22:10:48 -0500 Subject: [PATCH 1198/2173] Update sneep to 0.8 (#44799) * Update sneep to 0.8 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/sneep/meta.yaml | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/recipes/sneep/meta.yaml b/recipes/sneep/meta.yaml index 9eb96b1f9a664..97578dcf17ba2 100644 --- a/recipes/sneep/meta.yaml +++ b/recipes/sneep/meta.yaml @@ -1,19 +1,19 @@ - - -{% set name = "SNEEP" %} -{% set version = "0.7" %} +{% set name = "SNEEP" %} +{% set version = "0.8" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/SchulzLab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: ba199ca16ec1df120577114dc90a42774fe62bfc091270da94e908f4ca4531d7 + url: https://github.com/SchulzLab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 147e10e6f64056f6fde4fec609f7019d0a765a5b4b14ead954e1ef3071d95d49 build: skip: True # [py2k] number: 0 + run_exports: + - {{ pin_subpackage('sneep', max_pin="x.x") }} requirements: build: @@ -27,16 +27,17 @@ requirements: - python - numpy >=1.19 - scipy - - matplotlib-base + - matplotlib-base - bedtools >=2.27.1 test: commands: - differentialBindingAffinity_multipleSNPs -h - + about: home: https://github.com/SchulzLab/SNEEP dev_url: https://github.com/SchulzLab/SNEEP license: MIT - summary: Identify regulatory non-coding SNPs (rSNPs) + license_family: MIT + summary: Identify regulatory non-coding SNPs (rSNPs) From 66c188b17aaad8f0fdf32b380bd41653337cf1be Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 13 Dec 2023 22:13:02 -0500 Subject: [PATCH 1199/2173] Update btllib to 1.7.0 (#44791) * Update btllib to 1.7.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/btllib/meta.yaml | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/recipes/btllib/meta.yaml b/recipes/btllib/meta.yaml index 7e5179de80cf8..6a7e631686d5b 100644 --- a/recipes/btllib/meta.yaml +++ b/recipes/btllib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "btllib" %} -{% set version = "1.6.2" %} +{% set version = "1.7.0" %} package: name: {{ name|lower }} @@ -7,11 +7,13 @@ package: source: url: https://github.com/bcgsc/btllib/releases/download/v{{ version }}/{{ name|lower }}-{{ version }}.tar.gz - sha256: 06af0bccd68443bc6351d1d6d46599ae2a6e94752ae5fdf973067a77740d751c + sha256: a9a2b7d5c65865b20ee6467657c08ac05c9ea1f7c993bf44c3ffcf044b200def build: skip: true # [py < 38 or win] number: 0 + run_exports: + - {{ pin_subpackage('btllib', max_pin="x") }} requirements: build: @@ -47,6 +49,13 @@ test: about: home: https://github.com/bcgsc/btllib - license: GPL-3.0 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: 'Bioinformatics common code library in C++ with Python wrappers, from Bioinformatics Technology Lab' + doc_url: https://bcgsc.github.io/btllib/ + +extra: + identifiers: + - doi:10.21105/joss.04720 + - doi:10.1093/bioadv/vbad162 From b655bcd3cd68ef988315a830ea0aa5b2b582bd9e Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Thu, 14 Dec 2023 02:42:16 -0800 Subject: [PATCH 1200/2173] Update AmpliconSuite to 1.1.3 (#44808) * Add ampliconsuite * Fix ampliconsuite meta.yaml Fix ampliconsuite meta.yaml Fix ampliconsuite meta.yaml add "noarch: python" * Fix ampliconsuite meta.yaml * adjust recipe based on reviewer feedback * bugfix for ampliconarchitectlib src pathing * bump ampsuite version * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml include python in host section of requirements * Update meta.yaml * Update meta.yaml * Update build.sh expose amplicon_classifier.py and feature_similarity.py * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml add run_exports * Update meta.yaml typo * Update build.sh * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml --- recipes/ampliconsuite/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml index 1a8bf1a1d8a33..91920ebed86f4 100644 --- a/recipes/ampliconsuite/meta.yaml +++ b/recipes/ampliconsuite/meta.yaml @@ -1,6 +1,6 @@ {% set name="ampliconsuite" %} -{% set AS_version="1.1.2" %} -{% set AA_version="1.3.r6" %} +{% set AS_version="1.1.3" %} +{% set AA_version="1.3.r7" %} {% set AC_version="1.0.0" %} package: @@ -11,9 +11,9 @@ source: # the sha256 sum is generated by doing # $ wget -O- [URL] | shasum -a 256 - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz - sha256: 4483b38a89dfde309bc82e589c334df010de9315e34115790dd5c664f9f80bde + sha256: 9150307c559d942b820e6249d7b2c4737261d19b1bcaf2c7a487c222e683438d - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz - sha256: cc21a52d9853cd5e0b5b9374773a6ea24191241b9b9cf1d71e2a928ab3d97f01 + sha256: be65a0293da9ced3f6f744657db475c16dd4dcaf9f037e17ee1a19f4ceaa7430 folder: ampliconarchitectlib - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz sha256: d1f35e17827947f657892b08c93c9694e9b33947e30d45e8e515084a5c96638d From 3f3bcfe1c3bdf76c36856d088ea6e5648fae79d0 Mon Sep 17 00:00:00 2001 From: Julian Uszkoreit Date: Thu, 14 Dec 2023 15:45:17 +0100 Subject: [PATCH 1201/2173] PIA: Update OpenJDK dependency for newest version (#44813) --- recipes/pia/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pia/meta.yaml b/recipes/pia/meta.yaml index 1fe65791e2b82..0c8c94b59fac4 100644 --- a/recipes/pia/meta.yaml +++ b/recipes/pia/meta.yaml @@ -8,7 +8,7 @@ package: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('pia', max_pin="x") }} @@ -18,7 +18,7 @@ source: requirements: run: - - openjdk >=17 + - openjdk >=21 test: commands: From c3378aa4e7d3dd36a3762db092fef3446179a841 Mon Sep 17 00:00:00 2001 From: TPOB <19909103+TTTPOB@users.noreply.github.com> Date: Thu, 14 Dec 2023 23:14:24 +0800 Subject: [PATCH 1202/2173] Add scib start from 1.1.4 (#44765) * Add scib start from 1.1.4 * fix ci lint errors * fix: fix jinja2 template error * update dependencies constraint * relax version constraints * reset build number * use skip: statement to have separate python builds --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/scib/meta.yaml | 55 +++++++++++++++++++++++++++++++ recipes/scib/setup_compiler.patch | 21 ++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 recipes/scib/meta.yaml create mode 100644 recipes/scib/setup_compiler.patch diff --git a/recipes/scib/meta.yaml b/recipes/scib/meta.yaml new file mode 100644 index 0000000000000..a8598ccf3891c --- /dev/null +++ b/recipes/scib/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "scib" %} +{% set version = "1.1.4" %} + + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +build: + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + skip: True # [ py < 37 or py > 311] + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} + +source: + url: https://github.com/theislab/scib/archive/v{{ version }}.tar.gz + sha256: aebdad725b58a0bf8f3660a57e1ab81a06845632bb1b6cf9c64f6378d191154b + patches: + - setup_compiler.patch + +requirements: + host: + - python + - pip + - setuptools + build: + - {{ compiler('cxx') }} + run: + - anndata >=0.7.2 + - deprecated + - h5py + - igraph >=0.10 + - leidenalg + - llvmlite + - matplotlib-base + - numpy + - pandas + - pydot + - python + - scanpy >=1.5 + - scikit-learn + - scikit-misc + - scipy + - seaborn + - umap-learn + +test: + commands: + - python3 -c "import scib; print(scib.__version__)" + +about: + home: https://github.com/theislab/scib + license: MIT + summary: "Evaluating single-cell data integration methods" \ No newline at end of file diff --git a/recipes/scib/setup_compiler.patch b/recipes/scib/setup_compiler.patch new file mode 100644 index 0000000000000..5aedf1a1a7886 --- /dev/null +++ b/recipes/scib/setup_compiler.patch @@ -0,0 +1,21 @@ +diff --git a/setup.py b/setup.py +index 45677ce..ba1276c 100644 +--- a/setup.py ++++ b/setup.py +@@ -1,11 +1,15 @@ + import subprocess + import sys ++import os + + from setuptools import setup + ++# get compiler path ++gxx = os.environ.get("CXX", "g++") ++ + try: + cmd = ( +- "g++ -std=c++11 -O3 scib/knn_graph/knn_graph.cpp -o scib/knn_graph/knn_graph.o" ++ f"{gxx} -std=c++11 -O3 scib/knn_graph/knn_graph.cpp -o scib/knn_graph/knn_graph.o" + ) + sys.stdout.write("Compile knn_graph C++ code for LISI metric...\n") + sys.stdout.flush() From d6193910171d42a54c222bda86497536e331674a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 11:34:08 -0500 Subject: [PATCH 1203/2173] Update pybiolib to 1.1.1626 (#44816) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 4226a108463ae..ad8aa5fac7518 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1608" %} +{% set version = "1.1.1626" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: aec0b5b2ef10435d457939c800e88c07be113b49c99d5d3b014da1858b491351 + sha256: 6150f0964125c1b1abb44d6ae2972c9fb6cc4d7fbca22bbf45b95124ea418649 build: noarch: python From 3cc1e95513889fda34dfe965ac7dd4a4c3c135bd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 12:08:12 -0500 Subject: [PATCH 1204/2173] Update r-pipette to 0.15.1 (#44802) * Update r-pipette to 0.15.1 * Add r-baseset and update other dependencies --------- Co-authored-by: Michael Steinbaugh --- recipes/r-pipette/meta.yaml | 34 ++++++++++++++++++---------------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/recipes/r-pipette/meta.yaml b/recipes/r-pipette/meta.yaml index b88de4b723414..60def9f0c508a 100644 --- a/recipes/r-pipette/meta.yaml +++ b/recipes/r-pipette/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.15.0" %} +{% set version = "0.15.1" %} {% set github = "https://github.com/acidgenomics/r-pipette" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 9948eb9d6cee54f4b72a6dd6bf2496816a9a0746cd73488c27ee360e9b33eb0b + sha256: 0a8d090f52d882b8fc8d8b7286ef6ffe9ea0309969d0dd35945d715b5bddfe41 build: number: 0 @@ -27,20 +27,21 @@ requirements: - bioconductor-genomicranges >=1.52.0 - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.7.0 + - r-acidbase >=0.7.2 - r-acidcli >=0.3.0 - - r-acidgenerics >=0.6.13 - - r-goalie >=0.7.0 - - r-jsonlite >=1.8.7 - - r-matrix >=1.6.1 - - r-syntactic >=0.7.0 - - r-yaml >=2.3.7 + - r-acidgenerics >=0.7.5 + - r-goalie >=0.7.7 + - r-jsonlite >=1.8.8 + - r-matrix >=1.6.4 + - r-syntactic >=0.7.1 + - r-yaml >=2.3.8 # Suggests: - bioconductor-biocfilecache >=2.8.0 - bioconductor-biostrings >=2.68.0 - bioconductor-maftools >=2.16.0 - bioconductor-rsamtools >=2.16.0 - bioconductor-rtracklayer >=1.60.0 + - r-baseset >=0.9.0 - r-data.table >=1.14.8 - r-digest >=0.6.33 - r-httr2 >=0.2.3 @@ -58,20 +59,21 @@ requirements: - bioconductor-genomicranges >=1.52.0 - bioconductor-iranges >=2.34.0 - bioconductor-s4vectors >=0.38.0 - - r-acidbase >=0.7.0 + - r-acidbase >=0.7.2 - r-acidcli >=0.3.0 - - r-acidgenerics >=0.6.13 - - r-goalie >=0.7.0 - - r-jsonlite >=1.8.7 - - r-matrix >=1.6.1 - - r-syntactic >=0.7.0 - - r-yaml >=2.3.7 + - r-acidgenerics >=0.7.5 + - r-goalie >=0.7.7 + - r-jsonlite >=1.8.8 + - r-matrix >=1.6.4 + - r-syntactic >=0.7.1 + - r-yaml >=2.3.8 # Suggests: - bioconductor-biocfilecache >=2.8.0 - bioconductor-biostrings >=2.68.0 - bioconductor-maftools >=2.16.0 - bioconductor-rsamtools >=2.16.0 - bioconductor-rtracklayer >=1.60.0 + - r-baseset >=0.9.0 - r-data.table >=1.14.8 - r-digest >=0.6.33 - r-httr2 >=0.2.3 From de41dcd728dd311501844cc9308311bcceed0d93 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Fri, 15 Dec 2023 06:29:38 +1300 Subject: [PATCH 1205/2173] bioconda-repodata-patches: Bump patching for htslib-1.19 (#44785) * Bump for htslib-1.19 release * Remove inadvertently committed patch_instructions.json files And add to .gitignore to prevent this from happening again. --- recipes/bioconda-repodata-patches/.gitignore | 1 + .../gen_patch_json.py | 2 +- recipes/bioconda-repodata-patches/meta.yaml | 2 +- .../patches/linux-64/patch_instructions.json | 21693 --- .../patches/noarch/patch_instructions.json | 104187 --------------- .../patches/osx-64/patch_instructions.json | 12421 -- 6 files changed, 3 insertions(+), 138303 deletions(-) delete mode 100644 recipes/bioconda-repodata-patches/patches/linux-64/patch_instructions.json delete mode 100644 recipes/bioconda-repodata-patches/patches/noarch/patch_instructions.json delete mode 100644 recipes/bioconda-repodata-patches/patches/osx-64/patch_instructions.json diff --git a/recipes/bioconda-repodata-patches/.gitignore b/recipes/bioconda-repodata-patches/.gitignore index 6934129b9f64e..03e52d30471fb 100644 --- a/recipes/bioconda-repodata-patches/.gitignore +++ b/recipes/bioconda-repodata-patches/.gitignore @@ -1,2 +1,3 @@ __pycache__ cache +patches/*/patch_instructions.json diff --git a/recipes/bioconda-repodata-patches/gen_patch_json.py b/recipes/bioconda-repodata-patches/gen_patch_json.py index f3f76a04e3869..d6a8e38c8d273 100755 --- a/recipes/bioconda-repodata-patches/gen_patch_json.py +++ b/recipes/bioconda-repodata-patches/gen_patch_json.py @@ -169,7 +169,7 @@ def _gen_new_index(repodata, subdir): if has_dep(record, 'htslib'): # skip deps prior to 1.10, which was the first with soversion 3 # TODO adjust replacement (exclusive) upper bound with each new compatible HTSlib - _pin_looser(fn, record, 'htslib', min_lower_bound='1.10', upper_bound='1.19') + _pin_looser(fn, record, 'htslib', min_lower_bound='1.10', upper_bound='1.20') # future libdeflate versions are compatible until they bump their soversion; relax dependencies accordingly if record_name in ['htslib', 'staden_io_lib', 'fastp'] and has_dep(record, 'libdeflate'): diff --git a/recipes/bioconda-repodata-patches/meta.yaml b/recipes/bioconda-repodata-patches/meta.yaml index be5786f20cbcb..fba5666b40699 100644 --- a/recipes/bioconda-repodata-patches/meta.yaml +++ b/recipes/bioconda-repodata-patches/meta.yaml @@ -1,6 +1,6 @@ package: name: bioconda-repodata-patches - version: 20230918 # ensure that this is the "current" date, and always higher than the latest version in master + version: 20231213 # ensure that this is the "current" date, and always higher than the latest version in master source: path: . diff --git a/recipes/bioconda-repodata-patches/patches/linux-64/patch_instructions.json b/recipes/bioconda-repodata-patches/patches/linux-64/patch_instructions.json deleted file mode 100644 index 3e83a10d292c2..0000000000000 --- a/recipes/bioconda-repodata-patches/patches/linux-64/patch_instructions.json +++ /dev/null @@ -1,21693 +0,0 @@ -{ - "packages": { - "aria2-1.23.0-0.tar.bz2": { - "depends": [ - "c-ares", - "libgcc", - "libssh2", - "libxml2", - "openssl >=1.1.0,<=1.1.1", - "sqlite", - "zlib" - ] - }, - "aria2-1.23.0-1.tar.bz2": { - "depends": [ - "c-ares", - "libgcc", - "libssh2", - "libxml2", - "openssl >=1.1.0,<=1.1.1", - "sqlite", - "zlib 1.2.11*" - ] - }, - "aria2-1.34.0-0.tar.bz2": { - "depends": [ - "c-ares", - "libgcc", - "libssh2", - "libxml2", - "openssl >=1.1.0,<=1.1.1", - "sqlite", - "zlib 1.2.11*" - ] - }, - "bamhash-1.0-0.tar.bz2": { - "depends": [ - "libgcc", - "openssl >=1.1.0,<=1.1.1", - "zlib" - ] - }, - "bamhash-1.0-1.tar.bz2": { - "depends": [ - "libgcc", - "openssl >=1.1.0,<=1.1.1", - "zlib 1.2.11*" - ] - }, - "bamhash-1.1-0.tar.bz2": { - "depends": [ - "libgcc", - "openssl >=1.1.0,<=1.1.1", - "zlib" - ] - }, - "bamhash-1.1-1.tar.bz2": { - "depends": [ - "libgcc", - "openssl >=1.1.0,<=1.1.1", - "zlib 1.2.11*" - ] - }, - "bcbio-nextgen-0.9.5-py27_1.tar.bz2": { - "depends": [ - "arrow", - "azure", - "bioblend", - "biopython", - "boto", - "click", - "cython", - "cyvcf2", - "fabric", - "fadapa", - "gffutils", - "ipyparallel", - "ipython-cluster-helper", - "joblib", - "logbook", - "lxml", - "matplotlib", - "msgpack-python", - "nose", - "numpy", - "openpyxl", - "openssl >=1.1.0,<=1.1.1", - "pandas", - "path.py", - "patsy", - "pip", - "progressbar", - "psutil", - "pybedtools", - "pycrypto", - "pysam", - "python 2.7*", - "python-dateutil", - "pyvcf", - "pyyaml", - "pyzmq", - "reportlab", - "requests", - "scikit-learn", - "scipy", - "seaborn", - "seqcluster", - "sh", - "sqlalchemy", - "statsmodels", - "tabulate", - "toolz", - "tornado" - ] - }, - "bcbio-nextgen-0.9.6-py27_0.tar.bz2": { - "depends": [ - "arrow", - "azure", - "bioblend", - "biopython", - "boto", - "click", - "cython", - "cyvcf2", - "fabric", - "fadapa", - "gffutils", - "ipyparallel", - "ipython-cluster-helper", - "ipywidgets", - "joblib", - "logbook", - "lxml", - "matplotlib", - "msgpack-python", - "nose", - "numpy", - "openpyxl", - "openssl >=1.1.0,<=1.1.1", - "pandas", - "path.py", - "patsy", - "pip", - "progressbar", - "psutil", - "pybedtools", - "pycrypto", - "pysam", - "python 2.7*", - "python-dateutil", - "pyvcf", - "pyyaml", - "pyzmq", - "reportlab", - "requests", - "scikit-learn", - "scipy", - "seaborn", - "seqcluster", - "sh", - "sqlalchemy", - "statsmodels", - "tabulate", - "toolz", - "tornado" - ] - }, - "bcbio-nextgen-0.9.6a-py27_0.tar.bz2": { - "depends": [ - "arrow", - "azure", - "bioblend", - "biopython", - "boto", - "click", - "cython", - "cyvcf2", - "fabric", - "fadapa", - "gffutils", - "ipyparallel", - "ipython-cluster-helper", - "joblib", - "logbook", - "lxml", - "matplotlib", - "msgpack-python", - "nose", - "numpy", - "openpyxl", - "openssl >=1.1.0,<=1.1.1", - "pandas", - "path.py", - "patsy", - "pip", - "progressbar", - "psutil", - "pybedtools", - "pycrypto", - "pysam", - "python 2.7*", - "python-dateutil", - "pyvcf", - "pyyaml", - "pyzmq", - "reportlab", - "requests", - "scikit-learn", - "scipy", - "seaborn", - "seqcluster", - "sh", - "sqlalchemy", - "statsmodels", - "tabulate", - "toolz", - "tornado" - ] - }, - "bcbio-nextgen-0.9.6a-py27_1.tar.bz2": { - "depends": [ - "arrow", - "azure", - "bioblend", - "biopython", - "boto", - "click", - "cython", - "cyvcf2", - "fabric", - "fadapa", - "gffutils", - "ipyparallel", - "ipython-cluster-helper", - "joblib", - "logbook", - "lxml", - "matplotlib", - "msgpack-python", - "nose", - "numpy", - "openpyxl", - "openssl >=1.1.0,<=1.1.1", - "pandas", - "path.py", - "patsy", - "pip", - "progressbar", - "psutil", - "pybedtools", - "pycrypto", - "pysam", - "python 2.7*", - "python-dateutil", - "pyvcf", - "pyyaml", - "pyzmq", - "reportlab", - "requests", - "scikit-learn", - "scipy", - "seaborn", - "seqcluster", - "sh", - "sqlalchemy", - "statsmodels", - "tabulate", - "toolz", - "tornado" - ] - }, - "bcbio-nextgen-0.9.6a-py27_2.tar.bz2": { - "depends": [ - "arrow", - "azure", - "bioblend", - "biopython", - "boto", - "click", - "cython", - "cyvcf2", - "fabric", - "fadapa", - "gffutils", - "ipyparallel", - "ipython-cluster-helper", - "joblib", - "logbook", - "lxml", - "matplotlib", - "msgpack-python", - "nose", - "numpy", - "openpyxl", - "openssl >=1.1.0,<=1.1.1", - "pandas", - "path.py", - "patsy", - "pip", - "progressbar", - "psutil", - "pybedtools", - "pycrypto", - "pysam", - "python 2.7*", - "python-dateutil", - "pyvcf", - "pyyaml", - "pyzmq", - "reportlab", - "requests", - "scikit-learn", - "scipy", - "seaborn", - "seqcluster", - "sh", - "sqlalchemy", - "statsmodels", - "tabulate", - "toolz", - "tornado" - ] - }, - "bcbio-nextgen-0.9.6a-py27_3.tar.bz2": { - "depends": [ - "arrow", - "azure", - "bioblend", - "biopython", - "boto", - "click", - "cython", - "cyvcf2", - "fabric", - "fadapa", - "gffutils", - "ipyparallel", - "ipython-cluster-helper", - "ipywidgets", - "joblib", - "logbook", - "lxml", - "matplotlib", - "msgpack-python", - "nose", - "numpy", - "openpyxl", - "openssl >=1.1.0,<=1.1.1", - "pandas", - "path.py", - "patsy", - "pip", - "progressbar", - "psutil", - "pybedtools", - "pycrypto", - "pysam", - "python 2.7*", - "python-dateutil", - "pyvcf", - "pyyaml", - "pyzmq", - "reportlab", - "requests", - "scikit-learn", - "scipy", - "seaborn", - "seqcluster", - "sh", - "sqlalchemy", - "statsmodels", - "tabulate", - "toolz", - "tornado" - ] - }, - "bcbio-nextgen-0.9.7-py27_0.tar.bz2": { - "depends": [ - "arrow", - "azure", - "bioblend", - "biopython", - "boto", - "click", - "cython", - "cyvcf2", - "fabric", - "fadapa", - "gffutils", - "ipyparallel", - "ipython-cluster-helper", - "ipywidgets", - "joblib", - "logbook", - "lxml", - "matplotlib", - "msgpack-python", - "nose", - "numpy", - "openpyxl", - "openssl >=1.1.0,<=1.1.1", - "pandas", - "path.py", - "patsy", - "pip", - "progressbar", - "psutil", - "pybedtools", - "pycrypto", - "pysam", - "python 2.7*", - "python-dateutil", - "pyvcf", - "pyyaml", - "pyzmq", - "reportlab", - "requests", - "scikit-learn", - "scipy", - "seaborn", - "seqcluster", - "sh", - "sqlalchemy", - 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"boost-cpp >=1.70.0,<1.70.1.0a0", - "glib >=2.58.3,<3.0a0", - "libarbdb 6.0.6 h82bc0eb_8", - "libcxx >=4.0.1", - "tbb >=2019.9,<2021.0.0a0", - "zlib >=1.2.11,<1.3.0a0" - ] - }, - "sina-1.7.0-hadaa689_0.tar.bz2": { - "depends": [ - "arb-bio-tools", - "boost-cpp >=1.70.0,<1.70.1.0a0", - "glib >=2.58.3,<3.0a0", - "libarbdb 6.0.6 h82bc0eb_8", - "libcxx >=9.0.1", - "tbb >=2019.9,<2021.0.0a0", - "zlib >=1.2.11,<1.3.0a0" - ] - }, - "sina-1.7.1-hadaa689_0.tar.bz2": { - "depends": [ - "arb-bio-tools", - "boost-cpp >=1.70.0,<1.70.1.0a0", - "glib >=2.58.3,<3.0a0", - "libarbdb 6.0.6 h82bc0eb_8", - "libcxx >=9.0.1", - "tbb >=2019.9,<2021.0.0a0", - "zlib >=1.2.11,<1.3.0a0" - ] - }, - "sina-1.7.2-hadaa689_0.tar.bz2": { - "depends": [ - "arb-bio-tools", - "boost-cpp >=1.70.0,<1.70.1.0a0", - "glib >=2.58.3,<3.0a0", - "libarbdb 6.0.6 h82bc0eb_8", - "libcxx >=9.0.1", - "tbb >=2019.9,<2021.0.0a0", - "zlib >=1.2.11,<1.3.0a0" - ] - }, - "spydrpick-1.1.1-h04f5b5a_0.tar.bz2": { - "depends": [ - "libcxx >=4.0.1", - "pthread-stubs", - "tbb >=2019.3,<2021.0.0a0" - ] - }, - "spydrpick-1.2.0-h4f3e9b1_0.tar.bz2": { - "depends": [ - "libcxx >=4.0.1", - "pthread-stubs", - "tbb >=2019.9,<2021.0.0a0" - ] - }, - "squeakr-0.5-0.tar.bz2": { - "depends": [ - "boost 1.64*", - "bzip2", - "openssl >=1.1.0,<=1.1.1", - "zlib 1.2.8*" - ] - }, - "squeakr-0.5-1.tar.bz2": { - "depends": [ - "boost 1.64*", - "bzip2 1.0*", - "openssl >=1.1.0,<=1.1.1", - "zlib 1.2.11*" - ] - }, - "swipe-2.0.12-0.tar.bz2": { - "depends": [ - "libgcc", - "openmpi", - "tbb <2021.0.0a0" - ] - }, - "swipe-2.0.12-h470a237_1.tar.bz2": { - "depends": [ - "openmpi", - "tbb <2021.0.0a0" - ] - }, - "swipe-2.1.0-h15ae403_1.tar.bz2": { - "depends": [ - "openmpi >=4.0.4,<4.1.0a0", - "tbb <2021.0.0a0" - ] - }, - "swipe-2.1.0-h470a237_0.tar.bz2": { - "depends": [ - "openmpi", - "tbb <2021.0.0a0" - ] - }, - "ucsc-bedgraphtobigwig-308-0.tar.bz2": { - "depends": [ - "libpng", - "libuuid", - "mysql-connector-c", - "openssl >=1.1.0,<=1.1.1", - "zlib 1.2.11*" - ] - }, - "ucsc-bedjointaboffset-377-1.tar.bz2": { - "depends": [ - "libpng", - "libuuid", - "mysql-connector-c", - "openssl >=1.1.0,<=1.1.1", - "python", - "zlib" - ] - }, - "ucsc-bedjointaboffset-377-h527b516_2.tar.bz2": { - "depends": [ - "libpng", - "libuuid", - "mysql-connector-c", - "openssl >=1.1.0,<=1.1.1", - "python", - "zlib" - ] - }, - "ucsc-expmatrixtobarchartbed-377-1.tar.bz2": { - "depends": [ - "libpng", - "libuuid", - "mysql-connector-c", - "openssl >=1.1.0,<=1.1.1", - "python", - "zlib" - ] - }, - "ucsc-websync-377-1.tar.bz2": { - "depends": [ - "libpng", - "libuuid", - "mysql-connector-c", - "openssl >=1.1.0,<=1.1.1", - "python", - "zlib" - ] - }, - "ucsc-websync-377-h527b516_2.tar.bz2": { - "depends": [ - "libpng", - "libuuid", - "mysql-connector-c", - "openssl >=1.1.0,<=1.1.1", - "python", - "zlib" - ] - } - }, - "patch_instructions_version": 1, - "remove": [], - "revoke": [] -} \ No newline at end of file From 83f7ca3c6c33c1945dedb629ca6bc8007c05532a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 12:45:24 -0500 Subject: [PATCH 1206/2173] Update varvamp to 1.0.1 (#44817) --- recipes/varvamp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varvamp/meta.yaml b/recipes/varvamp/meta.yaml index 62528f05909fb..efbed07b77dd9 100644 --- a/recipes/varvamp/meta.yaml +++ b/recipes/varvamp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varvamp" %} -{% set version = "1.0" %} +{% set version = "1.0.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/varvamp-{{ version }}.tar.gz - sha256: 6cc45e06b19f3e74c70dc6df3fee6db6a02ed1d967f9cb286dfb00eeb1f72ab8 + sha256: 422a4a9dc8d5377242731e3027bba4510939e0dc91555d57636d7b45961261ab build: entry_points: From 2f22c53ce30ce92117f188757690a6ee09308e67 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 14 Dec 2023 17:52:04 +0000 Subject: [PATCH 1207/2173] bump shinyngs (#44814) --- recipes/r-shinyngs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-shinyngs/meta.yaml b/recipes/r-shinyngs/meta.yaml index 1f77aa4ab7e77..2c7fd3512a809 100644 --- a/recipes/r-shinyngs/meta.yaml +++ b/recipes/r-shinyngs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.8.4' %} +{% set version = '1.8.5' %} {% set d3heatmap_version = '0.6.1.2' %} package: @@ -7,7 +7,7 @@ package: source: - url: https://github.com/pinin4fjords/shinyngs/archive/refs/tags/v{{ version }}.tar.gz - sha256: "b30a615b38b4804d580695130ee28dedc823aca7fc957ab8f073e1454f090c10" + sha256: "79d5da8cb976c3752e925da34d475ab1dac5837e83544bbced4486b10e165909" folder: shinyngs - url: https://github.com/cran/d3heatmap/archive/refs/tags/{{ d3heatmap_version }}.tar.gz sha256: "bda213c4d335b199c38a48cb8e60027c929a8ba8ef6e14dc7de692967777c25a" From 6bff1598d7d5a9ea2a1047b0b0f428f2359a8edf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 12:55:40 -0500 Subject: [PATCH 1208/2173] Update lusstr to 0.8 (#44819) --- recipes/lusstr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/lusstr/meta.yaml b/recipes/lusstr/meta.yaml index a0440cbca5b25..0b597aa0df8f1 100644 --- a/recipes/lusstr/meta.yaml +++ b/recipes/lusstr/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7" %} -{% set sha256 = "3a889c33b8c4e39511d761786e1c40842c8732db72e3e6477bca0d77414fca9b" %} +{% set version = "0.8" %} +{% set sha256 = "0a0de8e921ec072843c9aba3d02c9fd7afd429df72246ddb335bbd6705b3f430" %} package: name: lusstr From cea48869fc03ab760588e5fc1831928f5e0b4717 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 13:10:19 -0500 Subject: [PATCH 1209/2173] Update gogstools to 0.1.2 (#44815) --- recipes/gogstools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gogstools/meta.yaml b/recipes/gogstools/meta.yaml index caf47a4d47b53..2ccbece7643eb 100644 --- a/recipes/gogstools/meta.yaml +++ b/recipes/gogstools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gogstools" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 65c94fe72ba529f9ba63f18c2a9fdc9c0ceeda350ae88faaab6f7185d5d968ae + sha256: 8fd83e481de68a9f7280a612043a72e851c102cca6536e12be4bf1dc7a008404 build: number: 0 From 249b49dfcaab13bdfe84afa9c31925c8b8b2bbb4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marius=20Bj=C3=B8rnstad?= Date: Thu, 14 Dec 2023 19:22:55 +0100 Subject: [PATCH 1210/2173] Update to CADD-scripts 1.6.post1 (#44775) --- recipes/cadd-scripts/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/cadd-scripts/meta.yaml b/recipes/cadd-scripts/meta.yaml index 06120015ec56c..97cc5f5adcd16 100644 --- a/recipes/cadd-scripts/meta.yaml +++ b/recipes/cadd-scripts/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "1.6" %} -{% set sha256 = "c02ebb88beebe1a4433e4f70da03ee4af062212189c30ef99a07cbedf5f44eb6" %} +{% set version = "1.6.post1" %} +{% set sha256 = "0f83361c2e3b0f4bbd096d2e07a8cda4593a0d8b82f68ebff3153b161cad78a4" %} package: name: cadd-scripts version: {{ version }} source: - url: https://github.com/kircherlab/CADD-scripts/archive/CADD{{ version }}.tar.gz + url: https://github.com/kircherlab/CADD-scripts/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('cadd-scripts', max_pin="x") }} requirements: run: From a27c785defbfc595b2cf43405c6d2a8e05cc9a08 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Siebren=20Fr=C3=B6lich?= <48289046+siebrenf@users.noreply.github.com> Date: Thu, 14 Dec 2023 19:38:47 +0100 Subject: [PATCH 1211/2173] pin matplotlib (#44740) --- recipes/ananse/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ananse/meta.yaml b/recipes/ananse/meta.yaml index f6d2cfe02bade..943b94d0a7e51 100644 --- a/recipes/ananse/meta.yaml +++ b/recipes/ananse/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 3c623ba6df0e824238ce3d381bcbf9e2991654c18d7180e63d05951bb509e747 build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv run_exports: @@ -26,7 +26,7 @@ requirements: - genomepy >=0.14.0 - gimmemotifs-minimal >=0.18.0 - loguru - - matplotlib-base >=3.3 + - matplotlib-base >=3.3, <=3.7 - networkx - numpy >=1.6 - openpyxl From 3a9b25839d033f29fad4d3e8b75d6ca9fd68cc20 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 15:01:22 -0500 Subject: [PATCH 1212/2173] Update pbstarphase to 0.7.3 (#44822) --- recipes/pbstarphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbstarphase/meta.yaml b/recipes/pbstarphase/meta.yaml index 91eed38e8b5fc..977430f8b9081 100644 --- a/recipes/pbstarphase/meta.yaml +++ b/recipes/pbstarphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbstarphase" %} -{% set version = "0.7.2" %} -{% set sha256 = "a10a1d4e9e7aaa3fc18c207ab0483cd39ac2624ef96730903aa5aac970fb4e7c" %} +{% set version = "0.7.3" %} +{% set sha256 = "b5dd73ba2e67d7adc0036d34371c596df0caeb900033043efed045f82a9c8c2f" %} package: name: {{ name }} From ea90d79d08ddeaa4d388a5757f17e08017dae02c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 15:46:02 -0500 Subject: [PATCH 1213/2173] Update rbpbench to 0.8.1 (#44823) --- recipes/rbpbench/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rbpbench/meta.yaml b/recipes/rbpbench/meta.yaml index 9feea28617aac..f1762fc9744cc 100644 --- a/recipes/rbpbench/meta.yaml +++ b/recipes/rbpbench/meta.yaml @@ -1,6 +1,6 @@ {% set name = "RBPBench" %} -{% set version = "0.8" %} -{% set sha256 = "05bdc4cb76c81337615dbc4125c42e2d27bd25376f8dc520d1d06bc0257fcf0c" %} +{% set version = "0.8.1" %} +{% set sha256 = "fad4d23adc743716732641cc34f256e59dbd93d084d352aadeaa4f96e8e5dbb2" %} package: name: {{ name|lower }} From 9f552bfbfeeac6e84590ae2a97cd70ce40a37f5f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 16:11:00 -0500 Subject: [PATCH 1214/2173] Update annonars to 0.31.0 (#44821) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 0a6f96ee740ea..2640f5b0523ea 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.30.1" %} +{% set version = "0.31.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 17b0116630f06d87c904c5d40666d10e34f6ae3a88c1b9b2b761ea396aa537fb + sha256: 62d92b27d14a1582d73c659af40ca276cdf43ff8068fab2527693272d338569c requirements: build: From 2ce6dd97441497ec176f1a6006800dfce9fce003 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 16:39:30 -0500 Subject: [PATCH 1215/2173] Update ncbi-datasets-pylib to 15.33.0 (#44820) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 00edc6fe33a31..9c93c9ac6f4e1 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.32.0" %} -{% set sha256 = "ab31148412f56be34b6ae2879f847139484a1be2b9b58298cb5c9ae88f245bfa" %} +{% set version = "15.33.0" %} +{% set sha256 = "9d11e390ad6c2e6eba3d491519158a6cc20f092e22a8d89499fc7bba3454462a" %} package: name: {{ name|lower }} From fd525147d5adf1d5abceffd1d76d890d16eb1f84 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 16:39:40 -0500 Subject: [PATCH 1216/2173] Update pybbi to 0.3.6 (#44824) --- recipes/pybbi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybbi/meta.yaml b/recipes/pybbi/meta.yaml index 67a1777cbac11..398f334dbcfd6 100644 --- a/recipes/pybbi/meta.yaml +++ b/recipes/pybbi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybbi" %} -{% set version = "0.3.5" %} +{% set version = "0.3.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "75b6888ff95bb99811321068213d9ce5618daaea2438cb3c370265186249257a" + sha256: "1733b49a86c56848bbdc286b653da7ecfdeb72164516bfac10e54f0f1d49fc2a" build: number: 0 From 685f1d19752ef34e4d177ed39f83577c5c85035b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 21:16:06 -0500 Subject: [PATCH 1217/2173] Update pyrle to 0.0.39 (#44818) * Update pyrle to 0.0.39 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/pyrle/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/pyrle/meta.yaml b/recipes/pyrle/meta.yaml index ac19aa6fb49b8..5dc32645ae5d5 100644 --- a/recipes/pyrle/meta.yaml +++ b/recipes/pyrle/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrle" %} -{% set version = "0.0.38" %} +{% set version = "0.0.39" %} package: name: '{{ name|lower }}' @@ -7,12 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8b382947a18c73eb4aeaa9e731cb89d0b755f85f75ccb49fc7e121ae3fb984be + sha256: 1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5 build: - number: 3 + number: 0 skip: True # [py2k] script: python setup.py install --single-version-externally-managed --record=record.txt + run_exports: + - {{ pin_subpackage('pyrle', max_pin="x.x") }} requirements: build: @@ -36,6 +38,7 @@ test: about: home: https://github.com/endrebak/pyrle license: MIT + license_family: MIT license_file: LICENSE summary: Genomic Rle-objects for Python From c346430fcb83e93cf8e8ef7575b449c1ddfea1a0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 14 Dec 2023 21:16:19 -0500 Subject: [PATCH 1218/2173] Update callingcardstools to 1.4.0 (#44825) --- recipes/callingcardstools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/callingcardstools/meta.yaml b/recipes/callingcardstools/meta.yaml index 23f0b4d081e5b..78a89a18cbb1b 100644 --- a/recipes/callingcardstools/meta.yaml +++ b/recipes/callingcardstools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "callingcardstools" %} -{% set version = "1.3.0" %} +{% set version = "1.4.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: db96c71fed2622a23a57b6700637cdda3ec70c4890378b8441944ad76b531b3d + sha256: 72c1cf118232674f784b59e0245463a913a98d4bfd4ce657a80ad0abf482accc build: noarch: python From b5c45cfd757919db0f35a01d40415fa0810a56a1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 15 Dec 2023 04:57:03 -0500 Subject: [PATCH 1219/2173] Update illumina-interop to 1.3.1 (#44830) --- recipes/illumina-interop/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 7d469d9e3a067..6417abb1d19e2 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.0" %} +{% set version = "1.3.1" %} {% set sha256 = "0335f20a6d46b3c57a7dd1c337594b156bc1e7558f44cb981f1100f396929baa" %} package: @@ -13,7 +13,7 @@ build: source: url: https://github.com/Illumina/interop/archive/v{{version}}.tar.gz - sha256: 982770eeb271d7111d7215f5102e7c09b198686e84d4f1c7dc256df64bd0a3ca + sha256: 8784a38f09719f12d12a37defb24eee05085471791a136a0ad13172145819673 requirements: build: From 09c7213190826ffc8a50961a3f6798df63b4f269 Mon Sep 17 00:00:00 2001 From: Sam W Date: Fri, 15 Dec 2023 14:05:16 +0000 Subject: [PATCH 1220/2173] Update artic 1.2.4 Recipe (#44834) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update artic to 1.2.4 * Update meta.yaml Actually update version and hash, oops * Fix bwa def typo * CONDA_OVERRIDE_CUDA env var * No quotes around conda_override_cuda * Update meta.yaml Added run_exports * Update meta.yaml Try adding cudatoolkit to trigger downloading cuda rather than using tensorflow * bump medaka version * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Relaxing requirements * Re-pin muscle * Repin pyfaidx * Increment build number --------- Co-authored-by: Thanh Lee Co-authored-by: Robert A. Petit III Co-authored-by: Andreas Sjödin --- recipes/artic/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml index 7d81c8941ea34..59642e631a4cb 100644 --- a/recipes/artic/meta.yaml +++ b/recipes/artic/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage('artic', max_pin='x.x') }} @@ -53,7 +53,7 @@ requirements: - pysam - pytest - pyvcf - - pyfaidx + - pyfaidx =0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE - requests - samtools - tqdm From 1bf04a4b180b95f32b660d6be04315643a25a482 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Fri, 15 Dec 2023 17:48:10 +0000 Subject: [PATCH 1221/2173] Update Tower CLI to v0.9.1 (#44642) * Update Tower CLI to v0.9.1 * Switch tower-cli to use jar file instead of binaries --- recipes/tower-cli/build.sh | 13 +++++-- recipes/tower-cli/meta.yaml | 19 +++++----- recipes/tower-cli/tw.sh | 70 +++++++++++++++++++++++++++++++++++++ 3 files changed, 89 insertions(+), 13 deletions(-) create mode 100644 recipes/tower-cli/tw.sh diff --git a/recipes/tower-cli/build.sh b/recipes/tower-cli/build.sh index 575b16556dc43..e2dd716479b3c 100644 --- a/recipes/tower-cli/build.sh +++ b/recipes/tower-cli/build.sh @@ -1,4 +1,11 @@ #!/bin/bash -mkdir -p $PREFIX/bin -cp $SRC_DIR/tw $PREFIX/bin/tw -chmod 755 $PREFIX/bin/tw + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p "$TGT" +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cp -p "$SRC_DIR"/*.jar "$TGT" + +cp $RECIPE_DIR/tw.sh $TGT/tw +ln -s $TGT/tw $PREFIX/bin +chmod 0755 "${PREFIX}/bin/tw" diff --git a/recipes/tower-cli/meta.yaml b/recipes/tower-cli/meta.yaml index ac215c84eab25..9c5222e351dbf 100644 --- a/recipes/tower-cli/meta.yaml +++ b/recipes/tower-cli/meta.yaml @@ -1,4 +1,6 @@ -{% set version = "0.9.0" %} +{% set name = "tw"%} +{% set version = "0.9.1" %} +{% set sha = "34ad5fe57df990605681c185691feef453902146564a8822938e4ed8fdfff60e" %} package: name: tower-cli @@ -6,20 +8,17 @@ package: build: number: 0 + noarch: generic run_exports: - {{ pin_subpackage("tower-cli", max_pin="x.x") }} source: - - url: https://github.com/seqeralabs/tower-cli/releases/download/v{{ version }}/tw-linux-x86_64 # [linux] - sha256: 55217d07e4615e12a46bb3d86057975113636c26f3f9ee57f5d79290d3c1606d # [linux] - fn: tw # [linux] - - url: https://github.com/seqeralabs/tower-cli/releases/download/v{{ version }}/tw-osx-x86_64 # [osx] - sha256: f809859e3de7e384ed42874d331e3a2c518292e4d6e2554054ec3c72649c808e # [osx] - fn: tw # [osx] - - url: https://github.com/seqeralabs/tower-cli/releases/download/{{ version }}/tw-windows-x86_64.exe # [win] - sha256: 97c6aed555e1450bb5e32e0e031fe7416caec271925a64f48a4a14b420b3e457 # [win] - fn: tw # [win] + - url: https://github.com/seqeralabs/tower-cli/releases/download/v{{ version }}/tw.jar + sha256: {{ sha }} +requirements: + run: + - openjdk >=17 test: commands: diff --git a/recipes/tower-cli/tw.sh b/recipes/tower-cli/tw.sh new file mode 100644 index 0000000000000..e1175961f7b93 --- /dev/null +++ b/recipes/tower-cli/tw.sh @@ -0,0 +1,70 @@ +#!/bin/bash +# tower-cli executable shell script +# adapted from picard.sh launch script +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 +jar_file="tw.jar" + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' + then + pass_args="$arg" + else + pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg + fi + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/$jar_file" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/$jar_file" $pass_args +fi +exit From 7a853666ea6c771b7df6952cf62743c282688fbe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 15 Dec 2023 14:41:39 -0500 Subject: [PATCH 1222/2173] Update regenie to 3.4 (#44826) * Update regenie to 3.4 * update patch for v3.4 --------- Co-authored-by: Joelle Mbatchou --- recipes/regenie/meta.yaml | 7 +- .../0012-update-cmakelist-file-for-v3.4.patch | 348 ++++++++++++++++++ 2 files changed, 352 insertions(+), 3 deletions(-) create mode 100644 recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch diff --git a/recipes/regenie/meta.yaml b/recipes/regenie/meta.yaml index bb864e50ed545..3cdfe87d4c7b0 100644 --- a/recipes/regenie/meta.yaml +++ b/recipes/regenie/meta.yaml @@ -1,6 +1,6 @@ {% set name = "regenie" %} -{% set version = "3.3" %} -{% set sha256 = "ee5ccffa89c5ae37b4d89c367da0d0d47d808f1e157152d4d60bcbe1ab3e5f53" %} +{% set version = "3.4" %} +{% set sha256 = "c4c87f86ac42dc0ebc57f701e24cc88acd5fbf6cb9e6e3dac8c1b1c9ba4e6922" %} package: name: {{ name|lower }} @@ -21,7 +21,8 @@ source: # - patches/0008-fix-cmakelist-file-for-osx-eigen4.patch # - patches/0009-update-cmake-file-for-conda.patch # - patches/0010-update-cmakelist-file-for-v3.2.7.patch - - patches/0011-update-cmakelist-file-for-v3.2.9.patch + # - patches/0011-update-cmakelist-file-for-v3.2.9.patch + - patches/0012-update-cmakelist-file-for-v3.4.patch build: number: 0 diff --git a/recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch b/recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch new file mode 100644 index 0000000000000..0e6278d726201 --- /dev/null +++ b/recipes/regenie/patches/0012-update-cmakelist-file-for-v3.4.patch @@ -0,0 +1,348 @@ +From 918db42f41961bd4556662ade1edc6ca3378da7f Mon Sep 17 00:00:00 2001 +From: Joelle Mbatchou +Date: Thu, 14 Dec 2023 17:33:24 -0500 +Subject: [PATCH] pdate cmakelist file for v3.4 + +--- + CMakeLists.txt | 243 +++++++++++++++++++------------------------------ + 1 file changed, 94 insertions(+), 149 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 5bb60d3..3609ab4 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -1,11 +1,3 @@ +-# For Intel MKL, set MKLROOT= when running cmake +-# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ +-# For OpenBLAS, set OPENBLAS_ROOT= when running cmake +-# note: it also requires lapacke library +-# For static compilation on Linux systems, set STATIC=1 when running cmake +-# -> this excludes GLIBC +- +- + cmake_minimum_required(VERSION 3.13) + + # detect OS architecture +@@ -33,57 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 + ###################################### + ######## check input variables + +-# check BGEN_PATH +-if("$ENV{BGEN_PATH}" STREQUAL "") +- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") +-else() +- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") +- if (NOT EXISTS ${BGEN_PATH}) +- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") +- endif() +-endif() +- + # check for static compilation +-if($ENV{STATIC}) ++if(BUILD_SHARED_LIBS) ++ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") ++ set(Boost_USE_STATIC_LIBS OFF) ++else() + set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") ++ set(Boost_USE_STATIC_LIBS ON) + message( STATUS "Static compilation mode") + endif() + +-# check Boost IOStreams +-if($ENV{HAS_BOOST_IOSTREAM}) +- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") +- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") +-else() +- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") +-endif() +- +-# check MKL +-if(NOT "$ENV{MKLROOT}" STREQUAL "") +- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") +- if (NOT EXISTS ${MKLROOT}) +- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") +- endif() +- message( STATUS "Will compile with Intel MKL library") +-endif() +- +-# check HTSlib +-if(NOT "$ENV{HTSLIB_PATH}" STREQUAL "") +- set(HTSLIB_PATH "$ENV{HTSLIB_PATH}" CACHE INTERNAL "Set HTSlib library path") +- if (NOT EXISTS ${HTSLIB_PATH}) +- message( FATAL_ERROR "Specified HTSlib library directory '${HTSLIB_PATH}' does not exist") +- endif() +- message( STATUS "Will compile with HTSlib") +-endif() +- +-# check OpenBLAS +-if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") +- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") +- if (NOT EXISTS ${OPENBLAS_ROOT}) +- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") +- endif() +- message( STATUS "Will compile with OpenBLAS library") +-endif() +- + ###################################### + ######## set flags and required libraries + +@@ -92,9 +43,10 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) + set(Boost_USE_DEBUG_LIBS OFF) + set(Boost_USE_MULTITHREADED ON) + set(Boost_USE_STATIC_RUNTIME OFF) ++set(MKLROOT "${CMAKE_PREFIX_PATH}") + +-# list each file specifically +-add_executable(regenie ++# list each file specifically ++add_executable(regenie + ${CMAKE_SOURCE_DIR}/src/Data.cpp + ${CMAKE_SOURCE_DIR}/src/Files.cpp + ${CMAKE_SOURCE_DIR}/src/Geno.cpp +@@ -112,32 +64,54 @@ add_executable(regenie + ${CMAKE_SOURCE_DIR}/src/MCC.cpp + ${CMAKE_SOURCE_DIR}/src/Ordinal.cpp + ) +-target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) ++target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) + + set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") +-add_definitions(-DVERSION_NUMBER="${RG_VERSION}") + ++find_package(OpenMP REQUIRED) ++target_link_libraries(regenie OpenMP::OpenMP_CXX) + if("${UNAME_S}" STREQUAL "Linux") +- find_package(OpenMP REQUIRED) +- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) + if(${BUILD_STATIC}) +- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) ++ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) + endif() + elseif("${UNAME_S}" STREQUAL "Darwin") +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") + endif() + +-set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) ++set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") ++target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) ++ ++# for BGEN (choose static if present first) ++find_library(ZSTD_LIBRARY zstd REQUIRED) ++find_library(DB_LIBRARY ++ NAMES libdb.a db ++ REQUIRED ++ ) ++find_library(SQLITE3_LIBRARY sqlite3 REQUIRED) ++find_package(Boost ++ REQUIRED COMPONENTS system filesystem thread ++ OPTIONAL_COMPONENTS iostreams ++ ) ++find_library(BGEN_LIBRARY ++ NAMES libbgen.a ++ REQUIRED ++ ) ++target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) ++target_include_directories(regenie ++ PUBLIC ++ $ ++ $ ++ $ ++ $ ++ ) ++add_definitions(${Boost_DEFINITIONS}) + +-# BGEN library and its dependencies +-find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) +-find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) +-find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) +-find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) +-find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) +-target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) +-target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) ++# Boost IO ++if(Boost_iostreams_FOUND) ++ add_definitions(-DHAS_BOOST_IOSTREAM) ++ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") ++ message( STATUS "Will compile with Boost Iostreams library") ++endif() + + # MVTNorm library + set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") +@@ -146,7 +120,7 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${MVTN_PATH} + ) +-target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) ++target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) + add_dependencies(regenie libMvtnorm) + + # QF library +@@ -156,7 +130,7 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${QF_PATH} + ) +-target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) ++target_link_libraries(regenie ${QF_PATH}/qf.a) + add_dependencies(regenie libqf) + + # Quadpack library +@@ -166,7 +140,7 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${QUAD_PATH} + ) +-target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) ++target_link_libraries(regenie ${QUAD_PATH}/libquad.a) + add_dependencies(regenie libquad) + + # PGEN library +@@ -176,100 +150,71 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${PGEN_PATH} + ) +-target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) +-target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) ++target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) ++target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) + add_dependencies(regenie pgenlib) + +-# REMETA library +-if(EXISTS ${HTSLIB_PATH}) +- set(REMETA_PATH "${EXTERN_LIBS_PATH}/remeta") +- add_custom_target( +- remeta +- COMMAND make HTSLIB_PATH=${HTSLIB_PATH} +- WORKING_DIRECTORY ${REMETA_PATH} +- ) +- target_link_libraries(regenie PUBLIC ${REMETA_PATH}/remeta.a) +- target_include_directories(regenie PUBLIC ${REMETA_PATH}) +- add_dependencies(regenie remeta) +- +- add_definitions(-DWITH_HTSLIB) +- find_library(HTSLIB libhts.a HINTS ${HTSLIB_PATH}) +- target_link_libraries(regenie PUBLIC ${HTSLIB}) +-endif() +- + # Intel MKL +-if(EXISTS ${MKLROOT}) ++if(DEFINED MKLROOT) + add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) +- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) +- if(${BUILD_STATIC}) # specify static libs +- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) +- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) ++ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) ++ find_library(MKL_LP64_LIB mkl_intel_lp64 ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ if("${UNAME_S}" STREQUAL "Linux") ++ find_library(MKL_THREAD_LIB mkl_gnu_thread ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ elseif("${UNAME_S}" STREQUAL "Darwin") ++ find_library(MKL_THREAD_LIB mkl_intel_thread ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ endif() ++ find_library(MKL_CORE_LIB mkl_core ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ if("${UNAME_S}" STREQUAL "Darwin") ++ target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB}) ++ elseif(${BUILD_STATIC}) ++ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) + else() # use dynamic libs +- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) +- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) ++ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) + endif() +-elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS +- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) +- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) +- find_library(LAPACK_LIB lapack REQUIRED) +- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) +- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) ++ message( STATUS "Will compile with Intel MKL library") + endif() + + # cxxopts (header-only) +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) ++target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) + + # LBFGS (header-only) +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) ++target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) + + # Eigen (header-only) +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/) +- +-# Boost IO +-if(${HAS_BOOST_IOSTREAM}) +- if("${UNAME_S}" STREQUAL "Darwin") +- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) +- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) +- elseif(${BUILD_STATIC}) +- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) +- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) +- else() +- target_link_libraries(regenie PRIVATE -lboost_iostreams) +- endif() +- add_definitions(-DHAS_BOOST_IOSTREAM) +- message( STATUS "Will compile with Boost Iostreams library") +-endif() ++target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/) + + # Other libraries +-find_library(ZLIB_LIBRARY libz.a z REQUIRED) +-find_library(M_LIB m REQUIRED) +-find_library(DL_LIB dl REQUIRED) +-find_library(BZ2_LIB libbz2.so) +-find_library(LZMA_LIB liblzma.so) +-find_library(CURL_LIB libcurl.so) +-find_library(CRYPTO_LIB libcrypto.so) ++find_library(ZLIB_LIBRARY z REQUIRED) ++find_library(M_LIB m REQUIRED) ++find_library(DL_LIB dl REQUIRED) + if("${UNAME_S}" STREQUAL "Linux") + set(GFORTRAN_LIBRARY "-lgfortran") + elseif("${UNAME_S}" STREQUAL "Darwin") + find_library(GFORTRAN_LIBRARY gfortran REQUIRED) + endif() +-target_link_libraries( +- regenie PRIVATE +- ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} +- ${BZ2_LIB} ${LZMA_LIB} +- ${CURL_LIB} ${CRYPTO_LIB} ${GFORTRAN_LIBRARY} +-) ++target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) + +-install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) ++add_definitions(-DVERSION_NUMBER="${RG_VERSION}") ++install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) + message( STATUS "REGENIE v" ${RG_VERSION}) + +-add_custom_target(full-clean +- COMMAND cd "${MVTN_PATH}" && make clean +- COMMAND cd "${QF_PATH}" && make clean +- COMMAND cd "${QUAD_PATH}" && make clean +- COMMAND cd "${PGEN_PATH}" && make clean +- ) ++write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) ++install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) ++ ++set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) ++set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) ++set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) ++include(CPack) +-- +2.34.1 + From 902ebd1b3673b2459bd86ac96f139dd42d657bb8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Dec 2023 16:13:07 -0500 Subject: [PATCH 1223/2173] Update clinvar-this to 0.14.6 (#44832) --- recipes/clinvar-this/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clinvar-this/meta.yaml b/recipes/clinvar-this/meta.yaml index 7fb142d5b12fe..630d30e4835df 100644 --- a/recipes/clinvar-this/meta.yaml +++ b/recipes/clinvar-this/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.14.5" %} -{% set sha256 = "88be8458f10043b7dec266395204e17332fe0a05ba1776f7586f50d36722aa6c" %} +{% set version = "0.14.6" %} +{% set sha256 = "cf900c0ca9e92e335d6332463b6353488716c110bb367eedaf3aae96b1b52f2f" %} package: name: clinvar-this From d0faacd72b5a753134051925cc33c9534a21ed2e Mon Sep 17 00:00:00 2001 From: Arafat Rahman Date: Sat, 16 Dec 2023 13:13:28 -0800 Subject: [PATCH 1224/2173] Update beav to v1.0.0 (#44831) * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/beav/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/beav/meta.yaml b/recipes/beav/meta.yaml index 0e0cce08fc38d..51c26396cf4a7 100644 --- a/recipes/beav/meta.yaml +++ b/recipes/beav/meta.yaml @@ -1,12 +1,12 @@ {% set name = "beav" %} -{% set version = "0.5.5" %} -{% set sha256 = "2ae8d96e2ada0686af9279e7a84abe6094acbd07c8ea3049f3a1974e78be2014" %} +{% set version = "1.0.0" %} +{% set sha256 = "b0e65b26c2e5760bfa31587d153d3df902ee34606bc0f4059622dbcb8269ffc4" %} {% set dbscan_git = "condabeav0.5" %} {% set dbscan_sha256 = "2fe08873026fe63a9992bfb997e59fecce7facb903778983dc6917c962573463" %} {% set gapmind_git = "Beav0.5.1conda" %} {% set gapmind_sha256 = "a5d0c4855d65355fa4675172a65b97cb03d4ec2e5098a08bece84f677e48a244" %} -{% set pycirclize_git = "v0.5.2-beav0.5.3" %} -{% set pycirclize_sha256 = "5ed895e82be37e651a897344d9a9b7dddf36bbf04b00526209f834db13734274" %} +{% set pycirclize_git = "v0.5.3_beav0.5.5" %} +{% set pycirclize_sha256 = "f2b40d9de0d7d37d376e7d159b0b487933b40891c5e07094d555fd1a0d4d70b0" %} package: name: {{ name }} @@ -27,7 +27,7 @@ source: build: noarch: generic - number: 1 + number: 0 run_exports: - {{ pin_subpackage("beav", max_pin='x.x') }} From 3274a0b196b8bbb4d9c155163ea487721555829f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Dec 2023 16:13:36 -0500 Subject: [PATCH 1225/2173] Update phykit to 1.12.4 (#44829) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index fa7d43baddc88..aad32847c93f2 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.12.3" %} +{% set version = "1.12.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 36001777df73aed39b4e41dc35d774d089439005aa45358de22db71b51130b63 + sha256: ce1c8b0202ceafaadb7d9a5b946c5f13ccd5062af00f4cb1f611c9b8ef0cf9b6 build: noarch: python From 838170a3be480f3e38f6b88be250a6cedab2038e Mon Sep 17 00:00:00 2001 From: richard morris Date: Sun, 17 Dec 2023 08:14:50 +1100 Subject: [PATCH 1226/2173] Update cogent3 recipe to version 2023 12 15a1 (#44828) * Update cogent3 to 2023.12.15a1 * Updating bioconda autobump to add changes to minimum supported python release, and numba NB: Max python support is constrained by most recent numba release --------- Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> --- recipes/cogent3/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/cogent3/meta.yaml b/recipes/cogent3/meta.yaml index c4c5a2efa8a74..8b5b4792d7e2f 100644 --- a/recipes/cogent3/meta.yaml +++ b/recipes/cogent3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cogent3" %} -{% set version = "2023.9.22a1" %} +{% set version = "2023.12.15a1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b842df9ca55f9bb8bcc4d66787ddf25afd796f88d22663c3d14c0954c115ffcb + sha256: 8cccfdb39aff746c9225b1e063a6506502c840276c843bcb93fea10bb2f31bfb build: noarch: python @@ -18,15 +18,15 @@ build: requirements: host: - - python >=3.8, <3.12 + - python >=3.9, <3.12 - pip - flit-core >=3.2, <4 run: - - python >=3.8, <3.12 + - python >=3.9, <3.12 - scipy - chardet - numpy - - numba >0.48.0 + - numba >0.53.0 - scitrack - tqdm - tinydb From ced26cd229c1bba65a3cd59f8142bfb4f1ebbced Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Dec 2023 16:16:17 -0500 Subject: [PATCH 1227/2173] Update pia to 1.5.0 (#44833) --- recipes/pia/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pia/meta.yaml b/recipes/pia/meta.yaml index 0c8c94b59fac4..187827de84b2a 100644 --- a/recipes/pia/meta.yaml +++ b/recipes/pia/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pia" %} -{% set version = "1.4.10" %} -{% set sha256 = "f42550b51ea244f38d351205b1d1b7fda5aff1341ff451ef9530f67e1e73a017" %} +{% set version = "1.5.0" %} +{% set sha256 = "1f7dee6522927dfec13fadaf12a75e209f6f19f16cf20e8bb2ffa27993d4d886" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: build: noarch: generic - number: 1 + number: 0 run_exports: - {{ pin_subpackage('pia', max_pin="x") }} From 8d8646210d38ad3b09e321558ed46a91ff5c868a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Dec 2023 16:16:35 -0500 Subject: [PATCH 1228/2173] Update jbrowse2 to 2.10.0 (#44835) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index fe00dc6c696ba..05698606f2fc5 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.9.0" %} +{% set version = "2.10.0" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 3557cea0f7a13c479364de9611f584d5f2e51f70a53c949ee1fc023e3c12db86 + sha256: c1dcb2c3e4edd544dcdd566d9f96ca51f93587c444ad6d16d5deff7d3e271862 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From 5b7e2e4ec0284accec00aae506887ae1e72e7441 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Dec 2023 16:17:06 -0500 Subject: [PATCH 1229/2173] Update callingcardstools to 1.4.1 (#44846) --- recipes/callingcardstools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/callingcardstools/meta.yaml b/recipes/callingcardstools/meta.yaml index 78a89a18cbb1b..dc887ec16da56 100644 --- a/recipes/callingcardstools/meta.yaml +++ b/recipes/callingcardstools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "callingcardstools" %} -{% set version = "1.4.0" %} +{% set version = "1.4.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 72c1cf118232674f784b59e0245463a913a98d4bfd4ce657a80ad0abf482accc + sha256: b5e312e790fc5f88f979885ee080284a67e7142308350dcd7ca0566ec4ffc8d1 build: noarch: python From 044b37889cda6f5d8294064a8440ec0f9cd8dd26 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Dec 2023 16:17:18 -0500 Subject: [PATCH 1230/2173] Update orthoflow to 0.3.0 (#44849) --- recipes/orthoflow/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/orthoflow/meta.yaml b/recipes/orthoflow/meta.yaml index 8f8d2b203e7d3..ca8111d636967 100644 --- a/recipes/orthoflow/meta.yaml +++ b/recipes/orthoflow/meta.yaml @@ -1,5 +1,5 @@ {% set name = "orthoflow" %} -{% set version = "0.2.0" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/orthoflow-{{ version }}.tar.gz - sha256: 60e5c8bf6ba3f5d3b6d2e3fa9953f4196c117b4e656c9e5c709a28a397451d93 + sha256: bdfb03dbdccec636adee9be5c8a5a8eec682c82f3435da90ae7c504a2899f9e6 build: entry_points: From f2f4fd1eb2757292a7f82a3e1376af31e5c3a2d2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Dec 2023 16:17:28 -0500 Subject: [PATCH 1231/2173] Update oakvar to 2.9.80 (#44850) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index f03193cbfd07e..1dbd8570084c8 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.78" %} -{% set sha256 = "5531a1c1bced07011bcc3a8c94426b443ef96d2f05bf17e72709c22d6c412eee" %} +{% set version = "2.9.80" %} +{% set sha256 = "9c525e5598b681d6103f40502d45f3b4c7a973cb0b1332423b46d558cfddd823" %} package: name: {{ name|lower }} From 509d6653c33ce052c29660b7fe3115f0bf690b8a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Dec 2023 16:17:37 -0500 Subject: [PATCH 1232/2173] Update easypqp to 0.1.41 (#44852) --- recipes/easypqp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/easypqp/meta.yaml b/recipes/easypqp/meta.yaml index 908940e435daf..4a30d6a72d21e 100644 --- a/recipes/easypqp/meta.yaml +++ b/recipes/easypqp/meta.yaml @@ -1,6 +1,6 @@ {% set name = "easypqp" %} -{% set version = "0.1.40" %} -{% set sha256 = "9ea5db3d58b7ed49972477240ab079e60cc42488bfccf508d2a74e2d7f357bc5" %} +{% set version = "0.1.41" %} +{% set sha256 = "367f15566082f248e26c423e125de7b13fc6aa6a006ed1170a0e86c6a48da9af" %} package: name: {{ name|lower }} From e9d3bb3be8f4baac1631b09de8f05ec62b3091b0 Mon Sep 17 00:00:00 2001 From: Lightning Auriga <8940921+lightning-auriga@users.noreply.github.com> Date: Sat, 16 Dec 2023 16:19:51 -0500 Subject: [PATCH 1233/2173] feat: update bcftools-gtc2vcf-plugin to htslib/bcftools 1.19 (#44838) --- recipes/bcftools-gtc2vcf-plugin/conda_build_config.yaml | 4 ++-- recipes/bcftools-gtc2vcf-plugin/meta.yaml | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/bcftools-gtc2vcf-plugin/conda_build_config.yaml b/recipes/bcftools-gtc2vcf-plugin/conda_build_config.yaml index fd3f1b994d373..f357a8e159d8b 100644 --- a/recipes/bcftools-gtc2vcf-plugin/conda_build_config.yaml +++ b/recipes/bcftools-gtc2vcf-plugin/conda_build_config.yaml @@ -1,7 +1,7 @@ htslib: - - 1.18 + - 1.19 bcftools: - - 1.18 + - 1.19 pin_run_as_build: htslib: x.x bcftools: x.x diff --git a/recipes/bcftools-gtc2vcf-plugin/meta.yaml b/recipes/bcftools-gtc2vcf-plugin/meta.yaml index 43d7495a44bc7..cc1e37047ad6f 100644 --- a/recipes/bcftools-gtc2vcf-plugin/meta.yaml +++ b/recipes/bcftools-gtc2vcf-plugin/meta.yaml @@ -1,7 +1,7 @@ {% set name = "bcftools-gtc2vcf-plugin" %} -{% set version = "1.18" %} -{% set sha256 = "1ec20db4c43c9e7685fa738972db5799ce0d488e39f72a1e6edb0e662c89e920" %} -{% set git_commit = "aea6d8a" %} +{% set version = "1.19" %} +{% set sha256 = "4fb67f39d9599970b202fe5af01d5549088710970d44256b00ee78c25c57289f" %} +{% set git_commit = "1898320" %} package: name: {{name|lower}} @@ -13,7 +13,7 @@ source: sha256: {{sha256}} - folder: bcftools url: https://github.com/samtools/bcftools/releases/download/{{version}}/bcftools-{{version}}.tar.bz2 - sha256: "d9b9d36293e4cc62ab7473aa2539389d4e1de79b1a927d483f6e91f3c3ceac7e" + sha256: "782b5f1bc690415192231e82213b3493b047f45e630dc8ef6f154d6126ab3e68" build: number: 0 From 82afe856fcc109d3d735cb2c6eeb3ff27dbcfc91 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Dec 2023 16:44:12 -0500 Subject: [PATCH 1234/2173] Update illumina-utils to 2.13 (#44848) * Update illumina-utils to 2.13 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/illumina-utils/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/illumina-utils/meta.yaml b/recipes/illumina-utils/meta.yaml index 77fca41a9c7e2..1e42b49f2ee70 100644 --- a/recipes/illumina-utils/meta.yaml +++ b/recipes/illumina-utils/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.12" %} +{% set version = "2.13" %} package: name: 'illumina-utils' @@ -6,12 +6,14 @@ package: source: url: https://pypi.io/packages/source/i/illumina-utils/illumina-utils-{{ version }}.tar.gz - sha256: '5a4835f8f1ef630e9cc501209202833f3f30f6d8fdb64d7ea1afde23f3052f7d' + sha256: 'e688ca221ea6178614073b72205fce7b4a54695237c7aa96713492ecd99bd56e' build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('illumina-utils', max_pin="x") }} requirements: host: @@ -37,6 +39,6 @@ test: about: home: https://github.com/meren/illumina-utils - license: GNU General Public v3 or later (GPLv3+) + license: GPL-3.0-or-later license_family: GPL3 summary: A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.8+). From c4ee90cd75c7b79863ef7ec04ea83ea261aa7bdd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 16 Dec 2023 16:51:00 -0500 Subject: [PATCH 1235/2173] Update sourmash to 4.8.5 (#44784) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/sourmash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sourmash/meta.yaml b/recipes/sourmash/meta.yaml index eacd787ef483c..4feaa4aaee077 100644 --- a/recipes/sourmash/meta.yaml +++ b/recipes/sourmash/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.8.4" %} +{% set version = "4.8.5" %} package: name: sourmash @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/sourmash/sourmash-{{ version }}.tar.gz - sha256: 43584c112c3310719771de175b89cba94f1c2d30b1aea46000eaf5a81efbae8a + sha256: 9016c338d6b01f152d2c7becf5631000b058ff657f4fc50daa6ef15373d8a02a build: number: 0 From d80f7184ba948d6d283332b65bb9408555c0ff73 Mon Sep 17 00:00:00 2001 From: LinXing Chen Date: Sat, 16 Dec 2023 14:07:06 -0800 Subject: [PATCH 1236/2173] Add recipe for cobra-meta (#44841) * Add recipe for cobra-meta * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update recipes/cobra-meta/meta.yaml edit dependencies * use doi: tag --------- Co-authored-by: Linxing Chen Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cobra-meta/meta.yaml | 45 ++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 recipes/cobra-meta/meta.yaml diff --git a/recipes/cobra-meta/meta.yaml b/recipes/cobra-meta/meta.yaml new file mode 100644 index 0000000000000..509ff1273ccc4 --- /dev/null +++ b/recipes/cobra-meta/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "cobra-meta" %} +{% set version = "1.2.2" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/linxingchen/cobra/archive/refs/tags/v{{ version }}.tar.gz + sha256: 26f3cab513f8bb78d0aeb5ccfa3aed57bafb62f42bee1ac814e74e43c330a390 + +build: + entry_points: + - cobra-meta = cobra:main + noarch: python + script: "{{ PYTHON }} -m pip install . -vv" + number: 0 + run_exports: + - {{ pin_subpackage('cobra-meta', max_pin="x") }} + +requirements: + host: + - python >=3.7 + - pip + run: + - python >=3.7 + - biopython + - pysam + - numpy + - blast >=2.14.0,<3.0.0 + +test: + commands: + - cobra-meta -v + +about: + home: https://github.com/linxingchen/cobra + license: MIT + summary: 'COBRA is a tool to get higher quality viral genomes assembled from metagenomes.' + +extra: + identifiers: + - doi:10.1101/2023.05.30.542503 + recipe-maintainers: + - linxingchen From f737026bb21167ae7a095a720f4ce136b7dda93f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 17 Dec 2023 06:46:21 -0500 Subject: [PATCH 1237/2173] Update r-erah to 2.0.0 (#44610) * Update r-erah to 2.0.0 * add run_exports * remove r-osd * remove r-osd * Update meta.yaml --------- Co-authored-by: joshuazhuang7 Co-authored-by: Christian Brueffer --- recipes/r-erah/meta.yaml | 47 +++++++++++++++++++++------------------- 1 file changed, 25 insertions(+), 22 deletions(-) diff --git a/recipes/r-erah/meta.yaml b/recipes/r-erah/meta.yaml index a16096f928c5f..7f320d446f07c 100644 --- a/recipes/r-erah/meta.yaml +++ b/recipes/r-erah/meta.yaml @@ -1,62 +1,65 @@ {% set name = "erah" %} -{% set posix = "m2-" if win else "" %} -{% set version = "1.1.2" %} +{% set version = "2.0.0" %} package: name: r-{{ name }} version: '{{ version }}' source: - url: https://cran.r-project.org/src/contrib/erah_{{ version }}.tar.gz - sha256: db34880f99cd0338e3154462a1145c4dd09254083686a023fa2985a2a458d237 + url: + - {{ cran_mirror }}/src/contrib/erah_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/erah/erah_{{ version }}.tar.gz + sha256: dc53f49339380e581945e90f68101854eb1d718e1d70e4fb75ba013a2e21c458 build: number: 0 merge_build_host: false script: R CMD INSTALL --build . run_exports: + - {{ pin_subpackage('r-erah', max_pin="x") }} rpaths: - lib/R/lib/ - lib/ requirements: build: - - cross-r-base {{ r_base }} # [build_platform != target_platform] - - autoconf # [unix] - - "{{ compiler('c') }}" # [unix] - - "{{ compiler('m2w64_c') }}" # [win] - - "{{ compiler('cxx') }}" # [unix] - - "{{ compiler('m2w64_cxx') }}" # [win] - - posix # [win] + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - cross-r-base {{ r_base }} # [build_platform != target_platform] host: - - r-XML - r-base + - r-hiclimr + - r-furrr + - r-future - r-igraph - - r-r.methodss3 - - r-ncdf4 - - r-nnls + - r-osd + - r-progress - r-quantreg - r-signal + - r-tibble run: - - r-XML - r-base + - r-hiclimr + - r-furrr + - r-future - r-igraph - - r-r.methodss3 - - r-ncdf4 - - r-nnls + - r-osd + - r-progress - r-quantreg - r-signal + - r-tibble test: commands: - - $R -e "library('erah')" # [not win] - - "\"%R%\" -e \"library('erah')\"" # [win] + - $R -e "library('erah')" about: home: https://CRAN.R-project.org/package=erah summary: Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. description: Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) . - license: 'GPL-2 | GPL-3' + license: GPL-2.0-or-later + license_file: + - {{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2 extra: recipe-maintainers: From 46c8eb3e99d9fc28291657f386083b2a4f580fe0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 17 Dec 2023 12:35:25 -0500 Subject: [PATCH 1238/2173] Update tower-cli to 0.9.2 (#44837) --- recipes/tower-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tower-cli/meta.yaml b/recipes/tower-cli/meta.yaml index 9c5222e351dbf..bad22f588a3a3 100644 --- a/recipes/tower-cli/meta.yaml +++ b/recipes/tower-cli/meta.yaml @@ -1,6 +1,6 @@ {% set name = "tw"%} -{% set version = "0.9.1" %} -{% set sha = "34ad5fe57df990605681c185691feef453902146564a8822938e4ed8fdfff60e" %} +{% set version = "0.9.2" %} +{% set sha = "c9ebabdfe7aaeea0ce823c39819b0091503e6e8bf751281f90b620d20d365cec" %} package: name: tower-cli From 1ef9ddbddbf92908ff0c19f826de91bd5af19269 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 17 Dec 2023 16:41:08 -0500 Subject: [PATCH 1239/2173] Update phykit to 1.12.5 (#44855) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index aad32847c93f2..65ffccc3794fc 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.12.4" %} +{% set version = "1.12.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: ce1c8b0202ceafaadb7d9a5b946c5f13ccd5062af00f4cb1f611c9b8ef0cf9b6 + sha256: 1a1b33a683663a6fb8be56e00a41803b7e7d09183fc46d7c3a0e193a79e7584b build: noarch: python From e8f870b1f52d1ce02d2dba0f05ac53386396a7d6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 17 Dec 2023 17:25:58 -0500 Subject: [PATCH 1240/2173] Update r-acidgenerics to 0.7.6 (#44844) --- recipes/r-acidgenerics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-acidgenerics/meta.yaml b/recipes/r-acidgenerics/meta.yaml index 0b0349f1f6021..98a2c9a3d8e1f 100644 --- a/recipes/r-acidgenerics/meta.yaml +++ b/recipes/r-acidgenerics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.5" %} +{% set version = "0.7.6" %} {% set github = "https://github.com/acidgenomics/r-acidgenerics" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: cc992d9e5b1c3245dd7334a63815c66d58e6085b9e587cb6f192b20c2b536c97 + sha256: 4769b11a73bc1d159772a6caf9fb2887dc4f6a1147c7e782b68c3fbfd125136b build: number: 0 From f2996338fa2379be4590246b498c92ae34cd0fcd Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sun, 17 Dec 2023 16:30:40 -0600 Subject: [PATCH 1241/2173] Update peptide-shaker to 3.0.4 (#44860) --- recipes/peptide-shaker/meta.yaml | 4 ++-- recipes/peptide-shaker/peptide-shaker.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/peptide-shaker/meta.yaml b/recipes/peptide-shaker/meta.yaml index 4185fdcc4869e..677a59a7abc65 100644 --- a/recipes/peptide-shaker/meta.yaml +++ b/recipes/peptide-shaker/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the peptide-shaker.py file {% set name = "PeptideShaker" %} -{% set version = "3.0.3" %} -{% set sha256 = "528a526595317c033534bf7bb5fbca3368139df6c3123d11e2397182c4f0007e" %} +{% set version = "3.0.4" %} +{% set sha256 = "e1317b51dda3e10348f74e544832169340939f056576d2f01ed13988e56e8214" %} package: name: peptide-shaker diff --git a/recipes/peptide-shaker/peptide-shaker.py b/recipes/peptide-shaker/peptide-shaker.py index cf551f496a7de..98a22145a4cda 100755 --- a/recipes/peptide-shaker/peptide-shaker.py +++ b/recipes/peptide-shaker/peptide-shaker.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'PeptideShaker-3.0.3.jar' +jar_file = 'PeptideShaker-3.0.4.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] From d18c2e446b3e40a0fe6396fef94644eebb5bff79 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sun, 17 Dec 2023 16:37:21 -0600 Subject: [PATCH 1242/2173] Update searchgui to 4.3.5 (#44859) * Update searchgui to 4.3.5 * bump version string --- recipes/searchgui/build.sh | 2 +- recipes/searchgui/meta.yaml | 10 +++++----- recipes/searchgui/searchgui.py | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/recipes/searchgui/build.sh b/recipes/searchgui/build.sh index c16005eb8e9e8..006bef370f758 100644 --- a/recipes/searchgui/build.sh +++ b/recipes/searchgui/build.sh @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash set -eu -o pipefail outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index a3ab75e2274aa..6108e9779ef2a 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the searchgui.py file {% set name = "SearchGUI" %} -{% set version = "4.3.3" %} -{% set sha256 = "503331735883d6ebbc7b3f77bc5ebaf9e609833d475b69920c69b05bad6d35b8" %} +{% set version = "4.3.5" %} +{% set sha256 = "51458d20745f83c88fe1041d0e3ff64b148538c63795a0b548c1aa3f7ca8f67d" %} {% set build = "0" %} package: @@ -23,13 +23,13 @@ source: requirements: host: - xtandem ==15.12.15.2 - - metamorpheus ==1.0.2 + - metamorpheus ==1.0.5 - blast >=2.14.0 run: - python - openjdk >=17 - xtandem ==15.12.15.2 - - metamorpheus ==1.0.2 + - metamorpheus ==1.0.5 - mono >=6.0.0 - fontconfig - fonts-conda-ecosystem @@ -47,7 +47,7 @@ test: about: home: https://github.com/compomics/searchgui - license: Apache License 2.0 + license: Apache-2.0 license_family: APACHE summary: User-friendly graphical tool for using proteomics identification search engines description: diff --git a/recipes/searchgui/searchgui.py b/recipes/searchgui/searchgui.py index 298cb9a26bcf3..f697c358d602e 100755 --- a/recipes/searchgui/searchgui.py +++ b/recipes/searchgui/searchgui.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'SearchGUI-4.3.3.jar' +jar_file = 'SearchGUI-4.3.5.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] From b8263d93560c98e3319110777f877a3c279496d7 Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 18 Dec 2023 09:15:37 +1000 Subject: [PATCH 1243/2173] add nohuman recipe (#44812) * add nohuman recipe * openssl * Update meta.yaml --------- Co-authored-by: Thanh Lee Co-authored-by: Robert A. Petit III --- recipes/nohuman/build.sh | 17 +++++++++++++++++ recipes/nohuman/meta.yaml | 39 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 recipes/nohuman/build.sh create mode 100644 recipes/nohuman/meta.yaml diff --git a/recipes/nohuman/build.sh b/recipes/nohuman/build.sh new file mode 100644 index 0000000000000..98067b0d04217 --- /dev/null +++ b/recipes/nohuman/build.sh @@ -0,0 +1,17 @@ +#!/bin/bash +set -ex + +RUST_BACKTRACE=full + +if [ "$(uname)" == "Darwin" ]; then + # apparently the HOME variable isn't set correctly, and circle ci output indicates the following as the home directory + export HOME="/Users/distiller" + export HOME=`pwd` + echo "HOME is $HOME" + + # according to https://github.com/rust-lang/cargo/issues/2422#issuecomment-198458960 removing circle ci default configuration solves cargo trouble downloading crates + #git config --global --unset url.ssh://git@github.com.insteadOf +fi + +cargo install -v --locked --root "$PREFIX" --path . +"$STRIP" "$PREFIX/bin/nohuman" \ No newline at end of file diff --git a/recipes/nohuman/meta.yaml b/recipes/nohuman/meta.yaml new file mode 100644 index 0000000000000..5256c6bbd5606 --- /dev/null +++ b/recipes/nohuman/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "0.1.0" %} +{% set name = "nohuman" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz + sha256: 6133ece500c543303f2ba3819b4f8d5d4f04778b04d942c5a9bd840a4ce6e41a + +build: + number: 0 + run_exports: + - {{ pin_subpackage('nohuman', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - rust >=1.70 + - openssl + run: + - kraken2 =2.1 + +test: + commands: + - nohuman --help + +about: + home: https://github.com/mbhall88/nohuman + license: MIT + license_family: MIT + summary: Remove human reads from a sequencing run + license_file: LICENSE + +extra: + recipe-maintainers: + - mbhall88 From 4f4ce8bb875190f2c6ae9e3114ed74527d8f8fad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 17 Dec 2023 18:57:17 -0500 Subject: [PATCH 1244/2173] Update r-acidbase to 0.7.3 (#44842) * Update r-acidbase to 0.7.3 * Update r-acidbase --------- Co-authored-by: Michael Steinbaugh --- recipes/r-acidbase/meta.yaml | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/recipes/r-acidbase/meta.yaml b/recipes/r-acidbase/meta.yaml index 5f697c4f9d056..bf7918867c609 100644 --- a/recipes/r-acidbase/meta.yaml +++ b/recipes/r-acidbase/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.2" %} +{% set version = "0.7.3" %} {% set github = "https://github.com/acidgenomics/r-acidbase" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 0e599ea7bcb5bc2f36f5f1a5a88f4b69c25120210ea69a48e92005d6ec2cd194 + sha256: 104b8c7907375ef5943217aa1565ef8fd01ac8bed4e4d9addc2aa489195b172d build: number: 0 @@ -20,28 +20,28 @@ requirements: # Depends: - r-base # Imports: - - bioconductor-biocgenerics >=0.46.0 - - bioconductor-s4vectors >=0.38.0 - - r-acidgenerics >=0.7.0 - - r-goalie >=0.7.0 + - bioconductor-biocgenerics >=0.48.0 + - bioconductor-s4vectors >=0.40.0 + - r-acidgenerics >=0.7.6 + - r-goalie >=0.7.7 # Suggests: - - r-acidcli >=0.2.8 + - r-acidcli >=0.3.0 - r-memuse >=4.2.3 - - r-processx >=3.8.2 - - r-withr >=2.5.1 + - r-processx >=3.8.3 + - r-withr >=2.5.2 run: # Depends: - r-base # Imports: - - bioconductor-biocgenerics >=0.46.0 - - bioconductor-s4vectors >=0.38.0 - - r-acidgenerics >=0.7.0 - - r-goalie >=0.7.0 + - bioconductor-biocgenerics >=0.48.0 + - bioconductor-s4vectors >=0.40.0 + - r-acidgenerics >=0.7.6 + - r-goalie >=0.7.7 # Suggests: - - r-acidcli >=0.2.8 + - r-acidcli >=0.3.0 - r-memuse >=4.2.3 - - r-processx >=3.8.2 - - r-withr >=2.5.1 + - r-processx >=3.8.3 + - r-withr >=2.5.2 test: commands: From 8e50bd734cfc051e2df95378de4bdd2fadec34f5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 17 Dec 2023 22:38:34 -0500 Subject: [PATCH 1245/2173] Update r-pipette to 0.15.2 (#44843) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/r-pipette/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-pipette/meta.yaml b/recipes/r-pipette/meta.yaml index 60def9f0c508a..0a64d3387eaec 100644 --- a/recipes/r-pipette/meta.yaml +++ b/recipes/r-pipette/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.15.1" %} +{% set version = "0.15.2" %} {% set github = "https://github.com/acidgenomics/r-pipette" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 0a8d090f52d882b8fc8d8b7286ef6ffe9ea0309969d0dd35945d715b5bddfe41 + sha256: 80298775063372e1275191ff800ec00b7feb9cc33fdb9afb453826499e3b54c0 build: number: 0 From f87db87fc4635bd4323dc4bcfa5a47aee7c8b234 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Dec 2023 05:46:21 -0500 Subject: [PATCH 1246/2173] Update multiqc to 1.19 (#44865) --- recipes/multiqc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index 5bcd8cc95d825..2d17086c661b8 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.18" %} +{% set version = "1.19" %} package: name: multiqc @@ -6,7 +6,7 @@ package: source: url: https://github.com/ewels/MultiQC/archive/v{{ version }}.tar.gz - sha256: a6b1409607a05ecac452c2f8cd76167afca5d8f3df0b71f02e88d6f809f82d3c + sha256: 7c1501c8306f69a6f32777fe732fb4a53f71b066512a2252a8b2b4b89f994ca8 build: number: 0 From f959d6ee5ceb4b51bc95d9eba4d38fefa0ceab62 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 18 Dec 2023 09:00:09 -0500 Subject: [PATCH 1247/2173] Update annonars to 0.31.1 (#44868) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 2640f5b0523ea..2dcdf26cf3636 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.31.0" %} +{% set version = "0.31.1" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 62d92b27d14a1582d73c659af40ca276cdf43ff8068fab2527693272d338569c + sha256: 4a437f71d88538bc95fdd6fac33c840530373daaa0097788ed8314bae305bff3 requirements: build: From 16babca25d9585d1ab031093e6aaeaf128f250c5 Mon Sep 17 00:00:00 2001 From: John Lees Date: Mon, 18 Dec 2023 17:06:45 +0000 Subject: [PATCH 1248/2173] Bump poppunk to v2.6.3 (#44870) --- recipes/poppunk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index 09f1470304214..57b87d23fbd98 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.6.2" %} +{% set version = "2.6.3" %} {% set name = "PopPUNK" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: c554fbc8b322836771acd6b2c0d13bb516227cf96dd8d85680b619472897082f + sha256: 4a305da07482a8d500213823b29c48b9be5465194f25beae53ee986f0ae111d0 build: number: 0 From 3b7a14b596caa1223887427df91eb8d26fcc7aca Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 04:24:28 -0500 Subject: [PATCH 1249/2173] Update ena-upload-cli to 0.7.0 (#44869) * Update ena-upload-cli to 0.7.0 * Update dependencies * syntax --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> --- recipes/ena-upload-cli/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/ena-upload-cli/meta.yaml b/recipes/ena-upload-cli/meta.yaml index e23c26eeacfdd..5e31554cbe1b8 100644 --- a/recipes/ena-upload-cli/meta.yaml +++ b/recipes/ena-upload-cli/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ena-upload-cli" %} -{% set version = "0.6.3" %} +{% set version = "0.7.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 199bff6a60d7c7d81da88545e909b87e487911edc15e54f90ce20b424091b957 + sha256: e82e086c84435f5c9d53373d1e3e124a87ce1ead0ba75b72050db534cd50eab9 build: number: 0 @@ -21,7 +21,7 @@ build: requirements: host: - pip - - python >=3.5 + - python >=3.7 run: - genshi ==0.7.* - lxml >=4.9.3,<=5.0.0 @@ -29,7 +29,9 @@ requirements: - pyyaml ==5.* - requests >=2.31.0,<=3.0.0 - openpyxl >=3.1.2,<=4.0.0 - - python >=3.5 + - jsonschema >=4.19.1 + - pytest ==7.4.* + - python >=3.7 test: imports: From 5cc9da34ba55bd0ce9e10d5d4a9f059518f68ce9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 19 Dec 2023 10:53:35 +0100 Subject: [PATCH 1250/2173] fix: update dependencies and versions of snakemake interface packages (#44857) * fix: update dependencies and versions of snakemake interface packages * Update meta.yaml * add missing dependencies --- recipes/snakemake-interface-common/meta.yaml | 9 ++++++--- .../snakemake-interface-executor-plugins/meta.yaml | 11 +++++------ 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index b428c3de168a4..6e68562e29c2e 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -12,17 +12,20 @@ source: build: noarch: python script: {{ PYTHON }} -m pip install . -vvv - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} requirements: host: - - python >=3.7,<4.0 + - python >=3.8,<4.0 - poetry-core - pip run: - - python >=3.7.0,<4.0.0 + - python >=3.8.0,<4.0.0 + - argparse-dataclass >=2.0.0,<3.0.0 + - configargparse >=1.7,<2.0 + test: imports: diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index 5b7ed68c2217a..8a1bac49c8df9 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "8.1.1" %} +{% set version = "8.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: f695c27fae5c750c7a2b3e628ea057d2a941ead592e219e37d14d57eb895f047 + sha256: efac28f52825b5151e66f93c642ee4ab96309aa90149047cd144b3332ba72ccb build: noarch: python @@ -18,14 +18,13 @@ build: requirements: host: - - python >=3.9,<4.0 + - python >=3.11,<4.0 - poetry-core - pip run: - - python >=3.9.0,<4.0.0 + - python >=3.11.0,<4.0.0 - argparse-dataclass >=2.0.0,<3.0.0 - - configargparse - - snakemake-interface-common + - snakemake-interface-common >=1.12.0,<2.0.0 - throttler >=1.2.2,<2.0.0 test: From 930c5415bf313a236b685f4fb8c76036a539d6a3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 07:01:06 -0500 Subject: [PATCH 1251/2173] Update ananse to 0.5.1 (#44890) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update ananse to 0.5.1 * Update meta.yaml --------- Co-authored-by: Siebren Frölich <48289046+siebrenf@users.noreply.github.com> --- recipes/ananse/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/ananse/meta.yaml b/recipes/ananse/meta.yaml index 943b94d0a7e51..dfb5cba2f79f0 100644 --- a/recipes/ananse/meta.yaml +++ b/recipes/ananse/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} package: name: ananse @@ -6,10 +6,10 @@ package: source: url: https://github.com/vanheeringen-lab/ANANSE/releases/download/v{{ version }}/ANANSE-{{ version }}.tar.gz - sha256: 3c623ba6df0e824238ce3d381bcbf9e2991654c18d7180e63d05951bb509e747 + sha256: 3ce5a41dbedb83913fdd451692cbf7df0e4ad3bd102d1ce67f9379329b35142b build: - number: 1 + number: 0 noarch: python script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv run_exports: @@ -26,7 +26,7 @@ requirements: - genomepy >=0.14.0 - gimmemotifs-minimal >=0.18.0 - loguru - - matplotlib-base >=3.3, <=3.7 + - matplotlib-base >=3.3 - networkx - numpy >=1.6 - openpyxl From d2bd37dfb9319183ccfeae9f7e2081213a41fc72 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 08:16:48 -0500 Subject: [PATCH 1252/2173] Update upimapi to 1.13.0 (#44892) --- recipes/upimapi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/upimapi/meta.yaml b/recipes/upimapi/meta.yaml index 5c952176f1640..5ce94c96013c9 100644 --- a/recipes/upimapi/meta.yaml +++ b/recipes/upimapi/meta.yaml @@ -1,6 +1,6 @@ {% set name = "upimapi" %} -{% set version = "1.12.3" %} -{% set sha256 = "2cb9fe4a345bd6a80437af7400d09446eaf6da56ed632757d8c957d3a57de4cd" %} +{% set version = "1.13.0" %} +{% set sha256 = "0460d1f9485a05cab875521991feb43c4835b637e4955cba6e85abc9a01defe5" %} package: name: {{ name|lower }} From def8a6aaf64252d0c24b6b535b91c9e8b9597078 Mon Sep 17 00:00:00 2001 From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com> Date: Wed, 20 Dec 2023 02:13:09 +1100 Subject: [PATCH 1253/2173] Update CCMetagen (#44862) * Update CCMetagen - Pin Python version - Add recipe maintainers * ccmetagen: increment build number --- recipes/ccmetagen/meta.yaml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/recipes/ccmetagen/meta.yaml b/recipes/ccmetagen/meta.yaml index 9a724a9a6a7d6..9adb565f54b77 100644 --- a/recipes/ccmetagen/meta.yaml +++ b/recipes/ccmetagen/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 script: "python -m pip install --no-deps --ignore-installed . " run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -21,7 +21,7 @@ requirements: - pip - python run: - - python + - python >=3.9,<3.12 - ete3 - pandas - kma >=1.3 @@ -38,3 +38,8 @@ about: license_family: "GPL3" license_file: "LICENSE" summary: "CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data." + +extra: + recipe-maintainers: + - vrmarcelino + - vinisalazar From b9b05dcc3d2c20c57efebbb21494afff88e773b6 Mon Sep 17 00:00:00 2001 From: Mohammed Alshehri <542855+dralshehri@users.noreply.github.com> Date: Tue, 19 Dec 2023 18:23:06 +0300 Subject: [PATCH 1254/2173] Update epiweeks to 2.3.0 (#44889) --- recipes/epiweeks/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/epiweeks/meta.yaml b/recipes/epiweeks/meta.yaml index a4234b5846380..33383ba6b530a 100644 --- a/recipes/epiweeks/meta.yaml +++ b/recipes/epiweeks/meta.yaml @@ -1,5 +1,5 @@ {% set name = "epiweeks" %} -{% set version = "2.2.0" %} +{% set version = "2.3.0" %} package: name: "{{ name|lower }}" @@ -7,19 +7,21 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e6f6de0952b36b7dd50d2a2eed7937f654cc50823329664d333ee753bbc5d026 + sha256: 3c64ee0b217d0a03f0896fce3c35b73c848c3717790504893cb4eb61b9364bac build: number: 0 noarch: python script: {{ PYTHON }} -m pip install . -vv + run_exports: + - {{ pin_subpackage('epiweeks', max_pin="x") }} requirements: host: + - python >=3.8 - pip - - python >=3.7 run: - - python >=3.7 + - python >=3.8 test: imports: From 8fc9819f403e15e821dd55b77992c6be787c3ce1 Mon Sep 17 00:00:00 2001 From: Neng Huang Date: Tue, 19 Dec 2023 10:24:31 -0500 Subject: [PATCH 1255/2173] Add compleasm 0.2.4 (#44876) * update compleasm to 0.2.4 * update compleasm to 0.2.4 * update compleasm to 0.2.4 * update compleasm to 0.2.4 --- recipes/compleasm/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/compleasm/meta.yaml b/recipes/compleasm/meta.yaml index d5fbb5f1394f8..7c5b0fa3c27f9 100644 --- a/recipes/compleasm/meta.yaml +++ b/recipes/compleasm/meta.yaml @@ -1,6 +1,6 @@ {% set name = "compleasm" %} -{% set version = "0.2.2" %} -{% set hash = "07772e567b6c058e2a685abbe4ab75d9636bd8aebb013b5348744383e4266766" %} +{% set version = "0.2.4" %} +{% set hash = "3658a8104716d2d9345b1d71215fdc200798f5d366ae7f450eca0431ed8b2976" %} package: name: "{{ name|lower }}" @@ -17,6 +17,8 @@ build: - compleasm=compleasm:main script: - {{ PYTHON }} -m pip install . -vv + run_exports: + - {{ pin_subpackage(name, max_pin="x.x.x") }} requirements: host: From 399a85ce85dcdc2e6c32485bd6f0207fa86a92f1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 10:28:11 -0500 Subject: [PATCH 1256/2173] Update wgd to 2.0.24 (#44863) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index 585956b3a5563..c67fb54a19082 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.23" %} +{% set version = "2.0.24" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: 7d36a63d77dc9fc354cca1f1644e19213b43b7b0e3a444eb6d61a85fdeb27b68 + sha256: 60c986d848cacff15037567e02931c908d7644306e201ba48952810c1ff0545a build: number: 0 From 78be515b56f5f25683dc1b9ca769cba016c453aa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 10:28:20 -0500 Subject: [PATCH 1257/2173] Update bamdash to 0.2.3 (#44864) --- recipes/bamdash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bamdash/meta.yaml b/recipes/bamdash/meta.yaml index 430d4923962fc..549a5ab5d04bd 100644 --- a/recipes/bamdash/meta.yaml +++ b/recipes/bamdash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bamdash" %} -{% set version = "0.2.2" %} +{% set version = "0.2.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/bamdash-{{ version }}.tar.gz - sha256: aebd3ea688fac17f9d87ebae87efc33f260a4dedc83d14036c97f2ace08631d6 + sha256: da43cd3539ba86b4d2800aded8a3361ba34f325f803b5acd2991c69473c0f398 build: entry_points: From 592ed03713f351b496c9c226c283c17820b6dc3c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 10:28:29 -0500 Subject: [PATCH 1258/2173] Update capcruncher to 0.3.9 (#44866) --- recipes/capcruncher/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/capcruncher/meta.yaml b/recipes/capcruncher/meta.yaml index e1b742d58f4fa..5d80b6b47cdef 100644 --- a/recipes/capcruncher/meta.yaml +++ b/recipes/capcruncher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "capcruncher" %} -{% set version = "0.3.8" %} +{% set version = "0.3.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/capcruncher-{{ version }}.tar.gz - sha256: 6124d6e7ff0ff269b434c1cd38bbc6e7bf69ff737024aa411f58d1ce5384d2e7 + sha256: 9f14ac76c24158878bbb5ddf06c3ae45da5620adbc22558bb219d0cc86a6f8f8 build: number: 0 From df77619dc9285df175020df9b928770d49935705 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 10:29:59 -0500 Subject: [PATCH 1259/2173] Update oakvar to 2.9.81 (#44873) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 1dbd8570084c8..cf39860937ea0 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.80" %} -{% set sha256 = "9c525e5598b681d6103f40502d45f3b4c7a973cb0b1332423b46d558cfddd823" %} +{% set version = "2.9.81" %} +{% set sha256 = "47aeed3fc65fcfe8914bb14bf7973e1a58811f5e348251b235e7636c583a51ea" %} package: name: {{ name|lower }} From 61e1e04491d88a7f02360039b185e0b78311ca5a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 10:30:08 -0500 Subject: [PATCH 1260/2173] Update easypqp to 0.1.42 (#44879) --- recipes/easypqp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/easypqp/meta.yaml b/recipes/easypqp/meta.yaml index 4a30d6a72d21e..3fea94c7a0227 100644 --- a/recipes/easypqp/meta.yaml +++ b/recipes/easypqp/meta.yaml @@ -1,6 +1,6 @@ {% set name = "easypqp" %} -{% set version = "0.1.41" %} -{% set sha256 = "367f15566082f248e26c423e125de7b13fc6aa6a006ed1170a0e86c6a48da9af" %} +{% set version = "0.1.42" %} +{% set sha256 = "5f7420d350769e7bc7defbae8e48dfed270ad4ae112ba0a74b47e39fedfbbe27" %} package: name: {{ name|lower }} From 1aab6c3d693e24cf1c90df584e7ea32c35c9def3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 10:30:19 -0500 Subject: [PATCH 1261/2173] Update abpoa to 1.4.3 (#44882) --- recipes/abpoa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abpoa/meta.yaml b/recipes/abpoa/meta.yaml index 4bd663c59d297..40d2677da1ceb 100644 --- a/recipes/abpoa/meta.yaml +++ b/recipes/abpoa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.2" %} +{% set version = "1.4.3" %} {% set program = "abpoa" %} {% set PROGRAM = "abPOA" %} @@ -8,7 +8,7 @@ package: source: url: https://github.com/yangao07/{{ PROGRAM }}/releases/download/v{{ version }}/{{ PROGRAM }}-v{{ version }}.tar.gz - sha256: 955109ee28ccdef60c371f7ad113e380d1a6d42b658243eafc00239b9e58a087 + sha256: c6e9f6e1e8938f5ecb47ef41c2571f3563fd7fdf5eb32e9500099cbd29e72612 build: number: 0 From 3423d3b503878b62d96c1eb0907092c5ecfce773 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 10:30:27 -0500 Subject: [PATCH 1262/2173] Update pypolca to 0.2.1 (#44885) --- recipes/pypolca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pypolca/meta.yaml b/recipes/pypolca/meta.yaml index 40f4fefedf5c0..6981ef124abde 100644 --- a/recipes/pypolca/meta.yaml +++ b/recipes/pypolca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pypolca" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 5534fb54316931a664a6e5eb0bb020d432b39687fd5d932b00cd1d5e6dea5ef8 + sha256: 104f9a794d21f36454eb8e89ef317bd086d452a7fc1d4e2433b1afaa8d649c5c build: number: 0 From 66a7c05a297dd472803d81234cf6fe2f5ea00658 Mon Sep 17 00:00:00 2001 From: boukn Date: Tue, 19 Dec 2023 10:31:35 -0500 Subject: [PATCH 1263/2173] Add static comilation support for fcs-gx (#44872) * add aria_split_16.patch to improve AWS downloads * add aria_split_16.patch to improve AWS downloads * update build number for linter * add patch that allows for working static builds of gx * bump build number --- recipes/ncbi-fcs-gx/meta.yaml | 3 ++- recipes/ncbi-fcs-gx/no_static.patch | 13 +++++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 recipes/ncbi-fcs-gx/no_static.patch diff --git a/recipes/ncbi-fcs-gx/meta.yaml b/recipes/ncbi-fcs-gx/meta.yaml index 8f25c0282f3b9..2ed106374b726 100644 --- a/recipes/ncbi-fcs-gx/meta.yaml +++ b/recipes/ncbi-fcs-gx/meta.yaml @@ -7,6 +7,7 @@ source: sha256: 2f6b6099584495e1a9115403a5e4cb5f5dac1ddbbc691da9a3158a75391ffe8a patches: - aria_split_16.patch + - no_static.patch requirements: @@ -25,7 +26,7 @@ requirements: - grep >=3.4 build: - number: 1 + number: 2 skip: True # [not linux or not x86_64] run_exports: - {{ pin_compatible('ncbi-fcs-gx', max_pin="0.5") }} diff --git a/recipes/ncbi-fcs-gx/no_static.patch b/recipes/ncbi-fcs-gx/no_static.patch new file mode 100644 index 0000000000000..3d09172fa9770 --- /dev/null +++ b/recipes/ncbi-fcs-gx/no_static.patch @@ -0,0 +1,13 @@ +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index b2d24ff..007a3ac 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -32,7 +32,7 @@ include_directories(${PROJECT_SOURCE_DIR}/include/) + + set_source_files_properties(main.cpp PROPERTIES COMPILE_FLAGS "-DGIT_REVISION=`../../build-support/git_describe.sh`") + +-link_libraries("-flto -pthread -Wl,--format=binary -Wl,../../LICENSE -Wl,--format=default") # see show-license command in main.cpp ++link_libraries("-flto -Wl,--whole-archive -lrt -lpthread -Wl,--no-whole-archive -Wl,--format=binary -Wl,../../LICENSE -Wl,--format=default") # see show-license command in main.cpp + + #add_compile_options(-fsanitize=address) + #add_link_options(-fsanitize=address) From 5edc716b327cfe34fc158879ca8f94ecbe51cc25 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 10:54:01 -0500 Subject: [PATCH 1264/2173] Update pybiolib to 1.1.1641 (#44887) * Update pybiolib to 1.1.1632 * Update pybiolib to 1.1.1641 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index ad8aa5fac7518..2f4da5d5e367d 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1626" %} +{% set version = "1.1.1641" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 6150f0964125c1b1abb44d6ae2972c9fb6cc4d7fbca22bbf45b95124ea418649 + sha256: 922a89734f035766aefc5c9698d30ea8554b7cf098089601014956d96f27bfe8 build: noarch: python From 25129b52ef427d8710d01d6b13bf61b60d33e313 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 10:54:11 -0500 Subject: [PATCH 1265/2173] Update ncbi-datasets-pylib to 15.34.0 (#44877) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 9c93c9ac6f4e1..189df41461626 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.33.0" %} -{% set sha256 = "9d11e390ad6c2e6eba3d491519158a6cc20f092e22a8d89499fc7bba3454462a" %} +{% set version = "15.34.0" %} +{% set sha256 = "3809be524170dc92911fb6465c8182e28af3d67e1b5aebc37e1b22c89d8caee5" %} package: name: {{ name|lower }} From e5e727546698da54e4bd4020ff8081c55e5c0abd Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Tue, 19 Dec 2023 09:55:45 -0600 Subject: [PATCH 1266/2173] Add recipe for tf-comb (#44881) * Add recipe for tf-comb * Add run_exports lint --------- Co-authored-by: Natasha Pavlovikj --- recipes/tf-comb/meta.yaml | 65 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 recipes/tf-comb/meta.yaml diff --git a/recipes/tf-comb/meta.yaml b/recipes/tf-comb/meta.yaml new file mode 100644 index 0000000000000..032969cfb9cc0 --- /dev/null +++ b/recipes/tf-comb/meta.yaml @@ -0,0 +1,65 @@ +{% set name = "TF-COMB" %} +{% set version = "1.1" %} +{% set sha256 = "5b718061660e0f9f94d86459eb742ca81de5851b0defd8b08c8a7a7e3370c253" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + skip: True # [py>=311 or py2k] + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('tf-comb', max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - python + - setuptools + - wheel + - cython + - numpy + - pip + run: + - python + - scipy + - pysam + - matplotlib-base >=2 + - pandas + - tobias >=0.11 + - networkx >=2.4 + - python-louvain + - python-graphviz + - statsmodels + - goatools + - uropa + - qnorm + - dill + - seaborn + - tqdm + - ipython + - {{ pin_compatible('numpy') }} + +test: + imports: + - tfcomb + +about: + summary: "Transcription Factor Co-Occurrence using Market Basket analysis" + license: MIT + license_family: MIT + license_file: LICENSE + home: https://tf-comb.readthedocs.io/ + doc_url: https://tf-comb.readthedocs.io/ + dev_url: https://github.com/loosolab/TF-COMB/ + +extra: + identifiers: + - doi:10.1016/j.csbj.2022.07.025 From 5e6cb4d96e912981cbfa15611506a5440f8f646c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 19 Dec 2023 17:17:26 +0100 Subject: [PATCH 1267/2173] add snakemake storage plugins and the corresponding interface (#43652) * add snakemake storage plugins and the corresponding interface * add run_exports * fixes * fixes * fixes * add home urls * remove import test --- .../meta.yaml | 47 +++++++++++++++++++ .../snakemake-storage-plugin-http/meta.yaml | 47 +++++++++++++++++++ recipes/snakemake-storage-plugin-s3/meta.yaml | 47 +++++++++++++++++++ 3 files changed, 141 insertions(+) create mode 100644 recipes/snakemake-interface-storage-plugins/meta.yaml create mode 100644 recipes/snakemake-storage-plugin-http/meta.yaml create mode 100644 recipes/snakemake-storage-plugin-s3/meta.yaml diff --git a/recipes/snakemake-interface-storage-plugins/meta.yaml b/recipes/snakemake-interface-storage-plugins/meta.yaml new file mode 100644 index 0000000000000..f3ebb462501db --- /dev/null +++ b/recipes/snakemake-interface-storage-plugins/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "snakemake-interface-storage-plugins" %} +{% set version = "3.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_storage_plugins-{{ version }}.tar.gz + sha256: f20d85ee7e86a1e2ffa3f72e2385dd5abb17fa7b58a26cba8ba59096872fe169 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage("snakemake-interface-storage-plugins", max_pin="x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.12.0,<2.0.0 + - wrapt >=1.15.0,<2.0.0 + - reretry >=0.11.8,<0.12.0 + - throttler >=1.2.2,<2.0.0 + +test: + imports: + - snakemake_interface_storage_plugins + commands: + - pip check + requires: + - pip + +about: + summary: This package provides a stable interface for interactions between Snakemake and its storage plugins. + home: https://github.com/snakemake/snakemake-interface-storage-plugins + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-storage-plugin-http/meta.yaml b/recipes/snakemake-storage-plugin-http/meta.yaml new file mode 100644 index 0000000000000..9a22c74f02554 --- /dev/null +++ b/recipes/snakemake-storage-plugin-http/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "snakemake-storage-plugin-http" %} +{% set version = "0.2.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_http-{{ version }}.tar.gz + sha256: e4944a7c134e98515d9473c867c4ce071e3b625a5a9002a00da6ac917bc0c0ad + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage("snakemake-storage-plugin-http", max_pin="x") }} + +requirements: + host: + - python >=3.11.0,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - requests >=2.31.0,<3.0.0 + - requests-oauthlib >=1.3.1,<2.0.0 + - snakemake-interface-common >=1.14.0,<2.0.0 + - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 + +test: + # We do not test the import as the plugin needs snakemake for importing, but adding + # it would create a circular dependency. + commands: + - pip check + requires: + - pip + +about: + summary: Snakemake storage plugin for donwloading input files from HTTP(s). + home: https://github.com/snakemake/snakemake-storage-plugin-http + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-storage-plugin-s3/meta.yaml b/recipes/snakemake-storage-plugin-s3/meta.yaml new file mode 100644 index 0000000000000..a0cc7611163bd --- /dev/null +++ b/recipes/snakemake-storage-plugin-s3/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "snakemake-storage-plugin-s3" %} +{% set version = "0.2.8" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_s3-{{ version }}.tar.gz + sha256: 4006be9cec5113aaead77a0c9f362be4f3af5409a5da1a3a0f7d69675b222605 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage("snakemake-storage-plugin-s3", max_pin="x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.14.0,<2.0.0 + - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 + - boto3 >=1.28.55,<2.0.0 + - botocore >=1.31.55,<2.0.0 + +test: + # We do not test the import as the plugin needs snakemake for importing, but adding + # it would create a circular dependency. + commands: + - pip check + requires: + - pip + +about: + summary: A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.) + home: https://github.com/snakemake/snakemake-storage-plugin-s3 + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab From 59a007b84c8171b7278a7f27b1870153169b2e79 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 11:39:57 -0500 Subject: [PATCH 1268/2173] Update seqfu to 1.20.3 (#44895) --- recipes/seqfu/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml index c0f03f2958763..b8c6278466772 100644 --- a/recipes/seqfu/meta.yaml +++ b/recipes/seqfu/meta.yaml @@ -1,6 +1,6 @@ {% set name = "seqfu" %} -{% set version = "1.20.2" %} -{% set sha256 = "a7e5f2bdf0810d4b4d4a00a7f25522e8e3df7d5acf96742d2b63fb93da04ac8e" %} +{% set version = "1.20.3" %} +{% set sha256 = "1b287b99f3f1ac7045f4d551e781d6780ce168ba8e0a7bfaa0f5490f32e15938" %} package: name: {{ name }} From 9678cb534ae647f689c01cbd624973bd5101a9d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 12:43:18 -0500 Subject: [PATCH 1269/2173] Update ncbi-vdb to 3.0.10 (#44901) --- recipes/ncbi-vdb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-vdb/meta.yaml b/recipes/ncbi-vdb/meta.yaml index 5a3e7c36fa4c9..61d789b3e0c6f 100644 --- a/recipes/ncbi-vdb/meta.yaml +++ b/recipes/ncbi-vdb/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.0.9" %} +{% set version = "3.0.10" %} package: name: ncbi-vdb @@ -12,7 +12,7 @@ build: source: url: https://github.com/ncbi/ncbi-vdb/archive/{{ version }}.tar.gz - sha256: 26c94e5259b0c7e98fdaa1e93d41201df29ffff56946dd19464c6a0cfb584f92 + sha256: 2e088a8542e6c3bc1aad01a5d2fca2ef5b745c36a3aafd3b0b42cb53b42b345d folder: ncbi-vdb requirements: From ffbd594e6196b82aabf8b2d67e28d238540dc6fa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 12:43:33 -0500 Subject: [PATCH 1270/2173] Update capcruncher to 0.3.10 (#44896) --- recipes/capcruncher/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/capcruncher/meta.yaml b/recipes/capcruncher/meta.yaml index 5d80b6b47cdef..da3b10db17215 100644 --- a/recipes/capcruncher/meta.yaml +++ b/recipes/capcruncher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "capcruncher" %} -{% set version = "0.3.9" %} +{% set version = "0.3.10" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/capcruncher-{{ version }}.tar.gz - sha256: 9f14ac76c24158878bbb5ddf06c3ae45da5620adbc22558bb219d0cc86a6f8f8 + sha256: 3c81d6228ff7a2f7a84301cbcc5e9cd1988952c5d670b0eaf0903d2cfa3e3ac1 build: number: 0 From c3efb908e1d2443ccb1d73d626018fb99dc6efe4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 13:05:24 -0500 Subject: [PATCH 1271/2173] Update physiofit to 3.3.2 (#44903) --- recipes/physiofit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/physiofit/meta.yaml b/recipes/physiofit/meta.yaml index 4338f309dcecc..097759c293e02 100644 --- a/recipes/physiofit/meta.yaml +++ b/recipes/physiofit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "physiofit" %} -{% set version = "3.3.1" %} +{% set version = "3.3.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/physiofit-{{ version }}.tar.gz - sha256: dc01bbf300f8dd19fadf5d9ed3032f37533cb28b9057a7ec434740de10e3d392 + sha256: 1512c9926e74255034e4b3bdba7fd72a11e297841f62532b8e835957aa6f0e77 build: entry_points: From a810b3c31274f3349f3c88e314478065f39006d7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 14:35:38 -0500 Subject: [PATCH 1272/2173] Update sra-tools to 3.0.10 (#44902) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/sra-tools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sra-tools/meta.yaml b/recipes/sra-tools/meta.yaml index 1059721198b5b..a108dacb2488c 100644 --- a/recipes/sra-tools/meta.yaml +++ b/recipes/sra-tools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sra-tools" %} -{% set version = "3.0.9" %} -{% set sha256 = "41159b817fb7649e42b41b3ca37bb3346d4fcb27049737d8a3bca5091ad74bb5" %} +{% set version = "3.0.10" %} +{% set sha256 = "93cfa802938506866b9d565a18a31ac84fd26f2929636b23f1f8dd9f39cf977d" %} package: name: {{ name }} From 88a9346c1b3d4a6530608e9aaac276ddc7555515 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 19 Dec 2023 14:35:49 -0500 Subject: [PATCH 1273/2173] Update ncbi-vdb-py to 3.0.10 (#44904) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ncbi-vdb-py/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-vdb-py/meta.yaml b/recipes/ncbi-vdb-py/meta.yaml index 270c44e2b6586..eebd27cd47135 100644 --- a/recipes/ncbi-vdb-py/meta.yaml +++ b/recipes/ncbi-vdb-py/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.0.9" %} -{% set sha256 = "26c94e5259b0c7e98fdaa1e93d41201df29ffff56946dd19464c6a0cfb584f92" %} +{% set version = "3.0.10" %} +{% set sha256 = "2e088a8542e6c3bc1aad01a5d2fca2ef5b745c36a3aafd3b0b42cb53b42b345d" %} package: name: ncbi-vdb-py From aed266c4fbc66eaa2c8134dcccfaa71dc5d48925 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 02:04:30 -0500 Subject: [PATCH 1274/2173] Update snakemake-interface-executor-plugins to 8.1.3 (#44906) --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index 8a1bac49c8df9..7972cf75a5c94 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "8.1.2" %} +{% set version = "8.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: efac28f52825b5151e66f93c642ee4ab96309aa90149047cd144b3332ba72ccb + sha256: 1bafb4de9ab4bcbfb71de5ed66c6e3d2367d6e551426be21b0d293f15411ec1d build: noarch: python From 25aa0499561c8cab761c85486dd0346e23e390a0 Mon Sep 17 00:00:00 2001 From: Marcel Martin Date: Wed, 20 Dec 2023 08:52:20 +0100 Subject: [PATCH 1275/2173] Update IgDiscover: Allow higher snakemake versions (#44909) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Allow higher snakemake versions IgDiscover works fine with newer Snakemake versions, so let’s remove the overly restrictive pin (which is causing problems for me). * Update meta.yaml * Update meta.yaml --- recipes/igdiscover/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/igdiscover/meta.yaml b/recipes/igdiscover/meta.yaml index 8da5d1628aacb..462ca5ddc11bc 100644 --- a/recipes/igdiscover/meta.yaml +++ b/recipes/igdiscover/meta.yaml @@ -9,9 +9,11 @@ source: sha256: 534f0e81b71acabe24577f0989832c61e69b73e0e562eb147b1af38c4c9bf725 build: - number: 1 + number: 2 noarch: python script: python -m pip install --no-deps --ignore-installed . + run_exports: + - {{ pin_subpackage("igdiscover", max_pin="x.x") }} requirements: host: @@ -23,7 +25,7 @@ requirements: - pandas >=1.0 - numpy >=1.17.5 - matplotlib-base >=3.1.0 - - snakemake-minimal 5.9.* + - snakemake-minimal >=5.9 - cutadapt >=3.5 - xopen >=1.2.0 - dnaio >=0.7.1 From 141dd825d6d21f60ebb49c9c0f44dafc4154e5b5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 03:18:16 -0500 Subject: [PATCH 1276/2173] Update nf-core to 2.11 (#44905) --- recipes/nf-core/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml index 0e898adb3cc52..beeac6ee1f6e1 100644 --- a/recipes/nf-core/meta.yaml +++ b/recipes/nf-core/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nf-core" %} -{% set version = "2.10" %} -{% set sha256 = "5d3b3d51844fd5b2cec73b84aa736980daac54eb548796243db39680ae39980d" %} +{% set version = "2.11" %} +{% set sha256 = "d1ce276205178162d28d88fe9e7c3086b68cda70a27baeb366797a0150058189" %} package: name: {{ name|lower }} From a9931b3d1dc22b3a86bf99d5eafacd900d3de945 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 05:29:45 -0500 Subject: [PATCH 1277/2173] Update prot-scriber to 0.1.5 (#44891) * Update prot-scriber to 0.1.5 * Update prot-scriber to 0.1.5 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/prot-scriber/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/prot-scriber/meta.yaml b/recipes/prot-scriber/meta.yaml index 2c77e9eecee10..c74897c5d6a79 100644 --- a/recipes/prot-scriber/meta.yaml +++ b/recipes/prot-scriber/meta.yaml @@ -1,12 +1,14 @@ -{% set version = "0.1.4" %} -{% set sha256 = "fe15fe6d11a2466af3169f33e61ba532333563d0b50a07054481c2e0c11a013f" %} +{% set version = "0.1.5" %} +{% set sha256 = "75d75e7a78b631716efb25f762b18405ada70eec3558a2b721c8c633c308269e" %} package: name: prot-scriber version: {{ version }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage("prot-scriber", max_pin="x") }} source: url: https://github.com/usadellab/prot-scriber/archive/v{{ version }}.tar.gz @@ -25,3 +27,4 @@ about: home: https://github.com/usadellab/prot-scriber license: GPL-3 summary: "Assigns short human readable descriptions (HRD) to query biological sequences using reference candidate descriptions." + license_file: LICENSE From 244d02f59813d11bc42986e6d2b0c300afd5f107 Mon Sep 17 00:00:00 2001 From: Lia Obinu <96196229+LiaOb21@users.noreply.github.com> Date: Wed, 20 Dec 2023 11:02:30 +0000 Subject: [PATCH 1278/2173] Add Oatk (#44871) * adding oatk recipe * adding run_exports * correcting run_exports * fixing meta.yaml * fixing meta.yaml * fixing meta.yaml * fixing meta.yaml * fixing meta.yaml * fixing meta.yaml * fixing meta.yaml * trying to solve C and zlib conflicts * applying suggested changes * applying suggested changes * applying suggested changes --- recipes/oatk/build.sh | 11 +++++++++++ recipes/oatk/meta.yaml | 40 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 recipes/oatk/build.sh create mode 100644 recipes/oatk/meta.yaml diff --git a/recipes/oatk/build.sh b/recipes/oatk/build.sh new file mode 100644 index 0000000000000..cff258fcdd73d --- /dev/null +++ b/recipes/oatk/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +# Use Conda environment variables for the C compiler and flags +make CC=$CC CFLAGS="$CFLAGS $LDFLAGS" +ls -la + +# Copying binaries to the $PREFIX/bin directory for them to be included in the Conda package +mkdir -p $PREFIX/bin + +cp oatk path_to_fasta pathfinder hmm_annotation syncasm $PREFIX/bin/ + diff --git a/recipes/oatk/meta.yaml b/recipes/oatk/meta.yaml new file mode 100644 index 0000000000000..d3b3d028c7c8e --- /dev/null +++ b/recipes/oatk/meta.yaml @@ -0,0 +1,40 @@ +package: + name: oatk + version: 1.0 + +source: + url: https://github.com/c-zhou/oatk/archive/refs/tags/1.0.tar.gz + sha256: 5d1a1f44750dac04b436b99f6877b531b19e2e87a3eab956627fbb5e70af463c + +build: + number: 0 + run_exports: + - {{ pin_subpackage('oatk', max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - make + host: + - zlib + run: + - zlib + - hmmer >=3.4 + +test: + commands: + - oatk 2>&1 | grep 'Usage' + - path_to_fasta 2>&1 | grep 'Usage' + - pathfinder 2>&1 | grep 'Usage' + - hmm_annotation 2>&1 | grep 'Usage' + - syncasm 2>&1 | grep 'Usage' + - nhmmscan 2>&1 | grep 'Usage' + +about: + home: https://github.com/c-zhou/oatk + license: MIT + summary: "Oatk: an organelle genome assembly toolkit" + +extra: + recipe-maintainers: + - LiaOb21 From 930dc1c3a5d783c6f734f19fc7589acd6d090acd Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Wed, 20 Dec 2023 05:55:55 -0800 Subject: [PATCH 1279/2173] Update AmpliconSuite to 1.2.0 (#44910) --- recipes/ampliconsuite/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml index 91920ebed86f4..84c00115d5bdf 100644 --- a/recipes/ampliconsuite/meta.yaml +++ b/recipes/ampliconsuite/meta.yaml @@ -1,7 +1,7 @@ {% set name="ampliconsuite" %} -{% set AS_version="1.1.3" %} +{% set AS_version="1.2.0" %} {% set AA_version="1.3.r7" %} -{% set AC_version="1.0.0" %} +{% set AC_version="1.1.0" %} package: name: {{ name }} @@ -11,12 +11,12 @@ source: # the sha256 sum is generated by doing # $ wget -O- [URL] | shasum -a 256 - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz - sha256: 9150307c559d942b820e6249d7b2c4737261d19b1bcaf2c7a487c222e683438d + sha256: 749aa74579aa19d400078fc045d1f1d943159b2ebdcd43a449ee7d5ab2d8ca6d - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz sha256: be65a0293da9ced3f6f744657db475c16dd4dcaf9f037e17ee1a19f4ceaa7430 folder: ampliconarchitectlib - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz - sha256: d1f35e17827947f657892b08c93c9694e9b33947e30d45e8e515084a5c96638d + sha256: e656b557fd8e1c598dd8df9b29e25d4208cb0e1c66e97235c27104751654b7f6 build: noarch: python From 67a5a1913b7cabdd0333bb249a6913d0b4bc2901 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 10:12:19 -0500 Subject: [PATCH 1280/2173] Update lotus2 to 2.31 (#44907) --- recipes/lotus2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/lotus2/meta.yaml b/recipes/lotus2/meta.yaml index 17d78892937f9..1b9451722cb34 100644 --- a/recipes/lotus2/meta.yaml +++ b/recipes/lotus2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "lotus2" %} -{% set version = "2.30" %} -{% set sha256 = "6bd815324f409c188d9d7533583a9d4a642ee2add4ed9aaef63cbb3bdac1d5de" %} +{% set version = "2.31" %} +{% set sha256 = "ee6eb9d31249077e5c0f9a5386b340d511a3a6826b5de8dcfad93c9980392970" %} package: name: {{ name }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin='x') }} From a6132597787aa792f58c474f8c2ff8aa3dc52822 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 10:13:18 -0500 Subject: [PATCH 1281/2173] Update melon to 0.1.2 (#44911) --- recipes/melon/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/melon/meta.yaml b/recipes/melon/meta.yaml index abb0bd264262a..0474c549414fa 100644 --- a/recipes/melon/meta.yaml +++ b/recipes/melon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "melon" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/xinehc/melon/archive/refs/tags/v{{ version }}.tar.gz - sha256: 2f2aefe5fa99064dc7f1cdbafbf1bfaf98907ce3487c75cee4758c79c827f6d2 + sha256: a9c1f3bfb09c204c9be760cc156f8e604ac9138525b5b6c6e5ecc965a637016d build: noarch: python From b6fbe517fa70b223831a0805a8c9a3d1126e2d00 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 10:13:40 -0500 Subject: [PATCH 1282/2173] Update pybiolib to 1.1.1644 (#44913) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 2f4da5d5e367d..922b7865e421e 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1641" %} +{% set version = "1.1.1644" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 922a89734f035766aefc5c9698d30ea8554b7cf098089601014956d96f27bfe8 + sha256: 1afc5d564531414f756bfef32b8fd1fcbb0d604be3cef8bb05e9823cda2966e4 build: noarch: python From c929d8c5b729fb14498bcfd942c3bc9b0e2d6c61 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 10:14:01 -0500 Subject: [PATCH 1283/2173] Update r-erah to 2.0.1 (#44914) --- recipes/r-erah/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-erah/meta.yaml b/recipes/r-erah/meta.yaml index 7f320d446f07c..78d36cf3c8adc 100644 --- a/recipes/r-erah/meta.yaml +++ b/recipes/r-erah/meta.yaml @@ -1,5 +1,5 @@ {% set name = "erah" %} -{% set version = "2.0.0" %} +{% set version = "2.0.1" %} package: name: r-{{ name }} @@ -9,7 +9,7 @@ source: url: - {{ cran_mirror }}/src/contrib/erah_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/erah/erah_{{ version }}.tar.gz - sha256: dc53f49339380e581945e90f68101854eb1d718e1d70e4fb75ba013a2e21c458 + sha256: bd7f89d671ff90f70228ed59c8c1554ca6b3ffab721d50e4ac873daf1e80dc8c build: number: 0 From 9af202cb5c55e8735355ccb25ac123ebcacf0b60 Mon Sep 17 00:00:00 2001 From: zhenxian <920596906@qq.com> Date: Wed, 20 Dec 2023 23:14:57 +0800 Subject: [PATCH 1284/2173] Update meta.yaml (#44912) --- recipes/clair3/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/clair3/meta.yaml b/recipes/clair3/meta.yaml index 7994450c7be40..057a47b092a51 100644 --- a/recipes/clair3/meta.yaml +++ b/recipes/clair3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clair3" %} -{% set version = "1.0.4" %} +{% set version = "1.0.5" %} package: name: {{ name }} @@ -7,10 +7,10 @@ package: source: url: http://www.bio8.cs.hku.hk/clair3/bioconda/Clair3_v{{ version }}.zip - sha256: aa7b7d7db44488c58122f12fec73ea0ca1feea0c6bd10199ca18a00b9308330d + sha256: 05ba9b4de25753ef1f20f0199521672d6d5a4f986d1b2b5d7dc77e5c4bcd3b9a build: - number: 3 + number: 0 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x") }} From 94f8ce74300890375ae09f30bdb5ac8fa4319c22 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 10:19:37 -0500 Subject: [PATCH 1285/2173] Update methylartist to 1.2.11 (#44759) * Update methylartist to 1.2.8 * Update methylartist to 1.2.11 --- recipes/methylartist/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/methylartist/meta.yaml b/recipes/methylartist/meta.yaml index 1011726558909..43fa87877feaf 100644 --- a/recipes/methylartist/meta.yaml +++ b/recipes/methylartist/meta.yaml @@ -1,5 +1,5 @@ {% set name = "methylartist" %} -{% set version = "1.2.7" %} +{% set version = "1.2.11" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 23005b717a317aa1aea813703f3d7011592d58268b16f111275df2d8694c41a4 + sha256: 63c3493e65352471836b54eda82ce5678e676bf7c2557c2bb56ab34ae04cf29e build: noarch: python From 675bf609000f9d5380525667f433ffbca1fb3d3f Mon Sep 17 00:00:00 2001 From: Benjamin Linard <22132778+blinard-BIOINFO@users.noreply.github.com> Date: Wed, 20 Dec 2023 16:21:34 +0100 Subject: [PATCH 1286/2173] Update rappas to v1.22 (#44584) * rappas updated to v1.22 --------- Co-authored-by: B. Linard h Co-authored-by: Benjamin Linard --- build-fail-blacklist | 1 - recipes/rappas/meta.yaml | 12 +++++++----- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 5406b11e29630..01cc3c5e5ceff 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -172,7 +172,6 @@ recipes/bwa/0.6.2 # fails compilation in bulk on Linux recipes/paragraph recipes/selectsequencesfrommsa -recipes/rappas recipes/centrifuge recipes/nasp recipes/mmvc diff --git a/recipes/rappas/meta.yaml b/recipes/rappas/meta.yaml index 36073809e86af..d0b213969ed33 100644 --- a/recipes/rappas/meta.yaml +++ b/recipes/rappas/meta.yaml @@ -1,18 +1,20 @@ package: name: rappas - version: '1.21' + version: '1.22' source: - url: https://github.com/blinard-BIOINFO/RAPPAS/archive/v1.21.tar.gz - sha256: d9eb91fc0412b6517278a19f0f35a69de5da193aac25376180af74819165274d + url: https://github.com/blinard-BIOINFO/RAPPAS/archive/v1.22.tar.gz + sha256: 52c5023f1fae57fad2cf0d0f8ecb1ae9f8dda99fa79de405ccc58288ba4cc09d build: - number: 1 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('rappas', max_pin="x.x") }} requirements: host: - - ant 1.10.0 + - ant >=1.10.0 - openjdk >=8.0.144 run: - openjdk >=8.0.144 From 806639cba43c9bcd8786d8d7125373e9cc2ab81f Mon Sep 17 00:00:00 2001 From: y4nnick8 <151630397+y4nnick8@users.noreply.github.com> Date: Wed, 20 Dec 2023 16:26:19 +0100 Subject: [PATCH 1287/2173] Add recipe for snapatac2 (#44806) * add recipe for snapatac2 * fix linting * use correct subpackage * Update meta.yaml * Update meta.yaml * add build requirements * remove noarch * include more run requirements --------- Co-authored-by: Pavankumar Videm --- recipes/snapatac2/meta.yaml | 62 +++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 recipes/snapatac2/meta.yaml diff --git a/recipes/snapatac2/meta.yaml b/recipes/snapatac2/meta.yaml new file mode 100644 index 0000000000000..52674eddb1726 --- /dev/null +++ b/recipes/snapatac2/meta.yaml @@ -0,0 +1,62 @@ +{% set name = "snapatac2" %} +{% set version = "2.5.1" %} +{% set sha256 = "c60fff185fb502d03518b440b63e24b794f8c6f9592df06cd94d85e156721fa6" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snapatac2-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + script: {{ PYTHON }} -m pip install . -vv + run_exports: + - {{ pin_subpackage('snapatac2', max_pin="x.x.x") }} + + +requirements: + build: + - make + - cmake + - rust + - {{ compiler('c') }} + + host: + - python + - pip + - setuptools-rust + + run: + - python + - anndata + - scanpy + - matplotlib-base + - pandas + - scipy + - seaborn + - h5py + - scikit-learn + - numba + - numpy + - umap-learn + - packaging + - rustworkx + - pooch + +test: + imports: + - snapatac2 + +about: + home: https://github.com/kaizhang/SnapATAC2 + summary: Python/Rust package for single-cell epigenomics analysis + license: MIT + license_file: LICENSE + +extra: + identifiers: + - biotools:snapatac + - doi:10.1101/2023.09.11.557221 From 9df3bfca439f1140c16d21bcd2df9ed4b07be843 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 11:59:45 -0500 Subject: [PATCH 1288/2173] Update nf-core to 2.11.1 (#44919) --- recipes/nf-core/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml index beeac6ee1f6e1..df210d833f8d2 100644 --- a/recipes/nf-core/meta.yaml +++ b/recipes/nf-core/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nf-core" %} -{% set version = "2.11" %} -{% set sha256 = "d1ce276205178162d28d88fe9e7c3086b68cda70a27baeb366797a0150058189" %} +{% set version = "2.11.1" %} +{% set sha256 = "f81e411a66a417b9355657eec4337e8d004b166d8690e39f337994763b0ecc63" %} package: name: {{ name|lower }} From 08d11fc8d979c41e3fadaddde2402259fe5d28e2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 20 Dec 2023 19:22:44 +0100 Subject: [PATCH 1289/2173] feat: add various snakemake executor plugins (#44900) * feat: add various snakemake executor plugins * add run exports * latest azure batch version * update versions * fixes --- .../meta.yaml | 50 ++++++++++++++++++ .../meta.yaml | 45 ++++++++++++++++ .../meta.yaml | 45 ++++++++++++++++ .../snakemake-executor-plugin-drmaa/meta.yaml | 46 +++++++++++++++++ .../meta.yaml | 51 +++++++++++++++++++ .../meta.yaml | 46 +++++++++++++++++ .../meta.yaml | 45 ++++++++++++++++ .../snakemake-executor-plugin-slurm/meta.yaml | 47 +++++++++++++++++ 8 files changed, 375 insertions(+) create mode 100644 recipes/snakemake-executor-plugin-azure-batch/meta.yaml create mode 100644 recipes/snakemake-executor-plugin-cluster-generic/meta.yaml create mode 100644 recipes/snakemake-executor-plugin-cluster-sync/meta.yaml create mode 100644 recipes/snakemake-executor-plugin-drmaa/meta.yaml create mode 100644 recipes/snakemake-executor-plugin-googlebatch/meta.yaml create mode 100644 recipes/snakemake-executor-plugin-kubernetes/meta.yaml create mode 100644 recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml create mode 100644 recipes/snakemake-executor-plugin-slurm/meta.yaml diff --git a/recipes/snakemake-executor-plugin-azure-batch/meta.yaml b/recipes/snakemake-executor-plugin-azure-batch/meta.yaml new file mode 100644 index 0000000000000..46334d0da48a9 --- /dev/null +++ b/recipes/snakemake-executor-plugin-azure-batch/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "snakemake-executor-plugin-azure-batch" %} +{% set version = "0.1.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_azure_batch-{{ version }}.tar.gz + sha256: 7883ecdc3983eb73ea0e1ae10010eeff1626510c7e99176203ee2050031f86e3 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.15.0,<2.0.0 + - snakemake-interface-executor-plugins >=8.1.1,<9.0.0 + - azure-storage-blob >=12.17.0,<13.0.0 + - azure-batch >=14.0.0,<15.0.0 + - azure-mgmt-batch >=17.0.0,<18.0.0 + - azure-identity >=1.14.0,<2.0.0 + - msrest >=0.7.1,<0.8.0 + +test: + imports: + - snakemake_executor_plugin_azure_batch + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-executor-plugin-azure-batch + summary: A Snakemake executor plugin for submitting jobs to Microsoft Azure Batch. + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-executor-plugin-cluster-generic/meta.yaml b/recipes/snakemake-executor-plugin-cluster-generic/meta.yaml new file mode 100644 index 0000000000000..0abb031d05075 --- /dev/null +++ b/recipes/snakemake-executor-plugin-cluster-generic/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "snakemake-executor-plugin-cluster-generic" %} +{% set version = "1.0.7" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_cluster_generic-{{ version }}.tar.gz + sha256: 093808e63cc48294a9d1eb0b620cdff8cc970806294a2f6ba127a49f8a81d473 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-executor-plugins >=8.1.0,<9.0.0 + - snakemake-interface-common >=1.13.0,<2.0.0 + +test: + imports: + - snakemake_executor_plugin_cluster_generic + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-executor-plugin-cluster-generic + summary: '' + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-executor-plugin-cluster-sync/meta.yaml b/recipes/snakemake-executor-plugin-cluster-sync/meta.yaml new file mode 100644 index 0000000000000..8c85124cc99e3 --- /dev/null +++ b/recipes/snakemake-executor-plugin-cluster-sync/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "snakemake-executor-plugin-cluster-sync" %} +{% set version = "0.1.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_cluster_sync-{{ version }}.tar.gz + sha256: c30fca6ccb98a3f7ca52ca8a95414c71360a3d4a835bd4a097a13445d6fce2ac + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.14.0,<2.0.0 + - snakemake-interface-executor-plugins >=8.1.0,<9.0.0 + +test: + imports: + - snakemake_executor_plugin_cluster_sync + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-executor-plugin-cluster-sync + summary: A Snakemake executor plugin for cluster jobs that are executed synchronously. + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-executor-plugin-drmaa/meta.yaml b/recipes/snakemake-executor-plugin-drmaa/meta.yaml new file mode 100644 index 0000000000000..ecc427cb7d15e --- /dev/null +++ b/recipes/snakemake-executor-plugin-drmaa/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "snakemake-executor-plugin-drmaa" %} +{% set version = "0.1.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_drmaa-{{ version }}.tar.gz + sha256: 1250d0f307bf3db3aa3f26f85ea5ecc7ae00b2598ea1e1afceab7a457042fa12 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.13.0,<2.0.0 + - snakemake-interface-executor-plugins >=8.1.0,<9.0.0 + - drmaa >=0.7.9,<0.8.0 + +test: + imports: + - snakemake_executor_plugin_drmaa + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-executor-plugin-drmaa + summary: A snakemake executor plugin for submission of jobs via DRMAA. + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml new file mode 100644 index 0000000000000..06a457c3e614b --- /dev/null +++ b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml @@ -0,0 +1,51 @@ +{% set name = "snakemake-executor-plugin-googlebatch" %} +{% set version = "0.1.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_googlebatch-{{ version }}.tar.gz + sha256: 12a25a51f4471d6fb774ed0e837a49c8f3cebbe5a6494a5b2daf96146df87925 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - google-cloud-batch >=0.17.1,<0.18.0 + - requests >=2.31.0,<3.0.0 + - google-api-core >=2.12.0,<3.0.0 + - google-cloud-storage >=2.12.0,<3.0.0 + - snakemake-interface-common >=1.14.0,<2.0.0 + - snakemake-interface-executor-plugins >=8.1.1,<9.0.0 + - jinja2 >=3.1.2,<4.0.0 + - google-cloud-logging >=3.8.0,<4.0.0 + +test: + imports: + - snakemake_executor_plugin_googlebatch + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-executor-plugin-googlebatch + summary: '' + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-executor-plugin-kubernetes/meta.yaml b/recipes/snakemake-executor-plugin-kubernetes/meta.yaml new file mode 100644 index 0000000000000..c355b079a0b3e --- /dev/null +++ b/recipes/snakemake-executor-plugin-kubernetes/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "snakemake-executor-plugin-kubernetes" %} +{% set version = "0.1.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_kubernetes-{{ version }}.tar.gz + sha256: c3aeac87939ec5d038efdc3ba7dbbef5eeb3171c1b718b8af850b6287b9c54ff + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.14.1,<2.0.0 + - snakemake-interface-executor-plugins >=8.0.2,<9.0.0 + - python-kubernetes >=27.2.0,<28.0.0 + +test: + imports: + - snakemake_executor_plugin_kubernetes + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-executor-plugin-kubernetes + summary: A snakemake executor plugin for submission of jobs to Kubernetes + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml b/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml new file mode 100644 index 0000000000000..dd3cfeedd0a26 --- /dev/null +++ b/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "snakemake-executor-plugin-slurm-jobstep" %} +{% set version = "0.1.8" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm_jobstep-{{ version }}.tar.gz + sha256: 60e28ceae224107bc415a06ebeeca6b5216765f62622bcbf8ef5ecbc28cd4695 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.13.0,<2.0.0 + - snakemake-interface-executor-plugins >=8.0.2,<9.0.0 + +test: + imports: + - snakemake_executor_plugin_slurm_jobstep + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-executor-plugin-slurm-jobstep + summary: A Snakemake executor plugin for running srun jobs inside of SLURM jobs (meant for internal use by snakemake-executor-plugin-slurm) + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml new file mode 100644 index 0000000000000..3f6877dafc3b2 --- /dev/null +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "snakemake-executor-plugin-slurm" %} +{% set version = "0.1.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz + sha256: 924cdeca812bc2e38478c120f0143d5113170e20204a2911a1e104cf4c2daace + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.13.0,<2.0.0 + - snakemake-interface-executor-plugins >=8.0.2,<9.0.0 + - snakemake-executor-plugin-slurm-jobstep >=0.1.5,<0.2.0 + - throttler >=1.2.2,<2.0.0 + +test: + imports: + - snakemake_executor_plugin_slurm + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-executor-plugin-slurm + summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster. + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab From 27dded0308204712d9a6768dad070d90f9ff7011 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 20 Dec 2023 20:53:44 +0100 Subject: [PATCH 1290/2173] feat: add snakemake storage plugins (#44899) * feat: add snakemake storage plugins * add storage plugins * fix azure dependency * fixes * fixes --- .../snakemake-storage-plugin-azure/meta.yaml | 48 +++++++++++++++++++ recipes/snakemake-storage-plugin-fs/meta.yaml | 46 ++++++++++++++++++ .../snakemake-storage-plugin-ftp/meta.yaml | 46 ++++++++++++++++++ .../snakemake-storage-plugin-gcs/meta.yaml | 45 +++++++++++++++++ .../snakemake-storage-plugin-http/meta.yaml | 4 +- .../snakemake-storage-plugin-irods/meta.yaml | 46 ++++++++++++++++++ recipes/snakemake-storage-plugin-s3/meta.yaml | 4 +- .../snakemake-storage-plugin-sftp/meta.yaml | 46 ++++++++++++++++++ .../snakemake-storage-plugin-zenodo/meta.yaml | 46 ++++++++++++++++++ 9 files changed, 327 insertions(+), 4 deletions(-) create mode 100644 recipes/snakemake-storage-plugin-azure/meta.yaml create mode 100644 recipes/snakemake-storage-plugin-fs/meta.yaml create mode 100644 recipes/snakemake-storage-plugin-ftp/meta.yaml create mode 100644 recipes/snakemake-storage-plugin-gcs/meta.yaml create mode 100644 recipes/snakemake-storage-plugin-irods/meta.yaml create mode 100644 recipes/snakemake-storage-plugin-sftp/meta.yaml create mode 100644 recipes/snakemake-storage-plugin-zenodo/meta.yaml diff --git a/recipes/snakemake-storage-plugin-azure/meta.yaml b/recipes/snakemake-storage-plugin-azure/meta.yaml new file mode 100644 index 0000000000000..0bea4ce30457f --- /dev/null +++ b/recipes/snakemake-storage-plugin-azure/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "snakemake-storage-plugin-azure" %} +{% set version = "0.1.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_azure-{{ version }}.tar.gz + sha256: dcfcf285c9f1b1aa89db359afbf02b28d9e57a97ddac66747d3e46832e7ddbff + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.15.0,<2.0.0 + - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 + - azure-storage-blob >=12.19.0,<13.0.0 + - azure-core >=1.29.5,<2.0.0 + - azure-identity >=1.15.0,<2.0.0 + +test: + # We do not test the import as the plugin needs snakemake for importing, but adding + # it would create a circular dependency. + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-storage-plugin-azure + summary: A Snakemake storage plugin to read and write from Azure Blob Storage + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-storage-plugin-fs/meta.yaml b/recipes/snakemake-storage-plugin-fs/meta.yaml new file mode 100644 index 0000000000000..2f0f622a761d0 --- /dev/null +++ b/recipes/snakemake-storage-plugin-fs/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "snakemake-storage-plugin-fs" %} +{% set version = "0.1.5" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_fs-{{ version }}.tar.gz + sha256: f1a54248008b6c65102a1fde2064e3b66aadd9f6795522bacb452deecfe181ad + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.14.2,<2.0.0 + - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 + - sysrsync >=1.1.1,<2.0.0 + +test: + # We do not test the import as the plugin needs snakemake for importing, but adding + # it would create a circular dependency. + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-storage-plugin-fs + summary: 'A Snakemake storage plugin that reads and writes from a locally mounted filesystem using rsync' + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-storage-plugin-ftp/meta.yaml b/recipes/snakemake-storage-plugin-ftp/meta.yaml new file mode 100644 index 0000000000000..48183cbe50141 --- /dev/null +++ b/recipes/snakemake-storage-plugin-ftp/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "snakemake-storage-plugin-ftp" %} +{% set version = "0.1.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_ftp-{{ version }}.tar.gz + sha256: 9daf4d0eee152f776848b4787dcaf1a3bc34785caabafe2273b3d13e5bd2119c + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.15.0,<2.0.0 + - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 + - ftputil >=5.0.4,<6.0.0 + +test: + # We do not test the import as the plugin needs snakemake for importing, but adding + # it would create a circular dependency. + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-storage-plugin-ftp + summary: A Snakemake plugin for handling input and output via FTP + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-storage-plugin-gcs/meta.yaml b/recipes/snakemake-storage-plugin-gcs/meta.yaml new file mode 100644 index 0000000000000..d9da699d0876f --- /dev/null +++ b/recipes/snakemake-storage-plugin-gcs/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "snakemake-storage-plugin-gcs" %} +{% set version = "0.1.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_gcs-{{ version }}.tar.gz + sha256: f0315596120160656b8c8afec66e3b31b4a2889b9d0cead2102f9d924ec0b326 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - google-cloud-storage >=2.12.0,<3.0.0 + - google-crc32c >=1.1.2,<2.0.0 + +test: + # We do not test the import as the plugin needs snakemake for importing, but adding + # it would create a circular dependency. + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-storage-plugin-gcs + summary: A Snakemake storage plugin for Google Cloud Storage + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-storage-plugin-http/meta.yaml b/recipes/snakemake-storage-plugin-http/meta.yaml index 9a22c74f02554..a7aee9ddf4eaf 100644 --- a/recipes/snakemake-storage-plugin-http/meta.yaml +++ b/recipes/snakemake-storage-plugin-http/meta.yaml @@ -12,9 +12,9 @@ source: build: noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 0 + number: 1 run_exports: - - {{ pin_subpackage("snakemake-storage-plugin-http", max_pin="x") }} + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: diff --git a/recipes/snakemake-storage-plugin-irods/meta.yaml b/recipes/snakemake-storage-plugin-irods/meta.yaml new file mode 100644 index 0000000000000..143d7d1b12075 --- /dev/null +++ b/recipes/snakemake-storage-plugin-irods/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "snakemake-storage-plugin-irods" %} +{% set version = "0.1.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_irods-{{ version }}.tar.gz + sha256: af823c0d18a4e3807d05e9bcfe5687c7ce6c711224fc37259fd74558917ec71d + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.15.0,<2.0.0 + - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 + - python-irodsclient >=1.1.9,<2.0.0 + +test: + # We do not test the import as the plugin needs snakemake for importing, but adding + # it would create a circular dependency. + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-storage-plugin-irods + summary: A Snakemake plugin for handling input and output on iRODS + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-storage-plugin-s3/meta.yaml b/recipes/snakemake-storage-plugin-s3/meta.yaml index a0cc7611163bd..9bc32ac5fff7f 100644 --- a/recipes/snakemake-storage-plugin-s3/meta.yaml +++ b/recipes/snakemake-storage-plugin-s3/meta.yaml @@ -12,9 +12,9 @@ source: build: noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 0 + number: 1 run_exports: - - {{ pin_subpackage("snakemake-storage-plugin-s3", max_pin="x") }} + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: diff --git a/recipes/snakemake-storage-plugin-sftp/meta.yaml b/recipes/snakemake-storage-plugin-sftp/meta.yaml new file mode 100644 index 0000000000000..78dd48ec129d7 --- /dev/null +++ b/recipes/snakemake-storage-plugin-sftp/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "snakemake-storage-plugin-sftp" %} +{% set version = "0.1.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_sftp-{{ version }}.tar.gz + sha256: 1b5f99a6baf334d74e209d6ec8a59e495e56098cf6e9a19954e472ba1501525c + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.14.3,<2.0.0 + - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 + - pysftp >=0.2.9,<0.3.0 + +test: + # We do not test the import as the plugin needs snakemake for importing, but adding + # it would create a circular dependency. + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-storage-plugin-sftp + summary: 'A Snakemake storage plugin that handles files on an SFTP server. ' + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab diff --git a/recipes/snakemake-storage-plugin-zenodo/meta.yaml b/recipes/snakemake-storage-plugin-zenodo/meta.yaml new file mode 100644 index 0000000000000..c5437300cae37 --- /dev/null +++ b/recipes/snakemake-storage-plugin-zenodo/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "snakemake-storage-plugin-zenodo" %} +{% set version = "0.1.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_zenodo-{{ version }}.tar.gz + sha256: 3675e76ae5dc930664bbcc1132a957c6490199c366e4e1e607d1491a7a46cf3d + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.14.4,<2.0.0 + - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 + - requests >=2.31.0,<3.0.0 + +test: + # We do not test the import as the plugin needs snakemake for importing, but adding + # it would create a circular dependency. + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/snakemake/snakemake-storage-plugin-zenodo + summary: A Snakemake storage plugin for reading from and writing to zenodo.org + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab From 203dff165235359ffa1e7722741dd6fa882c597a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 18:34:22 -0500 Subject: [PATCH 1291/2173] Update ribodetector to 0.2.9 (#44920) --- recipes/ribodetector/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ribodetector/meta.yaml b/recipes/ribodetector/meta.yaml index 18cd605993a9c..fb159ba48fc96 100644 --- a/recipes/ribodetector/meta.yaml +++ b/recipes/ribodetector/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.2.8" %} +{% set version = "0.2.9" %} package: name: ribodetector version: {{ version }} source: - url: https://files.pythonhosted.org/packages/88/e7/4b7bb1a97093600cf0ca66399b91262dcdbe77eeafa06ef07e9f3eb04e53/ribodetector-0.2.8.tar.gz - sha256: 9da4b60b09321e0261cb97f51d209bda21573e810820290ecc39d70690a57aff + url: https://files.pythonhosted.org/packages/4c/45/7eb2a0f87b44e6f98f451a422584d05d293b1058397b6f016a53372c80cd/ribodetector-0.2.9.tar.gz + sha256: cf98b4e3c306e48e79454bad4d062af8f13607a0a3e09a5c849162cd7ae8783d build: number: 0 From 1b62be1684111b2eed71b0da7194f952ac089786 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 18:34:31 -0500 Subject: [PATCH 1292/2173] Update pybiolib to 1.1.1648 (#44922) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 922b7865e421e..2c69aa37fc597 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1644" %} +{% set version = "1.1.1648" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 1afc5d564531414f756bfef32b8fd1fcbb0d604be3cef8bb05e9823cda2966e4 + sha256: 49d0e8ad018cf046c50fc6162f1b08a7ba96ab7348e045ca318ae4c1116e7059 build: noarch: python From dd64a0961b0cc97a0aaee860d7aeaf2de5d3b395 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 18:42:33 -0500 Subject: [PATCH 1293/2173] Update ncbi-datasets-pylib to 16.0.0 (#44927) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 189df41461626..2712a35e55419 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "15.34.0" %} -{% set sha256 = "3809be524170dc92911fb6465c8182e28af3d67e1b5aebc37e1b22c89d8caee5" %} +{% set version = "16.0.0" %} +{% set sha256 = "499f5664b768ae4c6e2e5ab2965e0b6e150de2f81c667ba89eb5f29a2e67ce1d" %} package: name: {{ name|lower }} From 624a980ef8e837c061babeb75ecf2473298fd9bd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 18:48:59 -0500 Subject: [PATCH 1294/2173] Update macsyfinder to 2.1.3 (#44894) * Update macsyfinder to 2.1.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/macsyfinder/meta.yaml | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/recipes/macsyfinder/meta.yaml b/recipes/macsyfinder/meta.yaml index aeb97eaa783a9..6e61954c4f6c9 100644 --- a/recipes/macsyfinder/meta.yaml +++ b/recipes/macsyfinder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MacSyFinder" %} -{% set version = "2.1.2" %} +{% set version = "2.1.3" %} package: name: "{{ name|lower }}" @@ -7,19 +7,28 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 19369dc15bdf08aac90c8e0bf8dfc51ffa409105738fa9c55131403435fde7c0 + sha256: 28078e2e742598124aa216b7767db473290257dd265dbd9deafa687a9dbdf91a build: noarch: python number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + entry_points: + - macsyfinder=macsypy.scripts.macsyfinder:main + - macsydata=macsypy.scripts.macsydata:main + - macsyprofile=macsypy.scripts.macsyprofile:main + - macsyconfig=macsypy.scripts.macsyconfig:main + - macsysplit=macsypy.scripts.macsy_gembase_split:main + - macsymerge=macsypy.scripts.macsy_merge_results:main + run_exports: + - {{ pin_subpackage('macsyfinder', max_pin="x") }} requirements: host: - pip - - python + - python >=3.7 run: - - python + - python >=3.7 - colorlog - PyYAML >=5.1.1 - packaging >=18.0 @@ -48,4 +57,3 @@ extra: identifiers: - biotools:macsyfinder - doi:10.1371/journal/pone.0110726 - From f92a45ac0e1cd2aebe9fdb967a953bfb12badffe Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 21 Dec 2023 00:52:04 +0100 Subject: [PATCH 1295/2173] Update fiji version (#44893) * update fiji version * try to set a run_export * put package name in run_exports * fix ij version in bunwarpj.sh --- recipes/fiji/bunwarpj.sh | 2 +- recipes/fiji/meta.yaml | 14 ++++++++------ 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/recipes/fiji/bunwarpj.sh b/recipes/fiji/bunwarpj.sh index b4a6a1b1adcf1..f595cfc165b1e 100644 --- a/recipes/fiji/bunwarpj.sh +++ b/recipes/fiji/bunwarpj.sh @@ -52,6 +52,6 @@ if [ "$jvm_mem_opts" == "" ]; then jvm_mem_opts="$default_jvm_mem_opts" fi -eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/ij-1.53q.jar:$PLUGINS_DIR/bUnwarpJ_-2.6.13.jar" "$bUnwarpJ" $pass_args +eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/ij-1.54f.jar:$PLUGINS_DIR/bUnwarpJ_-2.6.13.jar" "$bUnwarpJ" $pass_args exit diff --git a/recipes/fiji/meta.yaml b/recipes/fiji/meta.yaml index 29dabfb6eec60..055f596ba2279 100644 --- a/recipes/fiji/meta.yaml +++ b/recipes/fiji/meta.yaml @@ -1,15 +1,17 @@ package: name: fiji - version: 20220414 + version: 20231211 source: - - url: https://downloads.imagej.net/fiji/archive/20220414-1745/fiji-linux64.zip # [linux] - md5: 6e34f59fd28978f59875b22b838c7b98 # [linux] - - url: https://downloads.imagej.net/fiji/archive/20220414-1745/fiji-macosx.zip # [osx] - md5: b2b5975e9a105302cebea88f2f96fd2c # [osx] + - url: https://downloads.imagej.net/fiji/archive/20231211-1317/fiji-linux64.zip # [linux] + md5: 9292db721a289c13de35dbb882a84c2a # [linux] + - url: https://downloads.imagej.net/fiji/archive/20231211-1317/fiji-macosx.zip # [osx] + md5: 46959cc6a43b7ace2981a9a4a3486e4c # [osx] build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage("fiji", max_pin=None) }} requirements: host: From 6ec3d2d8ca6818dd7dc25f9bce69dca877cfc994 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 19:22:52 -0500 Subject: [PATCH 1296/2173] Update hlafreq to 0.0.3 (#44916) * Update hlafreq to 0.0.3 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/hlafreq/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/hlafreq/meta.yaml b/recipes/hlafreq/meta.yaml index ad13a124afa23..f9b65c5f5093b 100644 --- a/recipes/hlafreq/meta.yaml +++ b/recipes/hlafreq/meta.yaml @@ -1,5 +1,5 @@ {% set name = "HLAfreq" %} -{% set version = "0.0.2" %} +{% set version = "0.0.3" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e43d70a876a6a245ecc2d6117947c5e1f6bce5824738a4d86dfecbe6c53e07f7 + sha256: 93941536c4912180f12544251792d21098e47116a871c6c49565054987e1438f build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('hlafreq', max_pin="x.x") }} requirements: host: From 9c4e4d40f51a647f9f9813351d43b5b0d5188ed3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 19:23:02 -0500 Subject: [PATCH 1297/2173] Update cellxgene to 1.2.0 (#44908) * Update cellxgene to 1.2.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/cellxgene/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/cellxgene/meta.yaml b/recipes/cellxgene/meta.yaml index e9707286a7efb..c0c0b3cf36172 100644 --- a/recipes/cellxgene/meta.yaml +++ b/recipes/cellxgene/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cellxgene" %} -{% set version = "1.1.2" %} -{% set sha256 = "9cdf6e626b2d884d4efa4e8cf2dd42deb4a3f9d793134d53c1c70938e8dc0a9a" %} +{% set version = "1.2.0" %} +{% set sha256 = "1a4c5e93106283ecd1d6bd38170942d298ce8087ace533c2a6e294b67fb13c53" %} package: name: "{{ name|lower }}" @@ -15,7 +15,9 @@ build: noarch: python entry_points: - cellxgene = server.cli.cli:cli - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('cellxgene', max_pin="x") }} requirements: host: From f2c896d549c766266693fdf93343ace628fedd54 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 19:23:13 -0500 Subject: [PATCH 1298/2173] Update pomoxis to 0.3.15 (#44898) * Update pomoxis to 0.3.15 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/pomoxis/meta.yaml | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/recipes/pomoxis/meta.yaml b/recipes/pomoxis/meta.yaml index 2b2455b6e48e7..ae831a0fd1025 100644 --- a/recipes/pomoxis/meta.yaml +++ b/recipes/pomoxis/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pomoxis" %} -{% set version = "0.3.13" %} +{% set version = "0.3.15" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 732e3c641b4d6c542b62f6df8bfd0e7b49e1a1cb351f644b3a98c37b4ec026d3 + sha256: e54f7f2960290121676dda992b326341986b093e5da4586203b8b613cc356d2b build: number: 0 @@ -22,14 +22,19 @@ build: - long_fastx = pomoxis.util:extract_long_reads - pomoxis_path = pomoxis:show_prog_path - qscores_from_summary = pomoxis.qscores_from_summary:main + - reverse_bed = pomoxis.util:reverse_bed - split_fastx = pomoxis.util:split_fastx_cmdline - stats_from_bam = pomoxis.stats_from_bam:main - subsample_bam = pomoxis.subsample_bam:main + - filter_bam = pomoxis.filter_bam:main - summary_from_stats = pomoxis.summary_from_stats:main + - tag_bam = pomoxis.util:tag_bam - trim_alignments = pomoxis.trim_alignments:main - ref_seqs_from_bam = pomoxis.ref_seqs_from_bam:main - find_indels = pomoxis.find_indels:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('pomoxis', max_pin="x.x") }} requirements: host: @@ -79,12 +84,12 @@ test: about: home: https://github.com/nanoporetech/pomoxis - license: Mozilla Public License 2.0 + license: MPL-2.0 license_family: OTHER license_file: LICENSE.md summary: Assembly, consensensus, and analysis tools by ONT research doc_url: https://nanoporetech.github.io/pomoxis/index.html - dev_url: https://github.com/nanoporetech/pomoxis + dev_url: https://github.com/nanoporetech/pomoxis extra: recipe-maintainers: From f4fb203854f9bc280d3be84ac9cace04a7da82ee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 19:23:25 -0500 Subject: [PATCH 1299/2173] Update fgpyo to 0.1.2 (#44897) * Update fgpyo to 0.1.1 * Update fgpyo to 0.1.2 * add run_exports * revert to poetry --------- Co-authored-by: joshuazhuang7 --- recipes/fgpyo/meta.yaml | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/recipes/fgpyo/meta.yaml b/recipes/fgpyo/meta.yaml index 57d971af0c167..a92669798697a 100644 --- a/recipes/fgpyo/meta.yaml +++ b/recipes/fgpyo/meta.yaml @@ -1,6 +1,5 @@ {% set name = "fgpyo" %} -{% set version = "0.1.0" %} - +{% set version = "0.1.2" %} package: name: {{ name|lower }} @@ -8,12 +7,14 @@ package: source: url: https://github.com/fulcrumgenomics/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: 195dcc08580a1522417ed5399df70b9680c271eb7887b8990a81b54898e84585 + sha256: e305049a2961a400519de2426f6b06bac00cd0216ab68e7966ea24420593ab37 build: noarch: python number: 0 - script: {{ PYTHON }} -m pip install . -vv --no-deps + script: {{ PYTHON }} -m pip install . -vvv --no-build-isolation --no-deps + run_exports: + - {{ pin_subpackage('fgpyo', max_pin="x.x") }} requirements: host: @@ -22,10 +23,14 @@ requirements: - poetry run: - python >=3.7 - - typing_extensions >=3.7.4 #[py<38] - - typing_inspect >=0.3.1 #[py<38] + - typing_extensions >=3.7.4 # [py < 38] + - typing_inspect >=0.3.1 # [py < 38] - attrs >=19.3.0 - pysam >=0.20.0 + - pytest >=7.4.0 + run_constrained: + - sphinx 4.3.1 + - sphinx_rtd_theme >=1.3.0,<2.0.0 test: imports: @@ -35,7 +40,10 @@ about: home: https://pypi.org/project/fgpyo/ summary: Python bioinformatics and genomics library license: MIT + license_family: MIT license_file: LICENSE + dev_url: https://github.com/fulcrumgenomics/fgpyo + doc_url: https://fgpyo.readthedocs.io/en/latest/ extra: recipe-maintainers: From 892730564e9ba8ed80cd1f1a33b1e0cd21700336 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 20 Dec 2023 18:58:35 -0600 Subject: [PATCH 1300/2173] Build primer3-py on python 3.8-3.10 (#44928) * Build primer3-py on python 3.8-3.10 * bump build number --- recipes/primer3-py/build.sh | 2 +- recipes/primer3-py/meta.yaml | 9 +++++---- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/primer3-py/build.sh b/recipes/primer3-py/build.sh index 4a58171466a07..b1f1ebe131016 100755 --- a/recipes/primer3-py/build.sh +++ b/recipes/primer3-py/build.sh @@ -1,4 +1,4 @@ #!/bin/bash sed -i.bak '/^CC /d' primer3/src/libprimer3/Makefile -$PYTHON -m pip install . --use-pep517 --no-deps -vvv +$PYTHON -m pip install . --use-pep517 --no-deps --no-build-isolation -vvv diff --git a/recipes/primer3-py/meta.yaml b/recipes/primer3-py/meta.yaml index c791ccfc63b4f..dd28aab34137d 100644 --- a/recipes/primer3-py/meta.yaml +++ b/recipes/primer3-py/meta.yaml @@ -10,7 +10,8 @@ source: sha256: 30b549c568ae5712e3e6cde6c1f5b243f328247ec8d6ec89d4b705873a44e772 build: - number: 0 + number: 1 + skip: True # [py < 38] run_exports: - {{ pin_subpackage('primer3-py', max_pin="x") }} @@ -19,12 +20,12 @@ requirements: - {{ compiler('c') }} - make host: - - python >=3.8 + - python - cython - setuptools >=65.6.3 - pip run: - - python >=3.8 + - python test: imports: @@ -34,7 +35,7 @@ about: home: https://github.com/libnano/primer3-py summary: Python bindings for Primer3 license: GPL-2.0-only - license_family: GPL + license_family: GPL2 license_file: LICENSE doc_url: https://libnano.github.io/primer3-py/ From bb9a0fbabd331b877fab02f1296e17a809bbf662 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 20 Dec 2023 20:31:41 -0600 Subject: [PATCH 1301/2173] Update hatchet to 2.0.1 (#44929) * Update hatchet to 2.0.1 * edit tests --- build-fail-blacklist | 1 - recipes/hatchet/build.sh | 7 ++++--- recipes/hatchet/meta.yaml | 37 ++++++++++++++++++++++--------------- 3 files changed, 26 insertions(+), 19 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 01cc3c5e5ceff..e043d8ad3088c 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -21,7 +21,6 @@ recipes/octopus recipes/bttcmp recipes/bttoxin_scanner recipes/cgat-apps -recipes/hatchet recipes/hail recipes/monocle3-cli recipes/phenix diff --git a/recipes/hatchet/build.sh b/recipes/hatchet/build.sh index c44c6715da79a..dce0f2fc3250e 100755 --- a/recipes/hatchet/build.sh +++ b/recipes/hatchet/build.sh @@ -1,3 +1,5 @@ +#!/bin/bash + # Compile Gurobi if [[ "$OSTYPE" == "darwin"* ]]; then @@ -18,6 +20,5 @@ else cp $GUROBI_HOME/linux64/lib/libgurobi90.so $PREFIX/lib fi -export CXXFLAGS=-pthread -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - +export CXXFLAGS="-O3 -pthread -I${PREFIX}/include ${LDFLAGS}" +$PYTHON -m pip install . --no-build-isolation --no-deps -vvv diff --git a/recipes/hatchet/meta.yaml b/recipes/hatchet/meta.yaml index 42ac3f6a77603..595507d10c9e0 100755 --- a/recipes/hatchet/meta.yaml +++ b/recipes/hatchet/meta.yaml @@ -1,13 +1,13 @@ {% set name = "hatchet" %} -{% set version = "1.1.1" %} +{% set version = "2.0.1" %} package: name: '{{ name|lower }}' version: '{{ version }}' source: - - url: https://github.com/raphael-group/{{ name }}/archive/v{{ version }}.zip - sha256: db30183ffb2bbdfff4753e8ef1c58f7d93b59c65b5737f92b3ac1c5f2f3936a4 + - url: https://github.com/raphael-group/{{ name }}/archive/v{{ version }}.tar.gz + sha256: e8ca462fc4404bacc97b2195e734cd6086eebd40e7941d450c069967d294d988 - url: https://packages.gurobi.com/9.0/gurobi9.0.2_linux64.tar.gz # [not osx] sha256: 6527581aef11c3e425c52993d108861ef53ec13971d9931861bf9c88d9d111f3 # [not osx] @@ -17,44 +17,51 @@ source: sha256: 1d58586f9a33ac7035f51f6a04707248218f70bddbec78cb83f11c986ac652cd # [osx] build: - number: 1 + number: 0 skip: True # [py < 37] + entry_points: + - hatchet = hatchet.__main__:main + run_exports: + - {{ pin_subpackage('hatchet', max_pin="x") }} requirements: - build: + build: - {{ compiler('cxx') }} - - cmake>=3.9 + - cmake >=3.9 - make host: - python - - setuptools + - pip run: - python - - bcftools>=1.9 + - bcftools >=1.9 - biopython - hmmlearn - matplotlib-base - mosdepth - pandas - - picard + - picard-slim - psutil - pyomo - pysam - requests - - samtools>=1.9 - - seaborn + - samtools >=1.9 + - seaborn - scikit-learn - - scipy + - scipy - tabix test: imports: - - hatchet + - hatchet about: home: https://github.com/raphael-group/hatchet - license: BSD-3 - summary: "Holistic Allele-specific Tumor Copy-number Heterogeneity" + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE + summary: "A package to infer allele and clone-specific copy-number aberrations (CNAs)." + doc_url: https://raphael-group.github.io/hatchet/ description: | HATCHet is an algorithm to infer allele and clone-specific copy-number aberrations (CNAs), clone proportions, and whole-genome duplications From 8ef828b06c73d560ae2faf4d2e8617507d942dc8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 21:45:03 -0500 Subject: [PATCH 1302/2173] Update mitos to 2.1.4 (#44917) * Update mitos to 2.1.4 * run_exports * mitos: update biopython --------- Co-authored-by: Matthias Bernt --- recipes/mitos/meta.yaml | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/recipes/mitos/meta.yaml b/recipes/mitos/meta.yaml index 03969c94c83a3..b5365554ec4ca 100644 --- a/recipes/mitos/meta.yaml +++ b/recipes/mitos/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "2.1.3" %} +{% set version = "2.1.4" %} package: name: "{{ name|lower }}" @@ -7,19 +7,21 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 0a5bee0882a957457426baaa36655d968fbd36523e3fb06d96e2401f9f9bd285 + sha256: 5e9095a0bd73c7835204918f3b65741346c9b411e528efd4edf8d6ae0a3bee66 build: number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " noarch: python + run_exports: + - {{ pin_subpackage('mitos', max_pin="x.x") }} requirements: host: - pip - python >=3 run: - - biopython <1.68 + - biopython <1.78 - python >=3 - blast =2.9 - hmmer =3.2 @@ -29,12 +31,7 @@ requirements: - r-ggplot2 - r-reshape2 - openjdk >8 - # biopython -> reportlab -> pillow - # - does not work with newest libtiff - # - force to not install it from defaults - # xref https://github.com/conda-forge/pillow-feedstock/issues/135 - - conda-forge::pillow - - conda-forge::libtiff <4.5 + - reportlab test: imports: From d3ca1025f61655d9942ffd00f591f815ad86fef2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 21:45:18 -0500 Subject: [PATCH 1303/2173] Update pybiolib to 1.1.1651 (#44930) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 2c69aa37fc597..22ba2c69eb687 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1648" %} +{% set version = "1.1.1651" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 49d0e8ad018cf046c50fc6162f1b08a7ba96ab7348e045ca318ae4c1116e7059 + sha256: e9e68bd90f67e5a9e4e4a9b174102559dfd8316a1b749bdef4275dbb7a048bb5 build: noarch: python From 09208e91085c73094ba619bfbfe367ad876b7c55 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 20 Dec 2023 22:04:11 -0500 Subject: [PATCH 1304/2173] Update keggcharter to 1.0.0 (#44921) * Update keggcharter to 1.0.0 * add requests and lxml --------- Co-authored-by: joshuazhuang7 --- recipes/keggcharter/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/keggcharter/meta.yaml b/recipes/keggcharter/meta.yaml index c93435f02d255..fabef34dadb32 100644 --- a/recipes/keggcharter/meta.yaml +++ b/recipes/keggcharter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "keggcharter" %} -{% set version = "0.7.1" %} -{% set sha256 = "bbbe3cb4d371a631cfdca68787af4f4f2b183556de0d71f6350f256e3b11437e" %} +{% set version = "1.0.0" %} +{% set sha256 = "aa36605886bb6419f616dbec7c95e9328e7eb0eea0585ccc8c9b0e5607943699" %} package: name: {{ name|lower }} @@ -32,6 +32,8 @@ requirements: - openpyxl - poppler - mscorefonts + - requests + - lxml test: commands: From 8938580df7cd734e3bd5ad546c928999c4333f6b Mon Sep 17 00:00:00 2001 From: Samuel Aroney <41124903+AroneyS@users.noreply.github.com> Date: Thu, 21 Dec 2023 14:21:16 +1000 Subject: [PATCH 1305/2173] Add binchicken (#44931) * add binchicken * add metagenome to summary --- recipes/binchicken/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 recipes/binchicken/meta.yaml diff --git a/recipes/binchicken/meta.yaml b/recipes/binchicken/meta.yaml new file mode 100644 index 0000000000000..caebd6ed54297 --- /dev/null +++ b/recipes/binchicken/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "0.10.0" %} +{% set name = "binchicken" %} +{% set sha256 = "32d47924d8f137c0b5a142c8e8abc4a1632da9537a6e1f30d69bfe2377c3b6ab" %} + +package: + name: binchicken + version: {{ version }} + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('binchicken', max_pin="x") }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: {{ sha256 }} + +requirements: + host: + - python >=3.8 + - pip + run: + - python =3.10.* + - snakemake =7.32.* + - mamba =1.4.* + - networkx =3.1 + - bird_tool_utils_python =0.4.* + - extern =0.4.* + - ruamel.yaml =0.17.* + - polars =0.20.* + - pigz =2.3.* + - pyarrow =12.0.* + - parallel =20230522 + - pyopenssl >22.1.0 + +test: + commands: + - {{ name }} --version | grep '{{ version }}' + +about: + home: https://github.com/aroneys/binchicken + license: GNU General Public v3 (GPLv3) + license_family: GPL3 + license_file: LICENSE + summary: Targeted recovery of low abundance metagenome assembled genomes through intelligent coassembly From 6e4475e8eab352684cf614d3b9df14cd7d183c8c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Dec 2023 04:53:32 -0500 Subject: [PATCH 1306/2173] Update snakemake to 8.0.0 (#44925) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake to 8.0.0 * Update dependencies I went through the differences in setup.cfg between 7.32.4 and 8.0.0: https://github.com/snakemake/snakemake/compare/v7.32.4...v8.0.0#diff-fa602a8a75dc9dcc92261bac5f533c2a85e34fcceaff63b3a3a81d9acde2fc52 This should capture most changes --------- Co-authored-by: Cornelius Roemer Co-authored-by: Johannes Köster --- recipes/snakemake/meta.yaml | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 5b8327aee4bdc..37ccc5b85c637 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "7.32.4" %} +{% set version = "8.0.0" %} package: name: snakemake @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: fdc3f15dd7b06fabb7da30d460e0a3b1fba08e4ea91f9c32c47a83705cdc7b6e + sha256: 5e331a9401f7f571db3fe3c1e0b56360f3fc003d210d8475a9c6466edb41eb6c build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_subpackage("snakemake", max_pin="x") }} @@ -30,14 +30,8 @@ requirements: - python-irodsclient # aws s3 - boto3 - # check snakemake/setup.cfg's section [options.extras_require] - # options.extras_require: google-cloud - - google-cloud-storage - - google-api-python-client - - google-crc32c - - oauth2client # options.extras_require: messaging - - slacker + - slack_sdk # options.extras_require: pep - eido - peppy @@ -86,26 +80,28 @@ outputs: noarch: python script: python -m pip install --no-deps --ignore-installed . entry_points: - - snakemake = snakemake:main - - snakemake-bash-completion = snakemake:bash_completion + - snakemake = snakemake.cli:main + - snakemake-bash-completion = snakemake.cli:bash_completion run_exports: - {{ pin_subpackage("snakemake-minimal", max_pin="x") }} requirements: host: - - python >=3.7 + - python >=3.11 - pip - setuptools run: # Keep in sync with snakemake/setup.cfg - - python >=3.7,<3.12 + - python >=3.11,<3.13 - appdirs + - conda-inject >=1.3.1,<2.0 - configargparse - connection_pool >=0.0.3 - datrie - docutils - gitpython - humanfriendly + - immutables - jinja2 >=3.0,<4.0 - jsonschema - nbformat @@ -116,6 +112,9 @@ outputs: - requests >=2.8.1 - reretry - smart_open >=3.0 + - snakemake-interface-executor-plugins >=8.1.3,<9.0 + - snakemake-interface-common >=1.15.0,<2.0 + - snakemake-interface-storage-plugins >=3.0.0,<4.0 - stopit - tabulate - throttler From d99fb4bc9391ee93e65c38b67a9fafea7db05af4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Dec 2023 04:54:51 -0500 Subject: [PATCH 1307/2173] Update recentrifuge to 1.13.0 (#44933) --- recipes/recentrifuge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/recentrifuge/meta.yaml b/recipes/recentrifuge/meta.yaml index b22789af9d4a7..76f4032164e44 100644 --- a/recipes/recentrifuge/meta.yaml +++ b/recipes/recentrifuge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "recentrifuge" %} -{% set version = "1.12.2" %} +{% set version = "1.13.0" %} package: name: {{ name }} @@ -14,7 +14,7 @@ build: source: url: https://github.com/khyox/{{ name }}/archive/v{{ version }}.tar.gz - sha256: b2dc96faf702d32d98bc178e283bf64934a6628a783644c8338dd50cf9227c3a + sha256: 6b7c4d80ad53115bca363d72352ee4d9074aa3385ed2556840ce4e3f24855e17 requirements: host: From b2d26eab72a7530c2dd5918045bf287c0ef4320a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 21 Dec 2023 13:35:50 +0100 Subject: [PATCH 1308/2173] fix: cleanup dependencies in snakemake 8 recipe and upgrade to 8.0.1 (#44934) * fix: cleanup dependencies in snakemake 8 recipe * Update meta.yaml --- recipes/snakemake/meta.yaml | 17 +++-------------- 1 file changed, 3 insertions(+), 14 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 37ccc5b85c637..66d8213406374 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.0.0" %} +{% set version = "8.0.1" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 5e331a9401f7f571db3fe3c1e0b56360f3fc003d210d8475a9c6466edb41eb6c + sha256: 72f1158a345e8c53f73a14b3480bdfd6c1605f7c1c4a8a46f96fac489133ab80 build: number: 0 @@ -17,19 +17,8 @@ build: requirements: run: - snakemake-minimal ={{ version }} - # optional dependencies needed for the full experience - # require this dropbox version to ensure that a conda doesn't pick up the - # outdated version available - - dropbox >=7.2.1 - - ftputil >=3.2 - - filechunkio >=1.6 - - pysftp >=0.2.8 - - aioeasywebdav # pandas is optional, but required for many workflows - pandas - - python-irodsclient - # aws s3 - - boto3 # options.extras_require: messaging - slack_sdk # options.extras_require: pep @@ -81,7 +70,6 @@ outputs: script: python -m pip install --no-deps --ignore-installed . entry_points: - snakemake = snakemake.cli:main - - snakemake-bash-completion = snakemake.cli:bash_completion run_exports: - {{ pin_subpackage("snakemake-minimal", max_pin="x") }} @@ -93,6 +81,7 @@ outputs: run: # Keep in sync with snakemake/setup.cfg - python >=3.11,<3.13 + - immutables - appdirs - conda-inject >=1.3.1,<2.0 - configargparse From 70b1f991ab2f6b5bd59461cad2ca9778998498fc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Dec 2023 10:04:32 -0500 Subject: [PATCH 1309/2173] Update last to 1521 (#44939) --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 22cfbe700d846..2c8181378c734 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1519" %} +{% set version = "1521" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: 2c1ab2d5671fbe96f47e94c6f5d77805cdb36c1afda3906e07e18fb6bb77d013 + sha256: dcfe5339f048f635f02326d181e086469c16e54a0f674c5df814c4d54236fc26 build: number: 0 From c2b6aee8d7c7976edcb8c3a018f3c856bd3e27dc Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 21 Dec 2023 16:07:38 +0100 Subject: [PATCH 1310/2173] Update fiji-max_inscribed_circles to version 2.1.0 (#44926) * Use version 2.1.0 * add run_exports * write package name --- recipes/fiji-max_inscribed_circles/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/fiji-max_inscribed_circles/meta.yaml b/recipes/fiji-max_inscribed_circles/meta.yaml index 1548b969795c3..7e55a6d863130 100644 --- a/recipes/fiji-max_inscribed_circles/meta.yaml +++ b/recipes/fiji-max_inscribed_circles/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fiji-max_inscribed_circles" %} -{% set version = "2.0.0" %} +{% set version = "2.1.0" %} package: name: {{ name | lower }} @@ -7,11 +7,13 @@ package: source: url: https://maven.scijava.org/service/local/repositories/releases/content/ch/epfl/biop/MaxInscribedCircles/{{ version }}/MaxInscribedCircles-{{ version }}.jar - sha256: de0fe5e71d493a45aff07d9c636172d83b2ace0600ffaa24ba8f8072825fdfa7 + sha256: 59346b24ed4d17570701cdb190d55e4862030720287379e194fd4db90fac3692 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage ("fiji-max_inscribed_circles", max_pin="x") }} requirements: run: @@ -34,4 +36,4 @@ about: from the largest to the smallest. The code is written for Java 8, which is the currently supported Java version for Fiji and ImageJ. - dev_url: https://github.com/BIOP/ijp-max-inscribed-circles \ No newline at end of file + dev_url: https://github.com/BIOP/ijp-max-inscribed-circles From 543e8d13e3b8d5addfaceb3bb519108a6aa6ba61 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Dec 2023 10:47:01 -0500 Subject: [PATCH 1311/2173] Update hmftools-gripss to 2.3.5 (#44880) * Update hmftools-gripss to 2.3.5 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/hmftools-gripss/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-gripss/meta.yaml b/recipes/hmftools-gripss/meta.yaml index 83ceab912c633..a0aab8147d630 100644 --- a/recipes/hmftools-gripss/meta.yaml +++ b/recipes/hmftools-gripss/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.3.2" %} -{% set sha256 = "8d5e17ebe9f065d59782b45e0b8f9da2847fe9ed624da79237318362ef651aa1" %} +{% set version = "2.3.5" %} +{% set sha256 = "7df02379f416c6131de5f81ad062ab253277b68d7eb71eae0dc9e9bfe34f3bc6" %} package: name: hmftools-gripss @@ -12,6 +12,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-gripss', max_pin='x') }} requirements: run: From 9836844acef8a688223618de03a4a37c6571aa86 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Dec 2023 11:56:19 -0500 Subject: [PATCH 1312/2173] Update clair3-illumina to 1.0.5 (#44932) * Update clair3-illumina to 1.0.5 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/clair3-illumina/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/clair3-illumina/meta.yaml b/recipes/clair3-illumina/meta.yaml index 711765d55c0c3..0f7f70a0be418 100644 --- a/recipes/clair3-illumina/meta.yaml +++ b/recipes/clair3-illumina/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clair3-illumina" %} -{% set version = "1.0.4" %} +{% set version = "1.0.5" %} package: name: {{ name }} @@ -7,12 +7,13 @@ package: source: url: https://github.com/HKU-BAL/Clair3/archive/refs/tags/v{{ version }}.zip - sha256: 886e4b8f12df65b69c2eba2f02a95a57582cc2a78d4b84941b9afe98a3616ac3 + sha256: 515129dace446d48a58e7f156d40ce09eb8ef15484661e0b7ff53fe83e5ac40a build: number: 0 skip: True # [osx] - + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: - {{ compiler('cxx') }} From 1a6598cd50b7654f879323ebdcbd33fa3b884ea6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Dec 2023 11:56:34 -0500 Subject: [PATCH 1313/2173] Update ont-fast5-api to 4.1.2 (#44935) * Update ont-fast5-api to 4.1.2 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/ont-fast5-api/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ont-fast5-api/meta.yaml b/recipes/ont-fast5-api/meta.yaml index da79cfdf31793..f860d6263889c 100644 --- a/recipes/ont-fast5-api/meta.yaml +++ b/recipes/ont-fast5-api/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ont-fast5-api" %} -{% set version = "4.1.1" %} +{% set version = "4.1.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 71ea44087f310a2792d1a6c2ffbf5bc194367e769ce96a15961787f90ec7707b + sha256: c7c59c6100e992ef8bc239cdf91f7a8ab46abf57ecd689f94b2b98e72a9e9472 build: number: 0 @@ -19,6 +19,8 @@ build: - compress_fast5=ont_fast5_api.conversion_tools.compress_fast5:main - check_compression=ont_fast5_api.conversion_tools.check_file_compression:main script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: From 724f4fd5e9aee8d1ab128431931f805240f26290 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Dec 2023 19:06:12 -0500 Subject: [PATCH 1314/2173] Update gtfparse to 2.1.0 (#44943) --- recipes/gtfparse/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gtfparse/meta.yaml b/recipes/gtfparse/meta.yaml index a5ac6588aa3d5..2a89b763b912d 100644 --- a/recipes/gtfparse/meta.yaml +++ b/recipes/gtfparse/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gtfparse" %} -{% set version = "2.0.1" %} -{% set sha256 = "c45439af58cb48120910bebe4625371d8fb5735f12a749e8933c9d6f2b1a558c" %} +{% set version = "2.1.0" %} +{% set sha256 = "d1e94897f159a6cc89984fe4eb8b614fbd57b57ce6432ca00c15672eec7e7956" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: python script: {{ PYTHON }} -m pip install . --no-deps -vvv run_exports: From c6aaeb46ed849d6c4b23b20f040902719324c826 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Dec 2023 19:06:21 -0500 Subject: [PATCH 1315/2173] Update ribodetector to 0.3.0 (#44944) --- recipes/ribodetector/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ribodetector/meta.yaml b/recipes/ribodetector/meta.yaml index fb159ba48fc96..e0e1f6562be2f 100644 --- a/recipes/ribodetector/meta.yaml +++ b/recipes/ribodetector/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.2.9" %} +{% set version = "0.3.0" %} package: name: ribodetector version: {{ version }} source: - url: https://files.pythonhosted.org/packages/4c/45/7eb2a0f87b44e6f98f451a422584d05d293b1058397b6f016a53372c80cd/ribodetector-0.2.9.tar.gz - sha256: cf98b4e3c306e48e79454bad4d062af8f13607a0a3e09a5c849162cd7ae8783d + url: https://files.pythonhosted.org/packages/e3/92/be698538c8ca7f1929295f87f080352d56c20749e92ef3f9f97bed953058/ribodetector-0.3.0.tar.gz + sha256: 42922dfde736c8fb1b83a0fd2c3b77864a5e9a4b8b3a0b31f0bf3764556bf1f9 build: number: 0 From 2bd58407fe26b60b58e50c4f4e8a026d85644192 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Dec 2023 19:46:09 -0500 Subject: [PATCH 1316/2173] Update gseapy to 1.1.1 (#44945) --- recipes/gseapy/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index b7e7775daa4ff..2f28298f064f6 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -1,10 +1,10 @@ package: name: gseapy - version: "1.1.0" + version: "1.1.1" source: - url: https://files.pythonhosted.org/packages/6b/99/93b64bf596d9dee42cb338ffa557c0c2f327675c1f0e1148ff1115f76e35/gseapy-1.1.0.tar.gz - sha256: eba85ad99f55727bde7d1ac0172b29d5e07c8c879cdcbcc94c11df40a804ed8c + url: https://files.pythonhosted.org/packages/c9/1b/b8bba54953a7ba433b73d701343557103bd96dfd76652698544b75fe5439/gseapy-1.1.1.tar.gz + sha256: 5062fc8d625037beb3d41762cb0cd7cad25653bb3a0c71b8f188ba458da77d4a build: entry_points: From 8b97dabfba9ac570d3ceafc7796d801b4529b546 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Dec 2023 19:46:23 -0500 Subject: [PATCH 1317/2173] Update seqerakit to 0.4.5 (#44946) --- recipes/seqerakit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seqerakit/meta.yaml b/recipes/seqerakit/meta.yaml index 097bb053c1fe8..4ee5c9b1f6cd7 100644 --- a/recipes/seqerakit/meta.yaml +++ b/recipes/seqerakit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqerakit" %} -{% set version = "0.4.4" %} +{% set version = "0.4.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqerakit-{{ version }}.tar.gz - sha256: 04e4f7b930efd3b3581c56e7774696db00625124893ebb9969aaa7fd3cd7959f + sha256: 792bd4fa53de4b3959929413d1ad8f39e20587971c9c5451419da1ff68cf3f49 build: entry_points: From c6db2d90297f1b469ab88529cfce7cd82761ad8c Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Fri, 22 Dec 2023 02:07:28 +0100 Subject: [PATCH 1318/2173] Update hictkpy to v0.0.3 (#44853) * Update recipe * Bump min python version * Update URL * Update checksum * Debugging * Debugging * Debugging * Bugfix --- recipes/hictkpy/build.sh | 4 ++-- recipes/hictkpy/conanfile.txt.patch | 28 ++++++++++++++++------------ recipes/hictkpy/meta.yaml | 14 ++++++++------ 3 files changed, 26 insertions(+), 20 deletions(-) diff --git a/recipes/hictkpy/build.sh b/recipes/hictkpy/build.sh index 98554b96d5ffd..8b2e7f66b8bd2 100755 --- a/recipes/hictkpy/build.sh +++ b/recipes/hictkpy/build.sh @@ -30,7 +30,6 @@ conan install conanfile.txt \ --build="*" \ --output-folder=build/ - CMAKE_ARGS="-DCMAKE_PREFIX_PATH=$PWD/build" CMAKE_ARGS+=" ${CMAKE_PLATFORM_FLAGS[*]}" CMAKE_ARGS+=" -DPython_EXECUTABLE=$PYTHON" @@ -39,5 +38,6 @@ echo "$CMAKE_ARGS" export CMAKE_ARGS HICTKPY_SETUP_SKIP_CONAN=1 \ -"$PYTHON" -m pip install . -v +SETUPTOOLS_SCM_PRETEND_VERSION="$PKG_VERSION" \ +"$PYTHON" -m pip install "$SRC_DIR" -vv diff --git a/recipes/hictkpy/conanfile.txt.patch b/recipes/hictkpy/conanfile.txt.patch index 0a0004bc51819..34865b8af6ab4 100644 --- a/recipes/hictkpy/conanfile.txt.patch +++ b/recipes/hictkpy/conanfile.txt.patch @@ -1,24 +1,27 @@ diff --git a/conanfile.txt b/conanfile.txt -index bf2df0b..1a50e65 100644 +index 3bea10b..444d3d1 100644 --- a/conanfile.txt +++ b/conanfile.txt -@@ -3,26 +3,9 @@ - # SPDX-License-Identifier: MIT +@@ -4,30 +4,9 @@ [requires] --fast_float/5.2.0#9bf1a3fac625789f2b571d43efb8013b --fmt/10.1.0#1fae165cded07416f64960a5b6140317 --hdf5/1.14.0#011206975dc4c5ca80dd612d3a34cab3 --highfive/2.7.1#a73bc6937c9add30c9d47a7a70a466eb --libdeflate/1.18#3697b637656a9af04cabcbed50db9a7e - parallel-hashmap/1.3.11#719aed501c271a34e2347a7731ab3bfb --pybind11/2.10.4#dd44c80a5ed6a2ef11194380daae1248 --spdlog/1.12.0#248c215bc5f0718402fbf1de126ef847 + bshoshany-thread-pool/3.5.0#5aaea7ccf37107d3c1ba9ca9ab246e42 +-fast_float/5.3.0#efd9bda97d5f77fa5a98981e014092a0 +-fmt/10.1.1#cd63809a79574a2f9eb73ca35f16a243 +-hdf5/1.14.2#1e12ccecd5ebc9b5191433862e196743 +-highfive/2.8.0#19e1a6e78d9329851aa9da409f07d29a +-libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602 + parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7 +-pybind11/2.11.1#e24cefefdb5561ba8d8bc34ab5ba1607 + span-lite/0.10.3#1967d71abb32b314387c2ab9c558dd22 +-spdlog/1.12.0#0e390a2f5c3e96671d0857bc734e4731 +-xxhash/0.8.2#03fd1c9a839b3f9cdf5ea9742c312187 +-zstd/1.5.5#b87dc3b185caa4b122979ac4ae8ef7e8 [generators] CMakeDeps - [options] +-[options] -fmt*:header_only=True -hdf5*:enable_cxx=False -hdf5*:hl=False @@ -29,3 +32,4 @@ index bf2df0b..1a50e65 100644 -highfive*:with_opencv=False -highfive*:with_xtensor=False -spdlog*:header_only=True +-xxhash*:utility=False diff --git a/recipes/hictkpy/meta.yaml b/recipes/hictkpy/meta.yaml index f4500292f59e4..390777733a8ef 100644 --- a/recipes/hictkpy/meta.yaml +++ b/recipes/hictkpy/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictkpy" %} -{% set version = "0.0.2" %} -{% set sha256 = "9e9bf3399d5747c68ced564c5c098aa79567097d4c5c7a7152d62a84ad46ec38" %} +{% set version = "0.0.3" %} +{% set sha256 = "5f08caebedd88a389329549722b9f34b3fcb526c5be30c6eb793b855a26806cc" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: build: number: 0 - skip: True # [py < 36] + skip: True # [py < 37] run_exports: - {{ pin_subpackage('hictkpy', max_pin='x.x') }} @@ -33,9 +33,10 @@ requirements: - python - hdf5 >=1.12 - libdeflate - - numpy - - pandas - - scipy + - xxhash >=0.8 + - setuptools + - setuptools_scm + - zstd >=1.5 run: - python @@ -44,6 +45,7 @@ requirements: - numpy - pandas - scipy + - zstd >=1.5 about: home: https://github.com/paulsengroup/{{ name }} From 86b094daa9318683d6d156e182094e776a5e9fde Mon Sep 17 00:00:00 2001 From: Maurizio Camagna Date: Fri, 22 Dec 2023 10:13:52 +0900 Subject: [PATCH 1319/2173] Add hisat2-pipeline (#44854) * Add hisat2-pipeline v1.0.6 * Updated SHA256 * Added tests * Added run_exports * Removed duplicate key in meta.yaml * Fixed incorrect sha hash * Added pandas to run requirements * Changed license to corresponding SPDX identifier * Moved host requirements to run requirements and included further tests --------- Co-authored-by: mcamagna <> --- recipes/hisat2-pipeline/meta.yaml | 56 +++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 recipes/hisat2-pipeline/meta.yaml diff --git a/recipes/hisat2-pipeline/meta.yaml b/recipes/hisat2-pipeline/meta.yaml new file mode 100644 index 0000000000000..6941c76f0c96a --- /dev/null +++ b/recipes/hisat2-pipeline/meta.yaml @@ -0,0 +1,56 @@ +{% set name = "hisat2-pipeline" %} +{% set version = "1.0.6" %} +{% set sha256 = "cc218d21ba1443a6581a2934afef2434d26aaac4bdc974b9747341fd1bac9fd7" %} +{% set DOI = "https://doi.org/10.5281/zenodo.10389729" %} + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_subpackage('hisat2-pipeline', max_pin="x.x") }} + + +source: + url: https://github.com/mcamagna/HISAT2-pipeline/archive/refs/tags/v{{ version }}-bioconda.tar.gz + sha256: {{ sha256 }} + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - hisat2 + - stringtie + - samtools >=1.9 + - pandas + - openpyxl + +test: + commands: + - hisat2-pipeline --version + - stringtie --version + - hisat2 --version + - samtools --version + imports: + - pandas + requires: + - stringtie + - hisat2 + - samtools + +about: + home: https://github.com/mcamagna/HISAT2-pipeline + license: GPL-3.0-or-later + license_family: GPL + license_file: LICENSE + summary: 'A pipeline to automatically run an RNA-seq analysis using HISAT2/Stringtie using default settings' + +extra: + identifiers: + - {{ DOI }} From 4abcae5ba77975a706dafdd4dc2ac2910b60a790 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 21 Dec 2023 20:23:12 -0500 Subject: [PATCH 1320/2173] Update sevenbridges-python to 2.10.0 (#44936) * Update sevenbridges-python to 2.10.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/sevenbridges-python/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index ad3d7aadb8e07..7c534eeee72b4 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.9.2" %} -{% set sha256 = "716c7d883a3aee9b45d5c668a37fc886a3871c316e0ad82559aad15e836fcb41" %} +{% set version = "2.10.0" %} +{% set sha256 = "6e370de45b5af6574a2937e8a8aba76108f779f55982b360eb796a113e9399e6" %} package: name: sevenbridges-python @@ -12,7 +12,9 @@ source: build: noarch: python number: 0 - script: touch requirements.txt && {{PYTHON}} -m pip install --no-deps --ignore-installed --no-cache-dir . + script: touch requirements.txt && {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv + run_exports: + - {{ pin_subpackage('sevenbridges-python', max_pin="x") }} requirements: host: @@ -45,7 +47,7 @@ test: about: home: https://github.com/sbg/sevenbridges-python license: Apache-2.0 - license_family: Apache + license_family: APACHE license_file: LICENSE summary: SBG API python client bindings description: sevenbridges-python is a Python library that provides an interface for the Seven Bridges Platform the Cancer From 06533e65a0f3c30be0a6a036587c11859c9212f9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Dec 2023 05:06:22 -0500 Subject: [PATCH 1321/2173] Update delly to 1.2.6 (#44948) --- recipes/delly/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/delly/meta.yaml b/recipes/delly/meta.yaml index 89b9485cd2e33..ee0d6f0ea4c2d 100644 --- a/recipes/delly/meta.yaml +++ b/recipes/delly/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.8" %} -{% set sha256 = "f72a1143dc71449fc277fc8b3e337a4d35b2fe736f3693a14b1986efa8da4889" %} +{% set version = "1.2.6" %} +{% set sha256 = "1a71fcc5f2a55649c2104086f3f7163ed58c5868eaf040a25e45c777b0e1abb7" %} package: name: delly From d5edaed1773cb8dc7f18d405ce6df8040f5eec22 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Dec 2023 05:54:21 -0500 Subject: [PATCH 1322/2173] Update annonars to 0.31.2 (#44950) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 2dcdf26cf3636..6a78e3c350db0 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.31.1" %} +{% set version = "0.31.2" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 4a437f71d88538bc95fdd6fac33c840530373daaa0097788ed8314bae305bff3 + sha256: c7d953633d77c3c46cf3d9417e9b8e6d67afac2a529dea0e342da3d8bb0d6680 requirements: build: From b5d7b2f3cc6e2c89bc5715a81a7318c07e12a74a Mon Sep 17 00:00:00 2001 From: M Bernt Date: Fri, 22 Dec 2023 23:06:20 +0100 Subject: [PATCH 1323/2173] bump mitos1 (#44918) * bump mitos1 * bump to 1.1.3 * fix indentation * fix sha --- recipes/mitos/mitos1/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/mitos/mitos1/meta.yaml b/recipes/mitos/mitos1/meta.yaml index 8fb993e5a0e14..9ce262fca6fec 100644 --- a/recipes/mitos/mitos1/meta.yaml +++ b/recipes/mitos/mitos1/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "1.1.1" %} +{% set version = "1.1.3" %} package: name: "{{ name|lower }}" @@ -7,32 +7,35 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: be603dd526d7123e3652e47aecda010e7d3ab7d6af93a9c138f965ca4cf44005 + sha256: 0e750ada0f69626407e81bd953c83717a917c6b96f49d0f154bbe740a4b5fe12 build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " noarch: python + run_exports: + - {{ pin_subpackage('mitos', max_pin="x.x") }} requirements: host: - pip - python >=3 run: - - biopython <1.68 + - biopython <1.82 - python >=3 - blast-legacy =2.2 - infernal =1.0 - viennarna <2 - r-base >=4 - r-ggplot2 + - r-reshape2 - openjdk >8 - # biopython -> reportlab -> pillow + - reportlab # - does not work with newest libtiff # - force to not install it from defaults # xref https://github.com/conda-forge/pillow-feedstock/issues/135 - conda-forge::pillow - - conda-forge::libtiff <4.5 + - conda-forge::libtiff test: imports: From 1271056089172d374f3760015fba8c6a440053d1 Mon Sep 17 00:00:00 2001 From: April Shen Date: Fri, 22 Dec 2023 22:06:48 +0000 Subject: [PATCH 1324/2173] Add CMAT (#44938) * add CMAT recipe * lint and add run_exports * add requirements to host * attempt to avoid permission denied error --- recipes/cmat/build.sh | 11 ++++++++ recipes/cmat/meta.yaml | 64 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 recipes/cmat/build.sh create mode 100644 recipes/cmat/meta.yaml diff --git a/recipes/cmat/build.sh b/recipes/cmat/build.sh new file mode 100644 index 0000000000000..035f39b8879b4 --- /dev/null +++ b/recipes/cmat/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +$PYTHON -m pip install . + +CMAT="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}" +mkdir -p ${PREFIX}/bin ${CMAT} + +chmod 775 bin/cmat/* +cp bin/cmat/* ${PREFIX}/bin + +mv bin/ mappings/ pipelines/ ${CMAT} \ No newline at end of file diff --git a/recipes/cmat/meta.yaml b/recipes/cmat/meta.yaml new file mode 100644 index 0000000000000..69e11aa455e27 --- /dev/null +++ b/recipes/cmat/meta.yaml @@ -0,0 +1,64 @@ +{% set name = "cmat" %} +{% set version = "3.1.0" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/EBIvariation/CMAT/archive/v{{version}}.tar.gz + sha256: 1e46a83d3d7e46a41f9f62ff4af0c151851fbbebc1c6b129255f987d75b64079 + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + host: + - nextflow >=21.10 + - python >=3.8,<3.10 # restriction from biopython + - biopython ==1.77 + - coverage ==6.5.0 + - coveralls ==3.3.1 + - jsonschema ==3.2.0 + - numpy ==1.24.3 + - pandas ==1.5.3 + - pytest ==7.2.2 + - pytest-cov ==2.10.0 + - requests ==2.31.0 + - requests-mock ==1.8.0 + - retry ==0.9.2 + run: + - nextflow >=21.10.0 + - python >=3.8,<3.10 + - biopython ==1.77 + - coverage ==6.5.0 + - coveralls ==3.3.1 + - jsonschema ==3.2.0 + - numpy ==1.24.3 + - pandas ==1.5.3 + - pytest ==7.2.2 + - pytest-cov ==2.10.0 + - requests ==2.31.0 + - requests-mock ==1.8.0 + - retry ==0.9.2 + +test: + imports: + - cmat + commands: + - cmat + # rm to avoid this: https://github.com/bioconda/bioconda-utils/issues/172 + - cmat annotate --help && rm -rf .nextflow + +about: + home: https://github.com/EBIvariation/CMAT + summary: ClinVar Mapping and Annotation Toolkit + license: Apache-2.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - apriltuesday \ No newline at end of file From 3211a68f8a6500bdadbaf67d3c32b25cc27e2744 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Dec 2023 17:07:09 -0500 Subject: [PATCH 1325/2173] Update mitos to 2.1.5 (#44949) * Update mitos to 2.1.5 * bump biopython requirement and add reportlab which does not come with biopython automatically anymore * require only R3 --------- Co-authored-by: Matthias Bernt --- recipes/mitos/meta.yaml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/recipes/mitos/meta.yaml b/recipes/mitos/meta.yaml index b5365554ec4ca..ee2cddc84aeb1 100644 --- a/recipes/mitos/meta.yaml +++ b/recipes/mitos/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "2.1.4" %} +{% set version = "2.1.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 5e9095a0bd73c7835204918f3b65741346c9b411e528efd4edf8d6ae0a3bee66 + sha256: c82a48eeaf63f7733c3439047154c1869842ba0106e95bb4ab556131d161b428 build: number: 0 @@ -21,7 +21,7 @@ requirements: - pip - python >=3 run: - - biopython <1.78 + - biopython <1.82 - python >=3 - blast =2.9 - hmmer =3.2 @@ -32,6 +32,11 @@ requirements: - r-reshape2 - openjdk >8 - reportlab + # - does not work with newest libtiff + # - force to not install it from defaults + # xref https://github.com/conda-forge/pillow-feedstock/issues/135 + - conda-forge::pillow + - conda-forge::libtiff test: imports: From 454611a7537512857466784d33723553b8fa14ad Mon Sep 17 00:00:00 2001 From: Kez Cleal <42997789+kcleal@users.noreply.github.com> Date: Fri, 22 Dec 2023 22:12:55 +0000 Subject: [PATCH 1326/2173] gw version 0.9.1 (#44953) * gw v0.9.1 * Use GL=1 for v0.9.1 * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh --- recipes/gw/build.sh | 4 ++++ recipes/gw/meta.yaml | 6 +++--- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/gw/build.sh b/recipes/gw/build.sh index ad9024fc8c20e..d04ce0b29c4d9 100644 --- a/recipes/gw/build.sh +++ b/recipes/gw/build.sh @@ -1,5 +1,9 @@ #!/usr/bin/bash set -e +export USE_GL=1 +if [[ "$OSTYPE" != "darwin"* ]]; then + sed -i 's/-lEGL -lGLESv2/-lGL/' Makefile +fi make prep CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" make mkdir -p $PREFIX/bin diff --git a/recipes/gw/meta.yaml b/recipes/gw/meta.yaml index aa5a857b7a8f0..7bf6ab483b790 100644 --- a/recipes/gw/meta.yaml +++ b/recipes/gw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.8.2" %} -{% set sha256 = "519f06fac2635a59614517ff00dc1e86e4f78c2926df504b03ba62a66a5de3e8" %} +{% set version = "0.9.1" %} +{% set sha256 = "10a65107717811179a124e8bac5b2f202bdbde6679a9e6eb67ef97c990b7cf9d" %} package: name: gw @@ -13,7 +13,7 @@ source: build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('gw', max_pin="x") }} From f9c2a2344add45326f20ee75093b970466aa2abf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Dec 2023 17:15:05 -0500 Subject: [PATCH 1327/2173] Update annotsv to 3.3.8 (#44957) --- recipes/annotsv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annotsv/meta.yaml b/recipes/annotsv/meta.yaml index bf1cfc713ab97..e7d2ab3035882 100644 --- a/recipes/annotsv/meta.yaml +++ b/recipes/annotsv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "annotsv" %} -{% set version = "3.3.7" %} -{% set sha256 = "abf2a0a1604275d8ded66aba7a7084659430d43242eb28fa2a59467487efe7bf" %} +{% set version = "3.3.8" %} +{% set sha256 = "e06f016fcbf16fe13e839adb4979a626dfeb4753a8ca5dc348d2581531cfeecd" %} package: name: {{ name }} From 5db8b2148b8df7063fcafdbe9408ed5effa2dbe6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Dec 2023 17:15:16 -0500 Subject: [PATCH 1328/2173] Update tsebra to 1.1.2.1 (#44959) --- recipes/tsebra/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tsebra/meta.yaml b/recipes/tsebra/meta.yaml index 52af2306ddd96..35064ac4f90c6 100644 --- a/recipes/tsebra/meta.yaml +++ b/recipes/tsebra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.2" %} +{% set version = "1.1.2.1" %} {% set name = "tsebra" %} -{% set sha256 = "d2fcf571890a70f9c3b60c1ffdbf6e60fd6c7b3c7c71bc78462ba0a52aca6300" %} +{% set sha256 = "66133f393bfe22ff5b113770175f358e8e4aa897fa865296707aee956b2ce560" %} package: name: "{{ name }}" From f9aa5d9a62c649a8435683710207e4bbd8e01b4a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Dec 2023 17:15:26 -0500 Subject: [PATCH 1329/2173] Update keggcharter to 1.0.1 (#44961) --- recipes/keggcharter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/keggcharter/meta.yaml b/recipes/keggcharter/meta.yaml index fabef34dadb32..939febdb892e0 100644 --- a/recipes/keggcharter/meta.yaml +++ b/recipes/keggcharter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "keggcharter" %} -{% set version = "1.0.0" %} -{% set sha256 = "aa36605886bb6419f616dbec7c95e9328e7eb0eea0585ccc8c9b0e5607943699" %} +{% set version = "1.0.1" %} +{% set sha256 = "39e79c226a61ede80a1a95819293fde8fe69b1c2f0dc4713c6262db9b1fad4e2" %} package: name: {{ name|lower }} From edf978ac4e247813dc5d0efc01aa621c7cd9719e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Dec 2023 17:15:37 -0500 Subject: [PATCH 1330/2173] Update haplink to 1.1.0 (#44962) --- recipes/haplink/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/haplink/meta.yaml b/recipes/haplink/meta.yaml index d5cbd3f22bfe6..2c68e6831f118 100644 --- a/recipes/haplink/meta.yaml +++ b/recipes/haplink/meta.yaml @@ -1,6 +1,6 @@ {% set name = "haplink" %} -{% set version = "1.0.0" %} -{% set sha256 = "2e9459d8b84c01b4503b1b6a68c664f6ba062d1a3123516a9e46a6d4f354374a" %} +{% set version = "1.1.0" %} +{% set sha256 = "6a4dc2c4a6ef4b2eb2db32576755c8efabe8601ea3ac48455f162f97750cd469" %} package: name: {{ name|lower }} From 4e3aa4361e8f69b32cc341b07f68b119ea6c4025 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Dec 2023 17:40:51 -0500 Subject: [PATCH 1331/2173] Update piper to 0.14.0 (#44956) * Update piper to 0.14.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/piper/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/piper/meta.yaml b/recipes/piper/meta.yaml index 661aca1d96876..1ba5d74d77b4c 100644 --- a/recipes/piper/meta.yaml +++ b/recipes/piper/meta.yaml @@ -1,5 +1,5 @@ {% set name = "piper" %} -{% set version = "0.13.2" %} +{% set version = "0.14.0" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "edc68583bf7925a44ed0cf439cd059bec51499cd70b4ff8a81ed67a9b0093867" + sha256: "2d2b226689f2e992da0735f25ea432f16f230bfaef51e732ef50b1b495ce153c" build: number: 0 noarch: python - script: "2to3 . && {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv" + script: "2to3 . && {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('piper', max_pin="x.x") }} requirements: host: From 8308d4c034dfb28da34529ca2d48be063dd1cf35 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 22 Dec 2023 17:47:41 -0500 Subject: [PATCH 1332/2173] Update raxml-ng to 1.2.1 (#44955) * Update raxml-ng to 1.2.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/raxml-ng/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/raxml-ng/meta.yaml b/recipes/raxml-ng/meta.yaml index 8a71b9c015b1d..0da1caa7dbbc0 100644 --- a/recipes/raxml-ng/meta.yaml +++ b/recipes/raxml-ng/meta.yaml @@ -1,5 +1,5 @@ {% set name = "raxml-ng" %} -{% set version = "1.2.0" %} +{% set version = "1.2.1" %} package: name: {{ name|lower }} @@ -7,10 +7,12 @@ package: source: url: https://github.com/amkozlov/raxml-ng/releases/download/{{ version }}/{{ name }}_v{{ version }}_source.zip - sha256: 1dc1940e2fbd0d701142c8bfa0c0007c5b39642493a60adb6a4cfa2d10e27ac8 + sha256: e14ec2233f0c9d9f497eab8f77c73512c8c787e44ed3839bd25fd35658ef89e3 build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('raxml-ng', max_pin="x") }} requirements: build: From f545ab26222a851cef5e9215b2abdceb7be46de6 Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Sat, 23 Dec 2023 11:22:29 -0500 Subject: [PATCH 1333/2173] Update gsearch v0.1.7 (#44964) --- recipes/gsearch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gsearch/meta.yaml b/recipes/gsearch/meta.yaml index e705912ca1f85..8e51a1a1372fd 100644 --- a/recipes/gsearch/meta.yaml +++ b/recipes/gsearch/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.6" %} +{% set version = "0.1.7" %} package: name: gsearch @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/gsearch/archive/v{{ version }}.tar.gz - sha256: e57b53617e325195699d3e3a8e68acc7172775466ce8be37516df60dd71fbd12 + sha256: ceec9638cbb2bb8f588375a3c3283ca717ba436e9d550624a1039c9d00a76e8a requirements: build: From cc24f953f48a023fd8b0274c80a5887a1b3332b2 Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Sat, 23 Dec 2023 17:24:27 +0100 Subject: [PATCH 1334/2173] Update hictk to v0.0.4 (#44958) * wip * Update URL * Update URL * Update URL and sha256 --- recipes/hictk/conanfile.txt.patch | 26 ++++++++++++-------------- recipes/hictk/meta.yaml | 19 +++++++++---------- recipes/hictk/run_test.sh | 5 +++-- 3 files changed, 24 insertions(+), 26 deletions(-) diff --git a/recipes/hictk/conanfile.txt.patch b/recipes/hictk/conanfile.txt.patch index 91d076a10b7ac..096e64e4b8187 100644 --- a/recipes/hictk/conanfile.txt.patch +++ b/recipes/hictk/conanfile.txt.patch @@ -1,31 +1,30 @@ diff --git a/conanfile.txt b/conanfile.txt -index 31d9e7f..669629d 100644 +index 420c5b7..eb94f2c 100644 --- a/conanfile.txt +++ b/conanfile.txt -@@ -3,74 +3,12 @@ +@@ -3,72 +3,11 @@ # SPDX-License-Identifier: MIT [requires] --boost/1.83.0#f0c3932db7f65b606ed78357ecbdcbef - bshoshany-thread-pool/3.5.0#3c9fd1e21a688432b7f31b40d2d168ee +-boost/1.83.0#7825569cd0622461dec7bc87dfdf47ae + bshoshany-thread-pool/3.5.0#5aaea7ccf37107d3c1ba9ca9ab246e42 -cli11/2.3.2#1424b9b1d9e3682a7122f415b078b4d7 -eigen/3.4.0#2e192482a8acff96fe34766adca2b24c --fast_float/5.2.0#9bf1a3fac625789f2b571d43efb8013b --fmt/10.1.0#1fae165cded07416f64960a5b6140317 --hdf5/1.14.1#16047e4faf70ba5488d7525063c5cb2b --highfive/2.7.1#b1e846aa63f7b3ab0368faae2f004fbd +-fast_float/5.3.0#efd9bda97d5f77fa5a98981e014092a0 +-fmt/10.1.1#cd63809a79574a2f9eb73ca35f16a243 +-hdf5/1.14.2#1e12ccecd5ebc9b5191433862e196743 +-highfive/2.8.0#19e1a6e78d9329851aa9da409f07d29a -libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602 - parallel-hashmap/1.3.11#719aed501c271a34e2347a7731ab3bfb + parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7 readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83 span-lite/0.10.3#1967d71abb32b314387c2ab9c558dd22 --spdlog/1.12.0#248c215bc5f0718402fbf1de126ef847 --xxhash/0.8.2#03fd1c9a839b3f9cdf5ea9742c312187 --zstd/1.5.5#93372fe14bb7883bd4de82914e0a1841 +-spdlog/1.12.0#0e390a2f5c3e96671d0857bc734e4731 +-zstd/1.5.5#b87dc3b185caa4b122979ac4ae8ef7e8 [generators] CMakeDeps - [options] +-[options] -boost*:system_no_deprecated=True -boost*:asio_no_deprecated=True -boost*:filesystem_no_deprecated=True @@ -76,4 +75,3 @@ index 31d9e7f..669629d 100644 -highfive*:with_opencv=False -highfive*:with_xtensor=False -spdlog*:header_only=True --xxhash*:utility=False diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index a36deadc6e1bd..821f6aaed942b 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.3" %} -{% set sha256 = "f49657b9ef80ef9fa07f125a0b6f056923235c9ea77e19cee312b004384ea39e" %} +{% set version = "0.0.4" %} +{% set sha256 = "19f9b17f76e27603179abb946edbcf3447a813d08d143a9f42c46d99a309614b" %} package: name: {{ name|lower }} @@ -26,16 +26,17 @@ requirements: - eigen >=3.4 - fast_float >=5 - fmt >=10 - - highfive >=2.7 + - highfive >=2.8 - spdlog >=1.12 + host: - - boost >=1.80 + - boost-cpp >=1.80 - hdf5 >=1.12 - libdeflate - - xxhash >=0.8 - zstd >=1.5 + run: - - boost >=1.80 + - libboost >=1.80 - hdf5 >=1.12 - libdeflate - zstd >=1.5 @@ -51,7 +52,7 @@ about: test: requires: - curl - - cooler>=0.9.2 + - cooler>=0.9.3 - openjdk>=11 - perl-digest-sha1 - xz @@ -71,12 +72,10 @@ test: - test/scripts/hictk_dump_balanced.sh - test/scripts/hictk_fix_mcool.sh - test/scripts/hictk_load_coo.sh - - test/scripts/hictk_load_coo.sh - test/scripts/hictk_load_bg2.sh - - test/scripts/hictk_load_bg2.sh - - test/scripts/hictk_load_4dn.sh - test/scripts/hictk_load_4dn.sh - test/scripts/hictk_merge.sh + - test/scripts/hictk_rename_chromosomes.sh - test/scripts/hictk_validate.sh - test/scripts/hictk_zoomify.sh commands: diff --git a/recipes/hictk/run_test.sh b/recipes/hictk/run_test.sh index 0736a37cea981..045b9c4db17c7 100755 --- a/recipes/hictk/run_test.sh +++ b/recipes/hictk/run_test.sh @@ -40,11 +40,12 @@ test/scripts/hictk_load_coo.sh "$hictk" sorted test/scripts/hictk_load_coo.sh "$hictk" unsorted test/scripts/hictk_load_bg2.sh "$hictk" sorted test/scripts/hictk_load_bg2.sh "$hictk" unsorted -test/scripts/hictk_load_4dn.sh "$hictk" sorted -test/scripts/hictk_load_4dn.sh "$hictk" unsorted +test/scripts/hictk_load_4dn.sh "$hictk" test/scripts/hictk_merge.sh "$hictk" +test/scripts/hictk_rename_chromosomes.sh "$hictk" + test/scripts/hictk_validate.sh "$hictk" test/scripts/hictk_zoomify.sh "$hictk" From 2c7790c4440a839c3ae6583a47e0618c006837d2 Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Sat, 23 Dec 2023 11:26:44 -0500 Subject: [PATCH 1335/2173] final commit with ete3 v3.1.3 fixed and compatible pandas resolving issue #155 (#44947) --- recipes/mob_suite/meta.yaml | 9 ++++++--- recipes/mob_suite/run_test.sh | 2 ++ 2 files changed, 8 insertions(+), 3 deletions(-) create mode 100644 recipes/mob_suite/run_test.sh diff --git a/recipes/mob_suite/meta.yaml b/recipes/mob_suite/meta.yaml index b16baa7188321..6109fc03c7d76 100644 --- a/recipes/mob_suite/meta.yaml +++ b/recipes/mob_suite/meta.yaml @@ -12,7 +12,7 @@ source: build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -31,12 +31,12 @@ requirements: run: - python >=3.7 - {{ pin_compatible('numpy', max_pin="x") }} + - pandas >=0.22,<=1.5.3 - pytables - - pandas >=0.22.0,<2 - biopython >=1.8,<2 - {{ pin_compatible('pycurl') }} - {{ pin_compatible('scipy') }} - - ete3 >=3.1.3 + - ete3 ==3.1.3 - six - blast >=2.9.0 - mash >=2.0 @@ -44,10 +44,13 @@ requirements: test: imports: - mob_suite + requires: + - pytest commands: - mob_recon --help - mob_cluster --help - mob_typer --help + - mob_init --help about: home: 'https://pypi.org/project/mob-suite/' diff --git a/recipes/mob_suite/run_test.sh b/recipes/mob_suite/run_test.sh new file mode 100644 index 0000000000000..817113f2f503d --- /dev/null +++ b/recipes/mob_suite/run_test.sh @@ -0,0 +1,2 @@ +#!/usr/bin/env bash +pytest --pyargs mob_suite.tests.test_mobrecon::test_mob_recon_typical_run From cdfcc90bda417dcb32172412c7cc153a49c65857 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 23 Dec 2023 16:27:39 +0000 Subject: [PATCH 1336/2173] chore: Update version and checksum for HapLink (#44967) From b353e0d3261bd3e663ff54fdf4f99310709a12c5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 23 Dec 2023 11:29:26 -0500 Subject: [PATCH 1337/2173] Update dajin2 to 0.3.5 (#44963) --- recipes/dajin2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index cd35c58305925..ec633abd38945 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "DAJIN2" %} -{% set version = "0.3.4" %} +{% set version = "0.3.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: 0165301f801242d3fd9e09064d78e5ca162cf1e6b55fec5100efebd35a3e8243 + sha256: f6a6c20eda88b3b1a86ccde2e3ac1a63d934c503eda0f44604f4d83ca77441d5 build: entry_points: From 77473e954fae9c59fec8497beeb7420bf00e3b82 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 23 Dec 2023 11:29:35 -0500 Subject: [PATCH 1338/2173] Update igv-reports to 1.10.0 (#44965) --- recipes/igv-reports/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/igv-reports/meta.yaml b/recipes/igv-reports/meta.yaml index ec27473cd1014..6335f9d235f6d 100644 --- a/recipes/igv-reports/meta.yaml +++ b/recipes/igv-reports/meta.yaml @@ -1,5 +1,5 @@ {% set name = "igv-reports" %} -{% set version = "1.9.1" %} +{% set version = "1.10.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: f2f96cf0d16cea1b71a098c1385384a31f054e4e1da72062373c1306ef115f94 + sha256: 8cbe26d120ca4d599c7ffb8077dc4501a5ef29cf76a69f187ce1cd948ef0f451 build: noarch: python From 8a1b28b7b228684ac327677421c72969bec97a42 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 23 Dec 2023 11:29:43 -0500 Subject: [PATCH 1339/2173] Update ont-modkit to 0.2.4 (#44966) --- recipes/ont-modkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml index f7e04c144049a..452de044fa9b1 100644 --- a/recipes/ont-modkit/meta.yaml +++ b/recipes/ont-modkit/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.3" %} -{% set sha256 = "24f53d3725a5d54524c80698cbae017b7ff9f4158507ac8052e273cac0d22373" %} +{% set version = "0.2.4" %} +{% set sha256 = "fcf01e992a9a8fd1feccf8513370cbcdb630fd0b4c0d14ce76696bfef656fe79" %} package: name: ont-modkit From 975302fdbfa692828c2258984e84351c42173399 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 23 Dec 2023 11:29:51 -0500 Subject: [PATCH 1340/2173] Update pybiolib to 1.1.1660 (#44969) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 22ba2c69eb687..35f3335be4b20 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1651" %} +{% set version = "1.1.1660" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: e9e68bd90f67e5a9e4e4a9b174102559dfd8316a1b749bdef4275dbb7a048bb5 + sha256: 2fc826a95c7353c423428037e5eec7174f1b875d826eaf1f30594acf5d31eb1a build: noarch: python From 8382be40240ec233cc0b2fe07790fc446563dbb4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 23 Dec 2023 11:30:02 -0500 Subject: [PATCH 1341/2173] Update ms-entropy to 1.1.2 (#44970) --- recipes/ms-entropy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ms-entropy/meta.yaml b/recipes/ms-entropy/meta.yaml index 1acfdcb572439..1af55e2d4d2c2 100644 --- a/recipes/ms-entropy/meta.yaml +++ b/recipes/ms-entropy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ms-entropy" %} -{% set version = "1.1.1" %} +{% set version = "1.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms_entropy-{{ version }}.tar.gz - sha256: ec2df69651049853e0b9d645abb1f0f3f4042e8d79bf8bc8997ba3c52b116525 + sha256: 057309df41d13d3bc7d763025fab1bd6ad3a8a12031aec0ace9bd29d8dd2bee2 build: skip: true # [py<37] From c133f7c3fb204a376b893c1f7055ae315516ec64 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 23 Dec 2023 11:30:11 -0500 Subject: [PATCH 1342/2173] Update oakvar to 2.9.82 (#44973) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index cf39860937ea0..f4b045bd05e12 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.81" %} -{% set sha256 = "47aeed3fc65fcfe8914bb14bf7973e1a58811f5e348251b235e7636c583a51ea" %} +{% set version = "2.9.82" %} +{% set sha256 = "77865978a9b646ce02a6e728f3f74f203a801bb4cf3df816badaca46d71ab4d2" %} package: name: {{ name|lower }} From 3763cbffa9f24eb2a46e3c02d5ea087cc5d3a20f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 23 Dec 2023 12:08:34 -0500 Subject: [PATCH 1343/2173] Update tantan to 49 (#44968) * Update tantan to 49 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/tantan/meta.yaml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/recipes/tantan/meta.yaml b/recipes/tantan/meta.yaml index e7a25672a25d7..26e07ef7347b1 100644 --- a/recipes/tantan/meta.yaml +++ b/recipes/tantan/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "40" %} +{% set version = "49" %} package: name: tantan @@ -6,11 +6,13 @@ package: source: url: https://gitlab.com/mcfrith/tantan/-/archive/{{ version }}/tantan-{{ version }}.tar.gz - sha256: 61303c88cdf41fa5bcb5f77f674b4fac2a9bc0e4c9abb3b9d75af35c47162240 + sha256: 851eb8f1c0f169107cebe16cb9e973c49a54d0f00413063b514ea0edfa3a5238 build: - number: 2 + number: 0 script: make install prefix=$PREFIX + run_exports: + - {{ pin_subpackage('tantan', max_pin="None") }} requirements: build: @@ -29,5 +31,10 @@ test: about: home: https://gitlab.com/mcfrith/tantan license: GPL-3.0-or-later + license_family: GPL3 license_file: COPYING.txt summary: "tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences." + +extra: + identifiers: + - doi:10.1093/nar/gkq1212 From 5cc0afa5e901427b4f346917ea4c005a605726f4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 23 Dec 2023 21:50:50 -0500 Subject: [PATCH 1344/2173] Update sylph to 0.5.0 (#44974) --- recipes/sylph/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sylph/meta.yaml b/recipes/sylph/meta.yaml index 4ef0837272ca2..c47e58e9a61e1 100644 --- a/recipes/sylph/meta.yaml +++ b/recipes/sylph/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.1" %} +{% set version = "0.5.0" %} package: name: sylph @@ -11,7 +11,7 @@ build: source: url: https://github.com/bluenote-1577/sylph/archive/v{{ version }}.tar.gz - sha256: fd405d34e8ebd5a0f09a85631864b330594a29e30fd3509e7f4873f2946046a6 + sha256: dfa7859281aa0aabf01e0362c7016679024b8ab5f112bef12f7cffbb0b3dc1fc requirements: build: From 5e1b7dab47611b0e54f94ddd75503385f489e2b7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 23 Dec 2023 22:38:19 -0500 Subject: [PATCH 1345/2173] Update pypgx to 0.23.0 (#44976) --- recipes/pypgx/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pypgx/meta.yaml b/recipes/pypgx/meta.yaml index 8f066487f74da..85fe340272681 100644 --- a/recipes/pypgx/meta.yaml +++ b/recipes/pypgx/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pypgx" %} -{% set version = "0.22.0" %} +{% set version = "0.23.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 522f9dcba319ecef08af026a134a45bc6267c9b482d615e774a7f877dcc6462e + sha256: f38c23085b0102182cabc8cc0fc32eff05bc668bf68b6a751ad249c70b18242c build: number: 0 From d322b392b47456cd777a4e6d7fc6e2e38877e48d Mon Sep 17 00:00:00 2001 From: Afif Elghraoui Date: Tue, 26 Dec 2023 08:51:13 -0800 Subject: [PATCH 1346/2173] mcl: restore bioinformatics tools support (#44975) * mcl: Add back in the mc blast support scripts The developer admitted that they shouldn't have been dropped from the code base and promised to reintroduce them in the next release. Since that release is far off, we can incorporate them here for now. See https://github.com/micans/mcl/discussions/25 * mcl: add run_exports --- recipes/mcl/build.sh | 5 + recipes/mcl/meta.yaml | 5 +- recipes/mcl/scripts/README | 16 + recipes/mcl/scripts/mclblastline | 58 ++++ recipes/mcl/scripts/mcxdeblast | 490 +++++++++++++++++++++++++++++++ 5 files changed, 573 insertions(+), 1 deletion(-) create mode 100644 recipes/mcl/scripts/README create mode 100755 recipes/mcl/scripts/mclblastline create mode 100755 recipes/mcl/scripts/mcxdeblast diff --git a/recipes/mcl/build.sh b/recipes/mcl/build.sh index da82f0c1b33d7..066d521961a67 100644 --- a/recipes/mcl/build.sh +++ b/recipes/mcl/build.sh @@ -28,3 +28,8 @@ cd .. make -j"${CPU_COUNT}" make install make clean + +# Add back in the mcl/blast scripts. +# Remove this once the next release re-incorporates them. +# See https://github.com/micans/mcl/discussions/25 +cp $RECIPE_DIR/scripts/mc* $PREFIX/bin/ diff --git a/recipes/mcl/meta.yaml b/recipes/mcl/meta.yaml index 0471e62c50962..30a984029b69c 100644 --- a/recipes/mcl/meta.yaml +++ b/recipes/mcl/meta.yaml @@ -14,7 +14,9 @@ source: folder: cimfomfa build: - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('mcl', max_pin=None) }} requirements: build: @@ -33,6 +35,7 @@ test: - mcl --help - mcx -h - mcxarray --version + - mcxdeblast -h - mcxdump --version - mcxi -h - mcxload --version diff --git a/recipes/mcl/scripts/README b/recipes/mcl/scripts/README new file mode 100644 index 0000000000000..3266fe9c83f0c --- /dev/null +++ b/recipes/mcl/scripts/README @@ -0,0 +1,16 @@ +These scripts downloaded from + + +They should be removed after being re-introduced in the upcoming release. +See https://github.com/micans/mcl/discussions/25 + + +Only the header of mcxdeblast was changed. The change is as follows: + +-#!/usr/local/bin/perl -w ++#!/usr/bin/env perl ++ ++use warnings; + +- Afif Elghraoui / 0xaf1f + 2023-12-25 diff --git a/recipes/mcl/scripts/mclblastline b/recipes/mcl/scripts/mclblastline new file mode 100755 index 0000000000000..2af2d45f41896 --- /dev/null +++ b/recipes/mcl/scripts/mclblastline @@ -0,0 +1,58 @@ +#!/usr/bin/env perl + +# Copyright (C) 2003, 2004, 2005, 2006, 2007 Stijn van Dongen + # +# You can redistribute and/or modify this program under the terms of the GNU +# General Public License; either version 3 of the License or (at your option) +# any later version. + +use strict; + +$" = ' '; + +my $do_help = 0; +my $cline = "mclpipeline --parser=mcxdeblast --parser-tag=blast"; + +unless (grep { $_ =~ /^--ass-r[vei]?=/; } @ARGV) { + $cline .= " --ass-r=max"; +} + +$cline .= " @ARGV"; + +if (grep { $_ =~ /--(help|apropos)/; } @ARGV) { + $do_help = 1; +} +elsif (!@ARGV) { + $do_help = 1; + $cline .= " --help"; +} + +if ($do_help) { + print <<_help_; +mcxblastline wraps around the generic mclpipeline script. It fills in the name +of the BLAST parser (mcxdeblast) and the tag ('blast') used to propagate +mcxdeblast options through the pipeline to mcxdeblast itself. You can freely +use all mclpipeline options other than --parser= and +--parser-tag=. +_help_ +} +if (system $cline) { + print "mcxblastline wrapper: pipeline failed\n"; + print "cline: $cline\n"; + exit(1); +} +if ($do_help) { + print <<_help_; +________________ +The above options are generic pipeline options. You can pass any mcxdeblast +option by inserting the 'blast' tag in front of that particular option. For +example, the mcxdeblast --score=x option (where x is 'b' or 'e') should +be passed to mcxblastline as --blast-score=x. + +The mcxdeblast --xo-dat option is special; it must *not* be prefixed, as it is +shared with mclpipeline, as can be seen from the above listing. The mcxdeblast +--xi-dat option should not be used, as it encapsulated by the mclpipeline --xi +option. +_help_ +} + diff --git a/recipes/mcl/scripts/mcxdeblast b/recipes/mcl/scripts/mcxdeblast new file mode 100755 index 0000000000000..25eea8cc3285d --- /dev/null +++ b/recipes/mcl/scripts/mcxdeblast @@ -0,0 +1,490 @@ +#!/usr/bin/env perl + +use warnings; +use Getopt::Long; + +# (c) Copyright 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Stijn van Dongen +# (c) Copyright 2004 Jason Stajich (column output parsing) +# +# Other (C)ontributors; +# Dinakarpandian Deendayal (general comments) +# Abel Ureta-Vidal (general comments) +# Daniel Lundin (regexp tweak, warning) +# +# You can redistribute and/or modify this program under the terms of the GNU +# General Public License; either version 3 of the License or (at your option) +# any later version. + +# +# TODO +# +# - Optionally read from STDIN +# - Require tab file for line-mode={123,packed} +# +# - Infer hsp_len from long output (?) +# - (Perhaps) enable section parsing ala tribe, for finer control. +# - $:: usage is arbitrary and ugly. pipe down. +# - Is the m9/seenlfgt combination correct? +# - Check whether m9 output state is correct if errors occur. + + +$^W = 1; +use strict; + +$::mode_sort = 'o'; # a lphabetical + # o ccurrence + +$::mode_score = 'e'; # e value + # b it + +my $line_mode = ""; # default is raw mode, not line mode +$::name_out = '-'; + +$::bcut = 0; +$::ecut = 0; +$::rcut = 0; + +my $blastfix = ""; +my $addfix = ""; + +my $user_tabfile = ""; + +my %line_modes = qw ( abc 1 123 1); + +my $obase = ""; +my $stdhandler = 0; + +my $help = 0; +my $m9 = 0; +my $abc = 0; + + + +if +(! GetOptions + ( "help" => \$help + , "apropos" => \$help + , "sort=s" => \$::mode_sort + , "ecut=f" => \$::ecut + , "bcut=f" => \$::bcut + , "rcut=f" => \$::rcut + , "score=s" => \$::mode_score + , "m9" => \$m9 + , "tab=s" => \$user_tabfile + , "xo-dat=s" => \$addfix + , "xi-dat=s" => \$blastfix + , "base=s" => \$obase + , "stdhandler" => \$stdhandler + , "line-mode=s" => \$line_mode + , "out=s" => \$::name_out + ) +) + { print STDERR "option processing failed\n"; + exit(1); + } + +help() && exit(0) if $help; + +die "unknown sort mode <$::mode_sort>" + unless $::mode_sort =~ /^[ao]$/; +die "unknown line mode <$line_mode>" + if ($line_mode && !defined($line_modes{$line_mode})); +die "unknown sort mode <$::mode_score>" + unless $::mode_score =~ /^[ebr]$/; + + +my $fname = shift || die "please submit name of blast file\n"; +$obase = $fname unless $obase; + + +if ($blastfix) { + $obase = $fname; + if ($fname =~ /\Q.$blastfix\E$/) { + $obase =~ s/\Q.$blastfix\E$//; + } + else { + $fname .= ".$blastfix"; + } +} +if ($addfix) { + $obase .= ".$addfix"; +} + +my ($gix, $giy); +$::seenlft = {}; +$::seenrgt = {}; +my $tagTocc = {}; +my $me = "[$0] "; +my $lc = 0; +my $fhin = \*STDIN; + +if ($fname ne '-') { + open(F_BLAST, "<$fname") || die "cannot open $fname\n"; + $fhin = \*F_BLAST; +} + +$::TAB_user = {}; + +if ($user_tabfile) { + read_tab($user_tabfile, $::TAB_user); +} + + +$::f_raw = undef; +my $f_err = undef; + +if ($line_mode) { + if (!$::name_out || $::name_out eq '-') { + $::f_raw = \*STDOUT; + } + else { + open(F_RAW, ">$::name_out") || die "cannot open $::name_out"; + $::f_raw = \*F_RAW; + } + $f_err = \*STDERR; + + if ($line_mode eq 'abc') { + # print $::f_raw "#aa# (stream abc cookie)\n"; + } + elsif ($line_mode eq '123') { + # print $::f_raw "#11# (stream abc cookie)\n"; + } +} +else { + if ($stdhandler) { + $::f_raw = \*STDOUT; + $f_err = \*STDERR; + } + else { + open(F_RAW, ">$obase.raw") || die "cannot open $obase.raw\n"; + $::f_raw = \*F_RAW; + open(F_ERR, ">$obase.err") || die "cannot open $obase.err\n"; + $f_err = \*F_ERR; + } +} + +$::ID = 0; + +if ($m9) { + munge_linewise($fhin, $::f_raw, $line_mode); +} +else { + munge_long($fhin, $::f_raw, $line_mode); +} + +close $::f_raw; +$::CT = scalar keys %$::seenrgt; + + +my $alnum = 0; +my $occTmisc = {}; + +if (!$user_tabfile && !$line_mode) { + open(F_HDR, ">$obase.hdr") || die "cannot open $obase.hdr\n"; # header + open(F_MAP, ">$obase.map") || die "cannot open $obase.idx\n"; # map file + open(F_TAB, ">$obase.tab") || die "cannot open $obase.idx\n"; # indices + print F_TAB "# \n"; + if ($::mode_sort eq 'o') { + print F_TAB "# sort mode is by occurrence\n"; + } + elsif ($::mode_sort eq 'a') { + print F_TAB "# sort mode is alphabetical\n"; + } + if ($::mode_sort eq 'a') { + for (sort {$::a cmp $::b; } keys %$tagTocc) { + print F_TAB "$alnum $_\n"; + $occTmisc->{$tagTocc->{$_}} = [ $alnum, $_ ]; + $alnum++; + } + print STDERR "Index [$obase.tab] is sorted by alphabetic order\n"; + } + elsif ($::mode_sort eq 'o' || 1) { + for (sort {$tagTocc->{$::a} <=> $tagTocc->{$::b}; } keys %$tagTocc) { + print F_TAB "$alnum $_\n"; + $occTmisc->{$tagTocc->{$_}} = [ $alnum, $_ ]; + $alnum++; + } + print STDERR "Index [$obase.tab] is sorted by occurrence order\n"; + print STDERR "Primary and secondary occurrences are considered equal\n"; + } + my $ct = keys %$occTmisc; + print F_MAP "(mclheader\nmcltype matrix\ndimensions $ct", 'x', + "$ct\n)\n(mclmatrix\nbegin\n"; + for (sort {$::a <=> $::b; } keys %$occTmisc) { + # print F_MAP "$_ ", $occTmisc->{$_}[0], " ", $occTmisc->{$_}[1], "\n"; + print F_MAP "$_ $occTmisc->{$_}[0] \$\n"; + } + print F_MAP ")\n"; + + print F_HDR "(mclheader\nmcltype matrix\ndimensions "; + print F_HDR $::ID . 'x' . $::ID; + print F_HDR "\n)\n"; + close F_TAB; + close F_HDR; + close F_MAP; +} + + +my $n_err = 0; +for (sort keys %$::seenrgt) { + if (!$::seenlft->{$_}) { + print $f_err "secondary element $_ not seen as primary element\n"; + print $f_err "emergency measure: added the element to the primary list\n"; + $n_err++; + } +} + +if ($n_err) { + print STDERR $me, "$n_err secondary elements not seen as primary element\n"; + print STDERR $me, "I added all of them\n"; + print STDERR $me, "There were $::CT elements in all\n"; +} +else { + print STDERR $me, + "all secondary elements were also seen as primary elements (check ok)\n"; +} + + +sub munge_linewise { + + my ($fh_in, $fh_raw, $line_mode) = @_; + + my $gix_prev = ""; + + while (<$fh_in>) { + + next if /^#/; + chomp; + my $sc_abc = 0; + + my ($gix, $giy, $percent_id, $hsp_len, $mismatches, $gapsm, + $qstart, $qend,$hstart, $hend, $e, $b) + = + split; + + my $s = 0; + + my $idx = getid($gix, 1); + next unless $idx >= 0; + + if ($gix_prev ne $gix) { + if (!$line_mode) { + if ($gix_prev) { + print $fh_raw "\$\n"; + } + if( $idx >= 0 ) { + print $fh_raw "$idx "; + } + } + } + my $idy = getid($giy, 0); + + $s = getscore($e, $b, $hsp_len); + + if ($idy >= 0) { + if (!$line_mode) { + print $fh_raw "$idy:$s "; + } + else { + print $fh_raw "$gix\t$giy\t$s\n"; + } + } + $gix_prev = $gix; + } + + if ($gix_prev) { + print $fh_raw "\$\n" if !$line_mode; + } +} + + +sub munge_long { + + my ($fh_in, $fh_raw, $line_mode) = @_; + + my $need_query = 1; + my $need_hits = 2; + my $need_gi = 3; + + my $state = $need_query; + + while (<$fh_in>) { + $lc++; + chomp; + if (/^Query=\s+gi\|(\d+(_\d+)?)/ || /^Query=\s+(\S+).*$/) { +# warn "STATE query $1\n"; + if ($state != $need_query) { + print STDERR "Unexpected 'Query=' line\n"; + } + $gix = $1; + my $idx = getid($gix, 1); + + if ($idx >= 0) { + print $fh_raw "$idx " if !$line_mode; + } + $state = $need_hits; + } + elsif (/^Query=/) { + print STDERR "Query string not recognized: $_\n"; + } + elsif + ($state == $need_hits && /sequences producing significant alignments/i) { + $state = $need_gi; +# warn "STATE significant\n"; + } + elsif ($state == $need_hits && /no hits found/i) { + print STDERR "no hits found for gi $gix\n"; + print $fh_raw "\$\n" if !$line_mode; + $state = $need_query; + } + elsif + ( $state == $need_gi + && ! /^>/ + && (/^gi\|(\d+(_\d+)?)/ || /^(\S+)\s+.*$/) + ) + { $giy = $1; + my $idy = getid($giy, 0); + my ($s, $b, $e); + + if (/(\S+)\s+(\S+)\s*$/) { + $b = +$1; + $e = +$2; + } + else { + print STDERR "no scores in line $lc [$_]!\n"; + next; + } + + $s = getscore($e, $b, 0); + + if ($idy >= 0) { # fixme, void or explain. + if (!$line_mode) { + print $fh_raw "$idy:$s "; + } + else { + print $fh_raw "$giy\t$gix\t$s\n"; + } + } + } + elsif (/^\s*$/) { + # paragraph skip does not change state, including the $need_gi case. + } + elsif (/(Statistics|Parameters):/) { + $state = $need_query; + # this provides WU-blast compatibility. + } + elsif ($state == $need_gi) { + print $fh_raw "\$\n" if !$line_mode; + $state = $need_query; + } + } + + if ($state == $need_gi) { + print $f_err "run ended while expecting more secondary scores\n"; + print STDERR "run ended while expecting more secondary scores\n"; + print $fh_raw "\$\n" if !$line_mode; + } +} + + + + +sub read_tab { + my $file = shift; + my $tab = shift; + open (U_TAB, "<$file") || die "cannot open $file\n"; + while () { + if (/^\s*#/) { + next; + } + else { + if (/^(\d+)\s+(.*)/) { + $tab->{$2} = $1; + } + else { + print STDERR "___ cannot parse line: $_"; + } + } + } +} + + +sub getscore { + my ($e, $b, $hl) = @_; + my $s = 0; + + if ($::mode_score eq 'e') { + $e = "1$e" if $e =~ /^e/; + $s = $e > 0 ? -log($e)/log(10) : 200; + if ($s > 200) { + $s = 200; + } + $s = $s > $::ecut ? $s : 0; + } + elsif ($::mode_score eq 'b') { + $s = $b > $::bcut ? $b : 0; + } + elsif ($::mode_score eq 'r' && $hl) { + $s = $b / $hl; + $s = $s > $::rcut ? $s : 0; + } + return $s; +} + + +sub getid { + my ($gi, $is_a_query) = @_; + my $id = -1; + + if ($user_tabfile) { + if (defined($::TAB_user->{$gi})) { + $id = $::TAB_user->{$gi}; + } + else { + print STDERR "___ no user tab entry for label <$gi>\n"; + return -1; + } + } + else { + if (!exists($tagTocc->{$gi})) { +# warn "$is_a_query $gi <-> $::ID\n"; + $tagTocc->{$gi} = $::ID++; + } + $id = $tagTocc->{$gi}; + } + + $::seenrgt->{$id}++; + if ($is_a_query) { + $::seenlft->{$id}++; + } + return $id; +} + + +sub help { + print <<_help_; +Usage: mcxdeblast file-name +where file-name is in BLAST NCBI format. +mcxdeblast will create + base.hdr [to be read by mcxassemble] + base.raw [to be read by mcxassemble] + base.map [to be read by mcxassemble] + base.tab [to be read by clmformat] + base.err [error log] +where base is derived from or equal to file-name +Options: + --m9 Expect column (-m 9) input. + --line-mode=abc Output simple ID1 ID2 SCORE format. + --score= Use bit scores, E-values, + or bit scores normalized by hsp-length + --sort= Use alphabetic sorting (default) or occurrence. + --tab= Use user-supplied tab file. + --xi-dat= Strip from file-name to create output base name. + --xo-dat= Add to base name. + --bcut= Ignore hits below bit score + --ecut= Ignore hits below E-value + --rcut= Ignore hits below raw value + --out= Output file name ('-' for STDOUT) +_help_ +} + From 5164e415f1a5dd43055af124be5f3fc00004ab56 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 26 Dec 2023 11:51:38 -0500 Subject: [PATCH 1347/2173] Update pybiolib to 1.1.1666 (#44977) * Update pybiolib to 1.1.1662 * Update pybiolib to 1.1.1664 * Update pybiolib to 1.1.1666 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 35f3335be4b20..d1e5bb09bb712 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1660" %} +{% set version = "1.1.1666" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 2fc826a95c7353c423428037e5eec7174f1b875d826eaf1f30594acf5d31eb1a + sha256: 71888c84f4ad3cf97f461d2fc5e9955560d131e0c74d9a453e378d5d80262442 build: noarch: python From 0e3bb3aa5a870a7ca57a125024832c3122a4b36d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 26 Dec 2023 15:07:02 -0500 Subject: [PATCH 1348/2173] Update perl-math-bigint to 2.003001 (#44985) --- recipes/perl-math-bigint/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-math-bigint/meta.yaml b/recipes/perl-math-bigint/meta.yaml index ac8101ef2f026..ac043f49bd2c9 100644 --- a/recipes/perl-math-bigint/meta.yaml +++ b/recipes/perl-math-bigint/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-math-bigint" %} -{% set version = "2.002001" %} -{% set sha256 = "21a2874639a5830d9215ed2f1645b700069cb914d8bb92edac1ca27e0db5e60f" %} +{% set version = "2.003001" %} +{% set sha256 = "9e14c5b0b7eecd1dca6d7c1eca680befccf212f7e6683f0b874348375a0333fc" %} package: name: {{ name }} From 832ba3a73af7ee618f03e48f8a6289f0e7b28fa1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Dec 2023 05:46:14 -0500 Subject: [PATCH 1349/2173] Update keggcharter to 1.0.2 (#44992) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update keggcharter to 1.0.2 * Update meta.yaml Now put all TXTs and TSVs from "resources" folder into "share" folder. --------- Co-authored-by: João Sequeira --- recipes/keggcharter/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/keggcharter/meta.yaml b/recipes/keggcharter/meta.yaml index 939febdb892e0..b4284f829e7c1 100644 --- a/recipes/keggcharter/meta.yaml +++ b/recipes/keggcharter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "keggcharter" %} -{% set version = "1.0.1" %} -{% set sha256 = "39e79c226a61ede80a1a95819293fde8fe69b1c2f0dc4713c6262db9b1fad4e2" %} +{% set version = "1.0.2" %} +{% set sha256 = "605795641af04a7045cc92b6f37ee0b0c0b8e508b85fb70bcc6c00234b9d5d89" %} package: name: {{ name|lower }} @@ -16,7 +16,7 @@ build: script: > mkdir -p $PREFIX/bin && mkdir -p $PREFIX/share && - cp *.py resources/KEGGCharter_prokaryotic_maps.txt $PREFIX/share && + cp *.py resources/*.txt resources/*.tsv $PREFIX/share && chmod +x $PREFIX/share/keggcharter.py && ln -s $PREFIX/share/keggcharter.py $PREFIX/bin/keggcharter run_exports: From 6b4d6c4365672611d4ed73688c07329cb88c080c Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Wed, 27 Dec 2023 16:34:18 +0100 Subject: [PATCH 1350/2173] Update hictk to v0.0.5 (#44988) * Update conanfile.txt.patch * Bump version --- recipes/hictk/conanfile.txt.patch | 8 ++++---- recipes/hictk/meta.yaml | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/hictk/conanfile.txt.patch b/recipes/hictk/conanfile.txt.patch index 096e64e4b8187..05ea419f8ae85 100644 --- a/recipes/hictk/conanfile.txt.patch +++ b/recipes/hictk/conanfile.txt.patch @@ -1,5 +1,5 @@ diff --git a/conanfile.txt b/conanfile.txt -index 420c5b7..eb94f2c 100644 +index 0ea6184..eb94f2c 100644 --- a/conanfile.txt +++ b/conanfile.txt @@ -3,72 +3,11 @@ @@ -10,10 +10,10 @@ index 420c5b7..eb94f2c 100644 bshoshany-thread-pool/3.5.0#5aaea7ccf37107d3c1ba9ca9ab246e42 -cli11/2.3.2#1424b9b1d9e3682a7122f415b078b4d7 -eigen/3.4.0#2e192482a8acff96fe34766adca2b24c --fast_float/5.3.0#efd9bda97d5f77fa5a98981e014092a0 +-fast_float/6.0.0#6c8a953c57879453982a6ce69c0ba87c -fmt/10.1.1#cd63809a79574a2f9eb73ca35f16a243 --hdf5/1.14.2#1e12ccecd5ebc9b5191433862e196743 --highfive/2.8.0#19e1a6e78d9329851aa9da409f07d29a +-hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1 +-highfive/2.8.0#b1de99f678ff5699cce6fb5fcac44d2d -libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602 parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7 readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83 diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index 821f6aaed942b..02e7110847842 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.4" %} -{% set sha256 = "19f9b17f76e27603179abb946edbcf3447a813d08d143a9f42c46d99a309614b" %} +{% set version = "0.0.5" %} +{% set sha256 = "12a784bfb83e64c99c2fb36839bdcb2c4a579688dced1e342df8eb6da7c8506d" %} package: name: {{ name|lower }} From 1349ec5e2624a446e8364f0b759faf3e14c4dbf5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Dec 2023 11:38:59 -0500 Subject: [PATCH 1351/2173] Update perl-minion to 10.28 (#44495) --- recipes/perl-minion/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-minion/meta.yaml b/recipes/perl-minion/meta.yaml index bca6af67b1818..87a845511735d 100644 --- a/recipes/perl-minion/meta.yaml +++ b/recipes/perl-minion/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-minion" %} -{% set version = "10.27" %} -{% set sha256 = "c8c5c64d4b3ac8359ed78227b47992bd6ccc3496110849cef228191f895ceb54" %} +{% set version = "10.28" %} +{% set sha256 = "0bd774d2f42b36a5e1293cd3d5241ed35f45eb041599498e28d6f00f6ae910d5" %} package: name: {{ name }} From 45a0733f4028a8a3960af1b8088a07f631ad00fd Mon Sep 17 00:00:00 2001 From: DrYak Date: Wed, 27 Dec 2023 17:42:47 +0100 Subject: [PATCH 1352/2173] bugfix: strand deprecated and removed in BioPython 1.82 (#44987) - see: https://github.com/chapmanb/bcbb/issues/138 --- recipes/bcbio-gff/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/bcbio-gff/meta.yaml b/recipes/bcbio-gff/meta.yaml index 90f1c2105a763..ff55d1753cf3b 100644 --- a/recipes/bcbio-gff/meta.yaml +++ b/recipes/bcbio-gff/meta.yaml @@ -10,8 +10,10 @@ source: sha256: f7b3922ee274106f8716703f41f05a1795aa9d73e903f4e481995ed8f5f65d2d build: - number: 0 + number: 1 noarch: python + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" requirements: @@ -21,7 +23,8 @@ requirements: run: - python - six - - biopython + # see: https://github.com/chapmanb/bcbb/issues/138 + - biopython <=1.81 - bx-python test: From e381800b01529bca44f9668ee3c1180e7c3af409 Mon Sep 17 00:00:00 2001 From: DrYak Date: Wed, 27 Dec 2023 17:47:26 +0100 Subject: [PATCH 1353/2173] bugfix: breaking API change between ruamel.yaml 0.17.x and 0.18 (#44989) --- recipes/lollipop/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/lollipop/meta.yaml b/recipes/lollipop/meta.yaml index 89f213a8aeaa8..5680df67393eb 100644 --- a/recipes/lollipop/meta.yaml +++ b/recipes/lollipop/meta.yaml @@ -12,7 +12,9 @@ source: build: noarch: python - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} script: - {{ PYTHON }} -m pip install '.[cli]' --ignore-installed --no-deps -v - mkdir -p ${PREFIX}/share/{{ name }}/presets @@ -30,7 +32,8 @@ requirements: - scipy - pandas - zstandard - - ruamel.yaml + # NOTE: change of API between ruamel.yaml 0.17.x and 0.18 + - ruamel.yaml <0.18 - strictyaml - tqdm - click From 4a215e51045577abeed1864656c5edc1775e146c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Dec 2023 20:23:24 -0500 Subject: [PATCH 1354/2173] Update tsebra to 1.1.2.2 (#45000) --- recipes/tsebra/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tsebra/meta.yaml b/recipes/tsebra/meta.yaml index 35064ac4f90c6..d0c23407dc092 100644 --- a/recipes/tsebra/meta.yaml +++ b/recipes/tsebra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.2.1" %} +{% set version = "1.1.2.2" %} {% set name = "tsebra" %} -{% set sha256 = "66133f393bfe22ff5b113770175f358e8e4aa897fa865296707aee956b2ce560" %} +{% set sha256 = "e055efea29d3b73a6202c56fb9256bf6006005ef54c8a5de83b9aa0377fff27c" %} package: name: "{{ name }}" From 6748158253e57279f3d4c066cd1fcf1164ae3236 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 27 Dec 2023 20:23:46 -0500 Subject: [PATCH 1355/2173] Update sylph to 0.5.1 (#45001) --- recipes/sylph/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sylph/meta.yaml b/recipes/sylph/meta.yaml index c47e58e9a61e1..c83ec07b1e0fd 100644 --- a/recipes/sylph/meta.yaml +++ b/recipes/sylph/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} package: name: sylph @@ -11,7 +11,7 @@ build: source: url: https://github.com/bluenote-1577/sylph/archive/v{{ version }}.tar.gz - sha256: dfa7859281aa0aabf01e0362c7016679024b8ab5f112bef12f7cffbb0b3dc1fc + sha256: 300b0f4ae77e25c28a05fd2f5323c112003a13111130f136d7d4bf4ded90e10c requirements: build: From 4cc549718834d2e1d1f1259e897b1307ae836a80 Mon Sep 17 00:00:00 2001 From: TPOB <19909103+TTTPOB@users.noreply.github.com> Date: Thu, 28 Dec 2023 09:25:10 +0800 Subject: [PATCH 1356/2173] add r-misha 3.7.0 (history version) (#44981) * add misha version 3.7.0 (history version) * fix hash * fix compiler settings * use template variable to specify name * add run_export to lock version --- recipes/r-misha/3.7.0/build.sh | 2 ++ recipes/r-misha/3.7.0/meta.yaml | 45 +++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 recipes/r-misha/3.7.0/build.sh create mode 100644 recipes/r-misha/3.7.0/meta.yaml diff --git a/recipes/r-misha/3.7.0/build.sh b/recipes/r-misha/3.7.0/build.sh new file mode 100644 index 0000000000000..937ed18ca8d4d --- /dev/null +++ b/recipes/r-misha/3.7.0/build.sh @@ -0,0 +1,2 @@ +sed -i 's/CC=g++/CC=\$(CXX)/' src/Makefile +$R CMD INSTALL --build . diff --git a/recipes/r-misha/3.7.0/meta.yaml b/recipes/r-misha/3.7.0/meta.yaml new file mode 100644 index 0000000000000..29c2d9b973b1c --- /dev/null +++ b/recipes/r-misha/3.7.0/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "3.7.0" %} +{% set name = "r-misha" %} +{% set commit = "fb45473ac27833154724bac04136c601e7b2a6f0" %} + +package: + name: "{{ name|lower }}" + version: '{{ version }}' + +source: + url: 'https://github.com/tanaylab/misha/archive/{{ commit }}.zip' + sha256: a27885729422368972734cf7a657a0a4f8abada8aa5728cb9a4ac745f3184d5a + +build: + # https://github.com/tanaylab/misha/issues/9 + skip: True # [osx] + number: 0 + rpaths: + - lib/R/lib + - lib/ + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - sed + host: + - r-base + - r-devtools + run: + - r-base + +test: + commands: + - '$R -e "library(misha)"' + +about: + home: 'https://tanaylab.github.io/misha/index.html' + license: GPL-2 + summary: 'Toolkit for analysis of genomic data' + +extra: + maintainers: + - Misha Hoichman From f3e4809c9fede240ddcd1ef3149a1fc20332b008 Mon Sep 17 00:00:00 2001 From: TPOB <19909103+TTTPOB@users.noreply.github.com> Date: Thu, 28 Dec 2023 09:56:44 +0800 Subject: [PATCH 1357/2173] add r-misha 3.7.1 (history version) (#44984) * add r-misha 3.7.1 (history version) * fix: incorrect commit and hash --- recipes/r-misha/3.7.1/build.sh | 2 ++ recipes/r-misha/3.7.1/meta.yaml | 45 +++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 recipes/r-misha/3.7.1/build.sh create mode 100644 recipes/r-misha/3.7.1/meta.yaml diff --git a/recipes/r-misha/3.7.1/build.sh b/recipes/r-misha/3.7.1/build.sh new file mode 100644 index 0000000000000..937ed18ca8d4d --- /dev/null +++ b/recipes/r-misha/3.7.1/build.sh @@ -0,0 +1,2 @@ +sed -i 's/CC=g++/CC=\$(CXX)/' src/Makefile +$R CMD INSTALL --build . diff --git a/recipes/r-misha/3.7.1/meta.yaml b/recipes/r-misha/3.7.1/meta.yaml new file mode 100644 index 0000000000000..1a4b49c1cc2ec --- /dev/null +++ b/recipes/r-misha/3.7.1/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "3.7.1" %} +{% set name = "r-misha" %} +{% set commit = "eaf2e6122166f95b176c2c9746ef1505791683ef" %} + +package: + name: "{{ name|lower }}" + version: '{{ version }}' + +source: + url: 'https://github.com/tanaylab/misha/archive/{{ commit }}.zip' + sha256: 443b9ab461c36ff4da0f75868f7ac362ce3fff786574516d131ac6ddc671c4f1 + +build: + # https://github.com/tanaylab/misha/issues/9 + skip: True # [osx] + number: 0 + rpaths: + - lib/R/lib + - lib/ + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - sed + host: + - r-base + - r-devtools + run: + - r-base + +test: + commands: + - '$R -e "library(misha)"' + +about: + home: 'https://tanaylab.github.io/misha/index.html' + license: GPL-2 + summary: 'Toolkit for analysis of genomic data' + +extra: + maintainers: + - Misha Hoichman From 730a691e0e6ffc557a22fd8b61c0302ecf055f74 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Dec 2023 11:59:20 -0500 Subject: [PATCH 1358/2173] Update viguno to 0.2.0 (#44996) * Update viguno to 0.2.0 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/viguno/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/viguno/meta.yaml b/recipes/viguno/meta.yaml index 070e91018abd5..aee151869b737 100644 --- a/recipes/viguno/meta.yaml +++ b/recipes/viguno/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.1.6" %} -{% set sha256 = "c4696ba9dab271216b80c560f78cddf8e0010474b7d7b8b6c717e666fd13cebd" %} +{% set version = "0.2.0" %} +{% set sha256 = "a4217f7ba34d55cda76b392e774be8392c18d550e752eb9db81e6cc3afa53010" %} package: name: viguno @@ -8,6 +8,8 @@ package: build: skip: True # [osx] number: 0 + run_exports: + - {{ pin_subpackage("viguno", max_pin="x.x") }} source: url: https://github.com/bihealth/viguno/archive/v{{ version }}.tar.gz From 264014b3a65308e1a07b9fb8a0a99200367b4083 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Dec 2023 12:59:59 -0500 Subject: [PATCH 1359/2173] Update annonars to 0.32.0 (#45013) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 6a78e3c350db0..7cd859e346249 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.31.2" %} +{% set version = "0.32.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: c7d953633d77c3c46cf3d9417e9b8e6d67afac2a529dea0e342da3d8bb0d6680 + sha256: 467ebd15737c4a6451f5993fa1e93f52c5ecb4a1cdf0b0cd754b414261730f37 requirements: build: From 02cfff55f5bdf1296b55e4e28376d1095d600bb8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=A3o=20Sequeira?= Date: Fri, 29 Dec 2023 01:30:44 +0000 Subject: [PATCH 1360/2173] Fix recognizer (#45012) * Update recognizer to 1.10.0 * Update meta.yaml No more build.sh file * Update meta.yaml Forgot about the other TSV files * Removed build.sh --------- Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> --- recipes/recognizer/build.sh | 7 ------- recipes/recognizer/meta.yaml | 10 ++++++++-- 2 files changed, 8 insertions(+), 9 deletions(-) delete mode 100644 recipes/recognizer/build.sh diff --git a/recipes/recognizer/build.sh b/recipes/recognizer/build.sh deleted file mode 100644 index 96dd646713b92..0000000000000 --- a/recipes/recognizer/build.sh +++ /dev/null @@ -1,7 +0,0 @@ -dir="${PREFIX}/share" -mkdir -p "${dir}" -mkdir -p "${PREFIX}/bin" -cp recognizer.py "${dir}" -cp -r resources/* "${dir}" -chmod +x "${dir}/recognizer.py" -ln -s "${dir}/recognizer.py" "${PREFIX}/bin/recognizer" diff --git a/recipes/recognizer/meta.yaml b/recipes/recognizer/meta.yaml index e894c66dab43d..c8acd63dc115b 100644 --- a/recipes/recognizer/meta.yaml +++ b/recipes/recognizer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "recognizer" %} -{% set version = "1.9.4" %} -{% set sha256 = "36c3f08fff9c5eff6bf45491b3332eee44507d08f9839766b4fe81eeb8715630" %} +{% set version = "1.10.0" %} +{% set sha256 = "7f001a4fb888777a7b14707f76458f25fc98fe14299d1bdcbf2452eba7cab75f" %} package: name: {{ name|lower }} @@ -15,6 +15,12 @@ build: number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x") }} + script: > + mkdir -p $PREFIX/bin && + mkdir -p $PREFIX/share && + cp recognizer.py resources/*.tsv $PREFIX/share && + chmod +x $PREFIX/share/recognizer.py && + ln -s $PREFIX/share/recognizer.py $PREFIX/bin/recognizer requirements: run: From 1d887da2b72dde3b441defe4b0bf84ee2e12ba79 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Dec 2023 20:31:52 -0500 Subject: [PATCH 1361/2173] Update last to 1522 (#45011) --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 2c8181378c734..673ba234ef336 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1521" %} +{% set version = "1522" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: dcfe5339f048f635f02326d181e086469c16e54a0f674c5df814c4d54236fc26 + sha256: 0cc27dce53693c4d97864c012f9b9b34e4c02ebd0c38db23c5c5d978dbfd4d4e build: number: 0 From 28beeda5282ff1a81d32d0ff97856d6633f94403 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 28 Dec 2023 20:32:05 -0500 Subject: [PATCH 1362/2173] Update pcaone to 0.4.1 (#45009) --- recipes/pcaone/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml index 636c605ed4401..3f67d9dbac7c4 100644 --- a/recipes/pcaone/meta.yaml +++ b/recipes/pcaone/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.0" %} -{% set sha256 = "b6bf45c20dddcc42811dcc902c7d92c5901d03fb4c69675ee8da39b3c92763a9" %} +{% set version = "0.4.1" %} +{% set sha256 = "03f8afa9870507e03aa90a349a00f70f56bbf202b05a4d3d648148f3c30b6518" %} package: From 7930bc49304a8e6d73c5bf561b535a5360f24809 Mon Sep 17 00:00:00 2001 From: stuber Date: Thu, 28 Dec 2023 18:32:36 -0700 Subject: [PATCH 1363/2173] genoflu version 1.02 (#44995) * genoflu version 1.02 * Update meta.yaml * Update meta.yaml * https://spdx.org/licenses/GPL-3.0-or-later.html --------- Co-authored-by: Thanh Lee --- recipes/genoflu/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/genoflu/meta.yaml b/recipes/genoflu/meta.yaml index 9b8cdc7c00314..c7e66039d4536 100644 --- a/recipes/genoflu/meta.yaml +++ b/recipes/genoflu/meta.yaml @@ -1,8 +1,8 @@ {% set user = "USDA-VS" %} {% set name = "GenoFLU" %} -{% set version = "1.01" %} -{% set sha256 = "c97ad073c2cf14f1c14f1a705ddc3817189c30f03239ba97b068a1ddab90ceb8" %} +{% set version = "1.02" %} +{% set sha256 = "8cae43be805ee1822d6acc3d1d51a7c4445c5252b5004ab700b7f807fc78070d" %} package: name: {{ name|lower }} @@ -11,6 +11,8 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('genoflu', max_pin="x") }} source: url: https://github.com/{{ user }}/{{ name }}/archive/{{ version }}.tar.gz @@ -30,7 +32,7 @@ test: about: home: https://github.com/{{ user }}/{{ name }} - license: GPL3 + license: GPL-3.0-or-later license_file: LICENSE summary: Influenza data pipeline to automate genotyping assignment. - dev_url: https://github.com/USDA-VS/GenoFLU \ No newline at end of file + dev_url: https://github.com/USDA-VS/GenoFLU From 4bdfaf64842ca2a441ee4277b25c4d2cb7db81d7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 05:58:17 -0500 Subject: [PATCH 1364/2173] Update chromhmm to 1.25 (#45016) * Update chromhmm to 1.25 * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/chromhmm/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/chromhmm/meta.yaml b/recipes/chromhmm/meta.yaml index 76da70b8016ab..22303f5fee131 100644 --- a/recipes/chromhmm/meta.yaml +++ b/recipes/chromhmm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ChromHMM" %} -{% set version = "1.24" %} +{% set version = "1.25" %} package: name: {{ name|lower }} @@ -8,10 +8,12 @@ package: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('chromhmm', max_pin=None) }} source: url: https://github.com/jernst98/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 84e14ebb78c197abe946007e72965296980339d4e3155604bf6c6734319af30c + sha256: 96b5773f7400835f16cc1d86d4e42e6dcc038e74569311cd73da2d5c5002a5d2 requirements: run: @@ -27,6 +29,7 @@ about: home: https://github.com/jernst98/ChromHMM license: GPLv3 summary: 'ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks.' + license_file: LICENSE extra: notes: 'ChromHMM comes with about 36MB of example data which is not included in the recipe. This recipe installs a script, "download_chromhmm_data.sh", which downloads the data in the proper location, and which can be run after ChromHMM has been installed.' From df9f17acaebbd24dc72e18082e105f31c0d324cd Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Fri, 29 Dec 2023 23:42:46 +0900 Subject: [PATCH 1365/2173] Update ColabFold to 1.5.5 (#45008) * Update ColabFold to 1.5.4 * Use 1.5.5 instead, 1.5.4 had a bug * OpenMM 8.1 causes issues --- recipes/colabfold/fix-jax-04-nan.patch | 20 ------------------ recipes/colabfold/meta.yaml | 28 +++++++++++--------------- 2 files changed, 12 insertions(+), 36 deletions(-) delete mode 100644 recipes/colabfold/fix-jax-04-nan.patch diff --git a/recipes/colabfold/fix-jax-04-nan.patch b/recipes/colabfold/fix-jax-04-nan.patch deleted file mode 100644 index 9065fc61d3154..0000000000000 --- a/recipes/colabfold/fix-jax-04-nan.patch +++ /dev/null @@ -1,20 +0,0 @@ -diff --git a/alphafold/model/modules.py b/alphafold/model/modules.py -index 73f9cdd..4ca8827 100644 ---- a/alphafold/model/modules.py -+++ b/alphafold/model/modules.py -@@ -672,6 +672,7 @@ class Attention(hk.Module): - logits = jnp.einsum('bqhc,bkhc->bhqk', q, k) + bias - if nonbatched_bias is not None: - logits += jnp.expand_dims(nonbatched_bias, axis=0) -+ logits = jnp.clip(logits, -1e8, 1e8) - weights = jax.nn.softmax(logits) - weighted_avg = jnp.einsum('bhqk,bkhc->bqhc', weights, v) - -@@ -771,6 +772,7 @@ class GlobalAttention(hk.Module): - k = jnp.einsum('bka,ac->bkc', m_data, k_weights) - bias = (1e9 * (q_mask[:, None, :, 0] - 1.)) - logits = jnp.einsum('bhc,bkc->bhk', q, k) + bias -+ logits = jnp.clip(logits, -1e8, 1e8) - weights = jax.nn.softmax(logits) - weighted_avg = jnp.einsum('bhk,bkc->bhc', weights, v) - diff --git a/recipes/colabfold/meta.yaml b/recipes/colabfold/meta.yaml index 11697a3be4d8f..c8c5024145ad6 100644 --- a/recipes/colabfold/meta.yaml +++ b/recipes/colabfold/meta.yaml @@ -1,7 +1,7 @@ -{% set cf_version = "1.5.3" %} -{% set cf_hash = "1b2776f285981796559effbc3691ebbcfcde68514cc05559583ebab76c4c25e8" %} -{% set af_version = "2.3.5" %} -{% set af_hash = "6244c2143987dd4a6a87c1174c7a801c220034fbeb8d13f901b0f950b69d8543" %} +{% set cf_version = "1.5.5" %} +{% set cf_hash = "7fb0ad263c24ec00d46f2dff1611989234bc1351d71653dd06006f2c88f83dcb" %} +{% set af_version = "2.3.6" %} +{% set af_hash = "a5674257d92928511d70f94ec3261e275cb3442a7762b5210e01f445692d2182" %} package: name: colabfold @@ -14,7 +14,7 @@ build: python -m pip install --no-deps --ignore-installed alphafold/ run_exports: - {{ pin_subpackage('colabfold', max_pin="x") }} - number: 1 + number: 0 source: - url: https://github.com/sokrypton/ColabFold/archive/refs/tags/v{{ cf_version }}.tar.gz @@ -23,14 +23,12 @@ source: - url: https://github.com/steineggerlab/alphafold/archive/refs/tags/v{{ af_version }}.tar.gz sha256: {{ af_hash }} folder: alphafold - patches: - - fix-jax-04-nan.patch requirements: host: - pip - python - - poetry + - poetry-core >=1.0.0 run: - python - absl-py @@ -42,20 +40,18 @@ requirements: - pandas - appdirs - py3Dmol - - dm-haiku - dm-tree - ml-collections - - immutabledict - importlib-metadata - - biopython - - jax ==0.4.14 - - jaxlib ==0.4.14 - - chex ==0.1.8 - - tensorflow ==2.12.1=cpu* + - dm-haiku ==0.0.10 + - biopython <=1.82 + - jax >=0.4.14 + - jaxlib >=0.4.14 + - tensorflow >=2.12.1=cpu* - mmseqs2 >=15.6f452 - kalign2 >=2.04 - hhsuite >=3.3.0 - - openmm ==7.7.0 + - openmm >=7.7.0,<8.1.0 - pdbfixer test: From 38e48a39dbd65c525aa05be8fee236ec66642bd2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 10:32:41 -0500 Subject: [PATCH 1366/2173] Update expam to 1.2.2.4 (#45007) * Update expam to 1.2.2.4 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/expam/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/expam/meta.yaml b/recipes/expam/meta.yaml index a078e57679269..01df06215fcbd 100644 --- a/recipes/expam/meta.yaml +++ b/recipes/expam/meta.yaml @@ -1,5 +1,5 @@ {% set name = "expam" %} -{% set version = "1.2.2.3" %} +{% set version = "1.2.2.4" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1a57cd160115ead399bd1b577dd071e0142d31e09df982c83c017e6ddfabcf96 + sha256: c33b249351c13fd3cfcbd0b2411a9d61e5e1e6239d5b841c2d980dcb9a88debc build: number: 0 skip: true # [py < 38] - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('expam', max_pin="x") }} requirements: build: From 843a8fd3d978765a92e6888747b2f4c2c667748a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 10:35:33 -0500 Subject: [PATCH 1367/2173] Update upimapi to 1.13.1 (#45019) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: João Sequeira --- recipes/upimapi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/upimapi/meta.yaml b/recipes/upimapi/meta.yaml index 5ce94c96013c9..c146f7d09c704 100644 --- a/recipes/upimapi/meta.yaml +++ b/recipes/upimapi/meta.yaml @@ -1,6 +1,6 @@ {% set name = "upimapi" %} -{% set version = "1.13.0" %} -{% set sha256 = "0460d1f9485a05cab875521991feb43c4835b637e4955cba6e85abc9a01defe5" %} +{% set version = "1.13.1" %} +{% set sha256 = "72fd88f6c21b6982071c007e9ce9a92ffe2bbc75edff3f6eddcfb0653bced0d4" %} package: name: {{ name|lower }} From 8d86dab00ebf2b619821f0fe00ce993912dfbe54 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Fri, 29 Dec 2023 17:07:55 +0100 Subject: [PATCH 1368/2173] Update raptor (#44952) multiple binaries and a wrapper scripts depending on available instruction sets. --- recipes/raptor/build.sh | 47 +++++++++++++++++++++++++++++++++++----- recipes/raptor/meta.yaml | 2 +- recipes/raptor/raptor | 30 +++++++++++++++++++++++++ 3 files changed, 73 insertions(+), 6 deletions(-) create mode 100644 recipes/raptor/raptor diff --git a/recipes/raptor/build.sh b/recipes/raptor/build.sh index ae27ae77a6465..ea27c80c990bb 100644 --- a/recipes/raptor/build.sh +++ b/recipes/raptor/build.sh @@ -1,7 +1,44 @@ #!/bin/bash -mkdir -p build -cd build -cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-mavx2 -D__STDC_FORMAT_MACROS" -DRAPTOR_NATIVE_BUILD=OFF -DCMAKE_INSTALL_PREFIX="${PREFIX}" -make -j"${CPU_COUNT}" -make install +set -eux + +get_instruction_set_flags() { + local instruction_set="$1" + case "${instruction_set}" in + none) + echo "" + ;; + sse2) + echo "-msse2" + ;; + sse4.2) + echo "-msse4.2" + ;; + avx2) + echo "-mavx2" + ;; + avx512) + echo "-mavx512f -mavx512bw" + ;; + *) + echo "Unknown instruction set: ${instruction_set}" >&2 + exit 1 + ;; + esac +} + +for INSTRUCTION_SET in "none" "sse2" "sse4.2" "avx2" "avx512"; do + mkdir -p build/${INSTRUCTION_SET} + cd build/${INSTRUCTION_SET} + cmake ../.. -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_CXX_FLAGS="$(get_instruction_set_flags ${INSTRUCTION_SET}) -Wno-interference-size -D__STDC_FORMAT_MACROS" \ + -DRAPTOR_NATIVE_BUILD=OFF \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" + make -j"${CPU_COUNT}" + make install + mv "${PREFIX}/bin/raptor" "${PREFIX}/bin/raptor_${INSTRUCTION_SET}" + cd ../.. +done + +cp "${RECIPE_DIR}/raptor" "${PREFIX}/bin/raptor" +chmod +x "${PREFIX}/bin/raptor" diff --git a/recipes/raptor/meta.yaml b/recipes/raptor/meta.yaml index 60599432442f1..0b38ef4ed151c 100644 --- a/recipes/raptor/meta.yaml +++ b/recipes/raptor/meta.yaml @@ -10,7 +10,7 @@ source: sha256: be44e7b2635e110c940cf40ff132956200551a2e25765d9f057e844f7a3ccebb build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/raptor/raptor b/recipes/raptor/raptor new file mode 100644 index 0000000000000..180b5b084c99f --- /dev/null +++ b/recipes/raptor/raptor @@ -0,0 +1,30 @@ +#!/bin/bash + +set -eu + +# -c : return count +# -m 1 : stop after first match, i.e. count is either 0 or 1 +# -E : use extended regular expressions +# \b : matches any non alphanumeric character, i.e. space, tab, newline, etc. +HAS_SSE2=$(grep -c -m 1 -E '\bsse2\b' /proc/cpuinfo) +HAS_SSE4_2=$(grep -c -m 1 -E '\bsse4_2\b' /proc/cpuinfo) +HAS_AVX2=$(grep -c -m 1 -E '\bavx2\b' /proc/cpuinfo) +HAS_AVX512F=$(grep -c -m 1 -E '\bavx512f\b' /proc/cpuinfo) +HAS_AVX512BW=$(grep -c -m 1 -E '\bavx512bw\b' /proc/cpuinfo) +if [ ${HAS_AVX512F} -eq 1 ] && [ ${HAS_AVX512BW} -eq 1 ]; then + HAS_AVX512=1 +else + HAS_AVX512=0 +fi + +if [ ${HAS_AVX512} -eq 1 ]; then + raptor_avx512 "$@" +elif [ ${HAS_AVX2} -eq 1 ]; then + raptor_avx2 "$@" +elif [ ${HAS_SSE4_2} -eq 1 ]; then + raptor_sse4.2 "$@" +elif [ ${HAS_SSE2} -eq 1 ]; then + raptor_sse2 "$@" +else + raptor_none "$@" +fi From 54e0ae75fc13b47aaeb4d54c7d2ecc9d2e1eb685 Mon Sep 17 00:00:00 2001 From: Ray <851836818@qq.com> Date: Sat, 30 Dec 2023 00:58:06 +0800 Subject: [PATCH 1369/2173] add AnnoSINE2 recipes (#44980) * add strainscan recipes * add annosine2 recipes * Delete recipes/strainscan/meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/annosine2/meta.yaml | 59 +++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 recipes/annosine2/meta.yaml diff --git a/recipes/annosine2/meta.yaml b/recipes/annosine2/meta.yaml new file mode 100644 index 0000000000000..9c474c8c73b80 --- /dev/null +++ b/recipes/annosine2/meta.yaml @@ -0,0 +1,59 @@ +{% set name = "annosine2" %} +{% set version = "1.0.4" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: c9d12adec9875c4a429c6e9da5b76d31c760ef7474635caf742d25592378f34c + +build: + number: 0 + entry_points: + - annosine2 = AnnoSINE.AnnoSINE_v2:main + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + run_exports: + - {{ pin_subpackage('annosine2', max_pin="x") }} + noarch: python + +requirements: + host: + - pip + - python + run: + - cycler ==0.10.0 + - kiwisolver + - matplotlib-base + - numpy + - pillow + - pyparsing + - python + - python-dateutil + - six + - hmmer ==3.3.1 + - minimap2 ==2.26 + - nodejs ==18.12.1 + - trf ==4.09 + - irf ==3.08 + - cd-hit ==4.8.1 + - repeatmasker ==4.1.2.p1 + - seqtk ==1.4 + + +test: + imports: + - AnnoSINE + commands: + - annosine2 --help + +about: + home: https://github.com/liaoherui/AnnoSINE + license: MIT + license_family: MIT + summary: AnnoSINE2 - SINE Annotation Tool for Plant and Animal Genomes + +extra: + recipe-maintainers: + - liaoherui From 8b32ec89d796edb448cf9600b7e30bbde49009a7 Mon Sep 17 00:00:00 2001 From: "Alicia A. Evans" <108547992+aliciaaevans@users.noreply.github.com> Date: Fri, 29 Dec 2023 12:38:56 -0500 Subject: [PATCH 1370/2173] Bulk (#45014) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * a round of fixes and build-skips * add some build failures * correct version for bioconductor-data-packages * add build failure for STdeconvolve * [ci run] trigger bulk run * run_exports on bioconductor-data-packages * [ci run] trigger bulk run * build failure for omnipathr * [ci run] trigger bulk run * Build important packages first * [ci run] trigger bulk run * revert to full build * [ci run] trigger bulk run * build failure files * skip iclusterplus * skip bioconductor-lpsymphony * bump bioconda-repodata-patches build number * [ci run] * build failures * next round of high priority packages * [ci run] trigger bulk run * [ci run] add dependency * [ci run] finish priority packages * re-enable full bulk * [ci run] trigger bulk run * build failures * [ci run] trigger bulk run * next round of high priority packages * [ci run] trigger bulk run * build more high priority packages * [ci run] test local channel fix * [ci run] increase workers * Try building bioconductor-geoquery (#44726) * Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml * Update meta.yaml * try fixing parsing error * [ci run] try rebuilding bioconductor-coregx (#44727) * try rebuilding bioconductor-coregx * Update meta.yaml * add opencl loading libraries - will this work * [ci run] remove a few build failure files * [ci run] Bioconductor graph (#44733) * remove build failure file * trigger build * Update meta.yaml * add patch back [ci run] * build failures * [ci run] high priority packages * bulk wiki page * [ci run] add missing packges * build failure for bioconductor-sictools * [ci run] missed one * [ci run] full run * Update build.sh * [ci run] fix dexseq * [ci run] next round of high priority packages * [ci run] missing packages * [ci run] high priority package * [ci run] build all bioconductor-bsgenome * [ci run] remove failures associated with bioconductor-bsgenome dependency * full build * use bioconda-common version * build failures: test dev version of utils * escape characters correctly * build failure for bioconductor-pics * use branch * build failure for bioconductor-inspect * try to fix build failure git range * build failure for bioconductor-distinct * use head branch * trigger build failure wf * [ci run] trigger bulk run * build failures fetch depth * build failure for biconductor-benchdamic * build failures * build failures with log * don't run build failures if last commit has ci skip * [ci skip] test build failure wiki * test build failure wiki job * [ci run] reenable record-build-failures * re-add token for build failure updates * build failures add category column * trigger wiki update * fix libsbml version for bioconductor-rsbml * build failure updates * fix bioconductor-glad * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-wppi * [ci skip] add build failure record for recipe recipes/bioconductor-gars * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-metascope * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader * [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r * [ci skip] add build failure record for recipe recipes/bioconductor-gesper * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-seqcna * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-inpas * [ci skip] add build failure record for recipe recipes/bioconductor-factr * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble * [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile * [ci skip] add build failure record for recipe recipes/bioconductor-extrachips * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc * [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats * [ci skip] add build failure record for recipe recipes/bioconductor-chipqc * [ci skip] add build failure record for recipe recipes/bioconductor-outsplice * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-circseqaligntk * [ci skip] add build failure record for recipe recipes/bioconductor-ritan * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-vulcan * [ci skip] add build failure record for recipe recipes/bioconductor-singlecelltk * [ci skip] add build failure record for recipe recipes/bioconductor-scfeatures * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-deconvr * [ci skip] add build failure record for recipe recipes/bioconductor-ideal * [ci skip] add build failure record for recipe recipes/bioconductor-esatac * [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr * [ci skip] add build failure record for recipe recipes/bioconductor-inetgrate * [ci skip] add build failure record for recipe recipes/bioconductor-ataccogaps * [ci skip] add build failure record for recipe recipes/bioconductor-lemur * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-regionreport * [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-cageminer * [ci skip] add build failure record for recipe recipes/bioconductor-multicrispr * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-scpipe * Rbowtie2 (#44856) [ci run] fix rbowtie2 builds * [ci run] remove build file * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] remove build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * failure for bioconda-multirnaflow * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * bioconductor-lpsymphony fix from master * remove build failures for finished dependencies * restore skip osx-64 * fix bioconductor-rawrr * high priority packages * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] remove build failure record for recipe recipes/bioconductor-proloc * fix bioconductor-chemmineob * [ci run] remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * remove easy build failures * [ci run] next round of dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-pigengene * [ci skip] add build failure record for recipe recipes/bioconductor-repitools * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * build failure updates * [ci run] next batch of fixes * [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2 * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run]remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-gatom * [ci run] set failures to skip * [ci run] reduce resources that are wasted * [ci skip] add build failure record for recipe recipes/bioconductor-pd.barley1 * fix accidental reverts * add GSL to bioconductor-pics * add back fix from master for omnipathr * remove build failure * [ci run] skip root nodes to spread out builds * [ci run] include more root nodes in blacklist * update build failures * [ci run] add more blacklist items and do osx build * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * [ci skip] add build failure record for recipe recipes/bioconductor-mumosa * [ci skip] add build failure record for recipe recipes/bioconductor-chromscape * [ci skip] add build failure record for recipe recipes/bioconductor-scmerge * [ci skip] add build failure record for recipe recipes/bioconductor-tadcompare * fix build errors * [ci run] more skipped builds * [ci skip] add build failure record for recipe recipes/bioconductor-cghmcr * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-ccpromise * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-interactivedisplay * [ci run] reduce workers * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-tbsignatureprofiler * [ci run] manually distribute packages * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-condiments * [ci skip] add build failure record for recipe recipes/bioconductor-scclassify * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-gcapc * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-traviz * remove build failures * remove colon that breaks yaml parsing * remove temporary bioconductor bulk skips * [ci run] remaining packages * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-promise * [ci skip] add build failure record for recipe recipes/bioconductor-otubase * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * retry http error * [ci run] full bulk build * [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer * [ci skip] remove build failure record for recipe recipes/bioconductor-meb * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci run] categorize failures * add bioconductor-cdi * remove old failure files * update bioconductor-reusedata to 3.18 * remove failures for dependencies that have been built * [ci run] build certain packages * bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (#44986) * update bioconductor-ccfindr with gsl * update bioconductor-rjmcmcnucleosomes with gsl * [ci run] build updated recipes * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-reusedata * remove temporary changes from workflows * build got bumped in merge * remove temp files --------- Co-authored-by: Ryan Dale Co-authored-by: Björn Grüning Co-authored-by: Bjoern Gruening Co-authored-by: BiocondaBot --- .github/workflows/Bulk.yml | 14 +- .github/workflows/build-failures.yml | 2 +- build-fail-blacklist | 4 + recipes/bioconductor-a4/meta.yaml | 27 +-- recipes/bioconductor-a4base/meta.yaml | 35 ++-- recipes/bioconductor-a4classif/meta.yaml | 19 +- recipes/bioconductor-a4core/meta.yaml | 11 +- recipes/bioconductor-a4preproc/meta.yaml | 15 +- recipes/bioconductor-a4reporting/meta.yaml | 9 +- recipes/bioconductor-abarray/meta.yaml | 15 +- recipes/bioconductor-abseqr/meta.yaml | 15 +- recipes/bioconductor-absseq/meta.yaml | 11 +- recipes/bioconductor-acde/meta.yaml | 7 +- recipes/bioconductor-ace/meta.yaml | 19 +- recipes/bioconductor-acgh/meta.yaml | 15 +- recipes/bioconductor-acme/meta.yaml | 15 +- 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recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml create mode 100644 recipes/pxblat/build_failure.linux-64.yaml create mode 100644 recipes/pxblat/build_failure.osx-64.yaml create mode 100644 recipes/r-interpretmsspectrum/meta.yaml diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 0ccdf6aa9c9d3..e8eeb8712145d 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -15,7 +15,10 @@ jobs: runner: [0, 1, 2, 3, 4, 5] steps: - uses: actions/checkout@v3 - + with: + # checkout as BiocondaBot in order to have the permission to push fail logs + token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} + - name: set git user run: | git config user.name BiocondaBot @@ -68,7 +71,7 @@ jobs: bioconda-utils build recipes config.yml \ --worker-offset ${{ matrix.runner }} --n-workers 6 \ --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \ - --record-build-failures --skiplist-leafs + --lint --record-build-failures --skiplist-leafs conda clean -y --all build-osx: @@ -82,7 +85,10 @@ jobs: runner: [0, 1, 2, 3] steps: - uses: actions/checkout@v3 - + with: + # checkout as BiocondaBot in order to have the permission to push fail logs + token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} + - name: set git user run: | git config user.name BiocondaBot @@ -139,5 +145,5 @@ jobs: echo '============' bioconda-utils build recipes config.yml \ --worker-offset ${{ matrix.runner }} --n-workers 4 \ - --anaconda-upload --record-build-failures --skiplist-leafs + --lint --anaconda-upload --record-build-failures --skiplist-leafs conda clean -y --all diff --git a/.github/workflows/build-failures.yml b/.github/workflows/build-failures.yml index 3fcdc275e6547..5037e91ec987e 100644 --- a/.github/workflows/build-failures.yml +++ b/.github/workflows/build-failures.yml @@ -64,4 +64,4 @@ jobs: OWNER: bioconda REPO_NAME: bioconda-recipes MD_FOLDER: build-failures - + \ No newline at end of file diff --git a/build-fail-blacklist b/build-fail-blacklist index e043d8ad3088c..31d92e56cbae9 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1,3 +1,7 @@ +# ----- 2023-12-02 problematic on bulk ----- +r-ramclustr +# ------------------------------------------ + # Currently kills bulk, and dependants recipes/bioconductor-missmethyl recipes/bioconductor-conumee diff --git a/recipes/bioconductor-a4/meta.yaml b/recipes/bioconductor-a4/meta.yaml index 5b8e67556e076..5ce9102925ae3 100644 --- a/recipes/bioconductor-a4/meta.yaml +++ b/recipes/bioconductor-a4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5d945210d12e19d845e8949ef53b9d43 + md5: 54c9c4300db0c04edd9b531bb0f121a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4", max_pin="x.x") }}' noarch: generic # Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats requirements: host: - - 'bioconductor-a4base >=1.48.0,<1.49.0' - - 'bioconductor-a4classif >=1.48.0,<1.49.0' - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-a4reporting >=1.48.0,<1.49.0' + - 'bioconductor-a4base >=1.50.0,<1.51.0' + - 'bioconductor-a4classif >=1.50.0,<1.51.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-a4reporting >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-a4base >=1.48.0,<1.49.0' - - 'bioconductor-a4classif >=1.48.0,<1.49.0' - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-a4reporting >=1.48.0,<1.49.0' + - 'bioconductor-a4base >=1.50.0,<1.51.0' + - 'bioconductor-a4classif >=1.50.0,<1.51.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-a4reporting >=1.50.0,<1.51.0' - r-base test: commands: diff --git a/recipes/bioconductor-a4base/meta.yaml b/recipes/bioconductor-a4base/meta.yaml index c3bc1ab6eee23..8d52ef862f80d 100644 --- a/recipes/bioconductor-a4base/meta.yaml +++ b/recipes/bioconductor-a4base/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4Base" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4727840ebfa0c2fdb548b54320e4e39 + md5: 927ee5147653a1ee4df6380f52ad055a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4base", max_pin="x.x") }}' noarch: generic # Suggests: Cairo, ALL, hgu95av2.db, nlcv requirements: host: - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-annaffy >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-annaffy >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-glmnet - r-gplots - r-mpm run: - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-annaffy >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-annaffy >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-glmnet - r-gplots diff --git a/recipes/bioconductor-a4classif/meta.yaml b/recipes/bioconductor-a4classif/meta.yaml index 7690f421f98f1..c519e2749143a 100644 --- a/recipes/bioconductor-a4classif/meta.yaml +++ b/recipes/bioconductor-a4classif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4Classif" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 44dc4f5d280303effaedb954307fb336 + md5: 2af82160c9909dd6fdec620de5710cfa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4classif", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db, knitr, rmarkdown requirements: host: - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-glmnet - r-pamr - r-rocr - r-varselrf run: - - 'bioconductor-a4core >=1.48.0,<1.49.0' - - 'bioconductor-a4preproc >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-a4core >=1.50.0,<1.51.0' + - 'bioconductor-a4preproc >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-glmnet - r-pamr diff --git a/recipes/bioconductor-a4core/meta.yaml b/recipes/bioconductor-a4core/meta.yaml index b0135089b2ee1..581eed71adc05 100644 --- a/recipes/bioconductor-a4core/meta.yaml +++ b/recipes/bioconductor-a4core/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4Core" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f0cb8b9e0ac23f1cd176b17c4ef84aa + md5: fdca418afe3a74d9114d8d28afca2037 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4core", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-glmnet run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-glmnet test: diff --git a/recipes/bioconductor-a4preproc/meta.yaml b/recipes/bioconductor-a4preproc/meta.yaml index 3efdd56e61c2f..06b428d18d822 100644 --- a/recipes/bioconductor-a4preproc/meta.yaml +++ b/recipes/bioconductor-a4preproc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4Preproc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 268368ed5be41d5484b7b5967e2fa716 + md5: 5d9eea3d9957fc99156115052398f0cb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4preproc", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-a4reporting/meta.yaml b/recipes/bioconductor-a4reporting/meta.yaml index 6c2d318ba1aa4..2da455e03ce4c 100644 --- a/recipes/bioconductor-a4reporting/meta.yaml +++ b/recipes/bioconductor-a4reporting/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "a4Reporting" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aace068e89a5238b844b694e81ef185b + md5: 3ba7f3c5606c2f898d84314ba63208fa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-a4reporting", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-abarray/meta.yaml b/recipes/bioconductor-abarray/meta.yaml index cd518fd3629fd..7e528a9709f81 100644 --- a/recipes/bioconductor-abarray/meta.yaml +++ b/recipes/bioconductor-abarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "ABarray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2ae9c221317ee561584dec59cd0ed37 + md5: 59e686f9daf6990fbe6e1594b8676197 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-abarray", max_pin="x.x") }}' noarch: generic # Suggests: limma, LPE requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-abseqr/meta.yaml b/recipes/bioconductor-abseqr/meta.yaml index 48cccf87678f5..da20a9a3cd15d 100644 --- a/recipes/bioconductor-abseqr/meta.yaml +++ b/recipes/bioconductor-abseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "abseqR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aef896b0c639d90e59a64148f07587c5 + md5: f35214f635511b611297a3730386b205 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-abseqr", max_pin="x.x") }}' noarch: generic # Suggests: testthat # SystemRequirements: pandoc (>= 1.19.2.1) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base - r-circlize - r-flexdashboard @@ -43,8 +44,8 @@ requirements: - r-venndiagram - 'pandoc >=1.19.2.1' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base - r-circlize - r-flexdashboard diff --git a/recipes/bioconductor-absseq/meta.yaml b/recipes/bioconductor-absseq/meta.yaml index bac5358be9274..7b51b8e054377 100644 --- a/recipes/bioconductor-absseq/meta.yaml +++ b/recipes/bioconductor-absseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ABSSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e0e0790ae5c6424bf69ba5b2aa334204 + md5: d170bf2f9a37dcdffd2d91e233ce5132 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-absseq", max_pin="x.x") }}' noarch: generic # Suggests: edgeR requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit test: diff --git a/recipes/bioconductor-acde/meta.yaml b/recipes/bioconductor-acde/meta.yaml index 8a7985595713d..2d4644f22d888 100644 --- a/recipes/bioconductor-acde/meta.yaml +++ b/recipes/bioconductor-acde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "acde" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7902aed44029d52dacbac22cba66509c + md5: 9a324caddfceb2aa977e0fc9e7e41615 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-acde", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit requirements: diff --git a/recipes/bioconductor-ace/meta.yaml b/recipes/bioconductor-ace/meta.yaml index bb78545967250..9befebeb13c7e 100644 --- a/recipes/bioconductor-ace/meta.yaml +++ b/recipes/bioconductor-ace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ACE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0403b6c89b9bcf3502feed89309e5922 + md5: dd177150c01a5547ca8edabf82ef85d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ace", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base - r-ggplot2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-acgh/meta.yaml b/recipes/bioconductor-acgh/meta.yaml index c0be97797e3a6..ce96cf84127e5 100644 --- a/recipes/bioconductor-acgh/meta.yaml +++ b/recipes/bioconductor-acgh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "aCGH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4e5a21eaeab73202b57967602d0d19e + md5: 137af76dc5756a83094da18eb0bededa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-acgh", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-cluster - r-survival - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-cluster - r-survival diff --git a/recipes/bioconductor-acme/meta.yaml b/recipes/bioconductor-acme/meta.yaml index 701e468e22498..1a43fedf23501 100644 --- a/recipes/bioconductor-acme/meta.yaml +++ b/recipes/bioconductor-acme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.56.0" %} +{% set version = "2.58.0" %} {% set name = "ACME" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ccefadaea2ecb53dcede052ddb6846b2 + md5: 6668a82e0a26ac03c9697e2cf22eb75e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-acme", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-adacgh2/meta.yaml b/recipes/bioconductor-adacgh2/meta.yaml index 5b1d78c12bba2..1c71ce07f7657 100644 --- a/recipes/bioconductor-adacgh2/meta.yaml +++ b/recipes/bioconductor-adacgh2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "ADaCGH2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef58db06870d692ea9b0d7a065d0542d + md5: 0ce28a95b156205f60eeda851b36c958 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adacgh2", max_pin="x.x") }}' # Suggests: CGHregions, Cairo, limma requirements: host: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-snapcgh >=1.70.0,<1.71.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-snapcgh >=1.72.0,<1.73.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base - r-bit - r-cluster @@ -33,11 +34,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-snapcgh >=1.70.0,<1.71.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-snapcgh >=1.72.0,<1.73.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base - r-bit - r-cluster diff --git a/recipes/bioconductor-adam/meta.yaml b/recipes/bioconductor-adam/meta.yaml index 15009172ba8e2..ecee8bcc2ce80 100644 --- a/recipes/bioconductor-adam/meta.yaml +++ b/recipes/bioconductor-adam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "ADAM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d93cb7a12ab64f41db64cacdef965abe + md5: 7f051085afca603520dbb5cb010e58fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adam", max_pin="x.x") }}' # Suggests: testthat, rmarkdown, BiocStyle # SystemRequirements: C++11 requirements: host: - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=0.7.6' - 'r-dt >=0.4' @@ -34,9 +35,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=0.7.6' - 'r-dt >=0.4' diff --git a/recipes/bioconductor-adamgui/meta.yaml b/recipes/bioconductor-adamgui/meta.yaml index ebf62d0541668..d9cd81c8fabd7 100644 --- a/recipes/bioconductor-adamgui/meta.yaml +++ b/recipes/bioconductor-adamgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "ADAMgui" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c733676eecd9e6fe3acf3918534ee220 + md5: d6b76d93be7f193cd913f44f6ff41a64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adamgui", max_pin="x.x") }}' noarch: generic # Suggests: markdown, BiocStyle requirements: host: - - 'bioconductor-adam >=1.16.0,<1.17.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-adam >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - 'r-colorramps >=2.3' - 'r-data.table >=1.11.4' @@ -43,8 +44,8 @@ requirements: - r-testthat - 'r-varhandle >=2.0.3' run: - - 'bioconductor-adam >=1.16.0,<1.17.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-adam >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - 'r-colorramps >=2.3' - 'r-data.table >=1.11.4' diff --git a/recipes/bioconductor-adductdata/meta.yaml b/recipes/bioconductor-adductdata/meta.yaml index 63ebe10e796a1..ad2a3978ce00b 100644 --- a/recipes/bioconductor-adductdata/meta.yaml +++ b/recipes/bioconductor-adductdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "adductData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abd834104d02465a0f32a64be9974c64 + md5: bf0e3549ee672a31f32759f0535f360a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adductdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5) requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-adductdata/post-link.sh b/recipes/bioconductor-adductdata/post-link.sh index 4f61cf8d1d91c..d3605c39b51d2 100644 --- a/recipes/bioconductor-adductdata/post-link.sh +++ b/recipes/bioconductor-adductdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "adductdata-1.16.0" +installBiocDataPackage.sh "adductdata-1.18.0" diff --git a/recipes/bioconductor-adductomicsr/meta.yaml b/recipes/bioconductor-adductomicsr/meta.yaml index 3e5bf8e9fdc27..0dae0b1138261 100644 --- a/recipes/bioconductor-adductomicsr/meta.yaml +++ b/recipes/bioconductor-adductomicsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "adductomicsR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed852e0f573a83db85687be2f9fd6854 + md5: 82e24a09ba891b76e9497a6725b96fe0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adductomicsr", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop (>= 1.34.0), testthat requirements: host: - - 'bioconductor-adductdata >=1.16.0,<1.17.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-adductdata >=1.18.0,<1.19.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - 'r-ade4 >=1.7.6' - r-base - 'r-bootstrap >=2017.2' @@ -44,10 +45,10 @@ requirements: - 'r-smoother >=1.1' - 'r-zoo >=1.8' run: - - 'bioconductor-adductdata >=1.16.0,<1.17.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-adductdata >=1.18.0,<1.19.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - 'r-ade4 >=1.7.6' - r-base - 'r-bootstrap >=2017.2' diff --git a/recipes/bioconductor-adimpute/meta.yaml b/recipes/bioconductor-adimpute/meta.yaml index bca3ef416071c..dc9e7cde8ce66 100644 --- a/recipes/bioconductor-adimpute/meta.yaml +++ b/recipes/bioconductor-adimpute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ADImpute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7d4917d6ba8a14b93e6ccb52e93b677 + md5: 488025707dc1ae48d36b1e936cd86e18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adimpute", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-data.table @@ -35,10 +36,10 @@ requirements: - r-rsvd - r-saver run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-adme16cod.db/meta.yaml b/recipes/bioconductor-adme16cod.db/meta.yaml index 6dd4d7e465201..e4dce7a0d51e4 100644 --- a/recipes/bioconductor-adme16cod.db/meta.yaml +++ b/recipes/bioconductor-adme16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "adme16cod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3902516a40a503302ef732143b2394b9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adme16cod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-adsplit/meta.yaml b/recipes/bioconductor-adsplit/meta.yaml index f3475e35dc258..63e85226e64ef 100644 --- a/recipes/bioconductor-adsplit/meta.yaml +++ b/recipes/bioconductor-adsplit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "adSplit" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c31606f8e4de1045362077ae9e7f0cc3 + md5: 4d50affb50e6f6a11d8c4e379b6116d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adsplit", max_pin="x.x") }}' # Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-cluster >=1.9.1' - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-cluster >=1.9.1' build: diff --git a/recipes/bioconductor-adverscarial/build.sh b/recipes/bioconductor-adverscarial/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-adverscarial/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-adverscarial/meta.yaml b/recipes/bioconductor-adverscarial/meta.yaml new file mode 100644 index 0000000000000..4a8c254b26e82 --- /dev/null +++ b/recipes/bioconductor-adverscarial/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "adverSCarial" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 196840790cf7fd0a0cbfe6d1aeb60e07 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adverscarial", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, RUnit, BiocGenerics, TENxPBMCData, CHETAH, stringr, LoomExperiment +requirements: + host: + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-gtools + run: + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-gtools +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'adverSCarial, generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacks' + description: 'adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq classifiers to adversarial attacks. The package is versatile and provides a format for integrating any type of classifier. It offers functions for studying and generating two types of attacks, single gene attack and max change attack. The single gene attack involves making a small modification to the input to alter the classification. The max change attack involves making a large modification to the input without changing its classification. The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers against adversarial attacks.' + license_file: LICENSE + diff --git a/recipes/bioconductor-affixcan/meta.yaml b/recipes/bioconductor-affixcan/meta.yaml index e06e9f22978f5..239059a2abf23 100644 --- a/recipes/bioconductor-affixcan/meta.yaml +++ b/recipes/bioconductor-affixcan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "AffiXcan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4372aaaf131ef8bced13fa847b0b09d0 + md5: 0fdb85714a4ee94e3c04117e56d35724 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affixcan", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon test: diff --git a/recipes/bioconductor-affxparser/meta.yaml b/recipes/bioconductor-affxparser/meta.yaml index 874264d669dce..98a8b2a7afec4 100644 --- a/recipes/bioconductor-affxparser/meta.yaml +++ b/recipes/bioconductor-affxparser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "affxparser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 532d0815920747092ca64f439fc2677a + md5: 2b6b9373d749a0ccbf930f834df90b92 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affxparser", max_pin="x.x") }}' # Suggests: R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles requirements: host: diff --git a/recipes/bioconductor-affy/meta.yaml b/recipes/bioconductor-affy/meta.yaml index b282b1628b862..b6cfed74b149d 100644 --- a/recipes/bioconductor-affy/meta.yaml +++ b/recipes/bioconductor-affy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "affy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1b3ca024b5fc6804d66023f11c058955 + md5: 09376016b32f86f707ff9b8f8cb8a1a5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools + run_exports: '{{ pin_subpackage("bioconductor-affy", max_pin="x.x") }}' +# Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf requirements: host: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-biocmanager - - r-curl - - r-plogr - - r-rsqlite - libblas - liblapack run: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - bioconductor-annotationdbi - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-biocmanager - - r-curl - - r-plogr - - r-rsqlite build: - {{ compiler('c') }} - automake diff --git a/recipes/bioconductor-affycomp/meta.yaml b/recipes/bioconductor-affycomp/meta.yaml index 01d92610a5ec8..8637840fed6df 100644 --- a/recipes/bioconductor-affycomp/meta.yaml +++ b/recipes/bioconductor-affycomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "affycomp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 087b3614cc06dc45c424d3c9c8a2cafa + md5: f80b53dc57dcb88730eda3c0506b9df1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affycomp", max_pin="x.x") }}' noarch: generic # Suggests: splines, affycompData requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-affycompdata/meta.yaml b/recipes/bioconductor-affycompdata/meta.yaml index 0004ba77c7269..0095e5b77d597 100644 --- a/recipes/bioconductor-affycompdata/meta.yaml +++ b/recipes/bioconductor-affycompdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "affycompData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: adf2ee1552f1ee380e5ccbcf8246955d + md5: 205391e19fb160dcff1531892f28b006 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affycompdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affycomp >=1.76.0,<1.77.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affycomp >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affycomp >=1.76.0,<1.77.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affycomp >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affycompdata/post-link.sh b/recipes/bioconductor-affycompdata/post-link.sh index 44727c3422456..8afa441ea7552 100644 --- a/recipes/bioconductor-affycompdata/post-link.sh +++ b/recipes/bioconductor-affycompdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affycompdata-1.38.0" +installBiocDataPackage.sh "affycompdata-1.40.0" diff --git a/recipes/bioconductor-affycontam/meta.yaml b/recipes/bioconductor-affycontam/meta.yaml index 2bfac5ee1f649..5b27747fc443e 100644 --- a/recipes/bioconductor-affycontam/meta.yaml +++ b/recipes/bioconductor-affycontam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "affyContam" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 033e0738e646d2f9ba5ba1b0b072b915 + md5: eb7e98d31e923d77d4e6197e5cf8b02d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affycontam", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affydata >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affydata >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affydata >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affydata >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-affycoretools/meta.yaml b/recipes/bioconductor-affycoretools/meta.yaml index bd9a73302edd7..a986df1b11158 100644 --- a/recipes/bioconductor-affycoretools/meta.yaml +++ b/recipes/bioconductor-affycoretools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "affycoretools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4235bb5e8547acf64c3c6a7d11c98c56 + md5: 0e35c33fb3f3a4cdc7778efacbc45441 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affycoretools", max_pin="x.x") }}' noarch: generic # Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-glimma >=2.10.0,<2.11.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-reportingtools >=2.39.0,<2.40.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-glimma >=2.12.0,<2.13.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-reportingtools >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-ggplot2 @@ -42,18 +43,18 @@ requirements: - r-rsqlite - r-xtable run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-glimma >=2.10.0,<2.11.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-reportingtools >=2.39.0,<2.40.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-glimma >=2.12.0,<2.13.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-reportingtools >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-ggplot2 diff --git a/recipes/bioconductor-affydata/meta.yaml b/recipes/bioconductor-affydata/meta.yaml index 38fb326487ba1..2f929ae9839ca 100644 --- a/recipes/bioconductor-affydata/meta.yaml +++ b/recipes/bioconductor-affydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.1" %} +{% set version = "1.50.0" %} {% set name = "affydata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1c03aa529e4854f6680fcf4702d2bea7 + md5: 29caf389ca94d4c0c0b27d993f33354c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affydata", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2cdf, hgu133acdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230718 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affydata/post-link.sh b/recipes/bioconductor-affydata/post-link.sh index 998d4b687d633..d1076767bb073 100644 --- a/recipes/bioconductor-affydata/post-link.sh +++ b/recipes/bioconductor-affydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affydata-1.48.1" +installBiocDataPackage.sh "affydata-1.50.0" diff --git a/recipes/bioconductor-affyhgu133a2expr/meta.yaml b/recipes/bioconductor-affyhgu133a2expr/meta.yaml index 8833f245300de..c8a6b90c26c8e 100644 --- a/recipes/bioconductor-affyhgu133a2expr/meta.yaml +++ b/recipes/bioconductor-affyhgu133a2expr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Affyhgu133A2Expr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09a1e306ad46f08b9508343050ffa756 + md5: 56296960e5539a4fd84724344f30aaaa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyhgu133a2expr", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affyhgu133a2expr/post-link.sh b/recipes/bioconductor-affyhgu133a2expr/post-link.sh index 3489adaf54942..51c44933e7561 100644 --- a/recipes/bioconductor-affyhgu133a2expr/post-link.sh +++ b/recipes/bioconductor-affyhgu133a2expr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affyhgu133a2expr-1.36.0" +installBiocDataPackage.sh "affyhgu133a2expr-1.38.0" diff --git a/recipes/bioconductor-affyhgu133aexpr/meta.yaml b/recipes/bioconductor-affyhgu133aexpr/meta.yaml index 23dee4fe8b1a9..cb49ec76a1c59 100644 --- a/recipes/bioconductor-affyhgu133aexpr/meta.yaml +++ b/recipes/bioconductor-affyhgu133aexpr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "Affyhgu133aExpr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e745cf07453b1f7151f28ddddced6be1 + md5: 2cf458278c574450a3a5ffe64a2aa72b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyhgu133aexpr", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affyhgu133aexpr/post-link.sh b/recipes/bioconductor-affyhgu133aexpr/post-link.sh index c621da65bd9da..340a6ec306e19 100644 --- a/recipes/bioconductor-affyhgu133aexpr/post-link.sh +++ b/recipes/bioconductor-affyhgu133aexpr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affyhgu133aexpr-1.38.0" +installBiocDataPackage.sh "affyhgu133aexpr-1.40.0" diff --git a/recipes/bioconductor-affyhgu133plus2expr/meta.yaml b/recipes/bioconductor-affyhgu133plus2expr/meta.yaml index 22f780b7b0273..34d5b6c564a12 100644 --- a/recipes/bioconductor-affyhgu133plus2expr/meta.yaml +++ b/recipes/bioconductor-affyhgu133plus2expr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "Affyhgu133Plus2Expr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 210b20595daf5314b8d5b90b5497eab4 + md5: f8baac83db4de07f941552d7b62c8d62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyhgu133plus2expr", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affyhgu133plus2expr/post-link.sh b/recipes/bioconductor-affyhgu133plus2expr/post-link.sh index e4d6cb7fb5882..61b0c8692f259 100644 --- a/recipes/bioconductor-affyhgu133plus2expr/post-link.sh +++ b/recipes/bioconductor-affyhgu133plus2expr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affyhgu133plus2expr-1.34.0" +installBiocDataPackage.sh "affyhgu133plus2expr-1.36.0" diff --git a/recipes/bioconductor-affyilm/meta.yaml b/recipes/bioconductor-affyilm/meta.yaml index 575b77bd63e71..6433bba0da600 100644 --- a/recipes/bioconductor-affyilm/meta.yaml +++ b/recipes/bioconductor-affyilm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "affyILM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e65e974cee281a713155a14d5ecf6a6 + md5: 96d1989fb75742f6a9b0f9d8df1c3fc0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyilm", max_pin="x.x") }}' noarch: generic # Suggests: AffymetrixDataTestFiles, hgfocusprobe requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base test: commands: diff --git a/recipes/bioconductor-affyio/meta.yaml b/recipes/bioconductor-affyio/meta.yaml index e2614e93f4455..0338d5377855c 100644 --- a/recipes/bioconductor-affyio/meta.yaml +++ b/recipes/bioconductor-affyio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "affyio" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9fb97bfde087591251d7cda5c978e528 + md5: 9bd1e4acedbf756386f96d4c1ebb21f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyio", max_pin="x.x") }}' requirements: host: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-affylmgui/meta.yaml b/recipes/bioconductor-affylmgui/meta.yaml index 9ef33694a62a1..a22190a4e1974 100644 --- a/recipes/bioconductor-affylmgui/meta.yaml +++ b/recipes/bioconductor-affylmgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "affylmGUI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae4622fe7a135671ded4e68d2e857760 + md5: 22d9ba796444840fc24cf9b7384f81c9 build: - number: 0 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affylmgui", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-biocmanager - r-r2html - r-tkrplot - r-xtable run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-biocmanager - r-r2html diff --git a/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml b/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml index 4d5d904bd46aa..66437faa2f9b4 100644 --- a/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml +++ b/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "AffymetrixDataTestFiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3aa3891584be3bcdab25e2b72b092edc + md5: 57ecb8e4d3f0d7a9cdcedb2a9648dd1e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affymetrixdatatestfiles", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,14 +25,14 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: LGPL-2.1 - summary: 'Affymetrix data files (CEL, CDF, CHP, EXP, PGF, PSI) for testing' + summary: 'Affymetrix Data Files (CEL, CDF, CHP, EXP, PGF, PSI) for Testing' description: 'This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix'' Fusion SDK distribution and other official sources.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' diff --git a/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh b/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh index 3f6f79b4c0d41..e2ba7cf5c205a 100644 --- a/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh +++ b/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affymetrixdatatestfiles-0.38.0" +installBiocDataPackage.sh "affymetrixdatatestfiles-0.40.0" diff --git a/recipes/bioconductor-affymoe4302expr/meta.yaml b/recipes/bioconductor-affymoe4302expr/meta.yaml index d7d15bc46a474..2c17903299ff0 100644 --- a/recipes/bioconductor-affymoe4302expr/meta.yaml +++ b/recipes/bioconductor-affymoe4302expr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "Affymoe4302Expr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 277537172df894a0e7384d3e48d059b1 + md5: 4dcd432d350cf2f8000f67774d95481c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affymoe4302expr", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-affymoe4302expr/post-link.sh b/recipes/bioconductor-affymoe4302expr/post-link.sh index 5c867c283a151..1c18e0a13e6be 100644 --- a/recipes/bioconductor-affymoe4302expr/post-link.sh +++ b/recipes/bioconductor-affymoe4302expr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affymoe4302expr-1.38.0" +installBiocDataPackage.sh "affymoe4302expr-1.40.0" diff --git a/recipes/bioconductor-affyplm/meta.yaml b/recipes/bioconductor-affyplm/meta.yaml index 1b6dfa0e06c33..6f6f1faaf8e41 100644 --- a/recipes/bioconductor-affyplm/meta.yaml +++ b/recipes/bioconductor-affyplm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.1" %} +{% set version = "1.78.0" %} {% set name = "affyPLM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9aae2ea1fdeafc1e540428a6d9d988d2 + md5: cdfd69bc9c54f3c03b52b3fd6e9f86b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: affydata, MASS + run_exports: '{{ pin_subpackage("bioconductor-affyplm", max_pin="x.x") }}' +# Suggests: affydata, MASS, hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-affyrnadegradation/meta.yaml b/recipes/bioconductor-affyrnadegradation/meta.yaml index e7d30099c638b..0cc0bd45177a2 100644 --- a/recipes/bioconductor-affyrnadegradation/meta.yaml +++ b/recipes/bioconductor-affyrnadegradation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "AffyRNADegradation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81aaa5c79893376798c726d114779512 + md5: 4affd7f48b178750311671c1f2ac8c4f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-affyrnadegradation", max_pin="x.x") }}' noarch: generic -# Suggests: AmpAffyExample +# Suggests: AmpAffyExample, hgu133acdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-ag.db/meta.yaml b/recipes/bioconductor-ag.db/meta.yaml index 93456c5bae844..7b597e80ef24d 100644 --- a/recipes/bioconductor-ag.db/meta.yaml +++ b/recipes/bioconductor-ag.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "ag.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 925e808d2c9b21a11ed131d483e75ab6 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ag.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.at.tair.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.at.tair.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-agcdf/meta.yaml b/recipes/bioconductor-agcdf/meta.yaml index 5a63ca629b14e..312952757082a 100644 --- a/recipes/bioconductor-agcdf/meta.yaml +++ b/recipes/bioconductor-agcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "agcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5dd14bc6a6d2729f5e7b170105c78e48 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-agcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-agdex/meta.yaml b/recipes/bioconductor-agdex/meta.yaml index 3720941870845..4304a5d0cccc5 100644 --- a/recipes/bioconductor-agdex/meta.yaml +++ b/recipes/bioconductor-agdex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "AGDEX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73f6cbece97c53821c785468dabca2e8 + md5: 9e74a7202bdc2e422e2213f1fb7a23f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-agdex", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-aggregatebiovar/meta.yaml b/recipes/bioconductor-aggregatebiovar/meta.yaml index 90ddcba32e1fb..a32ad85909c4c 100644 --- a/recipes/bioconductor-aggregatebiovar/meta.yaml +++ b/recipes/bioconductor-aggregatebiovar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "aggregateBioVar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 480e81b8e909d164fa86ce05b7d412a1 + md5: f389a909fab4bbc4cb526505c68f22e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aggregatebiovar", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rlang - r-tibble run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rlang diff --git a/recipes/bioconductor-agilp/meta.yaml b/recipes/bioconductor-agilp/meta.yaml index 6d77d5bf3c196..e3c5bbb5a3261 100644 --- a/recipes/bioconductor-agilp/meta.yaml +++ b/recipes/bioconductor-agilp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.32.0" %} +{% set version = "3.34.0" %} {% set name = "agilp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 573fbba741e2d0b2a99db971555f598d + md5: 21b54a703747520483657dd63288f403 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-agilp", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-agimicrorna/meta.yaml b/recipes/bioconductor-agimicrorna/meta.yaml index ab7e912ca8bf9..5030fc363a442 100644 --- a/recipes/bioconductor-agimicrorna/meta.yaml +++ b/recipes/bioconductor-agimicrorna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.50.0" %} +{% set version = "2.52.0" %} {% set name = "AgiMicroRna" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d971cfaddf49f4b7296a833a4a818dd + md5: 1c1046ab29a7766af0c602c974b4ec21 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-agimicrorna", max_pin="x.x") }}' noarch: generic # Suggests: geneplotter,marray,gplots,gtools,gdata,codelink requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affycoretools >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affycoretools >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affycoretools >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affycoretools >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-agprobe/meta.yaml b/recipes/bioconductor-agprobe/meta.yaml index 4740b9dcb4668..c2ba8fe20c5c7 100644 --- a/recipes/bioconductor-agprobe/meta.yaml +++ b/recipes/bioconductor-agprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "agprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 08f7527d4c8a30d8b2f86016a53f075a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-agprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahcytobands/meta.yaml b/recipes/bioconductor-ahcytobands/meta.yaml index 1ee85ebf82f04..1fd99874310a1 100644 --- a/recipes/bioconductor-ahcytobands/meta.yaml +++ b/recipes/bioconductor-ahcytobands/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "AHCytoBands" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3dd85d02e7ed3fca4c7898b5e395edeb build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahcytobands", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahensdbs/meta.yaml b/recipes/bioconductor-ahensdbs/meta.yaml index e28373c8ea6a6..117aeb2c7ff6a 100644 --- a/recipes/bioconductor-ahensdbs/meta.yaml +++ b/recipes/bioconductor-ahensdbs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.8" %} +{% set version = "1.1.10" %} {% set name = "AHEnsDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2c8c9338f09f480a46e1155d985d08f + md5: 63aa3efc1c85d5a26e4d69d50f781a2a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahensdbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown requirements: host: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahensdbs/post-link.sh b/recipes/bioconductor-ahensdbs/post-link.sh index fa692e021139b..e004d994abd34 100644 --- a/recipes/bioconductor-ahensdbs/post-link.sh +++ b/recipes/bioconductor-ahensdbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahensdbs-1.1.8" +installBiocDataPackage.sh "ahensdbs-1.1.10" diff --git a/recipes/bioconductor-ahlrbasedbs/meta.yaml b/recipes/bioconductor-ahlrbasedbs/meta.yaml index bd2c3c2f62e9d..29db9f49d2eb6 100644 --- a/recipes/bioconductor-ahlrbasedbs/meta.yaml +++ b/recipes/bioconductor-ahlrbasedbs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.7.0" %} {% set name = "AHLRBaseDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1427836afe85a5b580f7277e7d2c08ca + md5: 5df6ef84988477d6262e54abd07c82da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahlrbasedbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahlrbasedbs/post-link.sh b/recipes/bioconductor-ahlrbasedbs/post-link.sh index cfac5d956723a..b59c08f98bc83 100644 --- a/recipes/bioconductor-ahlrbasedbs/post-link.sh +++ b/recipes/bioconductor-ahlrbasedbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahlrbasedbs-1.6.0" +installBiocDataPackage.sh "ahlrbasedbs-1.7.0" diff --git a/recipes/bioconductor-ahmassbank/meta.yaml b/recipes/bioconductor-ahmassbank/meta.yaml index 7fea5ede930f7..6db48bd579837 100644 --- a/recipes/bioconductor-ahmassbank/meta.yaml +++ b/recipes/bioconductor-ahmassbank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "AHMassBank" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05f8f3c29029047132ee58b4e2a1f4b0 + md5: b9ddc7dff0cabd4b170bc750cc3c47d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahmassbank", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown, methods, CompoundDb (>= 1.1.4) requirements: host: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-ahmeshdbs/meta.yaml b/recipes/bioconductor-ahmeshdbs/meta.yaml index b0c0131347691..f7efca97a5554 100644 --- a/recipes/bioconductor-ahmeshdbs/meta.yaml +++ b/recipes/bioconductor-ahmeshdbs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.7.0" %} {% set name = "AHMeSHDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7fe9c77aaff9175d842cb4f4b9313360 + md5: 9bbcae25794d2f854a122ba36a4e4c5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahmeshdbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahmeshdbs/post-link.sh b/recipes/bioconductor-ahmeshdbs/post-link.sh index 36a8a0bf2cf59..4b406789a1680 100644 --- a/recipes/bioconductor-ahmeshdbs/post-link.sh +++ b/recipes/bioconductor-ahmeshdbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahmeshdbs-1.6.0" +installBiocDataPackage.sh "ahmeshdbs-1.7.0" diff --git a/recipes/bioconductor-ahpathbankdbs/meta.yaml b/recipes/bioconductor-ahpathbankdbs/meta.yaml index 5caa56ea627f4..aa5554f14038d 100644 --- a/recipes/bioconductor-ahpathbankdbs/meta.yaml +++ b/recipes/bioconductor-ahpathbankdbs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.5" %} {% set name = "AHPathbankDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 70339eae8c03c47248b612b365bda4ff build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahpathbankdbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahpubmeddbs/meta.yaml b/recipes/bioconductor-ahpubmeddbs/meta.yaml index e15a881301fbb..8692df0e1a8d1 100644 --- a/recipes/bioconductor-ahpubmeddbs/meta.yaml +++ b/recipes/bioconductor-ahpubmeddbs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.7.0" %} {% set name = "AHPubMedDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91815a0aa91e19d171fad3b116d02eed + md5: b2db2eda6009bc9cdec579c4ab579f25 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahpubmeddbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ahpubmeddbs/post-link.sh b/recipes/bioconductor-ahpubmeddbs/post-link.sh index c24116e69908e..42e051ec75f48 100644 --- a/recipes/bioconductor-ahpubmeddbs/post-link.sh +++ b/recipes/bioconductor-ahpubmeddbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahpubmeddbs-1.6.0" +installBiocDataPackage.sh "ahpubmeddbs-1.7.0" diff --git a/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml b/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml index 02f5241e55a69..73c928b6ecca4 100644 --- a/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml +++ b/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.4" %} {% set name = "AHWikipathwaysDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ffa90f6d6e8832ae6f4b5bf8b151cd46 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ahwikipathwaysdbs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-aims/meta.yaml b/recipes/bioconductor-aims/meta.yaml index cd75109310927..4e9667789a111 100644 --- a/recipes/bioconductor-aims/meta.yaml +++ b/recipes/bioconductor-aims/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "AIMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37736eda0cf70c07064ae8930a25b930 + md5: 23ef11145babcac9430b2c94db4dfae3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aims", max_pin="x.x") }}' noarch: generic # Suggests: breastCancerVDX, hgu133a.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 test: diff --git a/recipes/bioconductor-airpart/meta.yaml b/recipes/bioconductor-airpart/meta.yaml index 21438ee070670..c343eeefb76a6 100644 --- a/recipes/bioconductor-airpart/meta.yaml +++ b/recipes/bioconductor-airpart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "airpart" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5c42ac799c2fa8c3364cb7cc965161a1 + md5: 59977674a0dc5eb9f4bd03ef89a73630 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-airpart", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr requirements: host: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clue - r-dplyr @@ -43,12 +44,12 @@ requirements: - r-rlang - r-smurf run: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clue - r-dplyr diff --git a/recipes/bioconductor-airway/meta.yaml b/recipes/bioconductor-airway/meta.yaml index 9c721d737617c..ba924b9263df0 100644 --- a/recipes/bioconductor-airway/meta.yaml +++ b/recipes/bioconductor-airway/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "airway" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c79ded2f4d44b3a865a1e489c6d151d + md5: ffed4ae3349ebeeeabff9f1456b8ba1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-airway", max_pin="x.x") }}' noarch: generic # Suggests: knitr, GEOquery, markdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-airway/post-link.sh b/recipes/bioconductor-airway/post-link.sh index b21924a129852..a8e50bfc60ff3 100644 --- a/recipes/bioconductor-airway/post-link.sh +++ b/recipes/bioconductor-airway/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "airway-1.20.0" +installBiocDataPackage.sh "airway-1.22.0" diff --git a/recipes/bioconductor-alabaster.base/meta.yaml b/recipes/bioconductor-alabaster.base/meta.yaml index 7e76be0f452d4..22787eb448ec7 100644 --- a/recipes/bioconductor-alabaster.base/meta.yaml +++ b/recipes/bioconductor-alabaster.base/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.1" %} {% set name = "alabaster.base" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4bfa805d3a2b3c8a6c9ee45807ff68c5 + md5: 2d6215dfe9b8412438f9b05b54be2331 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.base", max_pin="x.x") }}' # Suggests: BiocStyle, rmarkdown, knitr, testthat, digest, Matrix # SystemRequirements: C++17, GNU make requirements: host: - - 'bioconductor-alabaster.schemas >=1.0.0,<1.1.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.schemas >=1.2.0,<1.3.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-jsonlite - r-jsonvalidate @@ -32,10 +33,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-alabaster.schemas >=1.0.0,<1.1.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.schemas >=1.2.0,<1.3.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-jsonlite - r-jsonvalidate diff --git a/recipes/bioconductor-alabaster.bumpy/meta.yaml b/recipes/bioconductor-alabaster.bumpy/meta.yaml index f35a409108fe7..ab61aee778ded 100644 --- a/recipes/bioconductor-alabaster.bumpy/meta.yaml +++ b/recipes/bioconductor-alabaster.bumpy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.bumpy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7c4104e604cc3b9d6f7b3d8d9a81bfb1 + md5: 0d5111cd74d5b72fc88eb66ac5b670c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.bumpy", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, testthat, jsonlite requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-alabaster.files/build.sh b/recipes/bioconductor-alabaster.files/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-alabaster.files/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-alabaster.files/meta.yaml b/recipes/bioconductor-alabaster.files/meta.yaml new file mode 100644 index 0000000000000..a91a9a98a4880 --- /dev/null +++ b/recipes/bioconductor-alabaster.files/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "alabaster.files" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ea12d81dadbad7340c5f2d6be276a697 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.files", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation +requirements: + host: + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + run: + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Wrappers to Save Common File Formats' + description: 'Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.' + license_file: LICENSE + diff --git a/recipes/bioconductor-alabaster.mae/meta.yaml b/recipes/bioconductor-alabaster.mae/meta.yaml index 7625f9251190e..15bed2c113976 100644 --- a/recipes/bioconductor-alabaster.mae/meta.yaml +++ b/recipes/bioconductor-alabaster.mae/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.mae" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f6eceed081467ce7d72c747bb1a0d11a + md5: 43abcdda61fc9d69dbc24dbd1c91664d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.mae", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, SummarizedExperiment, BiocParallel, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster.matrix/meta.yaml b/recipes/bioconductor-alabaster.matrix/meta.yaml index ff390004bf852..73ee0d6404f07 100644 --- a/recipes/bioconductor-alabaster.matrix/meta.yaml +++ b/recipes/bioconductor-alabaster.matrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.matrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4b93a993b0f4a9b3333da48a8f49ad36 + md5: 099a01bbb4a95bdaf0f91ffd2b89653d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.matrix", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, BiocGenerics, BiocStyle, S4Vectors, chihaya +# Suggests: testthat, knitr, BiocStyle, chihaya requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-alabaster.ranges/meta.yaml b/recipes/bioconductor-alabaster.ranges/meta.yaml index 27bdfbd3ca23a..d912501aceef5 100644 --- a/recipes/bioconductor-alabaster.ranges/meta.yaml +++ b/recipes/bioconductor-alabaster.ranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.ranges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 846f2604ddc36ae98f28443f4b12d305 + md5: af5d849080999b0167cc39fc182721e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.ranges", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, jsonlite requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster.sce/meta.yaml b/recipes/bioconductor-alabaster.sce/meta.yaml index 0c99a764670fb..dbb5845379eba 100644 --- a/recipes/bioconductor-alabaster.sce/meta.yaml +++ b/recipes/bioconductor-alabaster.sce/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.sce" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a732c09296222711d8296d5b896ac62 + md5: e508f30fb84947c7246b093b63a5aea3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.sce", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster.schemas/meta.yaml b/recipes/bioconductor-alabaster.schemas/meta.yaml index b54d01a99b1e8..6a45f9d6cc290 100644 --- a/recipes/bioconductor-alabaster.schemas/meta.yaml +++ b/recipes/bioconductor-alabaster.schemas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "alabaster.schemas" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 07cb1f4f931f7fcde891ab11857ad443 + md5: 308883d85ab416d45eaa55428463d308 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.schemas", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-alabaster.se/meta.yaml b/recipes/bioconductor-alabaster.se/meta.yaml index a60bca1f22d7a..6a54ef0e020fa 100644 --- a/recipes/bioconductor-alabaster.se/meta.yaml +++ b/recipes/bioconductor-alabaster.se/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.se" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e93f0f6699394a9fbb4b8048567a5538 + md5: 25133d88cc71ec6029229772a1eee0e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.se", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat, BiocStyle, jsonlite requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.matrix >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.ranges >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.matrix >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.ranges >=1.0.0,<1.1.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster.spatial/meta.yaml b/recipes/bioconductor-alabaster.spatial/meta.yaml index 8981659d9e157..fa129e7aa9045 100644 --- a/recipes/bioconductor-alabaster.spatial/meta.yaml +++ b/recipes/bioconductor-alabaster.spatial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.spatial" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b8804e5e38ef912c8d1a04343f03f748 + md5: 906d73c492ba97e8eda563055c51bbfc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.spatial", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, rmarkdown, BiocStyle, magick, png, digest +# Suggests: testthat, knitr, rmarkdown, BiocStyle, DropletUtils, magick, png, digest requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.sce >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-jsonlite run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.sce >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-jsonlite test: diff --git a/recipes/bioconductor-alabaster.string/meta.yaml b/recipes/bioconductor-alabaster.string/meta.yaml index 332effb707a9e..3ab554683fc97 100644 --- a/recipes/bioconductor-alabaster.string/meta.yaml +++ b/recipes/bioconductor-alabaster.string/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "alabaster.string" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ca363e28ab6a9dd4cba70484a090f13 + md5: b7add7aa52b8835471b04038842da095 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.string", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, testthat requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster.vcf/meta.yaml b/recipes/bioconductor-alabaster.vcf/meta.yaml index b21377382c639..191429828c512 100644 --- a/recipes/bioconductor-alabaster.vcf/meta.yaml +++ b/recipes/bioconductor-alabaster.vcf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster.vcf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a512241aa940a4dd220d86da0b94aea4 + md5: e0873ba68051843f6a35b01fef673423 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster.vcf", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.string >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.string >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-alabaster/meta.yaml b/recipes/bioconductor-alabaster/meta.yaml index 89cfcdd85a328..2189836f4b577 100644 --- a/recipes/bioconductor-alabaster/meta.yaml +++ b/recipes/bioconductor-alabaster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "alabaster" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8755db5053974ae9995e52dc59ac6dd1 + md5: 359d26d34b8867dd418d0d277b0228c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alabaster", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.bumpy >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.mae >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.matrix >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.ranges >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.sce >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.spatial >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.string >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.vcf >=1.0.0,<1.1.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.bumpy >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.mae >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.spatial >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.vcf >=1.2.0,<1.3.0' - r-base run: - - 'bioconductor-alabaster.base >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.bumpy >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.mae >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.matrix >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.ranges >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.sce >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.se >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.spatial >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.string >=1.0.0,<1.1.0' - - 'bioconductor-alabaster.vcf >=1.0.0,<1.1.0' + - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.bumpy >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.mae >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.spatial >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' + - 'bioconductor-alabaster.vcf >=1.2.0,<1.3.0' - r-base test: commands: diff --git a/recipes/bioconductor-aldex2/meta.yaml b/recipes/bioconductor-aldex2/meta.yaml index 700bf9e091a1a..70392f9f4f9ec 100644 --- a/recipes/bioconductor-aldex2/meta.yaml +++ b/recipes/bioconductor-aldex2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "ALDEx2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 345d5814c97ec89e886d3cea6de71fc2 + md5: 359e47382b7cac1093aa1a5c24307cec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aldex2", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, BiocStyle, knitr, rmarkdown +# Suggests: testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern, ggplot2, cowplot, tidyverse, magick requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base + - r-directlabels + - r-lattice + - r-latticeextra - r-rfast - r-zcompositions run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base + - r-directlabels + - r-lattice + - r-latticeextra - r-rfast - r-zcompositions test: @@ -45,9 +52,9 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Analysis Of Differential Abundance Taking Sample Variation Into Account' - description: 'A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch''s t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report p-values and Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs.' + license: 'GPL (>=3)' + summary: 'Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account' + description: 'A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch''s t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report predicted p-values and posterior Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs. ALDEx2 can now be used to estimate the effect of scale on the results and report on the scale-dependent robustness of results.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: diff --git a/recipes/bioconductor-alevinqc/meta.yaml b/recipes/bioconductor-alevinqc/meta.yaml index ac2601164b7a3..619d9e458faed 100644 --- a/recipes/bioconductor-alevinqc/meta.yaml +++ b/recipes/bioconductor-alevinqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "alevinQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bced99162e87f3f524220f1609769e5a + md5: fa79ac8ac72e4d6d16c096886e9f759d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alevinqc", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, testthat (>= 3.0.0), BiocManager # SystemRequirements: C++11 requirements: host: - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-cowplot - r-dplyr - r-dt - r-ggally - - r-ggplot2 + - 'r-ggplot2 >=3.4.0' - r-rcpp - r-rjson - r-rlang @@ -37,13 +38,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-cowplot - r-dplyr - r-dt - r-ggally - - r-ggplot2 + - 'r-ggplot2 >=3.4.0' - r-rcpp - r-rjson - r-rlang @@ -61,6 +62,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Generate QC Reports For Alevin Output' - description: 'Generate QC reports summarizing the output from an alevin run. Reports can be generated as html or pdf files, or as shiny applications.' + description: 'Generate QC reports summarizing the output from an alevin, alevin-fry, or simpleaf run. Reports can be generated as html or pdf files, or as shiny applications.' license_file: LICENSE diff --git a/recipes/bioconductor-all/meta.yaml b/recipes/bioconductor-all/meta.yaml index db938a4bcb525..21dff1b6d6ed1 100644 --- a/recipes/bioconductor-all/meta.yaml +++ b/recipes/bioconductor-all/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "ALL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_{{ name|lower }}.tar.gz' - md5: 11b7809ea96d31a9f1bc3eb56a2650c1 + md5: b80eb482b4937ef4eac01027ac95a61a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-all", max_pin="x.x") }}' noarch: generic # Suggests: rpart requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-all/post-link.sh b/recipes/bioconductor-all/post-link.sh index 447c44b75808a..2c5b04230e97b 100644 --- a/recipes/bioconductor-all/post-link.sh +++ b/recipes/bioconductor-all/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "all-1.42.0" +installBiocDataPackage.sh "all-1.44.0" diff --git a/recipes/bioconductor-allelicimbalance/meta.yaml b/recipes/bioconductor-allelicimbalance/meta.yaml index 9180922a1fa1d..bcbc7a1991cf6 100644 --- a/recipes/bioconductor-allelicimbalance/meta.yaml +++ b/recipes/bioconductor-allelicimbalance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "AllelicImbalance" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c8e2b8b1555f07edd8140aaca21e530 + md5: 9eb6991f47f1337aef63f9ce750db08a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-allelicimbalance", max_pin="x.x") }}' noarch: generic # Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-gridextra - r-lattice @@ -42,20 +43,20 @@ requirements: - r-nlme - r-seqinr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-gridextra - r-lattice diff --git a/recipes/bioconductor-allmll/meta.yaml b/recipes/bioconductor-allmll/meta.yaml index 693c6f690c605..e181a78da8504 100644 --- a/recipes/bioconductor-allmll/meta.yaml +++ b/recipes/bioconductor-allmll/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "ALLMLL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4c0642007ed854280b06339d989d94f + md5: 669e7ff030b6fea51c8013816bd6fae7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-allmll", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-allmll/post-link.sh b/recipes/bioconductor-allmll/post-link.sh index 9fdf373467321..f9958cf78ac2a 100644 --- a/recipes/bioconductor-allmll/post-link.sh +++ b/recipes/bioconductor-allmll/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "allmll-1.40.0" +installBiocDataPackage.sh "allmll-1.42.0" diff --git a/recipes/bioconductor-alphabeta/meta.yaml b/recipes/bioconductor-alphabeta/meta.yaml index 7b455fcd87496..a5240ce1ab0a6 100644 --- a/recipes/bioconductor-alphabeta/meta.yaml +++ b/recipes/bioconductor-alphabeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "AlphaBeta" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3daff3508c604ad2d2bea4d51bfd3e9b + md5: b03e94ae649db2b4141f97a7859e0683 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alphabeta", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-data.table >=1.10' - 'r-dplyr >=0.7' @@ -33,7 +34,7 @@ requirements: - 'r-plotly >=4.9' - 'r-stringr >=1.3' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-data.table >=1.10' - 'r-dplyr >=0.7' diff --git a/recipes/bioconductor-alphamissense.v2023.hg19/meta.yaml b/recipes/bioconductor-alphamissense.v2023.hg19/meta.yaml new file mode 100644 index 0000000000000..c4e4b98feb206 --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg19/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "3.18.2" %} +{% set name = "AlphaMissense.v2023.hg19" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e8784ad000be637321f432188a5a3f45 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alphamissense.v2023.hg19", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg19' + description: 'Store Google DeepMind AlphaMissense v2023 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + diff --git a/recipes/bioconductor-alphamissense.v2023.hg19/post-link.sh b/recipes/bioconductor-alphamissense.v2023.hg19/post-link.sh new file mode 100644 index 0000000000000..ed7e4efe56562 --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg19/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "alphamissense.v2023.hg19-3.18.2" diff --git a/recipes/bioconductor-alphamissense.v2023.hg19/pre-unlink.sh b/recipes/bioconductor-alphamissense.v2023.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..410f375b8c15b --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ AlphaMissense.v2023.hg19 diff --git a/recipes/bioconductor-alphamissense.v2023.hg38/meta.yaml b/recipes/bioconductor-alphamissense.v2023.hg38/meta.yaml new file mode 100644 index 0000000000000..5974912274231 --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg38/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "3.18.2" %} +{% set name = "AlphaMissense.v2023.hg38" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bedac9523e18829c5067dec1ebf801d4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alphamissense.v2023.hg38", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg38' + description: 'Store Google DeepMind AlphaMissense v2023 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + diff --git a/recipes/bioconductor-alphamissense.v2023.hg38/post-link.sh b/recipes/bioconductor-alphamissense.v2023.hg38/post-link.sh new file mode 100644 index 0000000000000..7709b6ee909c5 --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg38/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "alphamissense.v2023.hg38-3.18.2" diff --git a/recipes/bioconductor-alphamissense.v2023.hg38/pre-unlink.sh b/recipes/bioconductor-alphamissense.v2023.hg38/pre-unlink.sh new file mode 100644 index 0000000000000..40728685a22f9 --- /dev/null +++ b/recipes/bioconductor-alphamissense.v2023.hg38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ AlphaMissense.v2023.hg38 diff --git a/recipes/bioconductor-alpinedata/meta.yaml b/recipes/bioconductor-alpinedata/meta.yaml index 513dca99acc28..d1b1d2ca09aad 100644 --- a/recipes/bioconductor-alpinedata/meta.yaml +++ b/recipes/bioconductor-alpinedata/meta.yaml @@ -31,7 +31,7 @@ requirements: - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-alpsnmr/meta.yaml b/recipes/bioconductor-alpsnmr/meta.yaml index cf21c958eebb1..6ae5496aa23be 100644 --- a/recipes/bioconductor-alpsnmr/meta.yaml +++ b/recipes/bioconductor-alpsnmr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.2.0" %} +{% set version = "4.4.0" %} {% set name = "AlpsNMR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8238f13c688c0a53bf17b60b321ca80f + md5: 938d77895e6337a35d98b6a57fa90303 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alpsnmr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - 'r-baseline >=1.2-1' - r-cli @@ -50,8 +51,8 @@ requirements: - r-tidyselect - 'r-vctrs >=0.3.0' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - 'r-baseline >=1.2-1' - r-cli diff --git a/recipes/bioconductor-altcdfenvs/meta.yaml b/recipes/bioconductor-altcdfenvs/meta.yaml index e5dc218de4db5..2f56521289f0e 100644 --- a/recipes/bioconductor-altcdfenvs/meta.yaml +++ b/recipes/bioconductor-altcdfenvs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.62.0" %} +{% set version = "2.64.0" %} {% set name = "altcdfenvs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8a3985abeef481d9886b0f0f566bf5e5 + md5: 8bd83d29c11857ae73a4046289748f90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-altcdfenvs", max_pin="x.x") }}' noarch: generic # Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-makecdfenv >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-makecdfenv >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-makecdfenv >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-makecdfenv >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml b/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml index 35216c97bee60..7d1ab3e0251b4 100644 --- a/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml +++ b/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "alternativeSplicingEvents.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b1acae776c9e9c5d961cf4884cadc58f build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alternativesplicingevents.hg19", max_pin="x.x") }}' noarch: generic # Suggests: data.frame, dplyr, GenomicRanges, S4Vectors requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml b/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml index d722f96d8bb48..30e73e4117234 100644 --- a/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml +++ b/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "alternativeSplicingEvents.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8d49710eebd62fb15a48cab252ff3eca build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alternativesplicingevents.hg38", max_pin="x.x") }}' noarch: generic # Suggests: dplyr, GenomicRanges, S4Vectors requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-amaretto/meta.yaml b/recipes/bioconductor-amaretto/meta.yaml index e6ac5fa2df802..687714cb9991a 100644 --- a/recipes/bioconductor-amaretto/meta.yaml +++ b/recipes/bioconductor-amaretto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "AMARETTO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 221ee4ff61c9784ce231a2632ff9d860 + md5: d6b16e06e3eb15ba4cac645265a43db1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-amaretto", max_pin="x.x") }}' # Suggests: testthat, MASS, knitr, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-curatedtcgadata >=1.22.0,<1.23.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-curatedtcgadata >=1.24.0,<1.25.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - 'r-callr >=3.0.0.9001' - r-circlize @@ -48,12 +49,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-curatedtcgadata >=1.22.0,<1.23.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-curatedtcgadata >=1.24.0,<1.25.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - 'r-callr >=3.0.0.9001' - r-circlize diff --git a/recipes/bioconductor-amountain/meta.yaml b/recipes/bioconductor-amountain/meta.yaml index 16cb11a74a7a2..e8e64af069238 100644 --- a/recipes/bioconductor-amountain/meta.yaml +++ b/recipes/bioconductor-amountain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "AMOUNTAIN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d999f893262716e598b8816f9d585b7 + md5: acf007b4bceaa196843cbcf221b762ba build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-amountain", max_pin="x.x") }}' # Suggests: BiocStyle, qgraph, knitr, rmarkdown # SystemRequirements: gsl requirements: diff --git a/recipes/bioconductor-ampaffyexample/meta.yaml b/recipes/bioconductor-ampaffyexample/meta.yaml index ca79fef896674..a4124743b758b 100644 --- a/recipes/bioconductor-ampaffyexample/meta.yaml +++ b/recipes/bioconductor-ampaffyexample/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "AmpAffyExample" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8863d31491bb756d0f630d09c012904 + md5: 3277d6d26f145ddbb45c3808273cd150 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ampaffyexample", max_pin="x.x") }}' noarch: generic # Suggests: hgu133acdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ampaffyexample/post-link.sh b/recipes/bioconductor-ampaffyexample/post-link.sh index 9c4b6ba62ddf7..2d12c440e0cea 100644 --- a/recipes/bioconductor-ampaffyexample/post-link.sh +++ b/recipes/bioconductor-ampaffyexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ampaffyexample-1.40.0" +installBiocDataPackage.sh "ampaffyexample-1.42.0" diff --git a/recipes/bioconductor-amplican/meta.yaml b/recipes/bioconductor-amplican/meta.yaml index 1cf3fc17c68a4..d57bcd680d241 100644 --- a/recipes/bioconductor-amplican/meta.yaml +++ b/recipes/bioconductor-amplican/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "amplican" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7cc66936261be4fa00c6cee261cce6ab + md5: 73fd9acdf5066ee76b1157068151f1f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-amplican", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, GenomicAlignments requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-cluster >=2.1.4' - 'r-data.table >=1.10.4-3' @@ -46,14 +47,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-cluster >=2.1.4' - 'r-data.table >=1.10.4-3' diff --git a/recipes/bioconductor-anaquin/meta.yaml b/recipes/bioconductor-anaquin/meta.yaml index 0510b163517c6..aa5132a62ebf8 100644 --- a/recipes/bioconductor-anaquin/meta.yaml +++ b/recipes/bioconductor-anaquin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "Anaquin" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7dbfecc409b693298ad398782947d682 + md5: a0b480fdac1e56d9b308c2c23518b4a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anaquin", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.2.0' - r-knitr @@ -30,8 +31,8 @@ requirements: - r-plyr - r-rocr run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.2.0' - r-knitr diff --git a/recipes/bioconductor-ancombc/meta.yaml b/recipes/bioconductor-ancombc/meta.yaml index bf379d0df9d84..25c2d9638dbc9 100644 --- a/recipes/bioconductor-ancombc/meta.yaml +++ b/recipes/bioconductor-ancombc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "ANCOMBC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,67 +11,60 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 877867a31ab16c43bbb1eab0b4a92bf1 + md5: 42059f62faa03e818d0cd15b7bcf0094 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ancombc", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat, DT, caret, microbiome, tidyverse +# Suggests: dplyr, knitr, rmarkdown, testthat, DT, tidyr, tidyverse, microbiome, magrittr requirements: host: - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-cvxr - r-desctools - r-doparallel - r-dorng - - r-dplyr - - r-emmeans - r-energy - r-foreach + - r-gtools - r-hmisc - r-lme4 - r-lmertest - - r-magrittr - r-mass + - r-matrix + - r-multcomp - r-nloptr - r-rdpack - - r-rlang - - r-rngtools - - r-tibble - - r-tidyr run: - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-cvxr - r-desctools - r-doparallel - r-dorng - - r-dplyr - - r-emmeans - r-energy - r-foreach + - r-gtools - r-hmisc - r-lme4 - r-lmertest - - r-magrittr - r-mass + - r-matrix + - r-multcomp - r-nloptr - r-rdpack - - r-rlang - - r-rngtools - - r-tibble - - r-tidyr test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-aneufinder/meta.yaml b/recipes/bioconductor-aneufinder/meta.yaml index ac862ee49cfa2..c0989067c743b 100644 --- a/recipes/bioconductor-aneufinder/meta.yaml +++ b/recipes/bioconductor-aneufinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "AneuFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a38ae17997909fe55521eeeb7927f47b + md5: 421efa90a617606c8db2c947d302c6b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aneufinder", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-aneufinderdata >=1.28.0,<1.29.0' - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-aneufinderdata >=1.30.0,<1.31.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-doparallel @@ -44,17 +45,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-aneufinderdata >=1.28.0,<1.29.0' - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-aneufinderdata >=1.30.0,<1.31.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-doparallel diff --git a/recipes/bioconductor-aneufinderdata/meta.yaml b/recipes/bioconductor-aneufinderdata/meta.yaml index 7d2ecb6161957..7556ff6e34b2c 100644 --- a/recipes/bioconductor-aneufinderdata/meta.yaml +++ b/recipes/bioconductor-aneufinderdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "AneuFinderData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 703ac91ee510ae00274632026f14a065 + md5: 895230cd9b780dbb286a012f3c8777eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aneufinderdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-aneufinderdata/post-link.sh b/recipes/bioconductor-aneufinderdata/post-link.sh index 2b407d94f6c62..25c0a75eda265 100644 --- a/recipes/bioconductor-aneufinderdata/post-link.sh +++ b/recipes/bioconductor-aneufinderdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "aneufinderdata-1.28.0" +installBiocDataPackage.sh "aneufinderdata-1.30.0" diff --git a/recipes/bioconductor-annaffy/meta.yaml b/recipes/bioconductor-annaffy/meta.yaml index 677262a02d32d..843f2adced6d4 100644 --- a/recipes/bioconductor-annaffy/meta.yaml +++ b/recipes/bioconductor-annaffy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "annaffy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 007b32dfee6b9d9584ba4d723fb523f6 + md5: a590578d3e87dbab236a5531f0a5bce0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annaffy", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2.db, multtest, tcltk requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-biocmanager - r-dbi run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-annmap/meta.yaml b/recipes/bioconductor-annmap/meta.yaml index 68d79ae0b90f4..54d7f473f442b 100644 --- a/recipes/bioconductor-annmap/meta.yaml +++ b/recipes/bioconductor-annmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "annmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 414b7e6fe75e48d8e3a612a51cb29d38 + md5: 4e793a7c30de8248f566e7c14bf3fa90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annmap", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, rjson, Gviz requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dbi - r-digest - r-lattice - 'r-rmysql >=0.6-0' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dbi - r-digest diff --git a/recipes/bioconductor-annotate/meta.yaml b/recipes/bioconductor-annotate/meta.yaml index ceefbf3fa9dae..0e27f09050df3 100644 --- a/recipes/bioconductor-annotate/meta.yaml +++ b/recipes/bioconductor-annotate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "annotate" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fb5187ca7fdd4e1be47a470d528397df + md5: 04d25cadc03401556364f8ca9c3b2a61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotate", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dbi - r-httr - r-xml - r-xtable run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dbi - r-httr diff --git a/recipes/bioconductor-annotationdbi/meta.yaml b/recipes/bioconductor-annotationdbi/meta.yaml index df46ea4a23f46..092d59455da59 100644 --- a/recipes/bioconductor-annotationdbi/meta.yaml +++ b/recipes/bioconductor-annotationdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.2" %} +{% set version = "1.64.1" %} {% set name = "AnnotationDbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e12679a9cb4533c5f24fc27458b8d8e6 + md5: 965300db0b7a8b527ed3eb00fdd6d10f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationdbi", max_pin="x.x") }}' noarch: generic # Suggests: utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rsqlite diff --git a/recipes/bioconductor-annotationfilter/meta.yaml b/recipes/bioconductor-annotationfilter/meta.yaml index 3d6de9ccd9af2..72a8de6d1d3e4 100644 --- a/recipes/bioconductor-annotationfilter/meta.yaml +++ b/recipes/bioconductor-annotationfilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "AnnotationFilter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2838a3b75e2f41d27325908586729c4f + md5: 512eececc247990236fd09aa1fc46966 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationfilter", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-lazyeval run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-lazyeval test: diff --git a/recipes/bioconductor-annotationforge/meta.yaml b/recipes/bioconductor-annotationforge/meta.yaml index 4aedb25498143..0ff1070736cfa 100644 --- a/recipes/bioconductor-annotationforge/meta.yaml +++ b/recipes/bioconductor-annotationforge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.2" %} +{% set version = "1.44.0" %} {% set name = "AnnotationForge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ed5d42ecb97e5ab9123d078ff766c66 + md5: 4aa011cdbdc464bbfe1542ec418e7749 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationforge", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, markdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rcurl - r-rsqlite - r-xml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rcurl diff --git a/recipes/bioconductor-annotationhub/meta.yaml b/recipes/bioconductor-annotationhub/meta.yaml index 98ee765be3f0b..06f8f353cee10 100644 --- a/recipes/bioconductor-annotationhub/meta.yaml +++ b/recipes/bioconductor-annotationhub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "AnnotationHub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 458bb90d5680afe0b2e6b7c75ce37f16 + md5: 9dcc8ea705c0e7f8ac8e9af262de876f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationhub", max_pin="x.x") }}' noarch: generic -# Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub +# Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocversion >=3.17.0,<3.18.0' - - 'bioconductor-interactivedisplaybase >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocversion >=3.18.0,<3.19.0' + - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-curl @@ -36,12 +37,12 @@ requirements: - r-rsqlite - r-yaml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocversion >=3.17.0,<3.18.0' - - 'bioconductor-interactivedisplaybase >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocversion >=3.18.0,<3.19.0' + - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-curl diff --git a/recipes/bioconductor-annotationhubdata/meta.yaml b/recipes/bioconductor-annotationhubdata/meta.yaml index 6ab68144f4d88..712e0387d8f7f 100644 --- a/recipes/bioconductor-annotationhubdata/meta.yaml +++ b/recipes/bioconductor-annotationhubdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "AnnotationHubData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d924856924548dfcd2814cb0247c60a7 + md5: 0c08db64bda6298ca0d673b190a90dee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationhubdata", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bioccheck >=1.36.0,<1.37.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bioccheck >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-dbi @@ -47,23 +48,23 @@ requirements: - r-rsqlite - r-xml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bioccheck >=1.36.0,<1.37.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bioccheck >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-annotationtools/meta.yaml b/recipes/bioconductor-annotationtools/meta.yaml index a4fadf6af1516..e72898bc9a532 100644 --- a/recipes/bioconductor-annotationtools/meta.yaml +++ b/recipes/bioconductor-annotationtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "annotationTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c04239bb8a757f32c045586db12761c + md5: 3b0a795d7898c0b6112ed596f9d2de27 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotationtools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-annotatr/meta.yaml b/recipes/bioconductor-annotatr/meta.yaml index 8165e5c27a448..a2faf6e30caba 100644 --- a/recipes/bioconductor-annotatr/meta.yaml +++ b/recipes/bioconductor-annotatr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "annotatr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 24fa1da45dd9a0e0af22f4d358970ec6 + md5: 433372717ce78a1ae23a91a80601f2b6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-annotatr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 - r-readr - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-anopheles.db0/meta.yaml b/recipes/bioconductor-anopheles.db0/meta.yaml index 9b13d37a1e2aa..df8ab3def33f1 100644 --- a/recipes/bioconductor-anopheles.db0/meta.yaml +++ b/recipes/bioconductor-anopheles.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "anopheles.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d26110289d806c4d1bd6e039c5873100 + md5: cd7b03fffb4ffd0cf0877a55a3636d93 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anopheles.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-anopheles.db0/post-link.sh b/recipes/bioconductor-anopheles.db0/post-link.sh index fb5a134da283e..9febec5c61f5f 100644 --- a/recipes/bioconductor-anopheles.db0/post-link.sh +++ b/recipes/bioconductor-anopheles.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "anopheles.db0-3.17.0" +installBiocDataPackage.sh "anopheles.db0-3.18.0" diff --git a/recipes/bioconductor-anota/meta.yaml b/recipes/bioconductor-anota/meta.yaml index 51d07f713c147..eabf4ab9ea756 100644 --- a/recipes/bioconductor-anota/meta.yaml +++ b/recipes/bioconductor-anota/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "anota" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 043ed2d07c85599feb160ff62e65369a + md5: dc1461d1c43ffdfedc8e0f49a2b4ac6b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anota", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base run: - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base test: commands: diff --git a/recipes/bioconductor-anota2seq/meta.yaml b/recipes/bioconductor-anota2seq/meta.yaml index dccb1f285651f..295afda5304e6 100644 --- a/recipes/bioconductor-anota2seq/meta.yaml +++ b/recipes/bioconductor-anota2seq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "anota2seq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 67cf3d06cd925a69936cf6b784da0a7a + md5: c14a5f4c2cd7c51fbc9c7ecd844ad0be build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anota2seq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitr requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-antiprofiles/meta.yaml b/recipes/bioconductor-antiprofiles/meta.yaml index c65773a4a3397..b885a849653a4 100644 --- a/recipes/bioconductor-antiprofiles/meta.yaml +++ b/recipes/bioconductor-antiprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "antiProfiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62ed7ee12254e32c8cb6c5820b53b230 + md5: 80b3c1174d02d3b00b3ebf5d14a75b90 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-antiprofiles", max_pin="x.x") }}' noarch: generic # Suggests: antiProfilesData, RColorBrewer requirements: diff --git a/recipes/bioconductor-antiprofilesdata/meta.yaml b/recipes/bioconductor-antiprofilesdata/meta.yaml index a2787e87c261b..4803d0b345804 100644 --- a/recipes/bioconductor-antiprofilesdata/meta.yaml +++ b/recipes/bioconductor-antiprofilesdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "antiProfilesData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d5eab300113940ec702cdd00de617761 + md5: dc40c00fb296b31cf65369e801d6f2f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-antiprofilesdata", max_pin="x.x") }}' noarch: generic # Suggests: frma, GEOquery, GEOmetadb requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-antiprofilesdata/post-link.sh b/recipes/bioconductor-antiprofilesdata/post-link.sh index cf588366537b0..7de926d0707ed 100644 --- a/recipes/bioconductor-antiprofilesdata/post-link.sh +++ b/recipes/bioconductor-antiprofilesdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "antiprofilesdata-1.36.0" +installBiocDataPackage.sh "antiprofilesdata-1.38.0" diff --git a/recipes/bioconductor-anvil/meta.yaml b/recipes/bioconductor-anvil/meta.yaml index b7d5c34b2696c..27898e91b994e 100644 --- a/recipes/bioconductor-anvil/meta.yaml +++ b/recipes/bioconductor-anvil/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.3" %} +{% set version = "1.14.0" %} {% set name = "AnVIL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c773fdc6581ece77262038390b7ffba0 + md5: 960614983c195ba60dca0a63a0fbf352 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anvil", max_pin="x.x") }}' noarch: generic # Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools requirements: diff --git a/recipes/bioconductor-anvilbilling/meta.yaml b/recipes/bioconductor-anvilbilling/meta.yaml index 86334e0faaadd..a68235d62783f 100644 --- a/recipes/bioconductor-anvilbilling/meta.yaml +++ b/recipes/bioconductor-anvilbilling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "AnVILBilling" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad02ff4c8be1fdf4e48b493b55fa4c8b + md5: 9e6cd90c2e4e31067dfab860b5130cf8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anvilbilling", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: diff --git a/recipes/bioconductor-anvilpublish/meta.yaml b/recipes/bioconductor-anvilpublish/meta.yaml index a74f9837912ea..60a805d1f9759 100644 --- a/recipes/bioconductor-anvilpublish/meta.yaml +++ b/recipes/bioconductor-anvilpublish/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "AnVILPublish" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ce3d510992dfb125c6fac3adfc84a42 + md5: bbd5bd8ab36e2563e7b4b01e2b11295d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anvilpublish", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, BiocManager, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-anvil >=1.12.0,<1.13.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' - r-base - r-httr - r-jsonlite @@ -30,7 +31,7 @@ requirements: - r-whisker - r-yaml run: - - 'bioconductor-anvil >=1.12.0,<1.13.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-anvilworkflow/meta.yaml b/recipes/bioconductor-anvilworkflow/meta.yaml index 39e81f1c3b85e..de05da6b61a56 100644 --- a/recipes/bioconductor-anvilworkflow/meta.yaml +++ b/recipes/bioconductor-anvilworkflow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "AnVILWorkflow" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 351e6afcc0568d82cb69f4fa6efb67ee + md5: af890e3cea3c42346ec887603ba12e40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anvilworkflow", max_pin="x.x") }}' noarch: generic # Suggests: knitr, tibble, BiocStyle requirements: host: - - 'bioconductor-anvil >=1.12.0,<1.13.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' - r-base - r-httr - r-jsonlite run: - - 'bioconductor-anvil >=1.12.0,<1.13.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-apalyzer/meta.yaml b/recipes/bioconductor-apalyzer/meta.yaml index 04317074d9d00..744b59ec3073e 100644 --- a/recipes/bioconductor-apalyzer/meta.yaml +++ b/recipes/bioconductor-apalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "APAlyzer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90cb4679a0915479395a3955c7c75cbb + md5: 88aebb2681d07ad9bc8b7e3499339d51 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-apalyzer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hybridmtest >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hybridmtest >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-ggplot2 @@ -38,16 +39,16 @@ requirements: - r-repmis - r-tidyr run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hybridmtest >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hybridmtest >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-apcomplex/meta.yaml b/recipes/bioconductor-apcomplex/meta.yaml index 53e5b265bec60..78e15d595cd68 100644 --- a/recipes/bioconductor-apcomplex/meta.yaml +++ b/recipes/bioconductor-apcomplex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.66.0" %} +{% set version = "2.68.0" %} {% set name = "apComplex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51e69711964aab117703064718f5fbf5 + md5: 03418539dfa5904bf05f430718789fde build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-apcomplex", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-apeglm/meta.yaml b/recipes/bioconductor-apeglm/meta.yaml index 938a77dfbe3cb..3d750a1756a2b 100644 --- a/recipes/bioconductor-apeglm/meta.yaml +++ b/recipes/bioconductor-apeglm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "apeglm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 79070e75b8ea4968e63f8e17afa73d38 + md5: 0f8e64bdd8eec2566238fdc487afabb8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-apeglm", max_pin="x.x") }}' # Suggests: DESeq2, airway, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-emdbook - r-rcpp @@ -30,8 +31,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-emdbook - r-rcpp diff --git a/recipes/bioconductor-apl/meta.yaml b/recipes/bioconductor-apl/meta.yaml index cc417acd554cd..3cefe27602f15 100644 --- a/recipes/bioconductor-apl/meta.yaml +++ b/recipes/bioconductor-apl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "APL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41f52a6b448fbb963f3ef02f3e9f319b + md5: 725b38bc042e6b6fd349aac0ff3d471c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-apl", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat # SystemRequirements: python, pytorch, numpy requirements: host: - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-ggplot2 - r-ggrepel @@ -37,11 +38,11 @@ requirements: - r-seurat - r-viridislite run: - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-appreci8r/meta.yaml b/recipes/bioconductor-appreci8r/meta.yaml index b3a99c97d31a0..fdbd9dac892ba 100644 --- a/recipes/bioconductor-appreci8r/meta.yaml +++ b/recipes/bioconductor-appreci8r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.1" %} {% set name = "appreci8R" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,73 +11,72 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47501e7afbbe98a31b837ea71d094727 + md5: 9165459dd4a98c9645928c87b934c081 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-appreci8r", max_pin="x.x") }}' noarch: generic -# Suggests: GO.db, org.Hs.eg.db +# Suggests: GO.db, org.Hs.eg.db, utils requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-cosmic.67 >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-cosmic.67 >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-mafdb.gnomadex.r2.1.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0' - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - r-base - r-dt - r-openxlsx - r-rentrez - - r-rsnps - r-seqinr - r-shiny - r-shinyjs - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-cosmic.67 >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-cosmic.67 >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-mafdb.gnomadex.r2.1.hs37d5 >=3.10.0,<3.11.0' - 'bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0' - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - r-base - r-dt - r-openxlsx - r-rentrez - - r-rsnps - r-seqinr - r-shiny - r-shinyjs diff --git a/recipes/bioconductor-arabidopsis.db0/meta.yaml b/recipes/bioconductor-arabidopsis.db0/meta.yaml index 59d8ccdd4d9fd..a353a6fe036e9 100644 --- a/recipes/bioconductor-arabidopsis.db0/meta.yaml +++ b/recipes/bioconductor-arabidopsis.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "arabidopsis.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 773844428cd90716c8e32f942328618d + md5: 5896dbae0f9f8fdc87712dba0bb6cbd1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arabidopsis.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-arabidopsis.db0/post-link.sh b/recipes/bioconductor-arabidopsis.db0/post-link.sh index ff530db18e421..45f1d087e4fb9 100644 --- a/recipes/bioconductor-arabidopsis.db0/post-link.sh +++ b/recipes/bioconductor-arabidopsis.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "arabidopsis.db0-3.17.0" +installBiocDataPackage.sh "arabidopsis.db0-3.18.0" diff --git a/recipes/bioconductor-aracne.networks/meta.yaml b/recipes/bioconductor-aracne.networks/meta.yaml index 4de189b8200a4..a1725ffbcf2bf 100644 --- a/recipes/bioconductor-aracne.networks/meta.yaml +++ b/recipes/bioconductor-aracne.networks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "aracne.networks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 766b50311db15b7c36dffbb945277382 + md5: 42657d0acf4c1ba54aa2057fa4525d51 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aracne.networks", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-aracne.networks/post-link.sh b/recipes/bioconductor-aracne.networks/post-link.sh index 62f03eb5bec12..a25ee53fa9383 100644 --- a/recipes/bioconductor-aracne.networks/post-link.sh +++ b/recipes/bioconductor-aracne.networks/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "aracne.networks-1.26.0" +installBiocDataPackage.sh "aracne.networks-1.28.0" diff --git a/recipes/bioconductor-aroma.light/meta.yaml b/recipes/bioconductor-aroma.light/meta.yaml index cbb3a8373f6eb..30e404c5a01cf 100644 --- a/recipes/bioconductor-aroma.light/meta.yaml +++ b/recipes/bioconductor-aroma.light/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.30.0" %} +{% set version = "3.32.0" %} {% set name = "aroma.light" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 479f763a3001b487d9b3111d6505eece + md5: 07d98bcf8be950a16c1d6aaae375f17d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aroma.light", max_pin="x.x") }}' noarch: generic # Suggests: princurve (>= 2.1.4) requirements: diff --git a/recipes/bioconductor-arrayexpress/meta.yaml b/recipes/bioconductor-arrayexpress/meta.yaml index eca4847f54ffb..6efa3dbf50684 100644 --- a/recipes/bioconductor-arrayexpress/meta.yaml +++ b/recipes/bioconductor-arrayexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "ArrayExpress" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9dc6f2a3298a96b6416d7b6cbacf59de + md5: 6232db8158e5ba9cde38da322b0c5163 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arrayexpress", max_pin="x.x") }}' noarch: generic # Suggests: affy requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' - r-base - r-httr - r-jsonlite - r-rlang run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-arraymvout/meta.yaml b/recipes/bioconductor-arraymvout/meta.yaml index 765e9efcc5abb..612d3124a7a6b 100644 --- a/recipes/bioconductor-arraymvout/meta.yaml +++ b/recipes/bioconductor-arraymvout/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "arrayMvout" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 496faed8293a47944fe26efa75276598 + md5: 7aa46c496dbe47218ea774cb02108800 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arraymvout", max_pin="x.x") }}' noarch: generic # Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affycontam >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-mdqc >=1.62.0,<1.63.0' - - 'bioconductor-parody >=1.58.0,<1.59.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affycontam >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-mdqc >=1.64.0,<1.65.0' + - 'bioconductor-parody >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affycontam >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-mdqc >=1.62.0,<1.63.0' - - 'bioconductor-parody >=1.58.0,<1.59.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affycontam >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-mdqc >=1.64.0,<1.65.0' + - 'bioconductor-parody >=1.60.0,<1.61.0' - r-base test: commands: diff --git a/recipes/bioconductor-arrayquality/meta.yaml b/recipes/bioconductor-arrayquality/meta.yaml index 0429256522126..c3c33beb6b5c6 100644 --- a/recipes/bioconductor-arrayquality/meta.yaml +++ b/recipes/bioconductor-arrayquality/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "arrayQuality" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05fac545dc5122c38913b83e9788c06e + md5: 9d875e31dc2f51e4c476d1a13330ad18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arrayquality", max_pin="x.x") }}' noarch: generic # Suggests: mclust, MEEBOdata, HEEBOdata requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-gridbase - r-hexbin - r-rcolorbrewer run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-gridbase - r-hexbin diff --git a/recipes/bioconductor-arrayqualitymetrics/meta.yaml b/recipes/bioconductor-arrayqualitymetrics/meta.yaml index 4b809dc9ebc2a..46f59c2bc01a2 100644 --- a/recipes/bioconductor-arrayqualitymetrics/meta.yaml +++ b/recipes/bioconductor-arrayqualitymetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.56.0" %} +{% set version = "3.58.0" %} {% set name = "arrayQualityMetrics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d6e27fd09971235379b22a11ec9a0e8 + md5: 65128c55b6181bdadb73d256e399091e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arrayqualitymetrics", max_pin="x.x") }}' noarch: generic # Suggests: ALLMLL, CCl4, BiocStyle, knitr requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-gridsvg >=1.4-3' - r-hmisc @@ -39,13 +40,13 @@ requirements: - r-svglite - r-xml run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-gridsvg >=1.4-3' - r-hmisc diff --git a/recipes/bioconductor-arrmdata/meta.yaml b/recipes/bioconductor-arrmdata/meta.yaml index 3360d61788513..a7fe1357a1d0d 100644 --- a/recipes/bioconductor-arrmdata/meta.yaml +++ b/recipes/bioconductor-arrmdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ARRmData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1a4ecc042b17945f8a02625fbfa97b5 + md5: 95475f869b8ff3d6344c0f45f2e616c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arrmdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-arrmdata/post-link.sh b/recipes/bioconductor-arrmdata/post-link.sh index ca315f09c39d6..92579cc4ac064 100644 --- a/recipes/bioconductor-arrmdata/post-link.sh +++ b/recipes/bioconductor-arrmdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "arrmdata-1.36.0" +installBiocDataPackage.sh "arrmdata-1.38.0" diff --git a/recipes/bioconductor-arrmnormalization/meta.yaml b/recipes/bioconductor-arrmnormalization/meta.yaml index 225d1b87b01ad..437968da022a4 100644 --- a/recipes/bioconductor-arrmnormalization/meta.yaml +++ b/recipes/bioconductor-arrmnormalization/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "ARRmNormalization" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1331a6d43b42563841b7712441e0d14d + md5: a6223cb64b7077670d38fb437638e0fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-arrmnormalization", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-arrmdata >=1.36.0,<1.37.0' + - 'bioconductor-arrmdata >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-arrmdata >=1.36.0,<1.37.0' + - 'bioconductor-arrmdata >=1.38.0,<1.39.0' - r-base test: commands: diff --git a/recipes/bioconductor-artms/meta.yaml b/recipes/bioconductor-artms/meta.yaml index 0f79e21cd6bd9..25f17daed6675 100644 --- a/recipes/bioconductor-artms/meta.yaml +++ b/recipes/bioconductor-artms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "artMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de4a453a5d57a20ee95302254d866981 + md5: d52a9405bcf6f4a3920ecb70be49c1d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-artms", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-bit64 - r-circlize @@ -50,10 +51,10 @@ requirements: - r-venndiagram - r-yaml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-bit64 - r-circlize diff --git a/recipes/bioconductor-asafe/meta.yaml b/recipes/bioconductor-asafe/meta.yaml index 74c736c362256..46bae4e0a4f2d 100644 --- a/recipes/bioconductor-asafe/meta.yaml +++ b/recipes/bioconductor-asafe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ASAFE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02ac2aeccd6067529507ff1b46c0fdaf + md5: e054d986c3b6f2574c26498eaf6e4f7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asafe", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat requirements: diff --git a/recipes/bioconductor-aseb/meta.yaml b/recipes/bioconductor-aseb/meta.yaml index 0efab8d563af3..185e0ab4c1db4 100644 --- a/recipes/bioconductor-aseb/meta.yaml +++ b/recipes/bioconductor-aseb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.3" %} {% set name = "ASEB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 205d8716d05f9046395de90b9d48cdc2 + md5: 7e9312371523d44d7f1cb759af2d150e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aseb", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-asgsca/meta.yaml b/recipes/bioconductor-asgsca/meta.yaml index 740cffa843961..2fd57fbdec08e 100644 --- a/recipes/bioconductor-asgsca/meta.yaml +++ b/recipes/bioconductor-asgsca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "ASGSCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db2fb611216db58fd5fa05720151ab2e + md5: c0e60b4fa228444ab7863044881fa8bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asgsca", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: diff --git a/recipes/bioconductor-ashkenazimsonchr21/meta.yaml b/recipes/bioconductor-ashkenazimsonchr21/meta.yaml index b4e1289ce168f..e111494e14c2a 100644 --- a/recipes/bioconductor-ashkenazimsonchr21/meta.yaml +++ b/recipes/bioconductor-ashkenazimsonchr21/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "AshkenazimSonChr21" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6180e43108e29d9194ed93bc0f208124 + md5: a4455fab1d47dcf8dc2411fec1066a2c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ashkenazimsonchr21", max_pin="x.x") }}' noarch: generic # Suggests: knitr, VariantAnnotation requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ashkenazimsonchr21/post-link.sh b/recipes/bioconductor-ashkenazimsonchr21/post-link.sh index 27d6400da0ce0..20f8d2ad38a7e 100644 --- a/recipes/bioconductor-ashkenazimsonchr21/post-link.sh +++ b/recipes/bioconductor-ashkenazimsonchr21/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ashkenazimsonchr21-1.30.0" +installBiocDataPackage.sh "ashkenazimsonchr21-1.32.0" diff --git a/recipes/bioconductor-asics/meta.yaml b/recipes/bioconductor-asics/meta.yaml index 52580c3dcf753..49a962cda7e85 100644 --- a/recipes/bioconductor-asics/meta.yaml +++ b/recipes/bioconductor-asics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "ASICS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7e6efa85c8bc0444a5cac2114338cff + md5: 526bfb1ebf38574a4914a434cd159769 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asics", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-pepsnmr >=1.18.0,<1.19.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-pepsnmr >=1.20.0,<1.21.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-glmnet @@ -35,10 +36,10 @@ requirements: - r-quadprog - r-zoo run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-pepsnmr >=1.18.0,<1.19.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-pepsnmr >=1.20.0,<1.21.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-glmnet diff --git a/recipes/bioconductor-asicsdata/meta.yaml b/recipes/bioconductor-asicsdata/meta.yaml index 47f0f44eabcb9..6863b79647e76 100644 --- a/recipes/bioconductor-asicsdata/meta.yaml +++ b/recipes/bioconductor-asicsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ASICSdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46a4e15b37bd49b3cd5693c1a900b581 + md5: afb117c0db733e23239bf2cf4e18d364 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asicsdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-asicsdata/post-link.sh b/recipes/bioconductor-asicsdata/post-link.sh index 5e413191611a5..cacabdb1a734e 100644 --- a/recipes/bioconductor-asicsdata/post-link.sh +++ b/recipes/bioconductor-asicsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "asicsdata-1.20.0" +installBiocDataPackage.sh "asicsdata-1.22.0" diff --git a/recipes/bioconductor-aspli/meta.yaml b/recipes/bioconductor-aspli/meta.yaml index 9008a0e8a4d46..7b9d0fd06dfdf 100644 --- a/recipes/bioconductor-aspli/meta.yaml +++ b/recipes/bioconductor-aspli/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "ASpli" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 718667b9b158c89ef2f05649516aa3aa + md5: abf86e5478e3191f21892ba2eb35e442 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aspli", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dt @@ -42,18 +43,18 @@ requirements: - r-tidyr - r-upsetr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dt diff --git a/recipes/bioconductor-assessorf/meta.yaml b/recipes/bioconductor-assessorf/meta.yaml index dc05bd73c91d6..b03bbb0dcf99d 100644 --- a/recipes/bioconductor-assessorf/meta.yaml +++ b/recipes/bioconductor-assessorf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "AssessORF" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f5157d6177c7915fc9776c5b4d8b214 + md5: b11ca260fff21c6afe98ee471d79b3ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-assessorf", max_pin="x.x") }}' noarch: generic # Suggests: AssessORFData, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-assessorfdata/meta.yaml b/recipes/bioconductor-assessorfdata/meta.yaml index e2efc67f2625b..59253cef5e2df 100644 --- a/recipes/bioconductor-assessorfdata/meta.yaml +++ b/recipes/bioconductor-assessorfdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "AssessORFData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7c0f6953391e3f1f610467f14384774 + md5: 0dd44e672021a9179762efe4959e8608 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-assessorfdata", max_pin="x.x") }}' noarch: generic # Suggests: AssessORF, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-decipher >=2.28.0,<2.29.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' - r-base run: - - 'bioconductor-decipher >=2.28.0,<2.29.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-assessorfdata/post-link.sh b/recipes/bioconductor-assessorfdata/post-link.sh index 6728e501cc5c3..dc7f9d707e3cd 100644 --- a/recipes/bioconductor-assessorfdata/post-link.sh +++ b/recipes/bioconductor-assessorfdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "assessorfdata-1.18.0" +installBiocDataPackage.sh "assessorfdata-1.20.0" diff --git a/recipes/bioconductor-asset/meta.yaml b/recipes/bioconductor-asset/meta.yaml index 96c79973b49fa..fe7f5b9cdda56 100644 --- a/recipes/bioconductor-asset/meta.yaml +++ b/recipes/bioconductor-asset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "ASSET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c92854756cfbc064a6843c69dfefbfd5 + md5: 395bcc1b0256acc248c5d3440bf5dfeb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asset", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr requirements: diff --git a/recipes/bioconductor-assign/meta.yaml b/recipes/bioconductor-assign/meta.yaml index f13680a216ae7..ce78d053d88c9 100644 --- a/recipes/bioconductor-assign/meta.yaml +++ b/recipes/bioconductor-assign/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ASSIGN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95d9e71f088aa3369298e6889fe82a2c + md5: c03c8eedec6379aa0fac65d11377fdf8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-assign", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown requirements: host: - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 - r-gplots @@ -29,7 +30,7 @@ requirements: - r-rlab - r-yaml run: - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-asurat/meta.yaml b/recipes/bioconductor-asurat/meta.yaml index 77d1a41e21d31..79307284cafc7 100644 --- a/recipes/bioconductor-asurat/meta.yaml +++ b/recipes/bioconductor-asurat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ASURAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7bc663de993eed55f2a14aaa4946385 + md5: a1cb615f6ddab8cb8b9ccb1a73ba39de build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-asurat", max_pin="x.x") }}' # Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cluster @@ -32,10 +33,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cluster diff --git a/recipes/bioconductor-ataccogaps/meta.yaml b/recipes/bioconductor-ataccogaps/meta.yaml index 9a6e32fe9f3cb..3988a44053f03 100644 --- a/recipes/bioconductor-ataccogaps/meta.yaml +++ b/recipes/bioconductor-ataccogaps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ATACCoGAPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 266f86c0e01ae75b62a42f9ff65d69e1 + md5: f8cf8dd559b05caf23934090510297de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ataccogaps", max_pin="x.x") }}' noarch: generic # Suggests: knitr, viridis requirements: host: - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-chromvar >=1.22.0,<1.23.0' - - 'bioconductor-cogaps >=3.19.0,<3.20.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-geneoverlap >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-chromvar >=1.24.0,<1.25.0' + - 'bioconductor-cogaps >=3.22.0,<3.23.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-geneoverlap >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-jaspar2016 >=1.28.0,<1.29.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-jaspar2016 >=1.30.0,<1.31.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - 'bioconductor-mus.musculus >=1.3.0,<1.4.0' - - 'bioconductor-projectr >=1.16.0,<1.17.0' - - 'bioconductor-rgreat >=2.2.0,<2.3.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-projectr >=1.18.0,<1.19.0' + - 'bioconductor-rgreat >=2.4.0,<2.5.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dplyr - r-gplots @@ -47,20 +48,20 @@ requirements: run: - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-chromvar >=1.22.0,<1.23.0' - - 'bioconductor-cogaps >=3.19.0,<3.20.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-geneoverlap >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-chromvar >=1.24.0,<1.25.0' + - 'bioconductor-cogaps >=3.22.0,<3.23.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-geneoverlap >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-jaspar2016 >=1.28.0,<1.29.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-jaspar2016 >=1.30.0,<1.31.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - 'bioconductor-mus.musculus >=1.3.0,<1.4.0' - - 'bioconductor-projectr >=1.16.0,<1.17.0' - - 'bioconductor-rgreat >=2.2.0,<2.3.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-projectr >=1.18.0,<1.19.0' + - 'bioconductor-rgreat >=2.4.0,<2.5.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dplyr - r-gplots diff --git a/recipes/bioconductor-atacseqqc/meta.yaml b/recipes/bioconductor-atacseqqc/meta.yaml index 0ee2956e6770a..46ba87f49caf2 100644 --- a/recipes/bioconductor-atacseqqc/meta.yaml +++ b/recipes/bioconductor-atacseqqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ATACseqQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,51 +11,52 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43463f55028e1db0b7f94d6014507700 + md5: 6742da3bbb4073be7aa5f2544b65df23 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-atacseqqc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-kernsmooth - r-preseqr - r-randomforest run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-kernsmooth - r-preseqr diff --git a/recipes/bioconductor-atacseqtfea/meta.yaml b/recipes/bioconductor-atacseqtfea/meta.yaml index f00ef0af0ce58..e11f613d103a9 100644 --- a/recipes/bioconductor-atacseqtfea/meta.yaml +++ b/recipes/bioconductor-atacseqtfea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ATACseqTFEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de251ce1a7cb6b4e6a670db088bb0c23 + md5: 30284cc31687d97f23d2a7c023e8561d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-atacseqtfea", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dplyr - r-ggplot2 @@ -39,17 +40,17 @@ requirements: - r-matrix - r-pracma run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-atena/meta.yaml b/recipes/bioconductor-atena/meta.yaml index f3faff83b15d8..f34d851d4bc20 100644 --- a/recipes/bioconductor-atena/meta.yaml +++ b/recipes/bioconductor-atena/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "atena" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7522b8df9e9bb705d981a2f10adf1b39 + md5: c7ae11b12240ed1d848301b4c40b019e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-atena", max_pin="x.x") }}' noarch: generic # Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-matrixstats - r-squarem run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-matrixstats diff --git a/recipes/bioconductor-ath1121501.db/meta.yaml b/recipes/bioconductor-ath1121501.db/meta.yaml index 1df20035f550b..ad07150ccead6 100644 --- a/recipes/bioconductor-ath1121501.db/meta.yaml +++ b/recipes/bioconductor-ath1121501.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "ath1121501.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c5d937ca9c6bcbb4385fb37a3b14ad15 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ath1121501.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.at.tair.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.at.tair.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ath1121501cdf/meta.yaml b/recipes/bioconductor-ath1121501cdf/meta.yaml index 288550799f467..24a018cde9f47 100644 --- a/recipes/bioconductor-ath1121501cdf/meta.yaml +++ b/recipes/bioconductor-ath1121501cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ath1121501cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8b63798143219b7c1c2666a91a1a2440 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ath1121501cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ath1121501probe/meta.yaml b/recipes/bioconductor-ath1121501probe/meta.yaml index e976c42b63525..b5f881e5be459 100644 --- a/recipes/bioconductor-ath1121501probe/meta.yaml +++ b/recipes/bioconductor-ath1121501probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ath1121501probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eeeae5e6550bb472ba3419d71bbd7dfb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ath1121501probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-atsnp/meta.yaml b/recipes/bioconductor-atsnp/meta.yaml index ee86773b673f5..22b2497f49120 100644 --- a/recipes/bioconductor-atsnp/meta.yaml +++ b/recipes/bioconductor-atsnp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "atSNP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d73cffb926671ee83a72e6f5cf34428 + md5: e7de15cd417026f8449b14841ff89bd2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-atsnp", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' - r-base - r-data.table - r-ggplot2 @@ -34,10 +35,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-attract/meta.yaml b/recipes/bioconductor-attract/meta.yaml index d15a94a2d8b3c..8bf0a00a35862 100644 --- a/recipes/bioconductor-attract/meta.yaml +++ b/recipes/bioconductor-attract/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "attract" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bc7912564093f9fbc689a27829012832 + md5: e7d563026d5d00b5dd3bd906268af221 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-attract", max_pin="x.x") }}' noarch: generic # Suggests: illuminaHumanv1.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - r-cluster run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - r-cluster test: diff --git a/recipes/bioconductor-aucell/meta.yaml b/recipes/bioconductor-aucell/meta.yaml index 5d91c15ceb337..806723573eb1a 100644 --- a/recipes/bioconductor-aucell/meta.yaml +++ b/recipes/bioconductor-aucell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "AUCell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20e4725a450ea1ef9ae1de7b6e0b2a4c + md5: 4d095823da2fd13bf83c831c037564ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-aucell", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh, Rtsne, testthat, zoo requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrix @@ -33,11 +34,11 @@ requirements: - r-r.utils - r-shiny run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrix diff --git a/recipes/bioconductor-autonomics/meta.yaml b/recipes/bioconductor-autonomics/meta.yaml index 10078e09c11a3..506a4b040c9ad 100644 --- a/recipes/bioconductor-autonomics/meta.yaml +++ b/recipes/bioconductor-autonomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.2" %} {% set name = "autonomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 79d945c34c8797df2eb8140818e05b57 + md5: 9034c755764d54d8bf0eb0e330f4e54f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-autonomics", max_pin="x.x") }}' noarch: generic # Suggests: affy, AnnotationDbi, BiocManager, BiocStyle, diagram, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, knitr, lme4, lmerTest, MASS, mixOmics, mpm, nlme, org.Hs.eg.db, org.Mm.eg.db, RCurl, remotes, rmarkdown, ropls, Rsubread, rtracklayer, seqinr, statmod, testthat requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - - r-assertive + - r-assertive.base + - r-assertive.files + - r-assertive.numbers + - r-assertive.sets - r-base - r-bit64 - r-colorspace @@ -49,16 +53,19 @@ requirements: - r-stringi - r-tidyr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - - r-assertive + - r-assertive.base + - r-assertive.files + - r-assertive.numbers + - r-assertive.sets - r-base - r-bit64 - r-colorspace diff --git a/recipes/bioconductor-awfisher/meta.yaml b/recipes/bioconductor-awfisher/meta.yaml index 3d0ec3cad3dd0..cc019247c8442 100644 --- a/recipes/bioconductor-awfisher/meta.yaml +++ b/recipes/bioconductor-awfisher/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "AWFisher" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a52828e4fdc882bcc16a7a4de22af840 + md5: ba9b2824782018cc7626ebc72b6bb81e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-awfisher", max_pin="x.x") }}' # Suggests: knitr, tightClust requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - libblas - liblapack run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-awst/meta.yaml b/recipes/bioconductor-awst/meta.yaml index 4e3ebced198fc..c735340e61235 100644 --- a/recipes/bioconductor-awst/meta.yaml +++ b/recipes/bioconductor-awst/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "awst" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88c6bfd36a182af8d3107bcb8cacba4a + md5: a7ca0636a8f728b63d6cf56729b856eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-awst", max_pin="x.x") }}' noarch: generic # Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-baalchip/meta.yaml b/recipes/bioconductor-baalchip/meta.yaml index 95ce06a3db06a..4596a55c8a87c 100644 --- a/recipes/bioconductor-baalchip/meta.yaml +++ b/recipes/bioconductor-baalchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "BaalChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d5b38867245ae1ce58e3d6e1f50f6e5f + md5: 5f2cf6dd86b26982d4d7ed693f961246 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-baalchip", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-coda - r-doby @@ -35,11 +36,11 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-coda - r-doby diff --git a/recipes/bioconductor-bacon/meta.yaml b/recipes/bioconductor-bacon/meta.yaml index 988a288f5b586..350eb69311bf0 100644 --- a/recipes/bioconductor-bacon/meta.yaml +++ b/recipes/bioconductor-bacon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "bacon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fdad543dfc946ebc8aa940e9f5a9da4e + md5: 3757e896d5a8253845a21e37e555044a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bacon", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ellipse - r-ggplot2 - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ellipse - r-ggplot2 diff --git a/recipes/bioconductor-bader/meta.yaml b/recipes/bioconductor-bader/meta.yaml index c86c6dd83e7e6..346caafa84021 100644 --- a/recipes/bioconductor-bader/meta.yaml +++ b/recipes/bioconductor-bader/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "BADER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec42e5966b46992505dacfb8880b24b0 + md5: 10d4e5e231ff178df7922078024f9d89 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bader", max_pin="x.x") }}' # Suggests: pasilla (>= 0.2.10) requirements: host: diff --git a/recipes/bioconductor-badregionfinder/meta.yaml b/recipes/bioconductor-badregionfinder/meta.yaml index e4d5277acfd58..18612ea8cae65 100644 --- a/recipes/bioconductor-badregionfinder/meta.yaml +++ b/recipes/bioconductor-badregionfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "BadRegionFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3fe981fffe29fd21bcc16672c1d46205 + md5: c492af1d6b1297cd322a79355e3d3664 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-badregionfinder", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-bags/meta.yaml b/recipes/bioconductor-bags/meta.yaml index 8e523dd945fc8..9aa67ffe4f606 100644 --- a/recipes/bioconductor-bags/meta.yaml +++ b/recipes/bioconductor-bags/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "BAGS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 206c6b841ff841017f5a6af951bcbbef + md5: 42c7a57422ddbb5c2d5263703a7e22d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bags", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-breastcancervdx >=1.38.0,<1.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-breastcancervdx >=1.40.0,<1.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-breastcancervdx >=1.38.0,<1.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-breastcancervdx >=1.40.0,<1.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-ballgown/meta.yaml b/recipes/bioconductor-ballgown/meta.yaml index e927ffedbda31..a9d3e0017fa92 100644 --- a/recipes/bioconductor-ballgown/meta.yaml +++ b/recipes/bioconductor-ballgown/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "ballgown" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8bf7da5968f9f4cc1aa14d8f0693d8e2 + md5: 805a1514b4080a8b00b4bdfce051dcda build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ballgown", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-bambu/meta.yaml b/recipes/bioconductor-bambu/meta.yaml index bb14fbe4730d8..0a5192523653c 100644 --- a/recipes/bioconductor-bambu/meta.yaml +++ b/recipes/bioconductor-bambu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.2.4" %} +{% set version = "3.4.0" %} {% set name = "bambu" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d9a12cd1329e08735800e7928b98fb97 + md5: 900e0e67c251f12989154113c54d2b32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bambu", max_pin="x.x") }}' # Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -41,17 +42,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-bamsignals/meta.yaml b/recipes/bioconductor-bamsignals/meta.yaml index 6e7abbf45ed04..fe49237768045 100644 --- a/recipes/bioconductor-bamsignals/meta.yaml +++ b/recipes/bioconductor-bamsignals/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "bamsignals" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee29481c743d792e65ebff380d4fdf1e + md5: e7b42351aa9651bdf7d429a6377143f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bamsignals", max_pin="x.x") }}' # Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-rcpp >=0.10.6' - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-rcpp >=0.10.6' build: diff --git a/recipes/bioconductor-bandits/meta.yaml b/recipes/bioconductor-bandits/meta.yaml index de9b008f4a75a..7ad9f0390a7b8 100644 --- a/recipes/bioconductor-bandits/meta.yaml +++ b/recipes/bioconductor-bandits/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.1" %} {% set name = "BANDITS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6ef9178205f8a59be55faea48e08b90 + md5: 2a65b9a4669d4075f5882047445491eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bandits", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings -# SystemRequirements: C++11 +# SystemRequirements: C++17 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-drimseq >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-drimseq >=1.30.0,<1.31.0' - r-base - r-data.table - r-doparallel @@ -36,8 +37,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-drimseq >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-drimseq >=1.30.0,<1.31.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-bandle/meta.yaml b/recipes/bioconductor-bandle/meta.yaml index 41051d877b568..c2bea3dd5035c 100644 --- a/recipes/bioconductor-bandle/meta.yaml +++ b/recipes/bioconductor-bandle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "bandle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 18a4217c592ace34eccbb1b9ea46295d + md5: 9c8dd928dd2b7900ff453ddc590ad6e4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bandle", max_pin="x.x") }}' # Suggests: coda (>= 0.19-4), testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-proloc >=1.40.0,<1.41.0' - - 'bioconductor-prolocdata >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-proloc >=1.42.0,<1.43.0' + - 'bioconductor-prolocdata >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-circlize @@ -45,13 +46,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-proloc >=1.40.0,<1.41.0' - - 'bioconductor-prolocdata >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-proloc >=1.42.0,<1.43.0' + - 'bioconductor-prolocdata >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-circlize diff --git a/recipes/bioconductor-banocc/meta.yaml b/recipes/bioconductor-banocc/meta.yaml index 0aff09d41f5b8..6c42e52f10707 100644 --- a/recipes/bioconductor-banocc/meta.yaml +++ b/recipes/bioconductor-banocc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "banocc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f67213c67fb7ef2fa721d0c38dceb1b0 + md5: 5a73975945814e725991bd67552349e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-banocc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, methods, testthat, BiocStyle requirements: diff --git a/recipes/bioconductor-barcodetrackr/meta.yaml b/recipes/bioconductor-barcodetrackr/meta.yaml index 56dad017f8320..c001ab2392527 100644 --- a/recipes/bioconductor-barcodetrackr/meta.yaml +++ b/recipes/bioconductor-barcodetrackr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "barcodetrackR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ef50b9baf6cb0f19e3ad67f6afb445e + md5: 34e3b62fbe85f743278fba96cfc8c618 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-barcodetrackr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, magick, rmarkdown, testthat requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cowplot @@ -42,8 +43,8 @@ requirements: - r-vegan - r-viridis run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cowplot diff --git a/recipes/bioconductor-barley1cdf/meta.yaml b/recipes/bioconductor-barley1cdf/meta.yaml index c86da8e98d869..462dda51f3f36 100644 --- a/recipes/bioconductor-barley1cdf/meta.yaml +++ b/recipes/bioconductor-barley1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "barley1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 16a2ca83f550518756d9fa3273672157 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-barley1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-barley1probe/meta.yaml b/recipes/bioconductor-barley1probe/meta.yaml index a6bb73c10d152..851b639c63da9 100644 --- a/recipes/bioconductor-barley1probe/meta.yaml +++ b/recipes/bioconductor-barley1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "barley1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 80595d8ecf83ba83ea84a722a24ab474 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-barley1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-basecallqc/meta.yaml b/recipes/bioconductor-basecallqc/meta.yaml index 20641673259f7..a9a2496602e83 100644 --- a/recipes/bioconductor-basecallqc/meta.yaml +++ b/recipes/bioconductor-basecallqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "basecallQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d01b22d917934112ec3feaad5268060 + md5: ad61b901f8e533f817dccfb4830b222a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basecallqc", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle # SystemRequirements: bcl2Fastq (versions >= 2.1.7) requirements: host: - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-data.table - r-dplyr @@ -39,7 +40,7 @@ requirements: - r-xml - r-yaml run: - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-basespacer/meta.yaml b/recipes/bioconductor-basespacer/meta.yaml index 0f6a9d240c07b..d19b37977de6b 100644 --- a/recipes/bioconductor-basespacer/meta.yaml +++ b/recipes/bioconductor-basespacer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "BaseSpaceR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 940b776f826fff5208c944e26a4fa538 + md5: b141511c6e978d4f26c8ec4c42c078c2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basespacer", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, IRanges, Rsamtools requirements: diff --git a/recipes/bioconductor-basic4cseq/meta.yaml b/recipes/bioconductor-basic4cseq/meta.yaml index 05f70073532b7..1a5adc44f4e62 100644 --- a/recipes/bioconductor-basic4cseq/meta.yaml +++ b/recipes/bioconductor-basic4cseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Basic4Cseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c3471249017f78eda382aba54e760ea + md5: b6e8e624b34a0626cfa015e9814d017b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basic4cseq", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-catools - r-rcircos run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-catools - r-rcircos diff --git a/recipes/bioconductor-basics/meta.yaml b/recipes/bioconductor-basics/meta.yaml index b2c87423a85e7..71548c210ade6 100644 --- a/recipes/bioconductor-basics/meta.yaml +++ b/recipes/bioconductor-basics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.3" %} +{% set version = "2.14.0" %} {% set name = "BASiCS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 148355fc63bab3ac6c9b742f6613286f + md5: 1252fa180b0da21a4a22e3400550ab93 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basics", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-coda @@ -47,14 +48,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-coda diff --git a/recipes/bioconductor-basicstan/meta.yaml b/recipes/bioconductor-basicstan/meta.yaml index 3f917708d53b6..5e7eecf766f1d 100644 --- a/recipes/bioconductor-basicstan/meta.yaml +++ b/recipes/bioconductor-basicstan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "BASiCStan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 130a35d534f52c5361f97c16bb7af5c2 + md5: b7179ffcf510240c0c3cc6e8e31b60d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basicstan", max_pin="x.x") }}' # Suggests: testthat (>= 3.0.0), knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-basics >=2.12.0,<2.13.0' - - 'bioconductor-glmgampoi >=1.12.0,<1.13.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basics >=2.14.0,<2.15.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bh >=1.66.0' - 'r-rcpp >=0.12.0' @@ -38,12 +39,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-basics >=2.12.0,<2.13.0' - - 'bioconductor-glmgampoi >=1.12.0,<1.13.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basics >=2.14.0,<2.15.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bh >=1.66.0' - 'r-rcpp >=0.12.0' diff --git a/recipes/bioconductor-basicstarrseq/meta.yaml b/recipes/bioconductor-basicstarrseq/meta.yaml index 603ee18b85d63..0962d27074600 100644 --- a/recipes/bioconductor-basicstarrseq/meta.yaml +++ b/recipes/bioconductor-basicstarrseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "BasicSTARRseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5309450baf05eaa4b75962a1c51a42d2 + md5: 45c21fe93b28467ae466fd4017792494 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basicstarrseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-basilisk.utils/meta.yaml b/recipes/bioconductor-basilisk.utils/meta.yaml index bbf7fae14022c..50279f87793f9 100644 --- a/recipes/bioconductor-basilisk.utils/meta.yaml +++ b/recipes/bioconductor-basilisk.utils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.1" %} {% set name = "basilisk.utils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4c999a6536d2c0b080b9f2ee83f3bd47 + md5: d5e61359283886e8653f772e65b0a898 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basilisk.utils", max_pin="x.x") }}' noarch: generic # Suggests: reticulate, knitr, rmarkdown, BiocStyle, testthat, basilisk requirements: host: - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base test: commands: diff --git a/recipes/bioconductor-basilisk/meta.yaml b/recipes/bioconductor-basilisk/meta.yaml index 1537a740c3827..8e6089e3f742c 100644 --- a/recipes/bioconductor-basilisk/meta.yaml +++ b/recipes/bioconductor-basilisk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.1" %} {% set name = "basilisk" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5335a9b864bad01710c0e326dabc29e3 + md5: b47dde22cc3bb45ec9c785fe025241a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-basilisk", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, callr requirements: host: - - 'bioconductor-basilisk.utils >=1.12.0,<1.13.0' - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base - r-reticulate run: - - 'bioconductor-basilisk.utils >=1.12.0,<1.13.0' - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base - r-reticulate test: diff --git a/recipes/bioconductor-batchelor/meta.yaml b/recipes/bioconductor-batchelor/meta.yaml index 9b702df1f403a..85f55bdbb422e 100644 --- a/recipes/bioconductor-batchelor/meta.yaml +++ b/recipes/bioconductor-batchelor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "batchelor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c513fab91211a116143880cf00fc0f60 + md5: e78aa00a2e343b79e7ad7aeb0fde1196 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-batchelor", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-residualmatrix >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-residualmatrix >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix @@ -41,19 +42,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-residualmatrix >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-residualmatrix >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix diff --git a/recipes/bioconductor-batchqc/meta.yaml b/recipes/bioconductor-batchqc/meta.yaml index 499d4b9ec9822..b8c5d00be9898 100644 --- a/recipes/bioconductor-batchqc/meta.yaml +++ b/recipes/bioconductor-batchqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "BatchQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b92d0d1fb1c172b3558a5c0505b32df + md5: c8940666878af6ea1981e6d90095bc98 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-batchqc", max_pin="x.x") }}' noarch: generic # Suggests: testthat # SystemRequirements: pandoc (http://pandoc.org/installing.html) for generating reports from markdown files. requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-corpcor - r-ggvis @@ -40,8 +41,8 @@ requirements: - r-shiny - pandoc run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-corpcor - r-ggvis diff --git a/recipes/bioconductor-bayesknockdown/meta.yaml b/recipes/bioconductor-bayesknockdown/meta.yaml index dffb36eda212c..34fc090aa009a 100644 --- a/recipes/bioconductor-bayesknockdown/meta.yaml +++ b/recipes/bioconductor-bayesknockdown/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "BayesKnockdown" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ba8a6b2608364a8b8cecee2d4ef1ba6 + md5: 6efc97e1bf0448a97ca0b3d595096a3d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bayesknockdown", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-bayesspace/meta.yaml b/recipes/bioconductor-bayesspace/meta.yaml index bd630d27942de..8c53962e97f47 100644 --- a/recipes/bioconductor-bayesspace/meta.yaml +++ b/recipes/bioconductor-bayesspace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "BayesSpace" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 674dcaf64d6130d014c2c1fbdf7d15a1 + md5: 5505178450768dc45884632e3e0a3baf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bayesspace", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-coda @@ -47,14 +48,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-coda diff --git a/recipes/bioconductor-baynorm/meta.yaml b/recipes/bioconductor-baynorm/meta.yaml index 62993041a0030..32927dab2124f 100644 --- a/recipes/bioconductor-baynorm/meta.yaml +++ b/recipes/bioconductor-baynorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "bayNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a17fbe6ef50d0b03b97ab29c7fa085c + md5: fda25f54086787e9a038cc59f0660a58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-baynorm", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bb - r-dosnow @@ -38,9 +39,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bb - r-dosnow diff --git a/recipes/bioconductor-bayseq/build.sh b/recipes/bioconductor-bayseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bayseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bayseq/meta.yaml b/recipes/bioconductor-bayseq/meta.yaml new file mode 100644 index 0000000000000..1060cb2108ad2 --- /dev/null +++ b/recipes/bioconductor-bayseq/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "2.36.0" %} +{% set name = "baySeq" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f46b63ebca2bda7c124133149aa7e552 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bayseq", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, BiocGenerics +requirements: + host: + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - r-abind + - r-base + run: + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - r-abind + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Empirical Bayesian analysis of patterns of differential expression in count data' + description: 'This package identifies differential expression in high-throughput ''count'' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-bbcanalyzer/meta.yaml b/recipes/bioconductor-bbcanalyzer/meta.yaml index 8f40477b642e7..953c2118d4578 100644 --- a/recipes/bioconductor-bbcanalyzer/meta.yaml +++ b/recipes/bioconductor-bbcanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "BBCAnalyzer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b6171b730ca7bc3859dd0964e928afd0 + md5: 33b123d417f53ee03c547220dfdb1612 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bbcanalyzer", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-bcellviper/meta.yaml b/recipes/bioconductor-bcellviper/meta.yaml index 33168059ab5e1..62edc4c0af227 100644 --- a/recipes/bioconductor-bcellviper/meta.yaml +++ b/recipes/bioconductor-bcellviper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "bcellViper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c35a1f30610cc929acc8bfdc79af1d13 + md5: 7e93bbaa204826358c77282e2a370074 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bcellviper", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bcellviper/post-link.sh b/recipes/bioconductor-bcellviper/post-link.sh index e892ee98f5a1b..00b243486be7d 100644 --- a/recipes/bioconductor-bcellviper/post-link.sh +++ b/recipes/bioconductor-bcellviper/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bcellviper-1.36.0" +installBiocDataPackage.sh "bcellviper-1.38.0" diff --git a/recipes/bioconductor-bcrank/meta.yaml b/recipes/bioconductor-bcrank/meta.yaml index 04a571ea243c0..e76407cf7cf0a 100644 --- a/recipes/bioconductor-bcrank/meta.yaml +++ b/recipes/bioconductor-bcrank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "BCRANK" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36cb7441c4c60585348d43c0a6b08692 + md5: 6c551ab389af456ab76449642c01881a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bcrank", max_pin="x.x") }}' # Suggests: seqLogo requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-bcseq/meta.yaml b/recipes/bioconductor-bcseq/meta.yaml index 8b0acc15f7949..272410c1503a5 100644 --- a/recipes/bioconductor-bcseq/meta.yaml +++ b/recipes/bioconductor-bcseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "bcSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 210e968615481f3c2a8671d9bf1f7a84 + md5: e582b114bc4743a328b6ada2953a74da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bcseq", max_pin="x.x") }}' # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-matrix - 'r-rcpp >=0.12.12' - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-matrix - 'r-rcpp >=0.12.12' diff --git a/recipes/bioconductor-beachmat.hdf5/build.sh b/recipes/bioconductor-beachmat.hdf5/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-beachmat.hdf5/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-beachmat.hdf5/meta.yaml b/recipes/bioconductor-beachmat.hdf5/meta.yaml new file mode 100644 index 0000000000000..d26114501a536 --- /dev/null +++ b/recipes/bioconductor-beachmat.hdf5/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "beachmat.hdf5" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b2ca9b6358fb05895101e6a911ca0e39 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beachmat.hdf5", max_pin="x.x") }}' +# Suggests: testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix +# SystemRequirements: C++17, GNU make +requirements: + host: + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - r-base + - r-rcpp + - libblas + - liblapack + run: + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - r-base + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'beachmat bindings for HDF5-backed matrices' + description: 'Extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-beachmat/meta.yaml b/recipes/bioconductor-beachmat/meta.yaml index 774c7927729ed..b7ae4f0aa3360 100644 --- a/recipes/bioconductor-beachmat/meta.yaml +++ b/recipes/bioconductor-beachmat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "beachmat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4401998e14a9c1cfc516bd3167b4c8cc + md5: ec47172a09aba997192731b4a5f2f284 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beachmat", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array -# SystemRequirements: C++11 +# SystemRequirements: C++17 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix - r-rcpp @@ -45,7 +48,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Compiling Bioconductor to Handle Each Matrix Type' - description: 'Provides a consistent C++ class interface for reading from and writing data to a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, third-party S4 classes may be supported by external linkage, while all other matrices are handled by DelayedArray block processing.' + description: 'Provides a consistent C++ class interface for reading from a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, along with a subset of the delayed operations implemented in the DelayedArray package. All other matrix-like objects are supported by calling back into R.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: parent_recipe: diff --git a/recipes/bioconductor-beadarray/meta.yaml b/recipes/bioconductor-beadarray/meta.yaml index 0aa5898a78f0a..16d2467732896 100644 --- a/recipes/bioconductor-beadarray/meta.yaml +++ b/recipes/bioconductor-beadarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.50.0" %} +{% set version = "2.52.0" %} {% set name = "beadarray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e9d095d2a6a7bd24581de5f6c0435e48 + md5: ed1729be533d0731833e523174b9dbb4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beadarray", max_pin="x.x") }}' # Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-beaddatapackr >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-beaddatapackr >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-hexbin @@ -35,14 +36,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-beaddatapackr >=1.52.0,<1.53.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-beaddatapackr >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-hexbin diff --git a/recipes/bioconductor-beadarrayexampledata/meta.yaml b/recipes/bioconductor-beadarrayexampledata/meta.yaml index e1ac0a8c19463..8a5709c7d1053 100644 --- a/recipes/bioconductor-beadarrayexampledata/meta.yaml +++ b/recipes/bioconductor-beadarrayexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "beadarrayExampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8607365b2ef3e8a20b33eac9ae52c51 + md5: d327e659adc868f1e3c7ae457c60087b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beadarrayexampledata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beadarrayexampledata/post-link.sh b/recipes/bioconductor-beadarrayexampledata/post-link.sh index 422f2ab789574..42281c8dc3e00 100644 --- a/recipes/bioconductor-beadarrayexampledata/post-link.sh +++ b/recipes/bioconductor-beadarrayexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beadarrayexampledata-1.38.0" +installBiocDataPackage.sh "beadarrayexampledata-1.40.0" diff --git a/recipes/bioconductor-beadarraysnp/meta.yaml b/recipes/bioconductor-beadarraysnp/meta.yaml index 0a37329c07dab..4302ccd7cd7b4 100644 --- a/recipes/bioconductor-beadarraysnp/meta.yaml +++ b/recipes/bioconductor-beadarraysnp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "beadarraySNP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 65dff50fe83456771977aa02caaa90e5 + md5: 748ed20ee2b38f5eee765be8125e5aca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beadarraysnp", max_pin="x.x") }}' noarch: generic # Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base test: commands: diff --git a/recipes/bioconductor-beadarrayusecases/meta.yaml b/recipes/bioconductor-beadarrayusecases/meta.yaml index 60801e1b3fd24..29e716cd61f24 100644 --- a/recipes/bioconductor-beadarrayusecases/meta.yaml +++ b/recipes/bioconductor-beadarrayusecases/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "BeadArrayUseCases" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f02d0ef2902c1223d8e240b55bf77b91 + md5: a939c03744773755b9a80de63a925c3e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beadarrayusecases", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db requirements: host: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beadarrayusecases/post-link.sh b/recipes/bioconductor-beadarrayusecases/post-link.sh index 82f46270f399b..60fda081d37d8 100644 --- a/recipes/bioconductor-beadarrayusecases/post-link.sh +++ b/recipes/bioconductor-beadarrayusecases/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beadarrayusecases-1.38.0" +installBiocDataPackage.sh "beadarrayusecases-1.40.0" diff --git a/recipes/bioconductor-beaddatapackr/meta.yaml b/recipes/bioconductor-beaddatapackr/meta.yaml index c18dfa1d34f87..6613cebb430b6 100644 --- a/recipes/bioconductor-beaddatapackr/meta.yaml +++ b/recipes/bioconductor-beaddatapackr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "BeadDataPackR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c17047b30d1353607cbbcce03c90c182 + md5: b1e73395e4f18af4b799a1f447487a87 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beaddatapackr", max_pin="x.x") }}' # Suggests: BiocStyle, knitr requirements: host: diff --git a/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml b/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml index 889e16cef92f4..c39f60e6e07de 100644 --- a/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml +++ b/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BeadSorted.Saliva.EPIC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c521cbcd30e56de9e00a659d9e349320 + md5: ca080a144452fad8ce1bdf8e86d88c74 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beadsorted.saliva.epic", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh b/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh index c8f7addca48d3..4ce7d05773879 100644 --- a/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh +++ b/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beadsorted.saliva.epic-1.8.0" +installBiocDataPackage.sh "beadsorted.saliva.epic-1.10.0" diff --git a/recipes/bioconductor-bearscc/meta.yaml b/recipes/bioconductor-bearscc/meta.yaml index 2189683b26e73..7c4d24a0d7462 100644 --- a/recipes/bioconductor-bearscc/meta.yaml +++ b/recipes/bioconductor-bearscc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BEARscc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 035ff6012c3c148dc0a38c75640a9f3b + md5: 44eee85006f40ec0a81fa5b6bf26f6c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bearscc", max_pin="x.x") }}' noarch: generic # Suggests: testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-data.table - r-ggplot2 run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-beat/meta.yaml b/recipes/bioconductor-beat/meta.yaml index 3c8ccf6974465..3305424e4dae2 100644 --- a/recipes/bioconductor-beat/meta.yaml +++ b/recipes/bioconductor-beat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "BEAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d41321849b8d11806159fbbe3ec9b636 + md5: 46e0caf216c816dbe7323a1b0117fbf6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beat", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base test: commands: diff --git a/recipes/bioconductor-beclear/meta.yaml b/recipes/bioconductor-beclear/meta.yaml index 7514638502fec..22a3733efe5e5 100644 --- a/recipes/bioconductor-beclear/meta.yaml +++ b/recipes/bioconductor-beclear/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "BEclear" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ce5326c16adef82ee0e2d563b10d9b9 + md5: bd34703e5a35dfc888f0029395df2c80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beclear", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, pander, seewave # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-abind - r-base - 'r-data.table >=1.11.8' @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-abind - r-base - 'r-data.table >=1.11.8' diff --git a/recipes/bioconductor-beer/meta.yaml b/recipes/bioconductor-beer/meta.yaml index 546117288f23e..db26d4c26e576 100644 --- a/recipes/bioconductor-beer/meta.yaml +++ b/recipes/bioconductor-beer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "beer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9af7a20cd4d9384bf123a7ef854572de + md5: c8e6192a3f9bd04b62ed564c8164ba00 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beer", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling # SystemRequirements: JAGS (4.3.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-phipdata >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-phipdata >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-progressr - r-rjags run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-phipdata >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-phipdata >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-progressr diff --git a/recipes/bioconductor-benchdamic/build.sh b/recipes/bioconductor-benchdamic/build.sh index c1d13421f5f1e..497f7b5bdb678 100644 --- a/recipes/bioconductor-benchdamic/build.sh +++ b/recipes/bioconductor-benchdamic/build.sh @@ -8,4 +8,5 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-benchdamic/build_failure.linux-64.yaml b/recipes/bioconductor-benchdamic/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..19d91cac3dd0e --- /dev/null +++ b/recipes/bioconductor-benchdamic/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 7993ff7f131f07a197238e7749097371f8ba7a13db8b1848d3a153e2501e2ab8 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-mast[version='>=1.28.0,<1.29.0']"), MatchSpec("r-microbiomestat")} +category: |- + dependency issue diff --git a/recipes/bioconductor-benchdamic/meta.yaml b/recipes/bioconductor-benchdamic/meta.yaml index b450a23c7ce83..bfe0f5be96b33 100644 --- a/recipes/bioconductor-benchdamic/meta.yaml +++ b/recipes/bioconductor-benchdamic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "benchdamic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,77 +11,94 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 60b5a20af2bcf5272457ab2427f7f702 + md5: ca158383ebf87138c91438c7946fe567 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-benchdamic", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, kableExtra, BiocStyle, SPsimSeq, testthat +# Suggests: knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat requirements: host: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' - - 'bioconductor-ancombc >=2.2.0,<2.3.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-dearseq >=1.12.0,<1.13.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-noiseq >=2.44.0,<2.45.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' + - 'bioconductor-ancombc >=2.4.0,<2.5.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-dearseq >=1.14.0,<1.15.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - r-base - - r-corncob - r-cowplot - r-ggdendro - r-ggplot2 - r-ggridges + - r-gunifrac - r-lme4 - r-mglm + - r-microbiomestat - r-plyr - r-rcolorbrewer - r-reshape2 - r-seurat - r-tidytext run: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' - - 'bioconductor-ancombc >=2.2.0,<2.3.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-dearseq >=1.12.0,<1.13.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-noiseq >=2.44.0,<2.45.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' + - 'bioconductor-ancombc >=2.4.0,<2.5.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-dearseq >=1.14.0,<1.15.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - r-base - - r-corncob - r-cowplot - r-ggdendro - r-ggplot2 - r-ggridges + - r-gunifrac - r-lme4 - r-mglm + - r-microbiomestat - r-plyr - r-rcolorbrewer - r-reshape2 - r-seurat - r-tidytext + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] test: commands: - - '$R -e "library(''{{ name }}'')"' + - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Benchmark of differential abundance methods on microbiome data' description: 'Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method''s distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.' +extra: + container: + extended-base: true diff --git a/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml b/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml index c4165ebe13f2c..2b84b56cb70ce 100644 --- a/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml +++ b/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "benchmarkfdrData2019" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b50a599a3c8ca8b276400e6dc523b894 + md5: 50ce7eb4100da1909ddd6c71c31e7e0c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-benchmarkfdrdata2019", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, testthat, SummarizedBenchmark, dplyr, ggplot2, rlang requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh b/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh index 3deac42f34a2e..1129bed5479d6 100644 --- a/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh +++ b/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "benchmarkfdrdata2019-1.14.0" +installBiocDataPackage.sh "benchmarkfdrdata2019-1.16.0" diff --git a/recipes/bioconductor-beta7/meta.yaml b/recipes/bioconductor-beta7/meta.yaml index 4c0bd96f335f4..47ad27c91e376 100644 --- a/recipes/bioconductor-beta7/meta.yaml +++ b/recipes/bioconductor-beta7/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "beta7" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0049331687b2d8ce06153507e09a4a03 + md5: 7beee3699282a97c765cf418036fc0ed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-beta7", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-beta7/post-link.sh b/recipes/bioconductor-beta7/post-link.sh index 4f0c62a57883d..8c038bab630b5 100644 --- a/recipes/bioconductor-beta7/post-link.sh +++ b/recipes/bioconductor-beta7/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beta7-1.38.0" +installBiocDataPackage.sh "beta7-1.40.0" diff --git a/recipes/bioconductor-bg2/meta.yaml b/recipes/bioconductor-bg2/meta.yaml index 09813ceea2158..707795e15d457 100644 --- a/recipes/bioconductor-bg2/meta.yaml +++ b/recipes/bioconductor-bg2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "BG2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 261572229e90f2182464a60b7e938b5b + md5: da6ea59dda3c728bdce70a5b43e4541e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bg2", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 3.0.0) requirements: diff --git a/recipes/bioconductor-bgeecall/meta.yaml b/recipes/bioconductor-bgeecall/meta.yaml index 5f5b52d928a09..75110cb7b2571 100644 --- a/recipes/bioconductor-bgeecall/meta.yaml +++ b/recipes/bioconductor-bgeecall/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.1" %} {% set name = "BgeeCall" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4320d2ccfdaf2088c987b762dd3ce930 + md5: d6ffd11b71faf135832b99515c7ba4cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bgeecall", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, AnnotationHub, httr # SystemRequirements: kallisto requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-data.table - r-dplyr @@ -35,12 +36,12 @@ requirements: - r-rslurm - r-sjmisc run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-bgeedb/meta.yaml b/recipes/bioconductor-bgeedb/meta.yaml index 04d135b56e86a..c84ee3e31ee05 100644 --- a/recipes/bioconductor-bgeedb/meta.yaml +++ b/recipes/bioconductor-bgeedb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "BgeeDB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5d66ef5cae6f2ee50528e452ebbdb68 + md5: 9b8f5e9e829bd05d9a8322b3ff3408dd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bgeedb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, testthat, rmarkdown, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-curl - r-data.table @@ -34,9 +35,9 @@ requirements: - r-rsqlite - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-bgx/meta.yaml b/recipes/bioconductor-bgx/meta.yaml index f2ea8223608db..a5f285e769368 100644 --- a/recipes/bioconductor-bgx/meta.yaml +++ b/recipes/bioconductor-bgx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "bgx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: afab2c381aa1f363f242c26c13c23e14 + md5: f068c237db58f3d75d3fef9cd5645cf4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bgx", max_pin="x.x") }}' # Suggests: affydata, hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base - 'r-rcpp >=0.11.0' - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base - 'r-rcpp >=0.11.0' build: diff --git a/recipes/bioconductor-bhc/meta.yaml b/recipes/bioconductor-bhc/meta.yaml index cd59cd3e4c9d7..0ee0b47bf9658 100644 --- a/recipes/bioconductor-bhc/meta.yaml +++ b/recipes/bioconductor-bhc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "BHC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b08d636ca1e237816a3c0ad4ddae86f + md5: 855087c8854bd3014111477e1c3cdcb9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bhc", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-bicare/meta.yaml b/recipes/bioconductor-bicare/meta.yaml index 5effab9942084..e703872a25ea2 100644 --- a/recipes/bioconductor-bicare/meta.yaml +++ b/recipes/bioconductor-bicare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "BicARE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7bdfe915b7a5fa05496b4dea685e3dc8 + md5: d2498da49d01723934f42b4bf235fa05 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bicare", max_pin="x.x") }}' # Suggests: hgu95av2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-bifet/meta.yaml b/recipes/bioconductor-bifet/meta.yaml index f1c53ba4c19bf..9355f41630d56 100644 --- a/recipes/bioconductor-bifet/meta.yaml +++ b/recipes/bioconductor-bifet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BiFET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df9b0e887f85ef2881e011ea1979ef57 + md5: 11fcc80fc0c2745e5a15524fd2279bed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bifet", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, testthat, knitr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-poibin run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-poibin test: diff --git a/recipes/bioconductor-biggr/build_failure.linux-64.yaml b/recipes/bioconductor-biggr/build_failure.linux-64.yaml index 8d80c1d161066..1f88c079d088c 100644 --- a/recipes/bioconductor-biggr/build_failure.linux-64.yaml +++ b/recipes/bioconductor-biggr/build_failure.linux-64.yaml @@ -1,34 +1,35 @@ -recipe_sha: 5e4fb5d121cf8aff07e93d0614aac6a517def277ef61149a3a34e4a932691581 # The commit at which this recipe failed to build. +recipe_sha: b7766d035130ae790cea751e3ffdd9b9db7a9ee165bdd6eac0deefe15615c9f1 # The commit at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue log: |- - conda-forge/linux-64 100%[2K[1A[2K[0G[] 7.5s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 7.6s conda-forge/linux-64 100%[2K[1A[2K[0Gconda-forge/linux-64 [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 1.4MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.6MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s [?25hMamba failed to solve: + - bioconductor-rsbml >=2.60.0,<2.61.0 + - r-stringr + - bioconductor-hyperdraw >=1.54.0,<1.55.0 - r-lim - r-base 4.3.* - - bioconductor-hypergraph >=1.72.0,<1.73.0 + - bioconductor-hypergraph >=1.74.0,<1.75.0 - r-limsolve - - r-stringr - - bioconductor-rsbml >=2.58.0,<2.59.0 - - bioconductor-hyperdraw >=1.52.0,<1.53.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - package bioconductor-hyperdraw-1.52.0-r43hba55f59_0 requires graphviz >=8.1.0,<9.0a0, but none of the providers can be installed + - - package bioconductor-hyperdraw-1.54.0-r43hba55f59_0 requires graphviz >=8.1.0,<9.0a0, but none of the providers can be installed - Leaving build/test directories: @@ -51,22 +52,23 @@ log: |- File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve raise RuntimeError("Solver could not find solution." error_string) RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-rsbml >=2.60.0,<2.61.0 + - r-stringr + - bioconductor-hyperdraw >=1.54.0,<1.55.0 - r-lim - r-base 4.3.* - - bioconductor-hypergraph >=1.72.0,<1.73.0 + - bioconductor-hypergraph >=1.74.0,<1.75.0 - r-limsolve - - r-stringr - - bioconductor-rsbml >=2.58.0,<2.59.0 - - bioconductor-hyperdraw >=1.52.0,<1.53.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - package bioconductor-hyperdraw-1.52.0-r43hba55f59_0 requires graphviz >=8.1.0,<9.0a0, but none of the providers can be installed + - - package bioconductor-hyperdraw-1.54.0-r43hba55f59_0 requires graphviz >=8.1.0,<9.0a0, but none of the providers can be installed - During handling of the above exception, another exception occurred: @@ -100,5 +102,5 @@ log: |- actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-hyperdraw==1.52.0=r43hba55f59_0"), MatchSpec("graphviz[version='>=8.1.0,<9.0a0']")} + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-hyperdraw==1.54.0=r43hba55f59_0"), MatchSpec("graphviz[version='>=8.1.0,<9.0a0']")} # Last 100 lines of the build log. diff --git a/recipes/bioconductor-biggr/meta.yaml b/recipes/bioconductor-biggr/meta.yaml index 605e46d2f9f9f..4ea339b2a2ef1 100644 --- a/recipes/bioconductor-biggr/meta.yaml +++ b/recipes/bioconductor-biggr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "BiGGR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f95dbd34a7f3f8c0a918b6460b1bf3ef + md5: 16eeec0ca7502101425cbb568e6eef15 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biggr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-hyperdraw >=1.52.0,<1.53.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-rsbml >=2.58.0,<2.59.0' + - 'bioconductor-hyperdraw >=1.54.0,<1.55.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-rsbml >=2.60.0,<2.61.0' - r-base - r-lim - r-limsolve - r-stringr run: - - 'bioconductor-hyperdraw >=1.52.0,<1.53.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-rsbml >=2.58.0,<2.59.0' + - 'bioconductor-hyperdraw >=1.54.0,<1.55.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-rsbml >=2.60.0,<2.61.0' - r-base - r-lim - r-limsolve diff --git a/recipes/bioconductor-bigmelon/meta.yaml b/recipes/bioconductor-bigmelon/meta.yaml index adc1e4a1657a3..0f7c8a2a7a8ee 100644 --- a/recipes/bioconductor-bigmelon/meta.yaml +++ b/recipes/bioconductor-bigmelon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "bigmelon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2793b4b6a4b2d2239f731c0f6fb60a4f + md5: 1c6944989ec4f16b1903143a34296bf0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bigmelon", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base test: commands: diff --git a/recipes/bioconductor-bindingsitefinder/meta.yaml b/recipes/bioconductor-bindingsitefinder/meta.yaml index 9a14cffb08f4d..0d45dbb551c79 100644 --- a/recipes/bioconductor-bindingsitefinder/meta.yaml +++ b/recipes/bioconductor-bindingsitefinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "2.0.0" %} {% set name = "BindingSiteFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,58 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: deb1c8c88ca7fbd1701582975f32808f + md5: b54f11a27c1f6f55b4cc60ad8986e029 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bindingsitefinder", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, ComplexHeatmap, forcats, scales +# Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr + - r-forcats + - r-ggdist - r-ggforce - r-ggplot2 + - r-kableextra + - r-lifecycle - r-matrixstats - r-plyr + - r-rcolorbrewer + - r-rlang - r-tibble - r-tidyr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr + - r-forcats + - r-ggdist - r-ggforce - r-ggplot2 + - r-kableextra + - r-lifecycle - r-matrixstats - r-plyr + - r-rcolorbrewer + - r-rlang - r-tibble - r-tidyr test: diff --git a/recipes/bioconductor-bioassayr/meta.yaml b/recipes/bioconductor-bioassayr/meta.yaml index da01d4f62b18f..af54b2e1f736c 100644 --- a/recipes/bioconductor-bioassayr/meta.yaml +++ b/recipes/bioconductor-bioassayr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "bioassayR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2df098a9b7bb4735e92bf3a0b0d87c4 + md5: 94ac7a2ff2a9de7b65d8ebd864513a31 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioassayr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - 'r-dbi >=0.3.1' - r-matrix @@ -30,8 +31,8 @@ requirements: - 'r-rsqlite >=1.0.0' - r-xml run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - 'r-dbi >=0.3.1' - r-matrix diff --git a/recipes/bioconductor-biobase/meta.yaml b/recipes/bioconductor-biobase/meta.yaml index 5b76df1093a7a..e09e97936223e 100644 --- a/recipes/bioconductor-biobase/meta.yaml +++ b/recipes/bioconductor-biobase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.60.0" %} +{% set version = "2.62.0" %} {% set name = "Biobase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e427b98c2208f6c1c81cf4ec64caffc + md5: 75a65eb015d58ca611f2bebca41f9d2d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biobase", max_pin="x.x") }}' # Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-biobroom/meta.yaml b/recipes/bioconductor-biobroom/meta.yaml index 3cabf34e8bbf7..629191ae0ef98 100644 --- a/recipes/bioconductor-biobroom/meta.yaml +++ b/recipes/bioconductor-biobroom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "biobroom" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5f8edee57c6cc7540b187ea4d0a9c457 + md5: b0a4b29e9aa3bbb99f42cd2cd19ca4d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biobroom", max_pin="x.x") }}' noarch: generic # Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, rmarkdown, SummarizedExperiment requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-broom - r-dplyr - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-broom - r-dplyr diff --git a/recipes/bioconductor-biobtreer/meta.yaml b/recipes/bioconductor-biobtreer/meta.yaml index 70fa6d16cef8a..c14de14924e0e 100644 --- a/recipes/bioconductor-biobtreer/meta.yaml +++ b/recipes/bioconductor-biobtreer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "biobtreeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94456402f79d5430e53b31d80ed2e3c1 + md5: c341e537e79161abfd6f1f3382d3eb90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biobtreer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr,testthat,rmarkdown,markdown requirements: diff --git a/recipes/bioconductor-biocancer/meta.yaml b/recipes/bioconductor-biocancer/meta.yaml index ce8ab589bd9c7..ff3219486924f 100644 --- a/recipes/bioconductor-biocancer/meta.yaml +++ b/recipes/bioconductor-biocancer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "bioCancer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cec03fe98717844d52ff9f282dc125b0 + md5: 2eff081b55d8bda988f08f1836420b24 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocancer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-genetclassifier >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.bt.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' - 'r-algdesign >=1.1.7.3' - r-base - 'r-diagrammer <=1.01' @@ -49,16 +50,16 @@ requirements: - r-visnetwork - 'r-xml >=3.98' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-genetclassifier >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.bt.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' - 'r-algdesign >=1.1.7.3' - r-base - 'r-diagrammer <=1.01' @@ -83,6 +84,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'AGPL-3 | file LICENSE' summary: 'Interactive Multi-Omics Cancers Data Visualization and Analysis' - description: 'bioCancer is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.' + description: 'This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.' license_file: LICENSE diff --git a/recipes/bioconductor-biocartaimage/build.sh b/recipes/bioconductor-biocartaimage/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocartaimage/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocartaimage/meta.yaml b/recipes/bioconductor-biocartaimage/meta.yaml new file mode 100644 index 0000000000000..61d3f51296c03 --- /dev/null +++ b/recipes/bioconductor-biocartaimage/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "BioCartaImage" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8190c93a49f3d53085b3e6e44d482ffa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocartaimage", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat, knitr, BiocStyle, ragg +requirements: + host: + - r-base + - r-magick + run: + - r-base + - r-magick +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'BioCarta Pathway Images' + description: 'The core functionality of the package is to provide coordinates of genes on the BioCarta pathway images and to provide methods to add self-defined graphics to the genes of interest.' + license_file: LICENSE + diff --git a/recipes/bioconductor-biocbaseutils/meta.yaml b/recipes/bioconductor-biocbaseutils/meta.yaml index 14c57e3b3e022..66db86820aac2 100644 --- a/recipes/bioconductor-biocbaseutils/meta.yaml +++ b/recipes/bioconductor-biocbaseutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "BiocBaseUtils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6cb786aff723f206bb901ed336af3d23 + md5: 23ed1406ff70165a763ca2040c46353e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocbaseutils", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, tinytest requirements: diff --git a/recipes/bioconductor-biocbook/build.sh b/recipes/bioconductor-biocbook/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocbook/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocbook/meta.yaml b/recipes/bioconductor-biocbook/meta.yaml new file mode 100644 index 0000000000000..03d10aeca7f90 --- /dev/null +++ b/recipes/bioconductor-biocbook/meta.yaml @@ -0,0 +1,73 @@ +{% set version = "1.0.0" %} +{% set name = "BiocBook" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6bcb226068f30b135b705960de603ff0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocbook", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, testthat (>= 3.0.0), rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - r-available + - r-base + - r-cli + - r-dplyr + - r-gert + - r-gh + - r-gitcreds + - r-glue + - r-httr + - r-purrr + - r-quarto + - r-renv + - r-rlang + - r-rprojroot + - r-stringr + - r-tibble + - r-usethis + - r-yaml + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - r-available + - r-base + - r-cli + - r-dplyr + - r-gert + - r-gh + - r-gitcreds + - r-glue + - r-httr + - r-purrr + - r-quarto + - r-renv + - r-rlang + - r-rprojroot + - r-stringr + - r-tibble + - r-usethis + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Write, containerize, publish and version Quarto books with Bioconductor' + description: 'A BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, ...) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).' + license_file: LICENSE + diff --git a/recipes/bioconductor-bioccheck/meta.yaml b/recipes/bioconductor-bioccheck/meta.yaml index e46357757fa10..2512f02beb7da 100644 --- a/recipes/bioconductor-bioccheck/meta.yaml +++ b/recipes/bioconductor-bioccheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "BiocCheck" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a476a077103abf378f09d9ccb3cf05a + md5: d003f035a6c197261bed5fa4cd989738 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioccheck", max_pin="x.x") }}' noarch: generic -# Suggests: RUnit, BiocGenerics, Biobase, jsonlite, rmarkdown, downloader, devtools (>= 1.4.1), usethis, BiocStyle, callr +# Suggests: RUnit, BiocGenerics, Biobase, jsonlite, rmarkdown, downloader, devtools (>= 1.4.1), usethis, BiocStyle, GenomicRanges, gert requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-biocmanager + - r-callr - r-codetools - r-httr - r-knitr - r-stringdist run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-biocmanager + - r-callr - r-codetools - r-httr - r-knitr diff --git a/recipes/bioconductor-biocfhir/meta.yaml b/recipes/bioconductor-biocfhir/meta.yaml index 63a838470cbd5..10c51d83594e6 100644 --- a/recipes/bioconductor-biocfhir/meta.yaml +++ b/recipes/bioconductor-biocfhir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "BiocFHIR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29abc8f873ab6dff5597cf23558e6778 + md5: 788951417cde10ad9434dd443db47f80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocfhir", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rjsoncons, igraph, BiocStyle requirements: host: - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-dplyr - r-dt @@ -31,8 +32,8 @@ requirements: - r-tidyr - r-visnetwork run: - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-biocfilecache/meta.yaml b/recipes/bioconductor-biocfilecache/meta.yaml index 50cb12f97189f..f7dcc3d5468c6 100644 --- a/recipes/bioconductor-biocfilecache/meta.yaml +++ b/recipes/bioconductor-biocfilecache/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.1" %} {% set name = "BiocFileCache" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8ad06bf5fc23d0aabde7ba149d4d675 + md5: 80f9b9c7ef6f3fcb9aaff7125b409137 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocfilecache", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown, rtracklayer requirements: diff --git a/recipes/bioconductor-biocgenerics/meta.yaml b/recipes/bioconductor-biocgenerics/meta.yaml index 785b193559280..d2b4a7afa324d 100644 --- a/recipes/bioconductor-biocgenerics/meta.yaml +++ b/recipes/bioconductor-biocgenerics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.46.0" %} +{% set version = "0.48.1" %} {% set name = "BiocGenerics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 619aadefdba5c7cebac0136ada0fb42a + md5: 77629e64c2a9a0324eb11bb59b53b126 build: - number: 0 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocgenerics", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray, Biostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, RUnit requirements: diff --git a/recipes/bioconductor-biocgraph/meta.yaml b/recipes/bioconductor-biocgraph/meta.yaml index adc493c692e0c..e66a514e3c4a8 100644 --- a/recipes/bioconductor-biocgraph/meta.yaml +++ b/recipes/bioconductor-biocgraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "biocGraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a46b4f9c1a38fa5576b0323a22ebbedc + md5: 5deb3ff8596eaf678592ad9ae15defe2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocgraph", max_pin="x.x") }}' noarch: generic # Suggests: fibroEset, geneplotter, hgu95av2.db requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-biochail/meta.yaml b/recipes/bioconductor-biochail/meta.yaml index 5ea8066b7b2d6..aeb4d1b333b34 100644 --- a/recipes/bioconductor-biochail/meta.yaml +++ b/recipes/bioconductor-biochail/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "BiocHail" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: deafe3a2c0dccb5619f29ac3f917a3e0 + md5: 4707c299d0bb3b41001065a753d89f33 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biochail", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, BiocStyle, ggplot2, DT requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dplyr - r-reticulate run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dplyr - r-reticulate diff --git a/recipes/bioconductor-biochubsshiny/meta.yaml b/recipes/bioconductor-biochubsshiny/meta.yaml index 65f3ba1f939a8..eda08864d20d6 100644 --- a/recipes/bioconductor-biochubsshiny/meta.yaml +++ b/recipes/bioconductor-biochubsshiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "BiocHubsShiny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 123a3f285b0653c760cbb5a11fcc84e8 + md5: bc7ef9bc6285eb045f191b7c72846d68 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biochubsshiny", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, BiocStyle, knitr, rmarkdown, sessioninfo, shinytest2 requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dt - r-htmlwidgets @@ -33,9 +34,9 @@ requirements: - r-shinythemes - r-shinytoastr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dt - r-htmlwidgets diff --git a/recipes/bioconductor-biocio/meta.yaml b/recipes/bioconductor-biocio/meta.yaml index 6daf6e7f521b9..71881e468ca28 100644 --- a/recipes/bioconductor-biocio/meta.yaml +++ b/recipes/bioconductor-biocio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "BiocIO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac5aad476739475cfec311c8f28e770b + md5: 6e0c18bdf6d9f707f9d1e431400fa1c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocio", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-biocneighbors/meta.yaml b/recipes/bioconductor-biocneighbors/meta.yaml index a44d39cfbe661..83929f7284c5a 100644 --- a/recipes/bioconductor-biocneighbors/meta.yaml +++ b/recipes/bioconductor-biocneighbors/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "BiocNeighbors" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e87784c01c3e3c48735ebb1d01ff80f0 + md5: 3cfb96ab6d42068c5b875fa6fcefd779 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocneighbors", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix - r-rcpp @@ -30,8 +31,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-bioconcotk/meta.yaml b/recipes/bioconductor-bioconcotk/meta.yaml index 5d7192e625bf5..278c1af519595 100644 --- a/recipes/bioconductor-bioconcotk/meta.yaml +++ b/recipes/bioconductor-bioconcotk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BiocOncoTK" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 271d492c165d6350550a05949466289f + md5: 2cd117f19ec3c614a5bcb1d8b27b6e64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioconcotk", max_pin="x.x") }}' noarch: generic # Suggests: knitr, dbplyr, org.Hs.eg.db, MultiAssayExperiment, BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE (>= 1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat, AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75, rmarkdown, rhdf5client, AnnotationHub requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-curatedtcgadata >=1.22.0,<1.23.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-curatedtcgadata >=1.24.0,<1.25.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bigrquery - r-car @@ -46,15 +47,15 @@ requirements: - r-scales - r-shiny run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-curatedtcgadata >=1.22.0,<1.23.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-curatedtcgadata >=1.24.0,<1.25.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bigrquery - r-car diff --git a/recipes/bioconductor-biocor/meta.yaml b/recipes/bioconductor-biocor/meta.yaml index 4b62b4d930e79..4f9b1efe69ee1 100644 --- a/recipes/bioconductor-biocor/meta.yaml +++ b/recipes/bioconductor-biocor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "BioCor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ac6d44e021d256002b563d53a8ac9ef + md5: 5d061581890948dc4341346b82f8d170 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocor", max_pin="x.x") }}' noarch: generic -# Suggests: airway, BiocStyle, boot, DESeq2, GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db, rmarkdown, spelling, targetscan.Hs.eg.db, testthat, WGCNA +# Suggests: airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1), GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db, rmarkdown, spelling, targetscan.Hs.eg.db, testthat, WGCNA requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-matrix run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-biocparallel/meta.yaml b/recipes/bioconductor-biocparallel/meta.yaml index 1af1c54af1acc..08b5cb5440130 100644 --- a/recipes/bioconductor-biocparallel/meta.yaml +++ b/recipes/bioconductor-biocparallel/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.2" %} +{% set version = "1.36.0" %} {% set name = "BiocParallel" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe2e530471e5ecb6a9f74f1f43cb4efe + md5: a6a331ac453920e713836ddd0de38e25 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocparallel", max_pin="x.x") }}' # Suggests: BiocGenerics, tools, foreach, BBmisc, doParallel, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools, data.table # SystemRequirements: C++11 requirements: diff --git a/recipes/bioconductor-biocpkgtools/meta.yaml b/recipes/bioconductor-biocpkgtools/meta.yaml index 2351fc85c2cd0..4c6bab59e87ca 100644 --- a/recipes/bioconductor-biocpkgtools/meta.yaml +++ b/recipes/bioconductor-biocpkgtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "BiocPkgTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5945211cb859f579d7b1900f8c0877d1 + md5: a0ab7353a78b22b286d22520faff6142 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocpkgtools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, lubridate, visNetwork, clipr, blastula, kableExtra, DiagrammeR, SummarizedExperiment # SystemRequirements: mailsend-go requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-biocmanager - r-dplyr @@ -45,10 +46,10 @@ requirements: - r-tibble - r-xml2 run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-biocmanager - r-dplyr diff --git a/recipes/bioconductor-biocset/meta.yaml b/recipes/bioconductor-biocset/meta.yaml index 5b0ccad529798..e2086fa5fd45a 100644 --- a/recipes/bioconductor-biocset/meta.yaml +++ b/recipes/bioconductor-biocset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "BiocSet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 643105ff3920c099e3713e749f724aac + md5: 69ab960333325b038fb2379781fe36c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocset", max_pin="x.x") }}' noarch: generic # Suggests: GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache, GO.db, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ontologyindex @@ -33,10 +34,10 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ontologyindex diff --git a/recipes/bioconductor-biocsingular/meta.yaml b/recipes/bioconductor-biocsingular/meta.yaml index 7fea0c7847a07..984b889689b96 100644 --- a/recipes/bioconductor-biocsingular/meta.yaml +++ b/recipes/bioconductor-biocsingular/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "BiocSingular" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df6d2dd2e0de6864dcc488127f9b0621 + md5: 9b4158e143f2cbefc140228c13090b35 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocsingular", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix -# SystemRequirements: C++11 +# SystemRequirements: C++17 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - r-base - r-irlba - r-matrix @@ -35,12 +36,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - r-base - r-irlba - r-matrix diff --git a/recipes/bioconductor-biocsklearn/meta.yaml b/recipes/bioconductor-biocsklearn/meta.yaml index d18885bab9193..5974e5fdc00d4 100644 --- a/recipes/bioconductor-biocsklearn/meta.yaml +++ b/recipes/bioconductor-biocsklearn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "BiocSklearn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92331b92237b4a3e82af8e2679cdb576 + md5: a3df49031172bfd2b2a3b1c242b7dd40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocsklearn", max_pin="x.x") }}' noarch: generic # Suggests: testthat, restfulSE, HDF5Array, BiocStyle, rmarkdown, knitr # SystemRequirements: python (>= 2.7), sklearn, numpy, pandas, h5py requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-reticulate - 'python >=2.7' run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-reticulate - 'python >=2.7' diff --git a/recipes/bioconductor-biocstyle/meta.yaml b/recipes/bioconductor-biocstyle/meta.yaml index d520d23a37171..0f8df92a25fe6 100644 --- a/recipes/bioconductor-biocstyle/meta.yaml +++ b/recipes/bioconductor-biocstyle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "BiocStyle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91272b7821e6d3955aab1ec46c5c8491 + md5: 22ceacb6ab374657de48283e78dedbb5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocstyle", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit, htmltools requirements: diff --git a/recipes/bioconductor-biocthis/meta.yaml b/recipes/bioconductor-biocthis/meta.yaml index fbb614fc53920..6e1853af5c371 100644 --- a/recipes/bioconductor-biocthis/meta.yaml +++ b/recipes/bioconductor-biocthis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.3" %} +{% set version = "1.12.0" %} {% set name = "biocthis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5f348f9b54ba6845ace32212b709dd64 + md5: 7ebf8e46d2b20a3a2bae3cc7a36264d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocthis", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, devtools, knitr, pkgdown, RefManageR, rmarkdown, sessioninfo, testthat, utils requirements: diff --git a/recipes/bioconductor-biocversion/meta.yaml b/recipes/bioconductor-biocversion/meta.yaml index d9949d2b05ba8..2f6a6eaf4f1d2 100644 --- a/recipes/bioconductor-biocversion/meta.yaml +++ b/recipes/bioconductor-biocversion/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.1" %} +{% set version = "3.18.1" %} {% set name = "BiocVersion" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fea6248fd1d5c6ef5f4c00848f870b4 + md5: 46dbe2f6ca9c058b24da1bd98f79631e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocversion", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-biocviews/meta.yaml b/recipes/bioconductor-biocviews/meta.yaml index d9d6ad8abd1a4..0627cb2e4f0f5 100644 --- a/recipes/bioconductor-biocviews/meta.yaml +++ b/recipes/bioconductor-biocviews/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.1" %} +{% set version = "1.70.0" %} {% set name = "biocViews" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b6115ebd1436da570b59dbbd35a9fa0 + md5: e258342a57f06fa23f3732c75539c58d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocviews", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, knitr, commonmark, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-biocmanager - r-rcurl - r-runit - r-xml run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-biocmanager - r-rcurl diff --git a/recipes/bioconductor-biocworkflowtools/meta.yaml b/recipes/bioconductor-biocworkflowtools/meta.yaml index ae38c9e0456e1..800ffd008347d 100644 --- a/recipes/bioconductor-biocworkflowtools/meta.yaml +++ b/recipes/bioconductor-biocworkflowtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "BiocWorkflowTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6696a65d716c89b060c4cee07dcded96 + md5: 412d30d47953d51e35e9fa188e28841e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocworkflowtools", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base - r-bookdown - r-git2r @@ -31,7 +32,7 @@ requirements: - r-stringr - r-usethis run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base - r-bookdown - r-git2r diff --git a/recipes/bioconductor-biodb/meta.yaml b/recipes/bioconductor-biodb/meta.yaml index fe5c913eb0e61..ad39c52b330b1 100644 --- a/recipes/bioconductor-biodb/meta.yaml +++ b/recipes/bioconductor-biodb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "biodb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2140155f6d5c482557f7838661adbfe7 + md5: 0716a73291fb80cc3d1f0909549cbaa8 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2, git2r + run_exports: '{{ pin_subpackage("bioconductor-biodb", max_pin="x.x") }}' +# Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2 requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-chk + - r-git2r - r-jsonlite - r-lgr - r-lifecycle @@ -42,9 +44,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-chk + - r-git2r - r-jsonlite - r-lgr - r-lifecycle diff --git a/recipes/bioconductor-biodbchebi/meta.yaml b/recipes/bioconductor-biodbchebi/meta.yaml index 4551636ba0935..4371bc0a4a43f 100644 --- a/recipes/bioconductor-biodbchebi/meta.yaml +++ b/recipes/bioconductor-biodbchebi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biodbChebi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ba9df9eafa05f15f032fec477606a21 + md5: 31f6ed155e1126b62c5a6cd7fbd6c742 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbchebi", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 test: diff --git a/recipes/bioconductor-biodbexpasy/meta.yaml b/recipes/bioconductor-biodbexpasy/meta.yaml index 8bf72de29d06f..11a9662f7a468 100644 --- a/recipes/bioconductor-biodbexpasy/meta.yaml +++ b/recipes/bioconductor-biodbexpasy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "biodbExpasy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98e5ae0c72615b4f1b7d1d2cf0398f7c + md5: b4c2596f2efc76e3ba7cba00fb3a6177 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbexpasy", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 - r-stringr run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 diff --git a/recipes/bioconductor-biodbhmdb/meta.yaml b/recipes/bioconductor-biodbhmdb/meta.yaml index ad27b96d7ac9f..43819b75e957a 100644 --- a/recipes/bioconductor-biodbhmdb/meta.yaml +++ b/recipes/bioconductor-biodbhmdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biodbHmdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51bfd87e591eab475ec0498eaf805fd1 + md5: b34c06c2ce8865b7eebedb869a1ab505 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbhmdb", max_pin="x.x") }}' # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 - r-rcpp - r-testthat + - r-zip - libblas - liblapack run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 - r-rcpp - r-testthat + - r-zip build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-biodbkegg/meta.yaml b/recipes/bioconductor-biodbkegg/meta.yaml index 4932d2d81b630..89f789f680e40 100644 --- a/recipes/bioconductor-biodbkegg/meta.yaml +++ b/recipes/bioconductor-biodbkegg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biodbKegg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e55170ed0b1512e058a3546348556e6 + md5: 868600b40fc5ce4c38ced82df890400d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbkegg", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, igraph, magick, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-lifecycle - r-r6 run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-lifecycle diff --git a/recipes/bioconductor-biodblipidmaps/meta.yaml b/recipes/bioconductor-biodblipidmaps/meta.yaml index d5aa32c044891..49e10385518b5 100644 --- a/recipes/bioconductor-biodblipidmaps/meta.yaml +++ b/recipes/bioconductor-biodblipidmaps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biodbLipidmaps" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bcb13e4a81639403a3203fe973736d1 + md5: 996886d796e7ffba7a1a19598573f9c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodblipidmaps", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, lgr, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-lifecycle - r-r6 run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-lifecycle - r-r6 diff --git a/recipes/bioconductor-biodbmirbase/meta.yaml b/recipes/bioconductor-biodbmirbase/meta.yaml index f38a72b0e2629..3fc5c553215d5 100644 --- a/recipes/bioconductor-biodbmirbase/meta.yaml +++ b/recipes/bioconductor-biodbmirbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.5.0" %} {% set name = "biodbMirbase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73a96ab8d432ed80ffc987b3f318044e + md5: af331cadc2f7575e4dbf5345f19c61e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbmirbase", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 - r-stringr run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 diff --git a/recipes/bioconductor-biodbncbi/meta.yaml b/recipes/bioconductor-biodbncbi/meta.yaml index e8985870974a5..95b4d06ff4236 100644 --- a/recipes/bioconductor-biodbncbi/meta.yaml +++ b/recipes/bioconductor-biodbncbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "biodbNcbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8e830a9655fd75706c8d4c75440ddec + md5: 5d2c3e8eade431a86e13d54be468832e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbncbi", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 - r-xml run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 diff --git a/recipes/bioconductor-biodbnci/meta.yaml b/recipes/bioconductor-biodbnci/meta.yaml index 501ca82a668bf..cc1d3f3405d9c 100644 --- a/recipes/bioconductor-biodbnci/meta.yaml +++ b/recipes/bioconductor-biodbnci/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "biodbNci" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f9eeae84d0fb3daf211823d114a5f772 + md5: 6dcd43d5c282054f4edfef08a2f597cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbnci", max_pin="x.x") }}' # Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 @@ -29,7 +30,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-chk - r-r6 diff --git a/recipes/bioconductor-biodbuniprot/meta.yaml b/recipes/bioconductor-biodbuniprot/meta.yaml index af50105117d6a..a4e0d9a6b658e 100644 --- a/recipes/bioconductor-biodbuniprot/meta.yaml +++ b/recipes/bioconductor-biodbuniprot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "biodbUniprot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cc363aa65d5193c61a478401c9f20b91 + md5: f4f5bcc32018b6472836efcc8c82671c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodbuniprot", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr, covr requirements: host: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 run: - - 'bioconductor-biodb >=1.8.0,<1.9.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' - r-base - r-r6 test: diff --git a/recipes/bioconductor-biodist/meta.yaml b/recipes/bioconductor-biodist/meta.yaml index b84db1943e599..638ca746d888c 100644 --- a/recipes/bioconductor-biodist/meta.yaml +++ b/recipes/bioconductor-biodist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "bioDist" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0ac96c334d2d0703297b260b9b9535c + md5: a0c907dc82834b4771074cd8164cf773 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biodist", max_pin="x.x") }}' noarch: generic # Suggests: locfit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-kernsmooth run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-kernsmooth test: diff --git a/recipes/bioconductor-bioimagedbs/meta.yaml b/recipes/bioconductor-bioimagedbs/meta.yaml index 088193acc1f0a..f7ebe42cadf2b 100644 --- a/recipes/bioconductor-bioimagedbs/meta.yaml +++ b/recipes/bioconductor-bioimagedbs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BioImageDbs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8af4040411218fcfd81ab927747eb48 + md5: 785e9ea81ef5699d70af969fd8d4703d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioimagedbs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, purrr requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-animation - r-base - r-einsum @@ -33,9 +34,9 @@ requirements: - r-markdown - r-rmarkdown run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-animation - r-base - r-einsum @@ -45,7 +46,7 @@ requirements: - r-markdown - r-rmarkdown - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bioimagedbs/post-link.sh b/recipes/bioconductor-bioimagedbs/post-link.sh index 97c361a68d9de..908f4e675bd43 100644 --- a/recipes/bioconductor-bioimagedbs/post-link.sh +++ b/recipes/bioconductor-bioimagedbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bioimagedbs-1.8.0" +installBiocDataPackage.sh "bioimagedbs-1.10.0" diff --git a/recipes/bioconductor-biomart/meta.yaml b/recipes/bioconductor-biomart/meta.yaml index 061a7013a2d8c..9682b4d2750eb 100644 --- a/recipes/bioconductor-biomart/meta.yaml +++ b/recipes/bioconductor-biomart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.56.1" %} +{% set version = "2.58.0" %} {% set name = "biomaRt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3ebbe9c8774fc0f1cb42a6a5c3d4ef2 + md5: dd18037fef27f7c50af56f5da2086e04 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biomart", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, mockery, rmarkdown, testthat, webmockr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-digest - r-httr @@ -32,8 +33,8 @@ requirements: - 'r-xml >=3.99-0.7' - r-xml2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-digest - r-httr diff --git a/recipes/bioconductor-biomartgogenesets/meta.yaml b/recipes/bioconductor-biomartgogenesets/meta.yaml new file mode 100644 index 0000000000000..df4009848c019 --- /dev/null +++ b/recipes/bioconductor-biomartgogenesets/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "0.99.11" %} +{% set name = "BioMartGOGeneSets" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f96a12703fd2f9c357442a60e5f2c764 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biomartgogenesets", max_pin="x.x") }}' + noarch: generic +# Suggests: biomaRt, GO.db, GenomeInfoDb, knitr, testthat, GetoptLong, DT +requirements: + host: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + run: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Gene Ontology Gene Sets from BioMart' + description: 'It contains pre-compiled Gene Ontology gene sets for all organisms available on the Ensembl database. It also includes GO gene sets for organisms on Ensembl Plants, Ensembl Metazoa, Ensembl Fungi and Ensembl Protists. The data was collected with the biomaRt package.' + license_file: LICENSE + diff --git a/recipes/bioconductor-biomartgogenesets/post-link.sh b/recipes/bioconductor-biomartgogenesets/post-link.sh new file mode 100644 index 0000000000000..19d29150eab0b --- /dev/null +++ b/recipes/bioconductor-biomartgogenesets/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "biomartgogenesets-0.99.11" diff --git a/recipes/bioconductor-biomartgogenesets/pre-unlink.sh b/recipes/bioconductor-biomartgogenesets/pre-unlink.sh new file mode 100644 index 0000000000000..ea56fd0d96116 --- /dev/null +++ b/recipes/bioconductor-biomartgogenesets/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BioMartGOGeneSets diff --git a/recipes/bioconductor-biomformat/meta.yaml b/recipes/bioconductor-biomformat/meta.yaml index 3f733d767388d..9baeccbf7f291 100644 --- a/recipes/bioconductor-biomformat/meta.yaml +++ b/recipes/bioconductor-biomformat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "biomformat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eff7e3b0449e543e14b8e3c4169a3e11 + md5: f35aaf72b454bc1872f1247642029006 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biomformat", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - 'r-jsonlite >=0.9.16' - 'r-matrix >=1.2' - 'r-plyr >=1.8' run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - 'r-jsonlite >=0.9.16' - 'r-matrix >=1.2' diff --git a/recipes/bioconductor-biomvcclass/meta.yaml b/recipes/bioconductor-biomvcclass/meta.yaml index 9dda455c81080..63e1563014b71 100644 --- a/recipes/bioconductor-biomvcclass/meta.yaml +++ b/recipes/bioconductor-biomvcclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "BioMVCClass" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7186d0439ac65d30681067b145eefa04 + md5: 72d762b9a59c4b75d79c378792250b48 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biomvcclass", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-mvcclass >=1.74.0,<1.75.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-mvcclass >=1.76.0,<1.77.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-mvcclass >=1.74.0,<1.75.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-mvcclass >=1.76.0,<1.77.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-biomvrcns/build.sh b/recipes/bioconductor-biomvrcns/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biomvrcns/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biomvrcns/meta.yaml b/recipes/bioconductor-biomvrcns/meta.yaml new file mode 100644 index 0000000000000..29c5079d7968d --- /dev/null +++ b/recipes/bioconductor-biomvrcns/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.42.1" %} +{% set name = "biomvRCNS" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 592c6d6f34e855eed52b4591b6b065e1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biomvrcns", max_pin="x.x") }}' +# Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene +requirements: + host: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - r-base + - r-mvtnorm + - libblas + - liblapack + run: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - r-base + - r-mvtnorm + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Copy Number study and Segmentation for multivariate biological data' + description: 'In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-bionar/meta.yaml b/recipes/bioconductor-bionar/meta.yaml index db31ce7f4be80..a1ef1fc42337d 100644 --- a/recipes/bioconductor-bionar/meta.yaml +++ b/recipes/bioconductor-bionar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.4" %} +{% set version = "1.4.0" %} {% set name = "BioNAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f78a59dea815f7b7cfad0682cae32708 + md5: 4cbc1fe5bd753444b3470a317029a885 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bionar", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR +# Suggests: knitr, BiocStyle, magick, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-synaptome.db >=0.99.0,<0.100.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-clustercons - r-cowplot @@ -35,6 +35,7 @@ requirements: - r-ggrepel - 'r-igraph >=1.4.0' - r-latex2exp + - r-matrix - r-minpack.lm - r-powerlaw - r-rdpack @@ -45,11 +46,10 @@ requirements: - r-viridis - r-wgcna run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-synaptome.db >=0.99.0,<0.100.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-clustercons - r-cowplot @@ -59,6 +59,7 @@ requirements: - r-ggrepel - 'r-igraph >=1.4.0' - r-latex2exp + - r-matrix - r-minpack.lm - r-powerlaw - r-rdpack diff --git a/recipes/bioconductor-bionero/meta.yaml b/recipes/bioconductor-bionero/meta.yaml index f3df186d26e2b..2ebcf257d05b5 100644 --- a/recipes/bioconductor-bionero/meta.yaml +++ b/recipes/bioconductor-bionero/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.5" %} +{% set version = "1.10.0" %} {% set name = "BioNERO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e673d1c24445c648a2a152f8408d4f09 + md5: 4cc77a8b8eb3cff071fbe5df15a6eb67 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bionero", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2, networkD3, covr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genie3 >=1.22.0,<1.23.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genie3 >=1.24.0,<1.25.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-dynamictreecut - r-ggdendro @@ -43,12 +44,12 @@ requirements: - r-rlang - r-wgcna run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genie3 >=1.22.0,<1.23.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genie3 >=1.24.0,<1.25.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-dynamictreecut - r-ggdendro diff --git a/recipes/bioconductor-bionet/meta.yaml b/recipes/bioconductor-bionet/meta.yaml index d9adb1f066cc9..ba12d6bab333a 100644 --- a/recipes/bioconductor-bionet/meta.yaml +++ b/recipes/bioconductor-bionet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "BioNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ff51b8ceee1e56fb2330eb25404c8db + md5: 7f2fb01406a2c73946981af9fa9c86c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bionet", max_pin="x.x") }}' noarch: generic # Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - 'r-igraph >=1.0.1' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - 'r-igraph >=1.0.1' test: diff --git a/recipes/bioconductor-bionetstat/meta.yaml b/recipes/bioconductor-bionetstat/meta.yaml index 431995c0950b8..41bdf3796be71 100644 --- a/recipes/bioconductor-bionetstat/meta.yaml +++ b/recipes/bioconductor-bionetstat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BioNetStat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed891791ee2df9a37085262b321eb994 + md5: c5de66f95b44aa3d98c077be1a27ae44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bionetstat", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-dt - r-ggplot2 @@ -40,8 +41,8 @@ requirements: - r-whisker - r-yaml run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-dt - r-ggplot2 diff --git a/recipes/bioconductor-bioplex/meta.yaml b/recipes/bioconductor-bioplex/meta.yaml index 4eb82837b603c..2861b800c834c 100644 --- a/recipes/bioconductor-bioplex/meta.yaml +++ b/recipes/bioconductor-bioplex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "BioPlex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a387711025f30513f09cf397c759e81 + md5: 77e38da3b194e7776fa7007a2cef42bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioplex", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq, ExperimentHub, GenomicFeatures, S4Vectors, depmap, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bioplex/post-link.sh b/recipes/bioconductor-bioplex/post-link.sh index b3b51db1f2b19..fbbc180637819 100644 --- a/recipes/bioconductor-bioplex/post-link.sh +++ b/recipes/bioconductor-bioplex/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bioplex-1.6.0" +installBiocDataPackage.sh "bioplex-1.8.0" diff --git a/recipes/bioconductor-bioqc/meta.yaml b/recipes/bioconductor-bioqc/meta.yaml index 41b4f55fc8ba8..1a1c326723051 100644 --- a/recipes/bioconductor-bioqc/meta.yaml +++ b/recipes/bioconductor-bioqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "BioQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef8c169f2a452603691a880ae671082d + md5: 9e9b338e001fdeb614091e4fa0cf50cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioqc", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-biosigner/meta.yaml b/recipes/bioconductor-biosigner/meta.yaml index 0e141f036996e..459f194a9ee3b 100644 --- a/recipes/bioconductor-biosigner/meta.yaml +++ b/recipes/bioconductor-biosigner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "biosigner" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c8af3938b2d60391138f896583af1056 + md5: 33d853127b5e108b0fa1c5dfea22517d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biosigner", max_pin="x.x") }}' noarch: generic # Suggests: BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-randomforest run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-randomforest diff --git a/recipes/bioconductor-biostrings/meta.yaml b/recipes/bioconductor-biostrings/meta.yaml index e55e0fa2c3827..fc1ca74c09cdb 100644 --- a/recipes/bioconductor-biostrings/meta.yaml +++ b/recipes/bioconductor-biostrings/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.68.1" %} +{% set version = "2.70.1" %} {% set name = "Biostrings" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12cef3d82ae3ac557ab16fabfb6f8646 + md5: 998fdd127f3613ca157917c847e22ac3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ -# Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit + run_exports: '{{ pin_subpackage("bioconductor-biostrings", max_pin="x.x") }}' +# Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon build: diff --git a/recipes/bioconductor-biotip/meta.yaml b/recipes/bioconductor-biotip/meta.yaml index db19a9a6fc203..89e01b63d03be 100644 --- a/recipes/bioconductor-biotip/meta.yaml +++ b/recipes/bioconductor-biotip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "BioTIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fbfda3e6fbf559c289827a25ae5b5213 + md5: 9a7765bd55ed7e2d7d09d4eff3b2127c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biotip", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, base, rmarkdown, ggplot2 requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-cluster - r-igraph @@ -30,8 +31,8 @@ requirements: - r-psych - r-stringr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-cluster - r-igraph diff --git a/recipes/bioconductor-biotmle/meta.yaml b/recipes/bioconductor-biotmle/meta.yaml index a09ecd90c450e..b7e9320cef7ee 100644 --- a/recipes/bioconductor-biotmle/meta.yaml +++ b/recipes/bioconductor-biotmle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "biotmle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8737aaa23cc2f9fbeca57ff59fb924c4 + md5: 10fcb7a34336492cbd49f3170a2f81ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biotmle", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-dplyr @@ -35,11 +36,11 @@ requirements: - r-superheat - r-tibble run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-biotmledata/meta.yaml b/recipes/bioconductor-biotmledata/meta.yaml index 8832917877b31..2413693fa7bec 100644 --- a/recipes/bioconductor-biotmledata/meta.yaml +++ b/recipes/bioconductor-biotmledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "biotmleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e21b4d8009abb77c03a67a9115c289dc + md5: 8c725d5c496f9bfe7ed4b5d5c538244a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biotmledata", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, SummarizedExperiment requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-biotmledata/post-link.sh b/recipes/bioconductor-biotmledata/post-link.sh index 93a932011f94d..f4cbb02679956 100644 --- a/recipes/bioconductor-biotmledata/post-link.sh +++ b/recipes/bioconductor-biotmledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "biotmledata-1.24.0" +installBiocDataPackage.sh "biotmledata-1.26.0" diff --git a/recipes/bioconductor-biovizbase/meta.yaml b/recipes/bioconductor-biovizbase/meta.yaml index 96b433d801613..47c84b5c85b74 100644 --- a/recipes/bioconductor-biovizbase/meta.yaml +++ b/recipes/bioconductor-biovizbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "biovizBase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2849083f8ce8e17c9fbfb8448571f482 + md5: 8430b2a7913fdcfe27b9bf52ba9aff7e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biovizbase", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dichromat - r-hmisc @@ -43,20 +44,20 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dichromat - r-hmisc diff --git a/recipes/bioconductor-birewire/meta.yaml b/recipes/bioconductor-birewire/meta.yaml index 0884d912fb1f7..94f5cee0bbfa8 100644 --- a/recipes/bioconductor-birewire/meta.yaml +++ b/recipes/bioconductor-birewire/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.32.0" %} +{% set version = "3.34.0" %} {% set name = "BiRewire" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d54730101e7164be2148f51d78790fe + md5: 2539b609076f98e95e044f33fe443bdf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-birewire", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: diff --git a/recipes/bioconductor-biscuiteer/meta.yaml b/recipes/bioconductor-biscuiteer/meta.yaml index 1760062a11885..ab11d6d9b3f44 100644 --- a/recipes/bioconductor-biscuiteer/meta.yaml +++ b/recipes/bioconductor-biscuiteer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "biscuiteer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 18e07fd7cd831b02d9762a4f25b30116 + md5: a38a486daf7d4c4dd682f20658039234 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biscuiteer", max_pin="x.x") }}' noarch: generic # Suggests: DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biscuiteerdata >=1.14.0,<1.15.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-dmrseq >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biscuiteerdata >=1.16.0,<1.17.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-dmrseq >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-mus.musculus >=1.3.0,<1.4.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-gtools @@ -50,26 +51,26 @@ requirements: - r-r.utils - r-readr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biscuiteerdata >=1.14.0,<1.15.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-dmrseq >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biscuiteerdata >=1.16.0,<1.17.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-dmrseq >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-mus.musculus >=1.3.0,<1.4.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-gtools diff --git a/recipes/bioconductor-biscuiteerdata/meta.yaml b/recipes/bioconductor-biscuiteerdata/meta.yaml index d0656d7a78a17..c4cfffd5a8b7c 100644 --- a/recipes/bioconductor-biscuiteerdata/meta.yaml +++ b/recipes/bioconductor-biscuiteerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "biscuiteerData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 143bedc239cf56a25dc8bf6c1e98d392 + md5: 9610f1ea2c2e8303acbb0b52204f8d3e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biscuiteerdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-curl run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-curl - curl - - bioconductor-data-packages>=20230713 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-biscuiteerdata/post-link.sh b/recipes/bioconductor-biscuiteerdata/post-link.sh index 45806f68b34b3..6c22e115a9ff9 100644 --- a/recipes/bioconductor-biscuiteerdata/post-link.sh +++ b/recipes/bioconductor-biscuiteerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "biscuiteerdata-1.14.1" +installBiocDataPackage.sh "biscuiteerdata-1.16.0" diff --git a/recipes/bioconductor-biseq/meta.yaml b/recipes/bioconductor-biseq/meta.yaml index c3e2ea0161860..93bf96e0a6e37 100644 --- a/recipes/bioconductor-biseq/meta.yaml +++ b/recipes/bioconductor-biseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "BiSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef582ccfe80af188e2c95e93917112f6 + md5: 76a46bdea0a83b3ead6a8ee87d6000ac build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-betareg - r-formula - r-lokern run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-betareg - r-formula diff --git a/recipes/bioconductor-blacksheepr/meta.yaml b/recipes/bioconductor-blacksheepr/meta.yaml index 6261dbb5aa447..956002139ea7c 100644 --- a/recipes/bioconductor-blacksheepr/meta.yaml +++ b/recipes/bioconductor-blacksheepr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "blacksheepr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ffc59bd1330fbd355d89f419d5378c36 + md5: 464b853300f0d97e2ad8f0a4188701c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-blacksheepr", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-pasilla >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-pasilla >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-rcolorbrewer - r-viridis run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-pasilla >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-pasilla >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-rcolorbrewer diff --git a/recipes/bioconductor-bladderbatch/meta.yaml b/recipes/bioconductor-bladderbatch/meta.yaml index e3c40acb29dbe..9eafff22e508e 100644 --- a/recipes/bioconductor-bladderbatch/meta.yaml +++ b/recipes/bioconductor-bladderbatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "bladderbatch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ab4457a6eebb75202730d4433d4aa245 + md5: d59d10a87e8d62c6ba10f7e9c0160a44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bladderbatch", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bladderbatch/post-link.sh b/recipes/bioconductor-bladderbatch/post-link.sh index 1f6b3e2258b10..fac44e79b40e2 100644 --- a/recipes/bioconductor-bladderbatch/post-link.sh +++ b/recipes/bioconductor-bladderbatch/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bladderbatch-1.38.0" +installBiocDataPackage.sh "bladderbatch-1.40.0" diff --git a/recipes/bioconductor-blima/meta.yaml b/recipes/bioconductor-blima/meta.yaml index 0ed1506388c12..dee6d37139ead 100644 --- a/recipes/bioconductor-blima/meta.yaml +++ b/recipes/bioconductor-blima/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "blima" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c2c14f23337c1135f6d65fd58fa7ac05 + md5: a0d7cbb46b78eabdbc06c4ee1b417bcb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-blima", max_pin="x.x") }}' # Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr requirements: host: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-rcpp >=0.12.8' - libblas - liblapack run: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-rcpp >=0.12.8' build: diff --git a/recipes/bioconductor-blimatestingdata/meta.yaml b/recipes/bioconductor-blimatestingdata/meta.yaml index 7befc4cd40a70..6d25e2e3e3f9e 100644 --- a/recipes/bioconductor-blimatestingdata/meta.yaml +++ b/recipes/bioconductor-blimatestingdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "blimaTestingData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17e9a4119b1beaf61f30fbe192b9a20a + md5: 3ae3da97d0d020e16feee29b93c24825 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-blimatestingdata", max_pin="x.x") }}' noarch: generic # Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-blimatestingdata/post-link.sh b/recipes/bioconductor-blimatestingdata/post-link.sh index 0137332d50d47..1418b77f265e3 100644 --- a/recipes/bioconductor-blimatestingdata/post-link.sh +++ b/recipes/bioconductor-blimatestingdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "blimatestingdata-1.20.0" +installBiocDataPackage.sh "blimatestingdata-1.22.0" diff --git a/recipes/bioconductor-blma/meta.yaml b/recipes/bioconductor-blma/meta.yaml index f16f88fab8d50..acbf15edf9540 100644 --- a/recipes/bioconductor-blma/meta.yaml +++ b/recipes/bioconductor-blma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "BLMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9040447a39ecba3f13decf927d02295e + md5: a09cb94872d4a064b9b6300945795cdf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-blma", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-padog >=1.42.0,<1.43.0' - - 'bioconductor-rontotools >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-padog >=1.44.0,<1.45.0' + - 'bioconductor-rontotools >=2.30.0,<2.31.0' - r-base - r-gsa - r-metafor run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-padog >=1.42.0,<1.43.0' - - 'bioconductor-rontotools >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-padog >=1.44.0,<1.45.0' + - 'bioconductor-rontotools >=2.30.0,<2.31.0' - r-base - r-gsa - r-metafor diff --git a/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml b/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml index 776134ad78ca8..d6fbe40747131 100644 --- a/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml +++ b/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BloodCancerMultiOmics2017" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d7ccf32b2249044c2b86aa4cf933372 + md5: d2b2dcb147bf904df505fedca2d1ea9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bloodcancermultiomics2017", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, IHW, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, xtable requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beeswarm - r-devtools @@ -39,9 +40,9 @@ requirements: - r-survival - r-tibble run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beeswarm - r-devtools @@ -57,7 +58,7 @@ requirements: - r-survival - r-tibble - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh b/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh index 6a011d5316aed..84e46bc91c92a 100644 --- a/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh +++ b/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bloodcancermultiomics2017-1.20.0" +installBiocDataPackage.sh "bloodcancermultiomics2017-1.22.0" diff --git a/recipes/bioconductor-bloodgen3module/meta.yaml b/recipes/bioconductor-bloodgen3module/meta.yaml index 88890177b4894..aad99351531e3 100644 --- a/recipes/bioconductor-bloodgen3module/meta.yaml +++ b/recipes/bioconductor-bloodgen3module/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BloodGen3Module" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37a265fa33d837fb54956f3347976869 + md5: c9957080f8c55f99ebcc89cdc652deb9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bloodgen3module", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, devtools, BiocGenerics, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-ggplot2 @@ -36,11 +37,11 @@ requirements: - r-testthat - r-v8 run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-bluster/meta.yaml b/recipes/bioconductor-bluster/meta.yaml index 24fd7a073cdab..2ba7e0232e16b 100644 --- a/recipes/bioconductor-bluster/meta.yaml +++ b/recipes/bioconductor-bluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "bluster" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a8d0bcd5ece8d29de23893d218538f35 + md5: baf91e0700b1f49eb80522be9eb8204d build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster + run_exports: '{{ pin_subpackage("bioconductor-bluster", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster, DirichletMultinomial, vegan, fastcluster # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-igraph @@ -32,9 +33,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-igraph diff --git a/recipes/bioconductor-bnbc/meta.yaml b/recipes/bioconductor-bnbc/meta.yaml index d3820552aca7c..b60b06813c282 100644 --- a/recipes/bioconductor-bnbc/meta.yaml +++ b/recipes/bioconductor-bnbc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.23.0" %} {% set name = "bnbc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e2882b1e727097ea7116bdb5941eabb0 + md5: 201f8c694f60da1dfa8112194f29ca18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bnbc", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-data.table - r-matrixstats @@ -37,16 +38,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-data.table - r-matrixstats diff --git a/recipes/bioconductor-bnem/meta.yaml b/recipes/bioconductor-bnem/meta.yaml index 00b86a14d90bc..c24854a74af32 100644 --- a/recipes/bioconductor-bnem/meta.yaml +++ b/recipes/bioconductor-bnem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "bnem" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cd61ea3a67e6032366b423e220d4b4de + md5: 84eb035082edc5cefe35763abde3093f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bnem", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle +# Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-binom - r-cluster @@ -40,16 +41,16 @@ requirements: - r-rmarkdown - r-snowfall run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-binom - r-cluster diff --git a/recipes/bioconductor-bobafit/meta.yaml b/recipes/bioconductor-bobafit/meta.yaml index c0cc7a0e533dc..4b504236c4870 100644 --- a/recipes/bioconductor-bobafit/meta.yaml +++ b/recipes/bioconductor-bobafit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "BOBaFIT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61cff94869967960f27a430de74624d4 + md5: 48b9cc5c35adf6469bd1dc2ca566bed1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bobafit", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' - r-base - r-dplyr - r-ggforce @@ -33,9 +34,9 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' - r-base - r-dplyr - r-ggforce diff --git a/recipes/bioconductor-bodymaprat/meta.yaml b/recipes/bioconductor-bodymaprat/meta.yaml index 30cd298b734df..a13f963c7a9e9 100644 --- a/recipes/bioconductor-bodymaprat/meta.yaml +++ b/recipes/bioconductor-bodymaprat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "bodymapRat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d15dd35c8ce1db80954afb9e4663fe29 + md5: fc575d7f33dd1ee73f1860fb076a840b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bodymaprat", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bodymaprat/post-link.sh b/recipes/bioconductor-bodymaprat/post-link.sh index 86e3dad9f97d4..d4ee9d2550175 100644 --- a/recipes/bioconductor-bodymaprat/post-link.sh +++ b/recipes/bioconductor-bodymaprat/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bodymaprat-1.16.0" +installBiocDataPackage.sh "bodymaprat-1.18.0" diff --git a/recipes/bioconductor-bovine.db/meta.yaml b/recipes/bioconductor-bovine.db/meta.yaml index ea439d5251876..29be66b899563 100644 --- a/recipes/bioconductor-bovine.db/meta.yaml +++ b/recipes/bioconductor-bovine.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "bovine.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dcc1180e8ac11247f9899f140082647e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bovine.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.bt.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.bt.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bovine.db0/meta.yaml b/recipes/bioconductor-bovine.db0/meta.yaml index 5708b4d9c6569..7014ea409a9c4 100644 --- a/recipes/bioconductor-bovine.db0/meta.yaml +++ b/recipes/bioconductor-bovine.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "bovine.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1e268d93f6206875bd73ad2caae53f27 + md5: 658829797db74aec87af1914483d1af7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bovine.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bovine.db0/post-link.sh b/recipes/bioconductor-bovine.db0/post-link.sh index 7506bd29e27b6..0c3dc1fc3f167 100644 --- a/recipes/bioconductor-bovine.db0/post-link.sh +++ b/recipes/bioconductor-bovine.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bovine.db0-3.17.0" +installBiocDataPackage.sh "bovine.db0-3.18.0" diff --git a/recipes/bioconductor-bovinecdf/meta.yaml b/recipes/bioconductor-bovinecdf/meta.yaml index 9ad4d03a221a3..3a8ad02076f2f 100644 --- a/recipes/bioconductor-bovinecdf/meta.yaml +++ b/recipes/bioconductor-bovinecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bovinecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e155fc7d5f84ee420d9b250a639af305 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bovinecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bovineprobe/meta.yaml b/recipes/bioconductor-bovineprobe/meta.yaml index 90f41fdf6fd4b..d4af93a9c72d3 100644 --- a/recipes/bioconductor-bovineprobe/meta.yaml +++ b/recipes/bioconductor-bovineprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bovineprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9f9e25fc8c7a76acf541745b7c09748b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bovineprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bprmeth/meta.yaml b/recipes/bioconductor-bprmeth/meta.yaml index c01464ce9e050..6a3d18505b240 100644 --- a/recipes/bioconductor-bprmeth/meta.yaml +++ b/recipes/bioconductor-bprmeth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.0" %} {% set name = "BPRMeth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b83f314896bec3879303077f2537c62 + md5: 8229c7c5175e3888c86a5a3a42eb7a8c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bprmeth", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-cowplot @@ -45,10 +46,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-cowplot diff --git a/recipes/bioconductor-brain/meta.yaml b/recipes/bioconductor-brain/meta.yaml index 69cd4b403220d..f5e9400cafc79 100644 --- a/recipes/bioconductor-brain/meta.yaml +++ b/recipes/bioconductor-brain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "BRAIN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e35f1ec745209c95a944114c34091b41 + md5: 575b879f058d01202c3bc33b0ff8e3f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-brain", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-lattice - r-polynomf run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-lattice - r-polynomf diff --git a/recipes/bioconductor-brainflowprobes/meta.yaml b/recipes/bioconductor-brainflowprobes/meta.yaml index 6099d55d781b5..5f35b40d260c6 100644 --- a/recipes/bioconductor-brainflowprobes/meta.yaml +++ b/recipes/bioconductor-brainflowprobes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "brainflowprobes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 00cceed929cbf95e9d1dcaf2b0248933 + md5: eb9efebe165aeeae35ccc6b115836937 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-brainflowprobes", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-derfinderplot >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-derfinderplot >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-genomicstate >=0.99.0,<0.100.0' - r-base - 'r-cowplot >=1.0.0' - 'r-ggplot2 >=3.1.1' - 'r-rcolorbrewer >=1.1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-derfinderplot >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-derfinderplot >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-genomicstate >=0.99.0,<0.100.0' - r-base - 'r-cowplot >=1.0.0' diff --git a/recipes/bioconductor-branchpointer/meta.yaml b/recipes/bioconductor-branchpointer/meta.yaml index 292fb0401dad9..b5aa55175fda0 100644 --- a/recipes/bioconductor-branchpointer/meta.yaml +++ b/recipes/bioconductor-branchpointer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "branchpointer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a86bfa6b36d075cba930e82d1148b850 + md5: 7a62abd020843736b7ea125ffc4a56e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-branchpointer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-cowplot @@ -39,14 +40,14 @@ requirements: - r-plyr - r-stringr run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-cowplot diff --git a/recipes/bioconductor-breakpointr/meta.yaml b/recipes/bioconductor-breakpointr/meta.yaml index d84838d2737df..f401d66f805fd 100644 --- a/recipes/bioconductor-breakpointr/meta.yaml +++ b/recipes/bioconductor-breakpointr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "breakpointR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ba29b07c5e6f5c0972109a7dd43c32c + md5: 96dddc1e7bbd8b880a89f8f1be145e66 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breakpointr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-breakpointrdata >=1.18.0,<1.19.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-breakpointrdata >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-doparallel @@ -36,14 +37,14 @@ requirements: - r-ggplot2 - r-gtools run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-breakpointrdata >=1.18.0,<1.19.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-breakpointrdata >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-doparallel diff --git a/recipes/bioconductor-breakpointrdata/meta.yaml b/recipes/bioconductor-breakpointrdata/meta.yaml index 2a17fb8938acf..904bd544168f7 100644 --- a/recipes/bioconductor-breakpointrdata/meta.yaml +++ b/recipes/bioconductor-breakpointrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "breakpointRdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59535154a02ede7347b6114c11292173 + md5: e3f74132513d150cb5d5cc62bfd49586 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breakpointrdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breakpointrdata/post-link.sh b/recipes/bioconductor-breakpointrdata/post-link.sh index 12ab5d0df96bb..726ec7f9888bf 100644 --- a/recipes/bioconductor-breakpointrdata/post-link.sh +++ b/recipes/bioconductor-breakpointrdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breakpointrdata-1.18.0" +installBiocDataPackage.sh "breakpointrdata-1.20.0" diff --git a/recipes/bioconductor-breastcancermainz/meta.yaml b/recipes/bioconductor-breastcancermainz/meta.yaml index 0d66189888bfe..e073dd94ff14c 100644 --- a/recipes/bioconductor-breastcancermainz/meta.yaml +++ b/recipes/bioconductor-breastcancermainz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerMAINZ" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d906d493af2aa3a2fbf00029aa6f843 + md5: 2b8df5af87b71c6706f909129212b504 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancermainz", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancermainz/post-link.sh b/recipes/bioconductor-breastcancermainz/post-link.sh index c37b0581a960d..4570fff6a22f3 100644 --- a/recipes/bioconductor-breastcancermainz/post-link.sh +++ b/recipes/bioconductor-breastcancermainz/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancermainz-1.38.0" +installBiocDataPackage.sh "breastcancermainz-1.40.0" diff --git a/recipes/bioconductor-breastcancernki/meta.yaml b/recipes/bioconductor-breastcancernki/meta.yaml index 6d47a0d8fb9ff..38686c35da078 100644 --- a/recipes/bioconductor-breastcancernki/meta.yaml +++ b/recipes/bioconductor-breastcancernki/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerNKI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61d8e072228b6bbb224793b35625d507 + md5: 0a0940593d75deaed0aa6f01954cf61c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancernki", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancernki/post-link.sh b/recipes/bioconductor-breastcancernki/post-link.sh index 9b89ba199b787..e92a07580eac6 100644 --- a/recipes/bioconductor-breastcancernki/post-link.sh +++ b/recipes/bioconductor-breastcancernki/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancernki-1.38.0" +installBiocDataPackage.sh "breastcancernki-1.40.0" diff --git a/recipes/bioconductor-breastcancertransbig/meta.yaml b/recipes/bioconductor-breastcancertransbig/meta.yaml index 593973e18a542..80be8500b3982 100644 --- a/recipes/bioconductor-breastcancertransbig/meta.yaml +++ b/recipes/bioconductor-breastcancertransbig/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerTRANSBIG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7117b6426a4cf52736db5835ccdc4ccc + md5: 170d89ddd3e554da50a0b2b5d040a96e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancertransbig", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancertransbig/post-link.sh b/recipes/bioconductor-breastcancertransbig/post-link.sh index 586835155b461..819f5330c62a7 100644 --- a/recipes/bioconductor-breastcancertransbig/post-link.sh +++ b/recipes/bioconductor-breastcancertransbig/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancertransbig-1.38.0" +installBiocDataPackage.sh "breastcancertransbig-1.40.0" diff --git a/recipes/bioconductor-breastcancerunt/meta.yaml b/recipes/bioconductor-breastcancerunt/meta.yaml index ea17ee7662462..938bc94e4da08 100644 --- a/recipes/bioconductor-breastcancerunt/meta.yaml +++ b/recipes/bioconductor-breastcancerunt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerUNT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fab6de14673763f649a3cfd14fc62579 + md5: 31e1b6d7e34b4acb9207e3e152539166 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancerunt", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancerunt/post-link.sh b/recipes/bioconductor-breastcancerunt/post-link.sh index 6408e7184bd12..0b186b89bdffc 100644 --- a/recipes/bioconductor-breastcancerunt/post-link.sh +++ b/recipes/bioconductor-breastcancerunt/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancerunt-1.38.0" +installBiocDataPackage.sh "breastcancerunt-1.40.0" diff --git a/recipes/bioconductor-breastcancerupp/meta.yaml b/recipes/bioconductor-breastcancerupp/meta.yaml index 20b68e52bd898..0bdf776792724 100644 --- a/recipes/bioconductor-breastcancerupp/meta.yaml +++ b/recipes/bioconductor-breastcancerupp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerUPP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37f0587a0149e1abe5525dd7bbc76a7f + md5: c5c10989a8a2dbfd20c228522474fac1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancerupp", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancerupp/post-link.sh b/recipes/bioconductor-breastcancerupp/post-link.sh index b8e19ca711332..7abd029d8fdcd 100644 --- a/recipes/bioconductor-breastcancerupp/post-link.sh +++ b/recipes/bioconductor-breastcancerupp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancerupp-1.38.0" +installBiocDataPackage.sh "breastcancerupp-1.40.0" diff --git a/recipes/bioconductor-breastcancervdx/meta.yaml b/recipes/bioconductor-breastcancervdx/meta.yaml index 0f60c65a37662..ed8c49c9a563f 100644 --- a/recipes/bioconductor-breastcancervdx/meta.yaml +++ b/recipes/bioconductor-breastcancervdx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "breastCancerVDX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a20c1e1a3060af883ced8843600a1614 + md5: 446ef46e0bdd1480e12de21ded7b58f0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-breastcancervdx", max_pin="x.x") }}' noarch: generic # Suggests: survcomp, genefu, Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-breastcancervdx/post-link.sh b/recipes/bioconductor-breastcancervdx/post-link.sh index a5e24a547d943..1269d20e15959 100644 --- a/recipes/bioconductor-breastcancervdx/post-link.sh +++ b/recipes/bioconductor-breastcancervdx/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancervdx-1.38.0" +installBiocDataPackage.sh "breastcancervdx-1.40.0" diff --git a/recipes/bioconductor-brendadb/meta.yaml b/recipes/bioconductor-brendadb/meta.yaml index 459cb8316015e..b084097d11c03 100644 --- a/recipes/bioconductor-brendadb/meta.yaml +++ b/recipes/bioconductor-brendadb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "brendaDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 048a034a1b3a87cfbd31ada86ee4b282 + md5: 35e521feef3f87b0122ac00ad0deae5b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-brendadb", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-crayon - r-dplyr @@ -37,8 +38,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-crayon - r-dplyr diff --git a/recipes/bioconductor-brgedata/meta.yaml b/recipes/bioconductor-brgedata/meta.yaml index f353e69bb3c67..39687c989b37a 100644 --- a/recipes/bioconductor-brgedata/meta.yaml +++ b/recipes/bioconductor-brgedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "brgedata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5b448f1cfae2bb44babb2b1720d12234 + md5: b8d26c8dfa756e9eb556e4662e3b3302 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-brgedata", max_pin="x.x") }}' noarch: generic -# Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome +# Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-brgedata/post-link.sh b/recipes/bioconductor-brgedata/post-link.sh index 1e48f726f3a24..267b22a18da9f 100644 --- a/recipes/bioconductor-brgedata/post-link.sh +++ b/recipes/bioconductor-brgedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "brgedata-1.22.0" +installBiocDataPackage.sh "brgedata-1.24.0" diff --git a/recipes/bioconductor-brgenomics/meta.yaml b/recipes/bioconductor-brgenomics/meta.yaml index 4bccede1a84b9..519fe73af34c1 100644 --- a/recipes/bioconductor-brgenomics/meta.yaml +++ b/recipes/bioconductor-brgenomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.13.0" %} {% set name = "BRGenomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96099779d34a4ffd00637a2da0d2888d + md5: 33a9bc55e58468faa4cc337617be743a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-brgenomics", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, apeglm, remotes, ggplot2, reshape2, Biostrings requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-bridgedbr/meta.yaml b/recipes/bioconductor-bridgedbr/meta.yaml index 13e09730ca229..f48e3b4fbacd2 100644 --- a/recipes/bioconductor-bridgedbr/meta.yaml +++ b/recipes/bioconductor-bridgedbr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "BridgeDbR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64a3933b9e01f5e9f8f7ca740fbf2e1a + md5: 2c155c28cb8d117e2dc1b69873b91d84 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bridgedbr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-bronchialil13/meta.yaml b/recipes/bioconductor-bronchialil13/meta.yaml index 16910d2d8dcb5..4084cc6bf0bff 100644 --- a/recipes/bioconductor-bronchialil13/meta.yaml +++ b/recipes/bioconductor-bronchialil13/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "bronchialIL13" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71116894de06b0faf014ae3be0f54b36 + md5: be303e29450fb15b03a10f6caaf30159 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bronchialil13", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bronchialil13/post-link.sh b/recipes/bioconductor-bronchialil13/post-link.sh index 49cb149982f5b..6ec47d8303721 100644 --- a/recipes/bioconductor-bronchialil13/post-link.sh +++ b/recipes/bioconductor-bronchialil13/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bronchialil13-1.38.0" +installBiocDataPackage.sh "bronchialil13-1.40.0" diff --git a/recipes/bioconductor-browserviz/meta.yaml b/recipes/bioconductor-browserviz/meta.yaml index e2aff600e6de8..a84be67b166ab 100644 --- a/recipes/bioconductor-browserviz/meta.yaml +++ b/recipes/bioconductor-browserviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "BrowserViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f26ddbc8b11670673e8aa1ba1d596da + md5: ae6366903bd754cbe0ca0d21168c6883 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-browserviz", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-httpuv >=1.5.0' - 'r-jsonlite >=1.5' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-httpuv >=1.5.0' - 'r-jsonlite >=1.5' diff --git a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml index dd0c23f97d22c..8b13956ebc368 100644 --- a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "BSgenome.Alyrata.JGI.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 64878499c633de66ccf4c5abc32c0aeb build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.alyrata.jgi.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml index 10447b66c3c39..ab05d12803a09 100644 --- a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Amellifera.BeeBase.assembly4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 77495ee5eba48fe52902c9cc4f9ba7cc build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.beebase.assembly4", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml index 9ff51c4de3714..be19401c6fca5 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Amellifera.NCBI.AmelHAv3.1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b119087dfe54805c90cb6bf901e8237e build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.ncbi.amelhav3.1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml index 51095fb8ab0e1..5ad72a039a442 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Amellifera.UCSC.apiMel2.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e7a7ff8cfce8e239b22116855456f23d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.ucsc.apimel2.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml index 6c642df024a66..03cf1f3dc82a3 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Amellifera.UCSC.apiMel2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 436ddf54868906e7d1135369d41a2ffe build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.ucsc.apimel2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml index 77d7c5b033f0f..cd38ff3980573 100644 --- a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.Aofficinalis.NCBI.V1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3f8fd13e74eee63895a5ef528004b60b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.aofficinalis.ncbi.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml index ad247c14857a0..4fdd444fe0fb6 100644 --- a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml +++ b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Athaliana.TAIR.04232008" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6b8a31a228dbcf4468974f5ec1d98467 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.athaliana.tair.04232008", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml index e03055053f540..5829649a04069 100644 --- a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml +++ b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Athaliana.TAIR.TAIR9" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8c6709a5f544616d59f4d39aac5787a7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.athaliana.tair.tair9", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml index a893da700aa30..5e00c72c1eb23 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 50f7da5907cbe0d08183dc7161a8ca56 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml index a7cfc076d2a11..cf3656257eb57 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fe6c4d5853f91c3db3e716ddbc773580 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau3", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml index 8f79033795b1a..27d7dfefcbef2 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau4.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7c5294349c7061adfb3948bc5659afeb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau4.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml index 1c30f83c63ff8..eab5a9891ec02 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 162cd253c719e347df5748ebb407a191 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau4", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml index f75c8d0eaa275..bbfbee0affde2 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau6.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a176de6b1b91854d47e783b8249dbf58 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau6.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml index b3832e58994bd..ce246f321d24a 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b22391e0678fc3743daa4b77ecc55f66 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau6", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml index 1c7c2e7b1f8d1..682d89e7f4c24 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau8" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 61ababa7b2b5360fceeb06f0bf49b208 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau8", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml index 4bda0bf0ac096..62f59fbac5296 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.4" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau9.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c96bd95c3b791d712aa5cb8c96f9c937 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau9.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau9 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.btaurus.ucsc.bostau9 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml index 87bc529b78d3e..3f586fcdbffff 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau9" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9b3343725d85c093999413d91218079d build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau9", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml index 5a326847bb631..648f18fbe0f64 100644 --- a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.Carietinum.NCBI.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: eef018ecce6d32852aa18ac39cf377c6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.carietinum.ncbi.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml index 997b63d67e600..7f4da58f4e64f 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 98a8ca836d6db23e46674552669d7942 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce10", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml index 4edbab45dbd80..c2b220fe98a18 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Celegans.UCSC.ce11" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b80e24149a0c6ed323d0c9a6d112ef52 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce11", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml index d41e5c535f971..32235e1365fe1 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b2bf7eec2b07685cf9dcdf42840db208 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce2", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml index 77e16d3a2e788..e42da8e5488ee 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cb86ff861d8f660c2abd8fc1907d84a6 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce6", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Celegans.UCSC.ce6.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml index 2392f4d5cf402..069fc1c59c867 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam2.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6f921533bb83f83f43b8d227b00a48cb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml index 4ade310b5153a..982e9034314f8 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b98f5289ed5d362cd815db9352598634 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam2", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml index 0492d4146ac81..0261f9eff5a17 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8e2246f51fc967dc2ed748cf967a7649 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml index b8e2a85ce5776..89560db448749 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: efcdc531042be86f99a734cd69c0688c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam3", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml index 29b734795a981..10417581a99fc 100644 --- a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml +++ b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Cjacchus.UCSC.calJac3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 41f927aa0d6ffbdaa6ad93c9135409e6 build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cjacchus.ucsc.caljac3", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml index 899af20c80879..516f9eb1efe23 100644 --- a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml +++ b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Cjacchus.UCSC.calJac4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b11d16ac2cfa81e04af74e2049e52670 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cjacchus.ucsc.caljac4", max_pin="x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20231202 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml b/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml index a506ea2b1c87e..462035d069539 100644 --- a/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ea536a15bd932af794f672d9b204c141 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml b/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml index 55e8df05bb417..c415b873854e9 100644 --- a/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml +++ b/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Creinhardtii.JGI.v5.6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2bd1be53d19249ac14ad7f39dc00af0e build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.creinhardtii.jgi.v5.6", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml index 11825bf9d2d6e..62a0b17986a8d 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm2.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ae7ca3053e97a0d6bd20bc2b9635ecce build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml index e3a3eef94ca81..7b1927e47450e 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ebc88df5595fc7aad588b8f3f7de4784 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm2", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml index 2f2cc231ae70f..6067d2d13f90e 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 592e7ec451d126b2d314ab6c75d86830 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml index f16df60d79dc6..c68d6516cefb1 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b7ceebf7bfee766596f602f9e808d069 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm3", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Dmelanogaster.UCSC.dm3.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml index d84b65dd7a732..feaea65b5861e 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f9d6e406b7893a17c08edd4521c2802f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm6", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml index 92aca3bfbc9a8..87a3b044b538d 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Drerio.UCSC.danRer10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b8dbcc8a338a021ed35656b27b3dd4c0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer10", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml index c45c38af3a531..95822ca277bba 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Drerio.UCSC.danRer11" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cd586da56ca88ccebb85804f992ba204 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer11", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml index 68aa11c6f335a..64e298e1c21eb 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer5.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8f0623bcbe1743754a56c55599b535f3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer5.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml index 43690e11e74d6..bf6871a4d5a7d 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b1fee4bcc0d9cebb2bbdec5cb851f00d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer5", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml index fc11125683fda..6b526c573e5c6 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer6.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 71c9b05c27b8d2e05735e6494a8f17ba build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer6.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml index f0a07f6245687..478b3e1bddeff 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 537d37d29d97ae0c31d77decc67b25b0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer6", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml index fe467e74c1a8a..019514752ee1c 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer7.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5d68af24477d006ed22e7342ff97ac16 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer7.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml index 05ea9322b3723..6c1a8c0e62b9d 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer7" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 766b407a46f20d69a143eab0809eb10a build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer7", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml b/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml index bfae8430f5959..0ce3c6e24705b 100644 --- a/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml +++ b/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Dvirilis.Ensembl.dvircaf1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6a6a6dc7b2d68a741c85525045a67890 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dvirilis.ensembl.dvircaf1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml index b99315e8e48ff..2f3ba681a1364 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Ecoli.NCBI.20080805" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c653e9cbee3faeb6fd5759b7575f234d build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ecoli.ncbi.20080805", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml index 4e8f686c998da..3a5920d510aaa 100644 --- a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Gaculeatus.UCSC.gasAcu1.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9d9b9e70f4f4624ee4a2b09a59d44510 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml index 64feabca6f667..6a6732255be3d 100644 --- a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Gaculeatus.UCSC.gasAcu1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 412aa0570d9c556861b7bb9a5bbc2007 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.gaculeatus.ucsc.gasacu1", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml index 58495ba4cfa9f..cf7403c1a2f0a 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ggallus.UCSC.galGal3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b3224e3a2b15de379c068e61cedfefa6 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml index 7d8a3cbcda3e5..e8b20a1070d3b 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ggallus.UCSC.galGal3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a463e5ccfc8c6d2c62a6ade0da65dbc4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal3", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml index 32c4ca424d92b..4b54412a74eac 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ggallus.UCSC.galGal4.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0166121ebd8d0b6a4d24d67e175cfe81 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal4.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml index ad3c3e3edc772..d54b800d51b31 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ggallus.UCSC.galGal4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c2cb4bfc39db93c060e78d8d12542c11 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal4", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml index 6274a0dcded2f..18a560405740b 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ggallus.UCSC.galGal5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 93b42354404edd848b21ea6781ca135c build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal5", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml index c5cf92c3d35ad..a44fab45df53d 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ggallus.UCSC.galGal6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 25ef08a5430fb337dbf752ca3378ea3e build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal6", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml b/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml index f607776b31e4a..fe9c07be232c6 100644 --- a/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml +++ b/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml @@ -1,6 +1,6 @@ {% set version = "4.0" %} {% set name = "BSgenome.Gmax.NCBI.Gmv40" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 421c045b993b2cfbc2b08c8103835c56 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.gmax.ncbi.gmv40", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml index 4d458f7e30969..7fb6b93796e7d 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "BSgenome.Hsapiens.1000genomes.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 164e1692d38fefa499c2c8ac5fc22793 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.1000genomes.hs37d5", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml index 506c403b47d19..04da6b9994ab5 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.NCBI.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 733d324b34d34d7da8c4bf38459f4fae build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ncbi.grch38", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml index 802f28ed1c51f..4f0ef091db55a 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 22a99174e1e17718e0b4f8b66f32fd9b build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml index fdaff26d7f794..7fb6eb6c52a75 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Hsapiens.UCSC.hg17.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ff6ee5196f234c5a2a3bcdd052c3c08e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg17.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml index 4a71b4fbb264b..eb46af4af2e48 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.UCSC.hg17" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cbea3029c3d3125a88e6c061c3d3abde build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg17", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml index 05ee40409117e..e950d5f76a8de 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Hsapiens.UCSC.hg18.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e6a31e3cba34ce5e0eb6f76d2c19870c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg18.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml index a0c785f26697d..33e4cdff26eae 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.UCSC.hg18" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 51bb2e1ed4009860bb21aaac32fffd9c build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg18", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Hsapiens.UCSC.hg18.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml index d4720898a70b4..5664f8236fb7e 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.993" %} {% set name = "BSgenome.Hsapiens.UCSC.hg19.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4424e1bda9cc005d75f5f05ba4a50c77 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg19.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml index 59cee391fb862..4280e60fd61df 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Hsapiens.UCSC.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bb3f864ab32450d895816b45f6105f4f build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml index 972385b4cccfb..2c99c40050795 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.9999" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c59f66e52d4982942bea2254223d58df build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor, testthat requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml index 6e69afb63c9df..9c2021c5d0a73 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.9999" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2cc3a612a2064624735d6a92910be7f3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major, testthat requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml index 0fe10479f56ac..5a69152654b1b 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.5" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,24 +13,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7570dd1b4f013b3c6acecd68602180b4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml index ca742fc10b820..caafd0d4f2854 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.5" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b2e670c27944eed77fbe9a9b55be40d2 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml index 71aeb4c9ab68c..6e76b23734749 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.4" %} {% set name = "BSgenome.Hsapiens.UCSC.hs1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5812c5670f51a5c58a9da9e042e7e440 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hs1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml index 97a0ef2a902cf..c4ab4bc879512 100644 --- a/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml +++ b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mdomestica.UCSC.monDom5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ff940f7446a275962f69a6f4cb84724c build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mdomestica.ucsc.mondom5", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml index 0784f336cd2a6..c888f310c4025 100644 --- a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mfascicularis.NCBI.5.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dba6ade39dc6b4f6d06f488141b5550b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mfascicularis.ncbi.5.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml index d1c7ea45dcfd8..d6051b0d89c9a 100644 --- a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Mfascicularis.NCBI.6.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 67272a96950f485d3c0770265f59c85c build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mfascicularis.ncbi.6.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml index 9c9837bf6ca14..561159c626803 100644 --- a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml +++ b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Mfuro.UCSC.musFur1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c33e71746ce551bcbcd22be1979aee63 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mfuro.ucsc.musfur1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml index 62544190199ee..075e65553bbe0 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2f2afe40d5dcf8d8620aa5e12e311fbc build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac10", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml index 80ef70b97663a..0f176b99d2e61 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac2.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7602d86b68df7e4c8d336fede4090a62 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml index 3a9195cd66f71..775d3ae08031f 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 90c43e127e76dfd7cea90de9e1af9a50 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac2", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml index 18733254bbef5..e99cfc364553a 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 94f8714865655d3144e14f6fc5c24e76 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml index 2216fcb5a526c..b7f2e7e8cd0b3 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dfa1ecb9d0bb7a5d9fa628092fb1c354 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac3", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml index 601e857dbfb7e..1e79bebdc1783 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac8" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e9ad1f70f652c62554e2c5af7638c015 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac8", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml index d58e64bc4ed81..82ebb44b2a53d 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Mmusculus.UCSC.mm10.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 40d51fb428a5fda8c05101a3dddb8957 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm10.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml index f1efa6f1fac69..8d717d8f96f31 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Mmusculus.UCSC.mm10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ffddc2e035527ed1a1e201ac4cc0b1f3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm10", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml index 69b0ae1f316ad..935b7d6e381f3 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Mmusculus.UCSC.mm39" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a130ef50dd55da9fd341e6c90b22637b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm39", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml index 7684f10eb95d2..7f6fd1ee3b55f 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmusculus.UCSC.mm8.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5809f925e0fe7c4b73b78a90c9a36fdd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm8.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml index 6e6c613171204..1015d037ec13c 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm8" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f6aa91cdce2607f30a34f6dd0d678aff build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm8", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml index 488f175b658b3..a388770cefc1a 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmusculus.UCSC.mm9.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a5dadab14e55cdfc39649ede7a8483d5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm9.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml index 48013ddb87342..c84701d12370e 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm9" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5a30ba2b4481a17e8e6979eb69eabf78 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm9", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml b/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml index ff0a3d3aa702d..163678ae1635a 100644 --- a/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml +++ b/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.2" %} {% set name = "BSgenome.Osativa.MSU.MSU7" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 80648058756a2f74aa5a246d38ecf576 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.osativa.msu.msu7", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml index b59be7d005417..85411a3df2b2e 100644 --- a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml +++ b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Ppaniscus.UCSC.panPan1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 186adb59264d468d17c0f6374e2eb1f6 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ppaniscus.ucsc.panpan1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml index e79c92349f3a6..f6c6a0c21e800 100644 --- a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml +++ b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Ppaniscus.UCSC.panPan2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 74973376a6377d6820d6cd7fb3655a19 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ppaniscus.ucsc.panpan2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml index f1f2ecf2167d5..456bbdeda57f3 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro2.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e6d069be23712b483b4e4c71554594cf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml index a2cfdf785362c..13287c4def47d 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 780200c315779ac75fcf0bdeb9a2eb8c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro2", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml index 9cbb09f9db090..ccedb52acf0fe 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 89e96b3796d3b8e8793146597506e3f5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml index c99aa78937b5e..4cced5a9b52a6 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4677c75befd60742f3fc2a54c7f60666 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro3", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml index 3787d51f36c05..e2c5ae5f72aaa 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5b88573dd9c3ef838699b65934f8abe3 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro5", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml index 693fc7176d78a..12604327f1864 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1df05d985374e9edc1dd7c3df5118338 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro6", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml index f14ab66ec392e..c583c872ec589 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn4.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7e2ea7df588b6b10515e07ea3868c568 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml index e86c0d8bc025e..1c86c50cd4dae 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3afe6729237781445d99ec38228ee1a8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn4", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Rnorvegicus.UCSC.rn4.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml index a42230bd9c169..89dbbafe4e2e5 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn5.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 663233774b79012cb2cc08224ac275ed build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml index ad6b2d180cde1..4297c1fcfc716 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 723b1f3ced395ef638b2d68053b05c86 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn5", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Rnorvegicus.UCSC.rn5.refGene requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml index 3916440396076..1ee39156f2de8 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 60d3fb201e0b1475912aaf681927096d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn6", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml index 8bb4b62e4b64c..07102a354264c 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn7" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c64f7dd9e30ff88ce02ecd3712e4c454 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn7", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml index a990ef8a02074..725432e3a6292 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ad4c29c16a9635088bf13872b4a02ed4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.scerevisiae.ucsc.saccer1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml index 804779df06c94..f65fa66ad4026 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f1025b4d0fa7891dc46301550163753e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.scerevisiae.ucsc.saccer2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml index d3c22fceff1e7..b386b9c86ea88 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7f2d8bba69c3dcebf426d9b19a6bed30 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.scerevisiae.ucsc.saccer3", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml index 56385b29b352b..e2ac5d79e3f68 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr11" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: db22832229e31e1a629d107df522dff9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.sscrofa.ucsc.susscr11", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml index a56dd58b2c65b..c116c67adf671 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr3.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fd240651d22d169fd1e27a2b66e40dd7 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml index 4c832870ef0c0..2903b8432bb02 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0457ca52a81c9d7ceadad5830169e6cf build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.sscrofa.ucsc.susscr3", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml index e4427a2dd78e1..c22953ef89cf7 100644 --- a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "BSgenome.Tgondii.ToxoDB.7.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f67644d1a897fe2ff4139832d4ceaf80 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tgondii.toxodb.7.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml index 2b2a95e49809c..44e84dd6f5b29 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut1.masked" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 63684abb5b330bb54ff89fe78f2e6444 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tguttata.ucsc.taegut1.masked", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml index 3cc5e5fc365cb..086df25bd94c0 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9753d9568d2a866a627673a518a1dd8a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tguttata.ucsc.taegut1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml index 7ae6cc8a0698c..fbca5f56adb3d 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1d39678fb060e643f7e9c4ec25e828c0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tguttata.ucsc.taegut2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml index f746388a13d54..ef55869bfb77c 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP12Xv0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3f791de6d699325a97080cd98be86d89 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.vvinifera.urgi.iggp12xv0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml index d59326e2d635e..32841939100f7 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP12Xv2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 95472e574ab46327c19e241c381b26a2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.vvinifera.urgi.iggp12xv2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml index 79a636e08497f..34e0332d217bc 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP8X" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fccaf60e5c9352b9c454f7a8ecac2a20 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.vvinifera.urgi.iggp8x", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsgenome/meta.yaml b/recipes/bioconductor-bsgenome/meta.yaml index 5a909a1c3dcc1..0958486077c61 100644 --- a/recipes/bioconductor-bsgenome/meta.yaml +++ b/recipes/bioconductor-bsgenome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.1" %} {% set name = "BSgenome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: deb582b34b2d5532bb811c223e8426a0 + md5: a94697b953c4fc9bb0ba15daf35a884d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenome", max_pin="x.x") }}' noarch: generic -# Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit +# Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit, BSgenomeForge requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-matrixstats test: diff --git a/recipes/bioconductor-bsgenomeforge/meta.yaml b/recipes/bioconductor-bsgenomeforge/meta.yaml index 7b4754b1911f5..0c189d94200e2 100644 --- a/recipes/bioconductor-bsgenomeforge/meta.yaml +++ b/recipes/bioconductor-bsgenomeforge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "BSgenomeForge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 630aec996209048e39553239dd20e563 + md5: ed03f4628533403765aae28991855bca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsgenomeforge", max_pin="x.x") }}' noarch: generic # Suggests: GenomicRanges, GenomicFeatures, testthat, knitr, rmarkdown, BiocStyle, devtools requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-bsseq/meta.yaml b/recipes/bioconductor-bsseq/meta.yaml index e0a4b601e8cd0..a707ba6ca86b9 100644 --- a/recipes/bioconductor-bsseq/meta.yaml +++ b/recipes/bioconductor-bsseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "bsseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3fa1d3c20a5204d8d336c3261174ecfd + md5: 0fee416655d94a260bf4a613b4a6321e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsseq", max_pin="x.x") }}' # Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), batchtools requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.11.8' - r-gtools @@ -47,22 +48,22 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.11.8' - r-gtools diff --git a/recipes/bioconductor-bsseqdata/meta.yaml b/recipes/bioconductor-bsseqdata/meta.yaml index e892d6dcf9b31..2c014a22b1551 100644 --- a/recipes/bioconductor-bsseqdata/meta.yaml +++ b/recipes/bioconductor-bsseqdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "bsseqData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aeca7a29ea03b49344cf7cc223389537 + md5: 514171e8133c8d38e6b1ad31eff722a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsseqdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsseq >=1.36.0,<1.37.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-bsseq >=1.36.0,<1.37.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsseqdata/post-link.sh b/recipes/bioconductor-bsseqdata/post-link.sh index 3679601aa6199..6f79c30564302 100644 --- a/recipes/bioconductor-bsseqdata/post-link.sh +++ b/recipes/bioconductor-bsseqdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bsseqdata-0.38.0" +installBiocDataPackage.sh "bsseqdata-0.40.0" diff --git a/recipes/bioconductor-bsubtiliscdf/meta.yaml b/recipes/bioconductor-bsubtiliscdf/meta.yaml index 706abfe6693c0..d9da46bade688 100644 --- a/recipes/bioconductor-bsubtiliscdf/meta.yaml +++ b/recipes/bioconductor-bsubtiliscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bsubtiliscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7d7893d28c601206805819ae0e49b31b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsubtiliscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bsubtilisprobe/meta.yaml b/recipes/bioconductor-bsubtilisprobe/meta.yaml index 6ff55a639a50b..7cfe3dece2b39 100644 --- a/recipes/bioconductor-bsubtilisprobe/meta.yaml +++ b/recipes/bioconductor-bsubtilisprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "bsubtilisprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83568fcea2122350b7ce982e79b7ec53 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bsubtilisprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bubbletree/meta.yaml b/recipes/bioconductor-bubbletree/meta.yaml index 01bb298429bc2..23898ead413c9 100644 --- a/recipes/bioconductor-bubbletree/meta.yaml +++ b/recipes/bioconductor-bubbletree/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "BubbleTree" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03eea1f59b31aa704ae501d2f8fc5854 + md5: 84649d9271ce193051e18a7bb56ff58e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bubbletree", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dplyr - r-e1071 @@ -40,13 +41,13 @@ requirements: - r-rcolorbrewer - r-writexls run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dplyr - r-e1071 diff --git a/recipes/bioconductor-bufferedmatrix/meta.yaml b/recipes/bioconductor-bufferedmatrix/meta.yaml index 2e9069b65c3f1..dbb18ad6dfccf 100644 --- a/recipes/bioconductor-bufferedmatrix/meta.yaml +++ b/recipes/bioconductor-bufferedmatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "BufferedMatrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b33976ecec4bcd9ddabec3ef8747bc78 + md5: a4ad95db528526463e6dfca80975815e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bufferedmatrix", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml index 595e58c396867..55a8f987f77dc 100644 --- a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml +++ b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "BufferedMatrixMethods" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6dfc8b00fbfc5e05576eeef80a6bf9d + md5: 57eb9e8db5a9dc58db25b88bbe5d2436 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bufferedmatrixmethods", max_pin="x.x") }}' # Suggests: affyio, affy requirements: host: - - 'bioconductor-bufferedmatrix >=1.64.0,<1.65.0' + - 'bioconductor-bufferedmatrix >=1.66.0,<1.67.0' - r-base - libblas - liblapack run: - - 'bioconductor-bufferedmatrix >=1.64.0,<1.65.0' + - 'bioconductor-bufferedmatrix >=1.66.0,<1.67.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-bugsigdbr/meta.yaml b/recipes/bioconductor-bugsigdbr/meta.yaml index 45bcd9de2cece..345d5d5fb9b45 100644 --- a/recipes/bioconductor-bugsigdbr/meta.yaml +++ b/recipes/bioconductor-bugsigdbr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.1" %} {% set name = "bugsigdbr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5580a7ce1e29f6e6138a62185f2a9364 + md5: 35aebe840ca55cd93f16af9d239ea806 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bugsigdbr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - - r-vroom run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - - r-vroom test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-bumhmm/meta.yaml b/recipes/bioconductor-bumhmm/meta.yaml index bfb19bbee28a7..853c6756464b6 100644 --- a/recipes/bioconductor-bumhmm/meta.yaml +++ b/recipes/bioconductor-bumhmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "BUMHMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e43e3eb5d210769b8d9c5b585ecd2af9 + md5: c70dbfec58330fd1fa6cd1aca5e16912 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bumhmm", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-devtools - r-gtools - r-stringi run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-devtools - r-gtools diff --git a/recipes/bioconductor-bumphunter/meta.yaml b/recipes/bioconductor-bumphunter/meta.yaml index def7d740c00be..44699549646a5 100644 --- a/recipes/bioconductor-bumphunter/meta.yaml +++ b/recipes/bioconductor-bumphunter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "bumphunter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0fba211d07df317c3d4722a85357a475 + md5: fea93f84b54daabaaf1686d658aeedfc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bumphunter", max_pin="x.x") }}' noarch: generic # Suggests: testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dorng - r-foreach @@ -36,14 +37,14 @@ requirements: - r-locfit - r-matrixstats run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dorng - r-foreach diff --git a/recipes/bioconductor-bumpymatrix/meta.yaml b/recipes/bioconductor-bumpymatrix/meta.yaml index aabf599c5e7d0..3087aebf5c9a1 100644 --- a/recipes/bioconductor-bumpymatrix/meta.yaml +++ b/recipes/bioconductor-bumpymatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BumpyMatrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1575e971c01dd864c690ca5b48627781 + md5: 6069ae96659170c765102c2513e44b58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bumpymatrix", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-bus/meta.yaml b/recipes/bioconductor-bus/meta.yaml index 95f003cf037ac..d0b152aca8a53 100644 --- a/recipes/bioconductor-bus/meta.yaml +++ b/recipes/bioconductor-bus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "BUS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10472148950ca1a1ccfecaadf43367d0 + md5: 788ab26ecf05f0df93667a7c37f564ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bus", max_pin="x.x") }}' requirements: host: - - 'bioconductor-minet >=3.58.0,<3.59.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' - r-base - r-infotheo - libblas - liblapack run: - - 'bioconductor-minet >=3.58.0,<3.59.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' - r-base - r-infotheo build: diff --git a/recipes/bioconductor-buscorrect/meta.yaml b/recipes/bioconductor-buscorrect/meta.yaml index d15129579ac74..9507deeddc21a 100644 --- a/recipes/bioconductor-buscorrect/meta.yaml +++ b/recipes/bioconductor-buscorrect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "BUScorrect" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcefe721755de842d0d1952acb19a459 + md5: 6d24bece1ac7982a2a157e5cccc01b99 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-buscorrect", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots build: diff --git a/recipes/bioconductor-busparse/meta.yaml b/recipes/bioconductor-busparse/meta.yaml index 42b0d95564295..6946225b5c956 100644 --- a/recipes/bioconductor-busparse/meta.yaml +++ b/recipes/bioconductor-busparse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "BUSpaRse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d08b55495020361901d1373d4df4339c + md5: 7d2decd570fd518ad9a06c10a5ecffb3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-busparse", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 # SystemRequirements: GNU make requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-dplyr @@ -50,19 +51,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-dplyr diff --git a/recipes/bioconductor-busseq/meta.yaml b/recipes/bioconductor-busseq/meta.yaml index 1bc0066302432..1efe83d6f0fd2 100644 --- a/recipes/bioconductor-busseq/meta.yaml +++ b/recipes/bioconductor-busseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "BUSseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3623f486d083ce7f0c38903eae323c93 + md5: ba606db2bfb17a5958ba686639ecefbe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-busseq", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, BiocGenerics requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots build: diff --git a/recipes/bioconductor-cadd.v1.6.hg19/meta.yaml b/recipes/bioconductor-cadd.v1.6.hg19/meta.yaml new file mode 100644 index 0000000000000..446a23d0973bb --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg19/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "3.18.1" %} +{% set name = "cadd.v1.6.hg19" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 10cc50d17dbca89406a2290f37d5203c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cadd.v1.6.hg19", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg19' + description: 'Store University of Washington CADD v1.6 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + diff --git a/recipes/bioconductor-cadd.v1.6.hg19/post-link.sh b/recipes/bioconductor-cadd.v1.6.hg19/post-link.sh new file mode 100644 index 0000000000000..1cccd56a142ff --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg19/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "cadd.v1.6.hg19-3.18.1" diff --git a/recipes/bioconductor-cadd.v1.6.hg19/pre-unlink.sh b/recipes/bioconductor-cadd.v1.6.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..010caf8ebc0f2 --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cadd.v1.6.hg19 diff --git a/recipes/bioconductor-cadd.v1.6.hg38/meta.yaml b/recipes/bioconductor-cadd.v1.6.hg38/meta.yaml new file mode 100644 index 0000000000000..1136468b55f7b --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg38/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "3.18.1" %} +{% set name = "cadd.v1.6.hg38" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 620a889ea8bc55f98811a80a3aec814d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cadd.v1.6.hg38", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg38' + description: 'Store University of Washington CADD v1.6 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + diff --git a/recipes/bioconductor-cadd.v1.6.hg38/post-link.sh b/recipes/bioconductor-cadd.v1.6.hg38/post-link.sh new file mode 100644 index 0000000000000..c954375b37933 --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg38/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "cadd.v1.6.hg38-3.18.1" diff --git a/recipes/bioconductor-cadd.v1.6.hg38/pre-unlink.sh b/recipes/bioconductor-cadd.v1.6.hg38/pre-unlink.sh new file mode 100644 index 0000000000000..3bd10bc74e89d --- /dev/null +++ b/recipes/bioconductor-cadd.v1.6.hg38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cadd.v1.6.hg38 diff --git a/recipes/bioconductor-cadra/build.sh b/recipes/bioconductor-cadra/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cadra/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cadra/meta.yaml b/recipes/bioconductor-cadra/meta.yaml new file mode 100644 index 0000000000000..72f0b311f64e6 --- /dev/null +++ b/recipes/bioconductor-cadra/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.1" %} +{% set name = "CaDrA" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9ac2bc6afe6632e5fbd00c687ca19bba +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cadra", max_pin="x.x") }}' +# Suggests: BiocManager, BiocStyle, devtools, knitr, magick, pheatmap, rmarkdown, testthat (>= 3.1.6) +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-doparallel + - r-ggplot2 + - r-gplots + - r-gtable + - r-mass + - r-misc3d + - r-plyr + - r-ppcor + - r-r.cache + - r-reshape2 + - libblas + - liblapack + run: + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-doparallel + - r-ggplot2 + - r-gplots + - r-gtable + - r-mass + - r-misc3d + - r-plyr + - r-ppcor + - r-r.cache + - r-reshape2 + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Candidate Driver Analysis' + description: 'Performs both stepwise and backward heuristic search for candidate (epi)genetic drivers based on a binary multi-omics dataset. CaDrA''s main objective is to identify features which, together, are significantly skewed or enriched pertaining to a given vector of continuous scores (e.g. sample-specific scores representing a phenotypic readout of interest, such as protein expression, pathway activity, etc.), based on the union occurence (i.e. logical OR) of the events.' + license_file: LICENSE + diff --git a/recipes/bioconductor-caen/meta.yaml b/recipes/bioconductor-caen/meta.yaml index da3cb9b5852b4..9430206502ac5 100644 --- a/recipes/bioconductor-caen/meta.yaml +++ b/recipes/bioconductor-caen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CAEN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0bad38df2fe80cade3ef9db7c9241188 + md5: 66decd595d2315a90c09b7d52df606c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-caen", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown,BiocManager,SummarizedExperiment,BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-poiclaclu run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-poiclaclu test: diff --git a/recipes/bioconductor-cafe/meta.yaml b/recipes/bioconductor-cafe/meta.yaml index 42660bfbef0ba..38e52b776a3fc 100644 --- a/recipes/bioconductor-cafe/meta.yaml +++ b/recipes/bioconductor-cafe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "CAFE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3327ab214fb57b43e0e88bd2249c3b17 + md5: 1a64370f203f198ad86163715decbebb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cafe", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-gridextra run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-cagefightr/meta.yaml b/recipes/bioconductor-cagefightr/meta.yaml index 36d6bebb1e13f..7c7717aa940e4 100644 --- a/recipes/bioconductor-cagefightr/meta.yaml +++ b/recipes/bioconductor-cagefightr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CAGEfightR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,49 +11,50 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c46d615668fe693b427295c88416052 + md5: 86c87a4bec49d7c37ef74a6a6081a685 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cagefightr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-assertthat >=0.2.0' - r-base - 'r-matrix >=1.2-12' - 'r-pryr >=0.1.3' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-assertthat >=0.2.0' - r-base - 'r-matrix >=1.2-12' diff --git a/recipes/bioconductor-cageminer/meta.yaml b/recipes/bioconductor-cageminer/meta.yaml index c31239d6fd788..f6b6d7035888b 100644 --- a/recipes/bioconductor-cageminer/meta.yaml +++ b/recipes/bioconductor-cageminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "cageminer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d85bf5a81347a582b161160ccf001d83 + md5: 02b96b12bfe145c4c9deefff49cd1015 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cageminer", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo requirements: host: - - 'bioconductor-bionero >=1.8.0,<1.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-bionero >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-ggtext - r-reshape2 - r-rlang run: - - 'bioconductor-bionero >=1.8.0,<1.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-bionero >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-ggtext diff --git a/recipes/bioconductor-cager/meta.yaml b/recipes/bioconductor-cager/meta.yaml index 7f748a4694dab..760142e82ee20 100644 --- a/recipes/bioconductor-cager/meta.yaml +++ b/recipes/bioconductor-cager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "CAGEr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4abf800289121fcb4795c1a30fd35cd + md5: 845c3a47631734b6fe7209f173e24100 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cager", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cagefightr >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cagefightr >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-formula.tools @@ -51,21 +52,21 @@ requirements: - r-vegan - r-vgam run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cagefightr >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cagefightr >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-formula.tools diff --git a/recipes/bioconductor-calm/meta.yaml b/recipes/bioconductor-calm/meta.yaml index 390e16252f8a9..d544112473d73 100644 --- a/recipes/bioconductor-calm/meta.yaml +++ b/recipes/bioconductor-calm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "calm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d6b0e35a1cf15fe23f6ac7138863a58d + md5: 9a2b4c48021193636c88c997331ede2d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-calm", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-camera/meta.yaml b/recipes/bioconductor-camera/meta.yaml index 0d3eca1b9f159..db1fce9160d3f 100644 --- a/recipes/bioconductor-camera/meta.yaml +++ b/recipes/bioconductor-camera/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "CAMERA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b627c870804005f6ef9c1f48ccf6eceb + md5: 1958cafb2c9dd92fa44a35cfc607f894 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-camera", max_pin="x.x") }}' # Suggests: faahKO, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-hmisc - r-igraph - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-hmisc - r-igraph diff --git a/recipes/bioconductor-cancer/meta.yaml b/recipes/bioconductor-cancer/meta.yaml index 0163ea2219ef7..1498a00e3bb28 100644 --- a/recipes/bioconductor-cancer/meta.yaml +++ b/recipes/bioconductor-cancer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "canceR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 942f2c8187c6686017489023ee793d0d + md5: 4311164fc68969a40252dc3761583f24 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cancer", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.1), knitr, rmarkdown, BiocStyle # SystemRequirements: Tktable, BWidget requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genetclassifier >=1.40.0,<1.41.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-phenotest >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-phenotest >=1.50.0,<1.51.0' - r-base - r-circlize - r-formula @@ -38,10 +39,10 @@ requirements: - r-survival - r-tkrplot run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genetclassifier >=1.40.0,<1.41.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-phenotest >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-phenotest >=1.50.0,<1.51.0' - r-base - r-circlize - r-formula diff --git a/recipes/bioconductor-cancerclass/meta.yaml b/recipes/bioconductor-cancerclass/meta.yaml index 7b84f85d34133..ee3fb82ad436d 100644 --- a/recipes/bioconductor-cancerclass/meta.yaml +++ b/recipes/bioconductor-cancerclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "cancerclass" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1b773f50fc0ab3bc1e0555a2807d9c76 + md5: b2e5d6ec200ee08476480fa1f0a1577d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cancerclass", max_pin="x.x") }}' # Suggests: cancerdata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-binom - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-binom build: diff --git a/recipes/bioconductor-cancerdata/meta.yaml b/recipes/bioconductor-cancerdata/meta.yaml index 6e8a1974a3587..8b5aaa6fb459c 100644 --- a/recipes/bioconductor-cancerdata/meta.yaml +++ b/recipes/bioconductor-cancerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "cancerdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 23d4242144544786e0327a3144d8a6c6 + md5: 7baa088ef320a0222a897987ea8c3e8b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cancerdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cancerdata/post-link.sh b/recipes/bioconductor-cancerdata/post-link.sh index 634f9917cbc85..f48bb85329be6 100644 --- a/recipes/bioconductor-cancerdata/post-link.sh +++ b/recipes/bioconductor-cancerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cancerdata-1.38.0" +installBiocDataPackage.sh "cancerdata-1.40.0" diff --git a/recipes/bioconductor-canine.db/meta.yaml b/recipes/bioconductor-canine.db/meta.yaml index 811c40b827bca..9afadfb4280f1 100644 --- a/recipes/bioconductor-canine.db/meta.yaml +++ b/recipes/bioconductor-canine.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "canine.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a876bb01eda62604a32a96b46e34162b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canine.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.cf.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.cf.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine.db0/meta.yaml b/recipes/bioconductor-canine.db0/meta.yaml index b83fd7ffeaf32..9e295898ab473 100644 --- a/recipes/bioconductor-canine.db0/meta.yaml +++ b/recipes/bioconductor-canine.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "canine.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: da4af1b026fe2775a020addd13920f71 + md5: dc4fff8ed0a758ddff3f52aa0e8652c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canine.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine.db0/post-link.sh b/recipes/bioconductor-canine.db0/post-link.sh index e7e67a934420c..e5e86dee05068 100644 --- a/recipes/bioconductor-canine.db0/post-link.sh +++ b/recipes/bioconductor-canine.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "canine.db0-3.17.0" +installBiocDataPackage.sh "canine.db0-3.18.0" diff --git a/recipes/bioconductor-canine2.db/meta.yaml b/recipes/bioconductor-canine2.db/meta.yaml index 6682cbee36fcb..6b4c2bc532688 100644 --- a/recipes/bioconductor-canine2.db/meta.yaml +++ b/recipes/bioconductor-canine2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "canine2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 24727f27cdf1e324f097a76db81dfc1d build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canine2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.cf.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.cf.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine2cdf/meta.yaml b/recipes/bioconductor-canine2cdf/meta.yaml index 37ab92dcedc44..9d689a5971930 100644 --- a/recipes/bioconductor-canine2cdf/meta.yaml +++ b/recipes/bioconductor-canine2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "canine2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 78740cde98c75e6680470564a4df74c3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canine2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canine2probe/meta.yaml b/recipes/bioconductor-canine2probe/meta.yaml index fb4c210c8fd5c..6f54871ac6b19 100644 --- a/recipes/bioconductor-canine2probe/meta.yaml +++ b/recipes/bioconductor-canine2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "canine2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7de0f4ea616e8662dc2eaa9ab78d1f13 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canine2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-caninecdf/meta.yaml b/recipes/bioconductor-caninecdf/meta.yaml index 70b08561a5922..f80e3709dcb35 100644 --- a/recipes/bioconductor-caninecdf/meta.yaml +++ b/recipes/bioconductor-caninecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "caninecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 656f845cc66890015a4e13c5304ec262 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-caninecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-canineprobe/meta.yaml b/recipes/bioconductor-canineprobe/meta.yaml index 1856806650678..a85ebdab28fe3 100644 --- a/recipes/bioconductor-canineprobe/meta.yaml +++ b/recipes/bioconductor-canineprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "canineprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e5467bc9b7e54c5adce6b409ba7df767 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-canineprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cardelino/meta.yaml b/recipes/bioconductor-cardelino/meta.yaml index 2fdbcbb7f4d20..684c1386c8a20 100644 --- a/recipes/bioconductor-cardelino/meta.yaml +++ b/recipes/bioconductor-cardelino/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "cardelino" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ba9264af6b626d01cb7700cd264ca4c7 + md5: 363c06547419f29e1cdfe473651e1861 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cardelino", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-combinat - r-ggplot2 @@ -35,12 +36,12 @@ requirements: - r-pheatmap - r-vcfr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-combinat - r-ggplot2 diff --git a/recipes/bioconductor-cardinal/meta.yaml b/recipes/bioconductor-cardinal/meta.yaml index a4fa219fb80e4..ebb5c8fde4502 100644 --- a/recipes/bioconductor-cardinal/meta.yaml +++ b/recipes/bioconductor-cardinal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.2.1" %} +{% set version = "3.4.3" %} {% set name = "Cardinal" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c28538283f8b6b79f6b7e66f5ac7fcb + md5: ee7f799a94a4c3cd1946feb2b1db9dd4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cardinal", max_pin="x.x") }}' # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-matter >=2.2.0,<2.3.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cardinalio >=1.0.0,<1.1.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-matter >=2.4.0,<2.5.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-irlba - r-magrittr @@ -34,18 +36,18 @@ requirements: - r-mclust - r-nlme - r-signal - - r-sp - r-viridislite - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-matter >=2.2.0,<2.3.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cardinalio >=1.0.0,<1.1.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-matter >=2.4.0,<2.5.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-irlba - r-magrittr @@ -53,7 +55,6 @@ requirements: - r-mclust - r-nlme - r-signal - - r-sp - r-viridislite build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cardinalio/build.sh b/recipes/bioconductor-cardinalio/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cardinalio/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cardinalio/meta.yaml b/recipes/bioconductor-cardinalio/meta.yaml new file mode 100644 index 0000000000000..e51480d5e4ba8 --- /dev/null +++ b/recipes/bioconductor-cardinalio/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "CardinalIO" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 746846f9fda38de9fe2c3dd4c49c18e1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cardinalio", max_pin="x.x") }}' +# Suggests: BiocStyle, testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-matter >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-ontologyindex + - libblas + - liblapack + run: + - 'bioconductor-matter >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-ontologyindex + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Read and write mass spectrometry imaging files' + description: 'Fast and efficient reading and writing of mass spectrometry imaging data files. Supports imzML and Analyze 7.5 formats. Provides ontologies for mass spectrometry imaging.' + diff --git a/recipes/bioconductor-cardinalworkflows/meta.yaml b/recipes/bioconductor-cardinalworkflows/meta.yaml index 55aa4097d3b5f..9935acb2c639a 100644 --- a/recipes/bioconductor-cardinalworkflows/meta.yaml +++ b/recipes/bioconductor-cardinalworkflows/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "CardinalWorkflows" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a8b9945c7f7b5287510917c6bc1e1a4 + md5: 54c51a2ec2f20f96ad9e60c16eeb2ccb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cardinalworkflows", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-cardinal >=3.2.0,<3.3.0' + - 'bioconductor-cardinal >=3.4.0,<3.5.0' - r-base run: - - 'bioconductor-cardinal >=3.2.0,<3.3.0' + - 'bioconductor-cardinal >=3.4.0,<3.5.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cardinalworkflows/post-link.sh b/recipes/bioconductor-cardinalworkflows/post-link.sh index 375cb5b31f89e..d557ce84baab0 100644 --- a/recipes/bioconductor-cardinalworkflows/post-link.sh +++ b/recipes/bioconductor-cardinalworkflows/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cardinalworkflows-1.32.0" +installBiocDataPackage.sh "cardinalworkflows-1.34.0" diff --git a/recipes/bioconductor-carnival/meta.yaml b/recipes/bioconductor-carnival/meta.yaml index f9fa8303cb483..565eefdb379a4 100644 --- a/recipes/bioconductor-carnival/meta.yaml +++ b/recipes/bioconductor-carnival/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "CARNIVAL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d92b0f48e86019ba880d96574038a7b2 + md5: c5457d5d859c16cbec56532338f64fb0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-carnival", max_pin="x.x") }}' noarch: generic # Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo requirements: diff --git a/recipes/bioconductor-casper/meta.yaml b/recipes/bioconductor-casper/meta.yaml index 557323da87a07..3142caba5767b 100644 --- a/recipes/bioconductor-casper/meta.yaml +++ b/recipes/bioconductor-casper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "casper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f43788dc14c1c51dcfde295920c6f5e6 + md5: 4c9fc29e3b92d5b493953ea97436556a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-casper", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' - - 'bioconductor-gaga >=2.46.0,<2.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - 'bioconductor-gaga >=2.48.0,<2.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-coda - r-gtools @@ -41,18 +42,18 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' - - 'bioconductor-gaga >=2.46.0,<2.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - 'bioconductor-gaga >=2.48.0,<2.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-coda - r-gtools diff --git a/recipes/bioconductor-catalyst/meta.yaml b/recipes/bioconductor-catalyst/meta.yaml index 5d2276155f31a..42b526eec0739 100644 --- a/recipes/bioconductor-catalyst/meta.yaml +++ b/recipes/bioconductor-catalyst/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "CATALYST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 727b6a6736deb00b2a649bffc267ade6 + md5: 6ce647576b86ebdf9fe0933fd87b79ce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-catalyst", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cowplot @@ -39,7 +40,6 @@ requirements: - r-ggrepel - r-ggridges - r-gridextra - - r-magrittr - r-matrix - r-matrixstats - r-nnls @@ -49,14 +49,14 @@ requirements: - r-rtsne - r-scales run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-cowplot @@ -67,7 +67,6 @@ requirements: - r-ggrepel - r-ggridges - r-gridextra - - r-magrittr - r-matrix - r-matrixstats - r-nnls @@ -83,6 +82,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Cytometry dATa anALYSis Tools' - description: 'Mass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.' + description: 'CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-category/meta.yaml b/recipes/bioconductor-category/meta.yaml index 19020d0a70faf..a746fe351958e 100644 --- a/recipes/bioconductor-category/meta.yaml +++ b/recipes/bioconductor-category/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.66.0" %} +{% set version = "2.68.0" %} {% set name = "Category" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6dbd5bb859ad4567680561e085cd0765 + md5: d84fb36419834bb84721436d7f956932 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-category", max_pin="x.x") }}' noarch: generic # Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-dbi - r-matrix run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-dbi - r-matrix diff --git a/recipes/bioconductor-categorycompare/meta.yaml b/recipes/bioconductor-categorycompare/meta.yaml index 316ebf2f21eaf..1a04329db5a0c 100644 --- a/recipes/bioconductor-categorycompare/meta.yaml +++ b/recipes/bioconductor-categorycompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "categoryCompare" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12b838d68868bdf213889ed07657d373 + md5: 9809c7142b4af81d181bf8d8f7e0f815 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-categorycompare", max_pin="x.x") }}' noarch: generic # Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown # SystemRequirements: Cytoscape (>= 3.6.1) (if used for visualization of results, heavily suggested) requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-colorspace - r-hwriter - 'cytoscape >=3.6.1' run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-colorspace - r-hwriter diff --git a/recipes/bioconductor-causalr/meta.yaml b/recipes/bioconductor-causalr/meta.yaml index b96b70a4f9a8b..19336b1df1182 100644 --- a/recipes/bioconductor-causalr/meta.yaml +++ b/recipes/bioconductor-causalr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "CausalR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1a92153e981da4a487d5c42ca15994a + md5: 408b3cc6bc7a45715e6c07095f61ca2b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-causalr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-cbaf/meta.yaml b/recipes/bioconductor-cbaf/meta.yaml index 8a3029fa4092c..8e99a667fb4cb 100644 --- a/recipes/bioconductor-cbaf/meta.yaml +++ b/recipes/bioconductor-cbaf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "cbaf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c4489ed5d1141f61152a666bec15104c + md5: e3c093194c8fdcbd04ca035dddeaf5f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cbaf", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-cbioportaldata >=2.12.0,<2.13.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base - r-gplots - r-openxlsx - r-rcolorbrewer run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-cbioportaldata >=2.12.0,<2.13.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base - r-gplots - r-openxlsx diff --git a/recipes/bioconductor-cbea/meta.yaml b/recipes/bioconductor-cbea/meta.yaml index 0b3b567cbbf5d..63e685b38f7f5 100644 --- a/recipes/bioconductor-cbea/meta.yaml +++ b/recipes/bioconductor-cbea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.3.0" %} +{% set version = "1.2.0" %} {% set name = "CBEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abb5373c75d6328cedad978f32f2c0e7 + md5: 20761b06df9cf37c59172508ff8cd01d build: - number: 0 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cbea", max_pin="x.x") }}' # Suggests: phyloseq, BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyverse, roxygen2, mia, purrr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocset >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocset >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-dplyr - r-fitdistrplus @@ -40,10 +41,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocset >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocset >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-dplyr - r-fitdistrplus diff --git a/recipes/bioconductor-cbioportaldata/meta.yaml b/recipes/bioconductor-cbioportaldata/meta.yaml index 3f964fd3b87ac..4508b5319a9db 100644 --- a/recipes/bioconductor-cbioportaldata/meta.yaml +++ b/recipes/bioconductor-cbioportaldata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "cBioPortalData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 876930b2b73eb4f6d2515d187b925278 + md5: fc51f3b952b9c31900365adc94f85585 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cbioportaldata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, survival, survminer, rmarkdown, testthat requirements: host: - - 'bioconductor-anvil >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-rtcgatoolbox >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-rtcgatoolbox >=2.32.0,<2.33.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-digest - r-dplyr @@ -40,17 +41,17 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-anvil >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-rtcgatoolbox >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-rtcgatoolbox >=2.32.0,<2.33.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-digest - r-dplyr diff --git a/recipes/bioconductor-cbnplot/meta.yaml b/recipes/bioconductor-cbnplot/meta.yaml index e261a401638c6..8ca2a36fb2135 100644 --- a/recipes/bioconductor-cbnplot/meta.yaml +++ b/recipes/bioconductor-cbnplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "CBNplot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0717efc5c7c4f3b2b957528ff99c8dea + md5: d589e9361caf3409d65345cc48e5ccee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cbnplot", max_pin="x.x") }}' noarch: generic # Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, DESeq2, GEOquery, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-depmap >=1.14.0,<1.15.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-depmap >=1.16.0,<1.17.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - 'r-bnlearn >=4.7' - r-dplyr @@ -48,13 +49,13 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-depmap >=1.14.0,<1.15.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-depmap >=1.16.0,<1.17.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - 'r-bnlearn >=4.7' - r-dplyr diff --git a/recipes/bioconductor-cbpmanager/meta.yaml b/recipes/bioconductor-cbpmanager/meta.yaml index 5e9b4e7ee8d5f..e35ef4a737405 100644 --- a/recipes/bioconductor-cbpmanager/meta.yaml +++ b/recipes/bioconductor-cbpmanager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "cbpManager" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 428adb2f63dce7a4cbcba310d13bb32a + md5: 6567afab9427e6ee44a029fa5be314e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cbpmanager", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-base - r-dplyr - r-dt @@ -33,13 +34,14 @@ requirements: - r-rapportools - r-reticulate - r-rintrojs + - r-rlang - r-shiny - r-shinybs - r-shinycssloaders - r-shinydashboard - r-vroom run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-base - r-dplyr - r-dt @@ -51,6 +53,7 @@ requirements: - r-rapportools - r-reticulate - r-rintrojs + - r-rlang - r-shiny - r-shinybs - r-shinycssloaders diff --git a/recipes/bioconductor-ccdata/meta.yaml b/recipes/bioconductor-ccdata/meta.yaml index 5f24f35515072..e552cec2d123c 100644 --- a/recipes/bioconductor-ccdata/meta.yaml +++ b/recipes/bioconductor-ccdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ccdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d21508b620d5328d66111ed0250bcaa8 + md5: 60cbd595e53467fd61e1edc4f8ea47e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ccdata/post-link.sh b/recipes/bioconductor-ccdata/post-link.sh index cdc12359a9a68..3c5a6ff31dcdd 100644 --- a/recipes/bioconductor-ccdata/post-link.sh +++ b/recipes/bioconductor-ccdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ccdata-1.26.0" +installBiocDataPackage.sh "ccdata-1.28.0" diff --git a/recipes/bioconductor-ccfindr/build_failure.osx-64.yaml b/recipes/bioconductor-ccfindr/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..f96432c2ea200 --- /dev/null +++ b/recipes/bioconductor-ccfindr/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 284d8b5d60d001aad42c11aa0f88615ff84ff828b15ac43defb45c3fd2d1f416 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + * installing to library /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library + * installing *source* package ccfindR ... + ** using staged installation + ** libs + dyld[12683]: Library not loaded: '@rpath/libclang-cpp.15.dylib' + Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/clang-15' + Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file) + using C compiler: NA + using C11 + using SDK: + x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + dyld[12689]: Library not loaded: '@rpath/libclang-cpp.15.dylib' + Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/clang-15' + Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file) + make: *** [/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/etc/Makeconf:200: RcppExports.o] Abort trap: 6 + ERROR: compilation failed for package ccfindR + * removing /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/ccfindR + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ccfindr/meta.yaml b/recipes/bioconductor-ccfindr/meta.yaml index 8669dd286eaa1..885a9ad43f114 100644 --- a/recipes/bioconductor-ccfindr/meta.yaml +++ b/recipes/bioconductor-ccfindr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ccfindR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8862cd343902a030a29603942d4dede8 + md5: 0a0dd7c35273c39673f992bed7fa952d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccfindr", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown +# SystemRequirements: gsl requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-gtools @@ -36,10 +38,11 @@ requirements: - r-rtsne - libblas - liblapack + - gsl run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-gtools @@ -51,6 +54,7 @@ requirements: - 'r-rdpack >=0.7' - r-rmpi - r-rtsne + - gsl build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-ccimpute/meta.yaml b/recipes/bioconductor-ccimpute/meta.yaml index 21b4a6711e712..14e1190d5d502 100644 --- a/recipes/bioconductor-ccimpute/meta.yaml +++ b/recipes/bioconductor-ccimpute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "ccImpute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 890c259cabc9cd35bab959d4f698f5d9 + md5: f402177e3fc7bbbcac504c956889dfa9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccimpute", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, SingleCellExperiment, mclust, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-simlr >=1.26.0,<1.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-simlr >=1.28.0,<1.29.0' - r-base - r-matrixstats - r-rcpp @@ -29,8 +30,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-simlr >=1.26.0,<1.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-simlr >=1.28.0,<1.29.0' - r-base - r-matrixstats - r-rcpp diff --git a/recipes/bioconductor-ccl4/meta.yaml b/recipes/bioconductor-ccl4/meta.yaml index d9f85af551bc9..6179644dbc14d 100644 --- a/recipes/bioconductor-ccl4/meta.yaml +++ b/recipes/bioconductor-ccl4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CCl4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0bfca2abdda039b9376e9cc8ec71333 + md5: 3247cf1db347f959d908e88b5e8febb5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccl4", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ccl4/post-link.sh b/recipes/bioconductor-ccl4/post-link.sh index e2e4e1647ae6f..8bd8b92dae2ca 100644 --- a/recipes/bioconductor-ccl4/post-link.sh +++ b/recipes/bioconductor-ccl4/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ccl4-1.38.0" +installBiocDataPackage.sh "ccl4-1.40.0" diff --git a/recipes/bioconductor-ccmap/meta.yaml b/recipes/bioconductor-ccmap/meta.yaml index c073c4775e256..765e1c9c198f5 100644 --- a/recipes/bioconductor-ccmap/meta.yaml +++ b/recipes/bioconductor-ccmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ccmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a1587c139647a148d00e216b0fc9653d + md5: d01f3e9dca6ce3403096f8fc00766755 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccmap", max_pin="x.x") }}' noarch: generic # Suggests: crossmeta, knitr, rmarkdown, testthat, lydata requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-ccdata >=1.26.0,<1.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-ccdata >=1.28.0,<1.29.0' - r-base - 'r-biocmanager >=1.30.4' - 'r-data.table >=1.10.4' @@ -31,8 +32,8 @@ requirements: - 'r-lsa >=0.73.1' - 'r-xgboost >=0.6.4' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-ccdata >=1.26.0,<1.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-ccdata >=1.28.0,<1.29.0' - r-base - 'r-biocmanager >=1.30.4' - 'r-data.table >=1.10.4' diff --git a/recipes/bioconductor-ccplotr/build.sh b/recipes/bioconductor-ccplotr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ccplotr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ccplotr/meta.yaml b/recipes/bioconductor-ccplotr/meta.yaml new file mode 100644 index 0000000000000..550ccfa7556d0 --- /dev/null +++ b/recipes/bioconductor-ccplotr/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.0.0" %} +{% set name = "CCPlotR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 913896518f29cd88d7ac9d57298f44de +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccplotr", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - r-base + - r-circlize + - r-dplyr + - r-forcats + - r-ggbump + - r-ggh4x + - r-ggplot2 + - r-ggraph + - r-ggtext + - r-igraph + - r-patchwork + - r-plyr + - r-rcolorbrewer + - r-scales + - r-scatterpie + - r-stringr + - r-tibble + - r-tidyr + - r-viridis + run: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - r-base + - r-circlize + - r-dplyr + - r-forcats + - r-ggbump + - r-ggh4x + - r-ggplot2 + - r-ggraph + - r-ggtext + - r-igraph + - r-patchwork + - r-plyr + - r-rcolorbrewer + - r-scales + - r-scatterpie + - r-stringr + - r-tibble + - r-tidyr + - r-viridis +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Plots For Visualising Cell-Cell Interactions' + description: 'CCPlotR is an R package for visualising results from tools that predict cell-cell interactions from single-cell RNA-seq data. These plots are generic and can be used to visualise results from multiple tools such as Liana, CellPhoneDB, NATMI etc.' + license_file: LICENSE + diff --git a/recipes/bioconductor-ccpromise/build_failure.linux-64.yaml b/recipes/bioconductor-ccpromise/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..72fc0dc3a0c09 --- /dev/null +++ b/recipes/bioconductor-ccpromise/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 722fb617600a55303b535b784f5387ef700db6e8486e427c054d57fb5deff1b6 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.3s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.4s + [2K[1A[2K[0Gconda-forge/linux-64 + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.1MB/s 0.0s + [?25hMamba failed to solve: + - r-base 4.3.* + - r-ccp + - bioconductor-biobase >=2.62.0,<2.63.0 + - bioconductor-gseabase >=1.64.0,<1.65.0 + - bioconductor-promise >=1.54.0,<1.55.0 + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-promise >=1.54.0,<1.55.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-base 4.3.* + - r-ccp + - bioconductor-biobase >=2.62.0,<2.63.0 + - bioconductor-gseabase >=1.64.0,<1.65.0 + - bioconductor-promise >=1.54.0,<1.55.0 + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-promise >=1.54.0,<1.55.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-promise[version='>=1.54.0,<1.55.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ccpromise/meta.yaml b/recipes/bioconductor-ccpromise/meta.yaml index f24d2e72bf027..a9de2cd528f55 100644 --- a/recipes/bioconductor-ccpromise/meta.yaml +++ b/recipes/bioconductor-ccpromise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "CCPROMISE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1efc8cd0ffc5444554a53bb13b32d2f4 + md5: 1b85c7bbed3be474abf4e4591882abdf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ccpromise", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-promise >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-promise >=1.54.0,<1.55.0' - r-base - r-ccp run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-promise >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-promise >=1.54.0,<1.55.0' - r-base - r-ccp test: diff --git a/recipes/bioconductor-cctutorial/meta.yaml b/recipes/bioconductor-cctutorial/meta.yaml index a679a121002ad..ba960ac374091 100644 --- a/recipes/bioconductor-cctutorial/meta.yaml +++ b/recipes/bioconductor-cctutorial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ccTutorial" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6515deef368eb06b2f0aabaa069b3f63 + md5: 20af731ec83a03f12ec5d87060f5d168 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cctutorial", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, Biobase(>= 2.5.5), xtable requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cctutorial/post-link.sh b/recipes/bioconductor-cctutorial/post-link.sh index b0c9b061fbc1f..3acf97540ef0e 100644 --- a/recipes/bioconductor-cctutorial/post-link.sh +++ b/recipes/bioconductor-cctutorial/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cctutorial-1.38.0" +installBiocDataPackage.sh "cctutorial-1.40.0" diff --git a/recipes/bioconductor-cdi/build.sh b/recipes/bioconductor-cdi/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cdi/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cdi/meta.yaml b/recipes/bioconductor-cdi/meta.yaml new file mode 100644 index 0000000000000..10184abeabdbc --- /dev/null +++ b/recipes/bioconductor-cdi/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.2" %} +{% set name = "CDI" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 64ebd520b0ba4613c3bddf06bb82dbc0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cdi", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-ggsci + - r-matrixstats + - r-reshape2 + - r-seurat + - r-seuratobject + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-ggsci + - r-matrixstats + - r-reshape2 + - r-seurat + - r-seuratobject +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Clustering Deviation Index (CDI)' + description: 'Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be accurate. However, there have not been unsupervised metric designed for scRNA-seq to evaluate clustering performance. Hence, we propose clustering deviation index (CDI), an unsupervised metric based on the modeling of scRNA-seq UMI counts to evaluate clustering of cells.' + license_file: LICENSE + diff --git a/recipes/bioconductor-celaref/meta.yaml b/recipes/bioconductor-celaref/meta.yaml index 58aa2360a02dc..f3530a6b4cb5d 100644 --- a/recipes/bioconductor-celaref/meta.yaml +++ b/recipes/bioconductor-celaref/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "celaref" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d4e594ba701e701ca005234d6224c518 + md5: 8c168c1e505d63f6372d6baac7051a06 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celaref", max_pin="x.x") }}' noarch: generic # Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -35,11 +36,11 @@ requirements: - r-rlang - r-tibble run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-celarefdata/meta.yaml b/recipes/bioconductor-celarefdata/meta.yaml index 95c7c8450dbb2..5babbe3604e80 100644 --- a/recipes/bioconductor-celarefdata/meta.yaml +++ b/recipes/bioconductor-celarefdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "celarefData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb23383ea6cb3e84ef6c66f0617cc69e + md5: 6864c27f1d574314fe10612b37f6c433 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celarefdata", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHub, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celarefdata/post-link.sh b/recipes/bioconductor-celarefdata/post-link.sh index f4fd72ae7f3c6..da558cc839610 100644 --- a/recipes/bioconductor-celarefdata/post-link.sh +++ b/recipes/bioconductor-celarefdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "celarefdata-1.18.0" +installBiocDataPackage.sh "celarefdata-1.20.0" diff --git a/recipes/bioconductor-celda/meta.yaml b/recipes/bioconductor-celda/meta.yaml index c6993b5108ae5..921775f6f1896 100644 --- a/recipes/bioconductor-celda/meta.yaml +++ b/recipes/bioconductor-celda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.1" %} {% set name = "celda" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7f8c768ce0dd749d8f815232bfe0977e + md5: 5b60cdee9ee9cbb13f4af0a40abdd177 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celda", max_pin="x.x") }}' # Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-data.table @@ -37,11 +38,11 @@ requirements: - r-foreach - r-ggplot2 - r-ggrepel + - r-gridextra - r-gtable - r-matrix - r-matrixstats - r-mcmcprecision - - r-multipanelfigure - r-plyr - r-rcolorbrewer - r-rcpp @@ -55,13 +56,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-data.table @@ -72,11 +73,11 @@ requirements: - r-foreach - r-ggplot2 - r-ggrepel + - r-gridextra - r-gtable - r-matrix - r-matrixstats - r-mcmcprecision - - r-multipanelfigure - r-plyr - r-rcolorbrewer - r-rcpp diff --git a/recipes/bioconductor-celegans.db/meta.yaml b/recipes/bioconductor-celegans.db/meta.yaml index 6dc9527545231..ea39dc2bada5e 100644 --- a/recipes/bioconductor-celegans.db/meta.yaml +++ b/recipes/bioconductor-celegans.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "celegans.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3cfa9df5a81ef538a890ed8c5d5a98ad build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celegans.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.ce.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.ce.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celeganscdf/meta.yaml b/recipes/bioconductor-celeganscdf/meta.yaml index eea808835386d..3e1337bd905c5 100644 --- a/recipes/bioconductor-celeganscdf/meta.yaml +++ b/recipes/bioconductor-celeganscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "celeganscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1098cd99bfc5000bf9858e4a3acaf452 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celeganscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celegansprobe/meta.yaml b/recipes/bioconductor-celegansprobe/meta.yaml index eed0867c6997e..b1c063a28735f 100644 --- a/recipes/bioconductor-celegansprobe/meta.yaml +++ b/recipes/bioconductor-celegansprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "celegansprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7454bba10ff2dd7c03bfe0f9d450f148 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celegansprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cellarepertorium/meta.yaml b/recipes/bioconductor-cellarepertorium/meta.yaml index d3550262c3003..26cde2ad158a4 100644 --- a/recipes/bioconductor-cellarepertorium/meta.yaml +++ b/recipes/bioconductor-cellarepertorium/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "CellaRepertorium" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51d58a44ea2047858aa0a1c0453290d6 + md5: eceb5905cee5e0f9b9ba1ea47db2f1d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellarepertorium", max_pin="x.x") }}' # Suggests: testthat, readr, knitr, rmarkdown, ggplot2, BiocStyle, ggdendro, broom, lme4, RColorBrewer, SingleCellExperiment, scater, broom.mixed, cowplot, igraph, ggraph requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-forcats @@ -40,9 +41,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-forcats diff --git a/recipes/bioconductor-cellbarcode/meta.yaml b/recipes/bioconductor-cellbarcode/meta.yaml index c412436d62627..27da6a1d0c2b9 100644 --- a/recipes/bioconductor-cellbarcode/meta.yaml +++ b/recipes/bioconductor-cellbarcode/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "CellBarcode" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b1eac1414aa90b4f31efa4acfbed68a + md5: d219d9d5c998fda5f5c02f817361c56a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellbarcode", max_pin="x.x") }}' # Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-ckmeans.1d.dp @@ -38,10 +39,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-ckmeans.1d.dp @@ -64,6 +65,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Cellular DNA Barcode Analysis toolkit' - description: 'This package performs Cellular DNA Barcode (genetic lineage tracing) analysis. The package can handle all kinds of DNA barcodes, as long as the barcode within a single sequencing read and has a pattern which can be matched by a regular expression. This package can handle barcode with flexible length, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing of some amplicon sequencing such as CRISPR gRNA screening, immune repertoire sequencing and meta genome data.' + description: 'The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.' license_file: LICENSE diff --git a/recipes/bioconductor-cellbaser/meta.yaml b/recipes/bioconductor-cellbaser/meta.yaml index bb9f42a99f6bc..a80228b09d7cc 100644 --- a/recipes/bioconductor-cellbaser/meta.yaml +++ b/recipes/bioconductor-cellbaser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "cellbaseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc80944f26d7d766c213f9330e8093ad + md5: 1540f788e9e1fba133da3a369fe2c8b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellbaser", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-data.table - r-doparallel @@ -33,8 +34,8 @@ requirements: - r-r.utils - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-cellbench/meta.yaml b/recipes/bioconductor-cellbench/meta.yaml index 18127f02e607d..6dbd1f801f5e5 100644 --- a/recipes/bioconductor-cellbench/meta.yaml +++ b/recipes/bioconductor-cellbench/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CellBench" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55a020a53f4d16c4df41022b0287f5dd + md5: 21b854517881e111491fd4b6dba0857c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellbench", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-assertthat - r-base - r-dplyr @@ -39,10 +40,10 @@ requirements: - r-tidyr - r-tidyselect run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-celldex/meta.yaml b/recipes/bioconductor-celldex/meta.yaml index 68406f4d3d174..36ae84f27c872 100644 --- a/recipes/bioconductor-celldex/meta.yaml +++ b/recipes/bioconductor-celldex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "celldex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fef4f15bc2e0a7427627cf1cd7d505dc + md5: 62419c915beb91f7c228e1a125df68f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celldex", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, DT, ensembldb requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-celldex/post-link.sh b/recipes/bioconductor-celldex/post-link.sh index a789c0707212f..d36c9de2e3d47 100644 --- a/recipes/bioconductor-celldex/post-link.sh +++ b/recipes/bioconductor-celldex/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "celldex-1.10.1" +installBiocDataPackage.sh "celldex-1.12.0" diff --git a/recipes/bioconductor-cellhts2/meta.yaml b/recipes/bioconductor-cellhts2/meta.yaml index 187d6f7e88090..9ea087124a5a1 100644 --- a/recipes/bioconductor-cellhts2/meta.yaml +++ b/recipes/bioconductor-cellhts2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.64.0" %} +{% set version = "2.66.0" %} {% set name = "cellHTS2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ba5f251e1fea747094ba827c4bd82eb + md5: 6f9dfcbf4583db914d89c9310e207c02 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellhts2", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-hwriter - r-locfit - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-hwriter - r-locfit diff --git a/recipes/bioconductor-cellid/meta.yaml b/recipes/bioconductor-cellid/meta.yaml index 656b75d49abd3..7aff6e471d46e 100644 --- a/recipes/bioconductor-cellid/meta.yaml +++ b/recipes/bioconductor-cellid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.1" %} {% set name = "CelliD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 65cfdcb7f5d87427061399fc6603eeea + md5: 91ef83db3f348575f3b90cf4c3753806 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellid", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-fastmatch @@ -45,11 +46,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-fastmatch diff --git a/recipes/bioconductor-cellity/meta.yaml b/recipes/bioconductor-cellity/meta.yaml index c5cf38ca92df6..3f533b5866143 100644 --- a/recipes/bioconductor-cellity/meta.yaml +++ b/recipes/bioconductor-cellity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "cellity" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aadb0954509cd1a297ab1adf15449b30 + md5: c6680442e176cef832fc19d82d49815a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellity", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, caret, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-e1071 - r-ggplot2 - r-mvoutlier - r-robustbase run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-e1071 - r-ggplot2 diff --git a/recipes/bioconductor-cellmapper/meta.yaml b/recipes/bioconductor-cellmapper/meta.yaml index 968c4f0352fd2..6cfb167524086 100644 --- a/recipes/bioconductor-cellmapper/meta.yaml +++ b/recipes/bioconductor-cellmapper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "CellMapper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 93d1fccce26fd0fb0d31bc0a89fdbb95 + md5: ca94af55dbc55bb2bf40c69f4965b553 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellmapper", max_pin="x.x") }}' noarch: generic # Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-cellmapperdata/meta.yaml b/recipes/bioconductor-cellmapperdata/meta.yaml index 45e0955d8f3f6..694aa257b25ef 100644 --- a/recipes/bioconductor-cellmapperdata/meta.yaml +++ b/recipes/bioconductor-cellmapperdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "CellMapperData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9d311ad83cec787788c967e93cb290b + md5: 5db37729dd49f26b6cba9ff4aff80b1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellmapperdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-cellmapper >=1.26.0,<1.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-cellmapper >=1.28.0,<1.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-cellmapper >=1.26.0,<1.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-cellmapper >=1.28.0,<1.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cellmapperdata/post-link.sh b/recipes/bioconductor-cellmapperdata/post-link.sh index 7963c56d1b0c3..a5db39ff29df7 100644 --- a/recipes/bioconductor-cellmapperdata/post-link.sh +++ b/recipes/bioconductor-cellmapperdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cellmapperdata-1.26.0" +installBiocDataPackage.sh "cellmapperdata-1.28.0" diff --git a/recipes/bioconductor-cellmigration/meta.yaml b/recipes/bioconductor-cellmigration/meta.yaml index e7215a9ecab0c..c4b413d5dc107 100644 --- a/recipes/bioconductor-cellmigration/meta.yaml +++ b/recipes/bioconductor-cellmigration/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "cellmigRation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f8e86c8cdb38e015e3a1b5927b834cf + md5: 61fc4a74a41e132fc3b760bc444ee5d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellmigration", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl requirements: diff --git a/recipes/bioconductor-cellmixs/meta.yaml b/recipes/bioconductor-cellmixs/meta.yaml index d088721b9191d..fbf1f4f06dd59 100644 --- a/recipes/bioconductor-cellmixs/meta.yaml +++ b/recipes/bioconductor-cellmixs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CellMixS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9882807e195ad678d59c5ef5704bd943 + md5: 67910c3dc01e01dc6be6ca3bb76d7794 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellmixs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -38,12 +39,12 @@ requirements: - r-tidyr - r-viridis run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr diff --git a/recipes/bioconductor-cellnoptr/meta.yaml b/recipes/bioconductor-cellnoptr/meta.yaml index 87c2f623319aa..c4a20e64f1c8a 100644 --- a/recipes/bioconductor-cellnoptr/meta.yaml +++ b/recipes/bioconductor-cellnoptr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "CellNOptR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09bf4fd709ce09ae2e28a60dbe412832 + md5: 22ea1e446726e7b83f26f1f5f614d74f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellnoptr", max_pin="x.x") }}' # Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, # SystemRequirements: Graphviz version >= 2.2 requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-igraph @@ -36,9 +37,9 @@ requirements: - liblapack - 'graphviz >=2.2' run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-igraph diff --git a/recipes/bioconductor-cellscore/meta.yaml b/recipes/bioconductor-cellscore/meta.yaml index 089bf0bf98800..91e7ab9ca06b4 100644 --- a/recipes/bioconductor-cellscore/meta.yaml +++ b/recipes/bioconductor-cellscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CellScore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: afb6d50cd4f4d6af1da07504b10d0650 + md5: c842a56a0f5067b891a0ab7c9f9b1e21 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellscore", max_pin="x.x") }}' noarch: generic -# Suggests: hgu133plus2CellScore, knitr +# Suggests: hgu133plus2CellScore, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-gplots >=3.0.1' - 'r-lsa >=0.73.1' - 'r-rcolorbrewer >=1.1-2' - 'r-squash >=1.0.8' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-gplots >=3.0.1' - 'r-lsa >=0.73.1' diff --git a/recipes/bioconductor-celltrails/meta.yaml b/recipes/bioconductor-celltrails/meta.yaml index ebd283155d0a6..81e50c10fe30a 100644 --- a/recipes/bioconductor-celltrails/meta.yaml +++ b/recipes/bioconductor-celltrails/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "CellTrails" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a9fc651c79c87dc1f49947350f660f6 + md5: 87b23b653d772f9b436b655e5e8af5ae build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-celltrails", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cba - r-dendextend @@ -38,10 +39,10 @@ requirements: - r-reshape2 - r-rtsne run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cba - r-dendextend diff --git a/recipes/bioconductor-cellxgenedp/meta.yaml b/recipes/bioconductor-cellxgenedp/meta.yaml index 331dfc1cac7e3..52a8b40eb76cb 100644 --- a/recipes/bioconductor-cellxgenedp/meta.yaml +++ b/recipes/bioconductor-cellxgenedp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.1" %} {% set name = "cellxgenedp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eadf41eb26e97613a500fa73807a60f5 + md5: dc1730a545f49b0b8c14991289f29a6b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cellxgenedp", max_pin="x.x") }}' noarch: generic # Suggests: zellkonverter, SingleCellExperiment, HDF5Array, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery requirements: diff --git a/recipes/bioconductor-cemitool/meta.yaml b/recipes/bioconductor-cemitool/meta.yaml index 911aa97898ae0..0b2b39b75ff26 100644 --- a/recipes/bioconductor-cemitool/meta.yaml +++ b/recipes/bioconductor-cemitool/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "CEMiTool" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 513c292bb3582042a443b20930d66aec + md5: df823e2602a3b994f889644e39e0eb8f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cemitool", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocManager requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - 'r-data.table >=1.9.4' - r-dplyr @@ -48,8 +49,8 @@ requirements: - r-stringr - r-wgcna run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - 'r-data.table >=1.9.4' - r-dplyr diff --git a/recipes/bioconductor-censcyt/meta.yaml b/recipes/bioconductor-censcyt/meta.yaml index 184a5c03e98bd..5ed00b98241a1 100644 --- a/recipes/bioconductor-censcyt/meta.yaml +++ b/recipes/bioconductor-censcyt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "censcyt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 25c65055473214240eb1102ffa7b39b1 + md5: e5f2a60dcafc6d878e1e97e85768f078 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-censcyt", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom.mixed - r-dirmult @@ -43,11 +44,11 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom.mixed - r-dirmult diff --git a/recipes/bioconductor-cepo/build_failure.linux-64.yaml b/recipes/bioconductor-cepo/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5ac0014c0d22a --- /dev/null +++ b/recipes/bioconductor-cepo/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b904f129759930c0079c8f1858105b52b54ce300d7c837bd4c417f305be8d2d0 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.2.3-pyhd8ed1ab_0 conda-forge + zlib: 1.2.13-hd590300_5 conda-forge + zstd: 1.5.5-hfc55251_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + [34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.1MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.4MB/s 0.0s + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.0MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.9MB/s 0.0s + [?25h + ## Package Plan ## + + environment location: /opt/conda/conda-bld/bioconductor-cepo_1703278295981/_build_env + + + Source cache directory is: /opt/conda/conda-bld/src_cache + INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: Cepo_1.8.0_9eee9f73ec.tar.gz + INFO:conda_build.source:Downloading source to cache: Cepo_1.8.0_9eee9f73ec.tar.gz + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Cepo_1.8.0.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Cepo_1.8.0.tar.gz + Success + INFO:conda_build.source:Success + Extracting download + source tree in: /opt/conda/conda-bld/bioconductor-cepo_1703278295981/work + export PREFIX=/opt/conda/conda-bld/bioconductor-cepo_1703278295981/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-cepo_1703278295981/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-cepo_1703278295981/work + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-cepo_1703278295981/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/library + * installing *source* package Cepo ... + ** using staged installation + ** R + ** data + ** inst + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** help + *** installing help indices + *** copying figures + ** building package indices + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** installing vignettes + ** testing if installed package can be loaded from temporary location + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** testing if installed package can be loaded from final location + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** testing if installed package keeps a record of temporary installation path + * creating tarball + packaged installation of Cepo as Cepo_1.8.0_R_x86_64-conda-linux-gnu.tar.gz + * DONE (Cepo) + + Resource usage statistics from building bioconductor-cepo: + Process count: 6 + CPU time: Sys=0:00:02.4, User=0:00:20.2 + Memory: 733.9M + Disk usage: 6.8K + Time elapsed: 0:00:27.8 + + + Packaging bioconductor-cepo + INFO:conda_build.build:Packaging bioconductor-cepo + Packaging bioconductor-cepo-1.8.0-r43hdfd78af_0 + INFO:conda_build.build:Packaging bioconductor-cepo-1.8.0-r43hdfd78af_0 + number of files: 30 + Fixing permissions + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2358, in build + newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1672, in bundle_conda + output['checksums'] = create_info_files(metadata, replacements, files, prefix=metadata.config.host_prefix) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1272, in create_info_files + copy_license(m) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 762, in copy_license + generic_copy(m, "license", "license_file") + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 800, in generic_copy + raise ValueError( + ValueError: License file given in about/license_file (/opt/recipe/LICENSE) does not exist in source root dir or in recipe root dir (with meta.yaml) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-cepo/meta.yaml b/recipes/bioconductor-cepo/meta.yaml index b7de86cbeccc6..3e7d32bc32c6d 100644 --- a/recipes/bioconductor-cepo/meta.yaml +++ b/recipes/bioconductor-cepo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "Cepo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa0bd806c84f9024c965b3de7bc6652b + md5: 9eee9f73ecd4d7dd782d14db0f60bd1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cepo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap, patchwork requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -36,14 +37,14 @@ requirements: - r-reshape2 - r-rlang run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -58,4 +59,5 @@ about: license: 'MIT + file LICENSE' summary: 'Cepo for the identification of differentially stable genes' description: 'Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.' + license_file: LICENSE diff --git a/recipes/bioconductor-cernanetsim/meta.yaml b/recipes/bioconductor-cernanetsim/meta.yaml index 49f97e8b5f8fe..06a85239a44fc 100644 --- a/recipes/bioconductor-cernanetsim/meta.yaml +++ b/recipes/bioconductor-cernanetsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ceRNAnetsim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3bd2c6360a6a11df8ccce61557d105dd + md5: 7a406a65a3e7bad478149f1587317a79 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cernanetsim", max_pin="x.x") }}' noarch: generic # Suggests: knitr, png, rmarkdown, testthat, covr requirements: diff --git a/recipes/bioconductor-cetf/meta.yaml b/recipes/bioconductor-cetf/meta.yaml index 35bc561332f75..a5a4a5da234e4 100644 --- a/recipes/bioconductor-cetf/meta.yaml +++ b/recipes/bioconductor-cetf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "CeTF" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e155847761cb9f297650b789c967ff7 + md5: b79bf3680b81b7b6945eef89f6babfc1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cetf", max_pin="x.x") }}' # Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat # SystemRequirements: libcurl4-openssl-dev, libxml2-dev, libssl-dev, gfortran, build-essential, libz-dev, zlib1g-dev requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr @@ -44,12 +45,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr diff --git a/recipes/bioconductor-cexor/meta.yaml b/recipes/bioconductor-cexor/meta.yaml index aac4f37c1f333..50afffdcd92be 100644 --- a/recipes/bioconductor-cexor/meta.yaml +++ b/recipes/bioconductor-cexor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CexoR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32ef736b70fcc811be756cbed73445c3 + md5: 53f7febbb51a7f925322329e89a8d619 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cexor", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-idr - r-rcolorbrewer run: - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-idr - r-rcolorbrewer diff --git a/recipes/bioconductor-cfassay/meta.yaml b/recipes/bioconductor-cfassay/meta.yaml index c8587570ddc98..96259a3f1aed1 100644 --- a/recipes/bioconductor-cfassay/meta.yaml +++ b/recipes/bioconductor-cfassay/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "CFAssay" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3fbd8b4078901da0139a5fc27d56cda8 + md5: 122c969248ffd92330d93a266db6cb3c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cfassay", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-cfdnakit/build.sh b/recipes/bioconductor-cfdnakit/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cfdnakit/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cfdnakit/meta.yaml b/recipes/bioconductor-cfdnakit/meta.yaml new file mode 100644 index 0000000000000..b7735232ce60f --- /dev/null +++ b/recipes/bioconductor-cfdnakit/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.0.0" %} +{% set name = "cfdnakit" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 967a84e96d20af4a0256e117afe272b7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cfdnakit", max_pin="x.x") }}' + noarch: generic +# Suggests: rmarkdown, knitr, roxygen2, BiocStyle +requirements: + host: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-pscbs + - r-rlang + run: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-pscbs + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)' + description: 'This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-cfdnapro/meta.yaml b/recipes/bioconductor-cfdnapro/meta.yaml index 55bda26419c1f..1b8813dc37295 100644 --- a/recipes/bioconductor-cfdnapro/meta.yaml +++ b/recipes/bioconductor-cfdnapro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "cfDNAPro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80295d2e20980978b268c420ee6c5acd + md5: 377fb633e850fcef49fbe86f3c4d1505 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cfdnapro", max_pin="x.x") }}' noarch: generic # Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ncbi.grch38 >=1.3.0,<1.4.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-dplyr >=0.8.3' - 'r-ggplot2 >=3.2.1' @@ -40,16 +41,16 @@ requirements: - 'r-stringr >=1.4.0' - r-tibble run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ncbi.grch38 >=1.3.0,<1.4.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-dplyr >=0.8.3' - 'r-ggplot2 >=3.2.1' diff --git a/recipes/bioconductor-cftools/meta.yaml b/recipes/bioconductor-cftools/meta.yaml index 325303e6f60fc..7ad4099a140e5 100644 --- a/recipes/bioconductor-cftools/meta.yaml +++ b/recipes/bioconductor-cftools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "cfTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc30acea96850944e511ea4bbf58e266 + md5: cf0f03a9654984b3214bcadac889fc28 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cftools", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-cftoolsdata >=1.0.0,<1.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-bh - r-r.utils @@ -29,8 +31,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-cftoolsdata >=1.0.0,<1.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-bh - r-r.utils diff --git a/recipes/bioconductor-cftoolsdata/meta.yaml b/recipes/bioconductor-cftoolsdata/meta.yaml new file mode 100644 index 0000000000000..4150a2a029bdb --- /dev/null +++ b/recipes/bioconductor-cftoolsdata/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.0" %} +{% set name = "cfToolsData" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 00bbf328a45fb8731b3c7262b3521e0b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cftoolsdata", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - r-base + run: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'ExperimentHub data for the cfTools package' + description: 'The cfToolsData package supplies the data for the cfTools package. It contains two pre-trained deep neural network (DNN) models for the cfSort function. Additionally, it includes the shape parameters of beta distribution characterizing methylation markers associated with four tumor types for the CancerDetector function, as well as the parameters characterizing methylation markers specific to 29 primary human tissue types for the cfDeconvolve function.' + license_file: LICENSE + diff --git a/recipes/bioconductor-cftoolsdata/post-link.sh b/recipes/bioconductor-cftoolsdata/post-link.sh new file mode 100644 index 0000000000000..76ff4ad0b782b --- /dev/null +++ b/recipes/bioconductor-cftoolsdata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "cftoolsdata-1.0.0" diff --git a/recipes/bioconductor-cftoolsdata/pre-unlink.sh b/recipes/bioconductor-cftoolsdata/pre-unlink.sh new file mode 100644 index 0000000000000..d8e309e01fa6c --- /dev/null +++ b/recipes/bioconductor-cftoolsdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cfToolsData diff --git a/recipes/bioconductor-cgen/meta.yaml b/recipes/bioconductor-cgen/meta.yaml index a45300a10267c..cc332a3a96b16 100644 --- a/recipes/bioconductor-cgen/meta.yaml +++ b/recipes/bioconductor-cgen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.36.1" %} +{% set version = "3.38.0" %} {% set name = "CGEN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0092d5b8a0127b2ad4b803fc41289f08 + md5: e62dd5874cfcaab65414fff648106633 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cgen", max_pin="x.x") }}' # Suggests: cluster requirements: host: diff --git a/recipes/bioconductor-cghbase/meta.yaml b/recipes/bioconductor-cghbase/meta.yaml index d4196e9ebd2df..6a9c029f439be 100644 --- a/recipes/bioconductor-cghbase/meta.yaml +++ b/recipes/bioconductor-cghbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "CGHbase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ac037567f6cec96bce84af4382d7481 + md5: 806f73dc042c0bf46989606a4aa4dbe8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cghbase", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-cghcall/meta.yaml b/recipes/bioconductor-cghcall/meta.yaml index 2ee30e29f42cf..0177f0dccb3bc 100644 --- a/recipes/bioconductor-cghcall/meta.yaml +++ b/recipes/bioconductor-cghcall/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.62.0" %} +{% set version = "2.64.0" %} {% set name = "CGHcall" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a593c642a5f01c37fd60caece6363f87 + md5: 7a43fd6ae1e6c288b98abd2b8824fed4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cghcall", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-snowfall run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-snowfall test: diff --git a/recipes/bioconductor-cghmcr/meta.yaml b/recipes/bioconductor-cghmcr/meta.yaml index ebda3d6609810..ed85eb3edecc1 100644 --- a/recipes/bioconductor-cghmcr/meta.yaml +++ b/recipes/bioconductor-cghmcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "cghMCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4df2110576ea48c62099f7eafb985866 + md5: b3db4bfc3f23e690592a37414db360c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cghmcr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cntools >=1.56.0,<1.57.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cntools >=1.58.0,<1.59.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cntools >=1.56.0,<1.57.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cntools >=1.58.0,<1.59.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-cghnormaliter/meta.yaml b/recipes/bioconductor-cghnormaliter/meta.yaml index b7cf959966a85..b09f4d2b885e1 100644 --- a/recipes/bioconductor-cghnormaliter/meta.yaml +++ b/recipes/bioconductor-cghnormaliter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "CGHnormaliter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab70a4d3f244ab250b735ad3b1fbbbd2 + md5: 948d3af66840226e7095e46d281df177 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cghnormaliter", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-cghregions/meta.yaml b/recipes/bioconductor-cghregions/meta.yaml index e3f1c469919d2..d10ed89bd1358 100644 --- a/recipes/bioconductor-cghregions/meta.yaml +++ b/recipes/bioconductor-cghregions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "CGHregions" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e445f33fe45b3f9773e5b433ab94c0aa + md5: 3ec8f1bb5db1987f92932d29a31d74fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cghregions", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-champdata/meta.yaml b/recipes/bioconductor-champdata/meta.yaml index 0bb20b2c6c55e..7e32b96919117 100644 --- a/recipes/bioconductor-champdata/meta.yaml +++ b/recipes/bioconductor-champdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "ChAMPdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf36209a25e3dbc4c8098a3fcb3327df + md5: b12bfec01a1cfdd103bc0cb9bd44d4aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-champdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-champdata/post-link.sh b/recipes/bioconductor-champdata/post-link.sh index 4d1b7c8156bb8..af3862f5f24b1 100644 --- a/recipes/bioconductor-champdata/post-link.sh +++ b/recipes/bioconductor-champdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "champdata-2.32.0" +installBiocDataPackage.sh "champdata-2.34.0" diff --git a/recipes/bioconductor-chemminedrugs/meta.yaml b/recipes/bioconductor-chemminedrugs/meta.yaml index dcf2b0360e313..97651c57e2bbe 100644 --- a/recipes/bioconductor-chemminedrugs/meta.yaml +++ b/recipes/bioconductor-chemminedrugs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "ChemmineDrugs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,25 +13,26 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2a3646e5173e93080fb5b49564f5d545 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chemminedrugs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitcitations,knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-rsqlite run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chemmineob/build.sh b/recipes/bioconductor-chemmineob/build.sh index 9ee117c0e7115..ee892d72037fc 100644 --- a/recipes/bioconductor-chemmineob/build.sh +++ b/recipes/bioconductor-chemmineob/build.sh @@ -8,4 +8,4 @@ CXX=$CXX -I$PREFIX/include/openbabel3 -I$PREFIX/include/eigen3 -L$PREFIX/lib CXX98=$CXX CXX11=$CXX CXX14=$CXX -I$PREFIX/include/openbabel3 -I$PREFIX/include/eigen3 -L$PREFIX/lib" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chemmineob/meta.yaml b/recipes/bioconductor-chemmineob/meta.yaml index 0b1c018320b76..e143fc83685a4 100644 --- a/recipes/bioconductor-chemmineob/meta.yaml +++ b/recipes/bioconductor-chemmineob/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ChemmineOB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,7 +11,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d721ca0fa36f8b42fecca0ab4f98910 + md5: 5bd759ca398ffb70214a8076028bf0b2 patches: - patch build: @@ -19,12 +19,13 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chemmineob", max_pin="x.x") }}' # Suggests: ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager, rmarkdown,RUnit # SystemRequirements: OpenBabel (>= 3.0.0) with headers (http://openbabel.org). Eigen3 with headers. requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - 'r-rcpp >=0.11.0' @@ -33,8 +34,8 @@ requirements: - openbabel >=3 - eigen run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - 'r-rcpp >=0.11.0' diff --git a/recipes/bioconductor-chemminer/meta.yaml b/recipes/bioconductor-chemminer/meta.yaml index 99ce170bcdabf..dec3edb5902fc 100644 --- a/recipes/bioconductor-chemminer/meta.yaml +++ b/recipes/bioconductor-chemminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.52.0" %} +{% set version = "3.54.0" %} {% set name = "ChemmineR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54601905e8a4a48d85b3c7a80f935eb5 + md5: 8dd1886811bdc4ac23c24fad60a9b238 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chemminer", max_pin="x.x") }}' # Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-base64enc - r-bh @@ -40,7 +41,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-base64enc - r-bh diff --git a/recipes/bioconductor-chetah/meta.yaml b/recipes/bioconductor-chetah/meta.yaml index d31c3271649f8..2dca0e66b8dbe 100644 --- a/recipes/bioconductor-chetah/meta.yaml +++ b/recipes/bioconductor-chetah/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CHETAH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0312f98ec3d18db1839da7f6980cf4d6 + md5: a6b920a4a3f3f931acb3cd950c7a74c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chetah", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr requirements: host: - - 'bioconductor-biodist >=1.72.0,<1.73.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biodist >=1.74.0,<1.75.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-corrplot - r-cowplot @@ -35,10 +36,10 @@ requirements: - r-reshape2 - r-shiny run: - - 'bioconductor-biodist >=1.72.0,<1.73.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biodist >=1.74.0,<1.75.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-corrplot - r-cowplot diff --git a/recipes/bioconductor-chic.data/meta.yaml b/recipes/bioconductor-chic.data/meta.yaml index 4a8fcf87e3a4f..f99fd578b9c16 100644 --- a/recipes/bioconductor-chic.data/meta.yaml +++ b/recipes/bioconductor-chic.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ChIC.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c846395a170d9e1601f20f2250b5b3e2 + md5: 34b50ea53e6b5c982dc044addc68c33b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chic.data", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' - r-base - 'r-caret >=6.0-78' - r-randomforest run: - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' - r-base - 'r-caret >=6.0-78' - r-randomforest - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chic.data/post-link.sh b/recipes/bioconductor-chic.data/post-link.sh index 52ba42a28c315..7b754bd9c9d5b 100644 --- a/recipes/bioconductor-chic.data/post-link.sh +++ b/recipes/bioconductor-chic.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chic.data-1.20.0" +installBiocDataPackage.sh "chic.data-1.22.0" diff --git a/recipes/bioconductor-chicago/meta.yaml b/recipes/bioconductor-chicago/meta.yaml index bc24031fe5277..c5b8124eaea7d 100644 --- a/recipes/bioconductor-chicago/meta.yaml +++ b/recipes/bioconductor-chicago/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Chicago" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cecb7a43534f59b758ad7c05a2c0e4fe + md5: 854dccdecc3b0fc55c9146908bdeec27 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chicago", max_pin="x.x") }}' noarch: generic # Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub requirements: diff --git a/recipes/bioconductor-chicken.db/meta.yaml b/recipes/bioconductor-chicken.db/meta.yaml index 0329c2be32619..3269f8ebba784 100644 --- a/recipes/bioconductor-chicken.db/meta.yaml +++ b/recipes/bioconductor-chicken.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "chicken.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 512f887df339529d4883aad3f3eb6fb8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chicken.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.gg.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.gg.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.gg.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.gg.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chicken.db0/meta.yaml b/recipes/bioconductor-chicken.db0/meta.yaml index 299fd377f924a..f807a281abb07 100644 --- a/recipes/bioconductor-chicken.db0/meta.yaml +++ b/recipes/bioconductor-chicken.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "chicken.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bfacdb3f67e914c4d364a512620ec50d + md5: 0f0c20a519a9490c0909b68ec67c206d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chicken.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chicken.db0/post-link.sh b/recipes/bioconductor-chicken.db0/post-link.sh index b88e8c6ac32e0..23df0c7fd0516 100644 --- a/recipes/bioconductor-chicken.db0/post-link.sh +++ b/recipes/bioconductor-chicken.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chicken.db0-3.17.0" +installBiocDataPackage.sh "chicken.db0-3.18.0" diff --git a/recipes/bioconductor-chickencdf/meta.yaml b/recipes/bioconductor-chickencdf/meta.yaml index 64bc0b66b2e3b..3aa18b57b0fe8 100644 --- a/recipes/bioconductor-chickencdf/meta.yaml +++ b/recipes/bioconductor-chickencdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "chickencdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ab0097b4b7b6c4d94360feb84ab69972 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chickencdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chickenprobe/meta.yaml b/recipes/bioconductor-chickenprobe/meta.yaml index 3b7f3bc49a4ff..21e051513a182 100644 --- a/recipes/bioconductor-chickenprobe/meta.yaml +++ b/recipes/bioconductor-chickenprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "chickenprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b33599081ce1ba768ff7992e143c01d0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chickenprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chihaya/meta.yaml b/recipes/bioconductor-chihaya/meta.yaml index 6166022377359..48ed2f9721a59 100644 --- a/recipes/bioconductor-chihaya/meta.yaml +++ b/recipes/bioconductor-chihaya/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "chihaya" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 52743ecddbcf6548ab5ed19e629ad989 + md5: fc8e24fa8ec373d01c938fbfe12c3b9a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chihaya", max_pin="x.x") }}' # Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr # SystemRequirements: C++17, GNU make requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-chimeraviz/meta.yaml b/recipes/bioconductor-chimeraviz/meta.yaml index 3a0ccce4245d3..e05583b96cc73 100644 --- a/recipes/bioconductor-chimeraviz/meta.yaml +++ b/recipes/bioconductor-chimeraviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "chimeraviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 53ba0b753dbd0c0459d5ba1131a95ea9 + md5: 30227635634cb01d8196626c86dabc26 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chimeraviz", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, devtools, knitr, lintr # SystemRequirements: bowtie, samtools, and egrep are required for some functionalities requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-checkmate - r-data.table @@ -51,22 +52,22 @@ requirements: - r-rmarkdown - bowtie2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-chimp.db0/meta.yaml b/recipes/bioconductor-chimp.db0/meta.yaml index 6e58d8964a591..ef4f45937f147 100644 --- a/recipes/bioconductor-chimp.db0/meta.yaml +++ b/recipes/bioconductor-chimp.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "chimp.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a1382e14c2ace3a9cdc3daf7d7e4013 + md5: afb020cefb808101626234257bf71f69 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chimp.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chimp.db0/post-link.sh b/recipes/bioconductor-chimp.db0/post-link.sh index 9fbda934665a5..1298c3be4a0f5 100644 --- a/recipes/bioconductor-chimp.db0/post-link.sh +++ b/recipes/bioconductor-chimp.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chimp.db0-3.17.0" +installBiocDataPackage.sh "chimp.db0-3.18.0" diff --git a/recipes/bioconductor-chimphumanbraindata/meta.yaml b/recipes/bioconductor-chimphumanbraindata/meta.yaml index 80e8eb58a1ccc..36d967d68a6ee 100644 --- a/recipes/bioconductor-chimphumanbraindata/meta.yaml +++ b/recipes/bioconductor-chimphumanbraindata/meta.yaml @@ -34,7 +34,7 @@ requirements: - r-hexbin - r-statmod - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipanalyser/meta.yaml b/recipes/bioconductor-chipanalyser/meta.yaml index 2206c35d793a2..252bfb7c4953c 100644 --- a/recipes/bioconductor-chipanalyser/meta.yaml +++ b/recipes/bioconductor-chipanalyser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ChIPanalyser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75932168cfbb3bf4013b82f2cf95bf97 + md5: 21d3f8fe9fc90548452dab5a3a8e5c0d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipanalyser", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-rcolorbrewer - r-rcpproll - r-rocr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-rcolorbrewer diff --git a/recipes/bioconductor-chipcomp/meta.yaml b/recipes/bioconductor-chipcomp/meta.yaml index 2966e785af696..df3945bf8cc83 100644 --- a/recipes/bioconductor-chipcomp/meta.yaml +++ b/recipes/bioconductor-chipcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "ChIPComp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f3b60264992ea88c72e1d8da73dfa48 + md5: 5294eab6ada6b66e52935843dd9acc6b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipcomp", max_pin="x.x") }}' # Suggests: BiocStyle,RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-chipenrich.data/meta.yaml b/recipes/bioconductor-chipenrich.data/meta.yaml index 9fdd15ef6c4ec..d82da5fbc76ab 100644 --- a/recipes/bioconductor-chipenrich.data/meta.yaml +++ b/recipes/bioconductor-chipenrich.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "chipenrich.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4d9f38a90b43fad02b6448ecfbd36f2d + md5: 4918da98125fee82afaeee84930051a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipenrich.data", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat, GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-readr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-readr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipenrich.data/post-link.sh b/recipes/bioconductor-chipenrich.data/post-link.sh index fba74203f871f..90df321032f62 100644 --- a/recipes/bioconductor-chipenrich.data/post-link.sh +++ b/recipes/bioconductor-chipenrich.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipenrich.data-2.24.0" +installBiocDataPackage.sh "chipenrich.data-2.26.0" diff --git a/recipes/bioconductor-chipenrich/meta.yaml b/recipes/bioconductor-chipenrich/meta.yaml index 16735153cd287..9f53939b6e86e 100644 --- a/recipes/bioconductor-chipenrich/meta.yaml +++ b/recipes/bioconductor-chipenrich/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "chipenrich" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 85368fc7467101b17025a23231af5ff9 + md5: bb047e41aba2de216b8384322bb6a7aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipenrich", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chipenrich.data >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chipenrich.data >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-lattice - r-latticeextra @@ -43,19 +44,19 @@ requirements: - r-rms - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chipenrich.data >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chipenrich.data >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-lattice - r-latticeextra diff --git a/recipes/bioconductor-chipexoqual/meta.yaml b/recipes/bioconductor-chipexoqual/meta.yaml index cab6dcfe66cd7..eaacba6ed4f3c 100644 --- a/recipes/bioconductor-chipexoqual/meta.yaml +++ b/recipes/bioconductor-chipexoqual/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ChIPexoQual" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 840ba226b952bac3081c94fb133d1c53 + md5: c5fc56e308fbcfdf0630f2559c3556a3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipexoqual", max_pin="x.x") }}' noarch: generic # Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-broom >=0.4' - 'r-data.table >=1.9.6' @@ -40,14 +41,14 @@ requirements: - 'r-scales >=0.4.0' - 'r-viridis >=0.3' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-broom >=0.4' - 'r-data.table >=1.9.6' diff --git a/recipes/bioconductor-chipexoqualexample/meta.yaml b/recipes/bioconductor-chipexoqualexample/meta.yaml index 47a99c910c890..b98adbff5998f 100644 --- a/recipes/bioconductor-chipexoqualexample/meta.yaml +++ b/recipes/bioconductor-chipexoqualexample/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ChIPexoQualExample" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8a88d767a542955c8dfa93a67c843de + md5: 5ebb67a1848aa0e69557e795d236e24b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipexoqualexample", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipexoqualexample/post-link.sh b/recipes/bioconductor-chipexoqualexample/post-link.sh index b2682c689a4f7..4cb76a02b9673 100644 --- a/recipes/bioconductor-chipexoqualexample/post-link.sh +++ b/recipes/bioconductor-chipexoqualexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipexoqualexample-1.24.0" +installBiocDataPackage.sh "chipexoqualexample-1.26.0" diff --git a/recipes/bioconductor-chippeakanno/meta.yaml b/recipes/bioconductor-chippeakanno/meta.yaml index 37eec2d81105c..67ad871c9926b 100644 --- a/recipes/bioconductor-chippeakanno/meta.yaml +++ b/recipes/bioconductor-chippeakanno/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.34.1" %} +{% set version = "3.36.0" %} {% set name = "ChIPpeakAnno" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c57887a1682adde2e3a9e3ebf5389575 + md5: d9773752fca7bd32e512d3a5b72236e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chippeakanno", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dbi - r-dplyr @@ -48,26 +49,26 @@ requirements: - r-matrixstats - r-venndiagram run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dbi - r-dplyr diff --git a/recipes/bioconductor-chipqc/meta.yaml b/recipes/bioconductor-chipqc/meta.yaml index 3a35946828413..2eb975a8384db 100644 --- a/recipes/bioconductor-chipqc/meta.yaml +++ b/recipes/bioconductor-chipqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ChIPQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10738588f2408b35b805c47ade29958a + md5: b7437c357c5ba27db1f2721a50c15f13 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipqc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-diffbind >=3.10.0,<3.11.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-diffbind >=3.12.0,<3.13.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' @@ -45,17 +46,17 @@ requirements: - r-nozzle.r1 - r-reshape2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-diffbind >=3.10.0,<3.11.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-diffbind >=3.12.0,<3.13.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' diff --git a/recipes/bioconductor-chipseeker/meta.yaml b/recipes/bioconductor-chipseeker/meta.yaml index ce1d8465acf6d..fe501701d99dd 100644 --- a/recipes/bioconductor-chipseeker/meta.yaml +++ b/recipes/bioconductor-chipseeker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ChIPseeker" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40fc097874f59ebe1b216c661f812b8e + md5: 4e7b7622d7d9d1b3de7b8f9bf49eb8c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipseeker", max_pin="x.x") }}' noarch: generic # Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, prettydoc requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-aplot - r-base @@ -43,15 +44,15 @@ requirements: - r-tibble - r-yulab.utils run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-aplot - r-base diff --git a/recipes/bioconductor-chipseq/meta.yaml b/recipes/bioconductor-chipseq/meta.yaml index d651e8addd8b8..9b132ed73d2bc 100644 --- a/recipes/bioconductor-chipseq/meta.yaml +++ b/recipes/bioconductor-chipseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "chipseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf6ac7d66b1527716768e6218f0468e9 + md5: 5cf8ab297fc95d0a36b4359488c50358 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipseq", max_pin="x.x") }}' # Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-lattice - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-lattice build: diff --git a/recipes/bioconductor-chipseqdbdata/meta.yaml b/recipes/bioconductor-chipseqdbdata/meta.yaml index 7fd9e17b951bb..51ec45e800c2a 100644 --- a/recipes/bioconductor-chipseqdbdata/meta.yaml +++ b/recipes/bioconductor-chipseqdbdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "chipseqDBData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9417adbf6ebe305a0caf0d0eba440cac + md5: a6e50016d2d7c0cb085df2c4254b5f84 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipseqdbdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipseqdbdata/post-link.sh b/recipes/bioconductor-chipseqdbdata/post-link.sh index 2079dff585ed8..3d5e5956052e4 100644 --- a/recipes/bioconductor-chipseqdbdata/post-link.sh +++ b/recipes/bioconductor-chipseqdbdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipseqdbdata-1.16.0" +installBiocDataPackage.sh "chipseqdbdata-1.18.0" diff --git a/recipes/bioconductor-chipseqr/meta.yaml b/recipes/bioconductor-chipseqr/meta.yaml index a69b3f5e17171..c6349e5dc015c 100644 --- a/recipes/bioconductor-chipseqr/meta.yaml +++ b/recipes/bioconductor-chipseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ChIPseqR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c1a94747eb45fbf4d791cbb05961424 + md5: 8696d6a783d26d8c6225ec4e3f294110 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipseqr", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-fbasics - r-timsac - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-fbasics - r-timsac diff --git a/recipes/bioconductor-chipsim/meta.yaml b/recipes/bioconductor-chipsim/meta.yaml index 74820f192e5f3..f81fdb6e13dc2 100644 --- a/recipes/bioconductor-chipsim/meta.yaml +++ b/recipes/bioconductor-chipsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ChIPsim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f3239589cefb4c8db5fafe013dcd926 + md5: e6f1bd9d18f542abace1039c37ada326 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipsim", max_pin="x.x") }}' noarch: generic # Suggests: actuar, zoo requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base test: commands: diff --git a/recipes/bioconductor-chipxpress/meta.yaml b/recipes/bioconductor-chipxpress/meta.yaml index 05e6214d06fb8..3d91446325661 100644 --- a/recipes/bioconductor-chipxpress/meta.yaml +++ b/recipes/bioconductor-chipxpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "ChIPXpress" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 31093ed51ee07a043038f30f431b8df0 + md5: bed7bbe60d0a51fb667cee9b01e4c407 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipxpress", max_pin="x.x") }}' noarch: generic # Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chipxpressdata >=1.38.0,<1.39.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chipxpressdata >=1.40.0,<1.41.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-biganalytics - r-bigmemory run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chipxpressdata >=1.38.0,<1.39.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chipxpressdata >=1.40.0,<1.41.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-biganalytics - r-bigmemory diff --git a/recipes/bioconductor-chipxpressdata/meta.yaml b/recipes/bioconductor-chipxpressdata/meta.yaml index 45808acdeb8cb..5651a2b0910c0 100644 --- a/recipes/bioconductor-chipxpressdata/meta.yaml +++ b/recipes/bioconductor-chipxpressdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ChIPXpressData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d764e5abb6fadab9aa4184222665fd25 + md5: 029086a630df9533dedea4babd28f0d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chipxpressdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -26,7 +27,7 @@ requirements: - r-base - r-bigmemory - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chipxpressdata/post-link.sh b/recipes/bioconductor-chipxpressdata/post-link.sh index de10fb5bf2753..82a974e07cf07 100644 --- a/recipes/bioconductor-chipxpressdata/post-link.sh +++ b/recipes/bioconductor-chipxpressdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipxpressdata-1.38.0" +installBiocDataPackage.sh "chipxpressdata-1.40.0" diff --git a/recipes/bioconductor-chopsticks/meta.yaml b/recipes/bioconductor-chopsticks/meta.yaml index ce6e6f825a531..17c378b1395b0 100644 --- a/recipes/bioconductor-chopsticks/meta.yaml +++ b/recipes/bioconductor-chopsticks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "chopsticks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d89502b5d2b8124bcf02def4af198d1e + md5: b63b111068a6d42f7812010d1dc31047 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chopsticks", max_pin="x.x") }}' # Suggests: hexbin requirements: host: diff --git a/recipes/bioconductor-chromdraw/meta.yaml b/recipes/bioconductor-chromdraw/meta.yaml index 619ff6d5788fa..e92f8c236b474 100644 --- a/recipes/bioconductor-chromdraw/meta.yaml +++ b/recipes/bioconductor-chromdraw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "chromDraw" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 396784bb969985d07948449d9370a7ea + md5: a2cb0f03cdde9853f68662b1783a2edb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromdraw", max_pin="x.x") }}' # SystemRequirements: Rtools (>= 3.1) requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - 'r-rcpp >=0.11.1' - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - 'r-rcpp >=0.11.1' build: diff --git a/recipes/bioconductor-chromheatmap/meta.yaml b/recipes/bioconductor-chromheatmap/meta.yaml index fcd97fa3d6695..b777bfe8ed021 100644 --- a/recipes/bioconductor-chromheatmap/meta.yaml +++ b/recipes/bioconductor-chromheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ChromHeatMap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a643aa848bc97a9893f442798ab63d51 + md5: ee08133257bb6da21d100e03fd720323 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromheatmap", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-chromhmmdata/meta.yaml b/recipes/bioconductor-chromhmmdata/meta.yaml index 31e71bfc05c6f..0dabce226994f 100644 --- a/recipes/bioconductor-chromhmmdata/meta.yaml +++ b/recipes/bioconductor-chromhmmdata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.2" %} {% set name = "chromhmmData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: eec85c20139b3d826f00264c7b28207c build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromhmmdata", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chromplot/meta.yaml b/recipes/bioconductor-chromplot/meta.yaml index c679f8ff551d5..38a0a8e56bf16 100644 --- a/recipes/bioconductor-chromplot/meta.yaml +++ b/recipes/bioconductor-chromplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "chromPlot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e79af2916f986d3381e6b4bad3a0b03 + md5: a9a3e6d499f082698be0bf88f6432103 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromplot", max_pin="x.x") }}' noarch: generic # Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base test: commands: diff --git a/recipes/bioconductor-chromscape/meta.yaml b/recipes/bioconductor-chromscape/meta.yaml index 39884d28d7f71..06a80351408c4 100644 --- a/recipes/bioconductor-chromscape/meta.yaml +++ b/recipes/bioconductor-chromscape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ChromSCape" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f10af25260d45879be22b5009d675957 + md5: a95b9c5be176f95c178ac7d3a1c26496 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromscape", max_pin="x.x") }}' # Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr requirements: host: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colorramps - r-colourpicker @@ -75,20 +76,20 @@ requirements: - libblas - liblapack run: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colorramps - r-colourpicker diff --git a/recipes/bioconductor-chromstar/meta.yaml b/recipes/bioconductor-chromstar/meta.yaml index 7bf4d86cf9264..c2f40c3c66293 100644 --- a/recipes/bioconductor-chromstar/meta.yaml +++ b/recipes/bioconductor-chromstar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "chromstaR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7cd6c65772e7ed8857f0c4a7fbde5f2 + md5: 4288983863e4523b5c7e7750691e8987 build: skip: True # [osx] number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromstar", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, testthat, biomaRt requirements: host: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chromstardata >=1.26.0,<1.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chromstardata >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach @@ -39,15 +40,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chromstardata >=1.26.0,<1.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chromstardata >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-chromstardata/meta.yaml b/recipes/bioconductor-chromstardata/meta.yaml index 292e8684ef5a8..1a844f8b5b766 100644 --- a/recipes/bioconductor-chromstardata/meta.yaml +++ b/recipes/bioconductor-chromstardata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "chromstaRData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 316680e584e9e31c3000a87e666fda3b + md5: 7f4a965a6b5aa71874a5cca39046cabf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromstardata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-chromstardata/post-link.sh b/recipes/bioconductor-chromstardata/post-link.sh index 8fe48b9d0b2e1..3707fe3b3448a 100644 --- a/recipes/bioconductor-chromstardata/post-link.sh +++ b/recipes/bioconductor-chromstardata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chromstardata-1.26.0" +installBiocDataPackage.sh "chromstardata-1.28.0" diff --git a/recipes/bioconductor-chromvar/meta.yaml b/recipes/bioconductor-chromvar/meta.yaml index 71bf356fd7b8c..dc83da4dba182 100644 --- a/recipes/bioconductor-chromvar/meta.yaml +++ b/recipes/bioconductor-chromvar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "chromVAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 457ef63195af94e9b077f852ff950120 + md5: 8e42f2454ce39606fae40e85e437b47b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chromvar", max_pin="x.x") }}' # Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dt - r-ggplot2 @@ -47,17 +48,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-dt - r-ggplot2 diff --git a/recipes/bioconductor-chronos/meta.yaml b/recipes/bioconductor-chronos/meta.yaml index 74f6e5ec5794e..d599b7baf0635 100644 --- a/recipes/bioconductor-chronos/meta.yaml +++ b/recipes/bioconductor-chronos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CHRONOS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36aa4b9e641e13b99c425fceaea51902 + md5: 7d2e5d9c89ea0163868d7b51bfd1c952 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-chronos", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, rmarkdown # SystemRequirements: Java version >= 1.7, Pandoc requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-circlize - r-doparallel @@ -36,9 +37,9 @@ requirements: - r-xml - openjdk run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-circlize - r-doparallel diff --git a/recipes/bioconductor-cicero/meta.yaml b/recipes/bioconductor-cicero/meta.yaml index c9a1f8ea9da63..3eccb1e945ea0 100644 --- a/recipes/bioconductor-cicero/meta.yaml +++ b/recipes/bioconductor-cicero/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "cicero" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: df17d0a24bd82617cc2eb0358cb2c01b + md5: 642264199171ac5b31a4f296c855dbb7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cicero", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-assertthat >=0.2.0' - r-base - 'r-data.table >=1.10.4' @@ -45,13 +46,13 @@ requirements: - r-tidyr - 'r-vgam >=1.0-5' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-assertthat >=0.2.0' - r-base - 'r-data.table >=1.10.4' diff --git a/recipes/bioconductor-cimice/meta.yaml b/recipes/bioconductor-cimice/meta.yaml index 167de8864400d..fdd7c4e3115bd 100644 --- a/recipes/bioconductor-cimice/meta.yaml +++ b/recipes/bioconductor-cimice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CIMICE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2b25b8cfb634948761ef0ab0cea2573a + md5: 510ab010752cd50654467583c6159ba1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cimice", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, webshot requirements: host: - - 'bioconductor-maftools >=2.16.0,<2.17.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' - r-assertthat - r-base - r-dplyr @@ -38,7 +39,7 @@ requirements: - r-tidyr - r-visnetwork run: - - 'bioconductor-maftools >=2.16.0,<2.17.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-cindex/meta.yaml b/recipes/bioconductor-cindex/meta.yaml index 1ac85c185c36e..b76d809749c35 100644 --- a/recipes/bioconductor-cindex/meta.yaml +++ b/recipes/bioconductor-cindex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CINdex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e7b2c4eea3f63ef70beb69855c13e8d + md5: 2616a2a02791d966dbf54a54f2ad5f42 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cindex", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens, R.utils requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bitops - r-dplyr @@ -34,10 +35,10 @@ requirements: - r-som - r-stringr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bitops - r-dplyr diff --git a/recipes/bioconductor-circrnaprofiler/meta.yaml b/recipes/bioconductor-circrnaprofiler/meta.yaml index 28a7828103941..169e8226f8928 100644 --- a/recipes/bioconductor-circrnaprofiler/meta.yaml +++ b/recipes/bioconductor-circrnaprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "circRNAprofiler" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 185095e44fb0afd5f381d76f4a9d11b8 + md5: 5cd7f621f355f9d816938675dd550e2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-circrnaprofiler", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gwascat >=2.32.0,<2.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-universalmotif >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gwascat >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-universalmotif >=1.20.0,<1.21.0' - r-base - r-dplyr - r-ggplot2 @@ -46,19 +47,19 @@ requirements: - r-stringi - r-stringr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gwascat >=2.32.0,<2.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-universalmotif >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gwascat >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-universalmotif >=1.20.0,<1.21.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-circseqaligntk/meta.yaml b/recipes/bioconductor-circseqaligntk/meta.yaml index 8762be109cfe7..1552ea1595ddc 100644 --- a/recipes/bioconductor-circseqaligntk/meta.yaml +++ b/recipes/bioconductor-circseqaligntk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "CircSeqAlignTk" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5afd52c06cc2be5978037ddbaf1c6b9d + md5: 2c3b93fca2c2974a45af093edf7d9558 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-circseqaligntk", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, R.utils, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rhisat2 >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rhisat2 >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dplyr - r-ggplot2 @@ -36,14 +37,14 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rhisat2 >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rhisat2 >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-cispath/meta.yaml b/recipes/bioconductor-cispath/meta.yaml index 198ea08df04db..cc4f2f6708169 100644 --- a/recipes/bioconductor-cispath/meta.yaml +++ b/recipes/bioconductor-cispath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "cisPath" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9fb575eb3e75ecca9e49aae03f99e16 + md5: 958a35281b9aa98b2d5c3a5c4e9c8824 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cispath", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-citefuse/meta.yaml b/recipes/bioconductor-citefuse/meta.yaml index c401b9e42dab4..b64daab89d292 100644 --- a/recipes/bioconductor-citefuse/meta.yaml +++ b/recipes/bioconductor-citefuse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "CiteFuse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a24d3bcaca6d446c6992c8f337deb15 + md5: d612b20352aa6e753d90baa4f24b058f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-citefuse", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-compositions - r-cowplot @@ -47,11 +48,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-compositions - r-cowplot diff --git a/recipes/bioconductor-citruscdf/meta.yaml b/recipes/bioconductor-citruscdf/meta.yaml index a1500a296707c..650b3066528a8 100644 --- a/recipes/bioconductor-citruscdf/meta.yaml +++ b/recipes/bioconductor-citruscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "citruscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4af821a0c1ae1adf42b7dc5ce7458593 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-citruscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-citrusprobe/meta.yaml b/recipes/bioconductor-citrusprobe/meta.yaml index 762e4af7c0c8f..2c386ee4e5874 100644 --- a/recipes/bioconductor-citrusprobe/meta.yaml +++ b/recipes/bioconductor-citrusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "citrusprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 259b114f96d5307c447d000bd27a7d15 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-citrusprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml b/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml index 7584a97d8f7b3..85c5b7c172edf 100644 --- a/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml +++ b/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomdhumanprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 01cb1a5cc4674750b6ce5988cd62fad3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomdhumanprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml index ae9a312dc03a3..a76e5a52dc2cb 100644 --- a/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomdhumantranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 80739a70d77ab785231a9367938035a8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomdhumantranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml index daa168f43926a..d70ad9cdca7f4 100644 --- a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomshumanhttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6a5e8e1f9768694be99277aafcc0a69a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomshumanhttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml index 264f39fc4cc19..794a3936044f0 100644 --- a/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomshumantranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 309b29e044e1227da6d4825bbdf04b76 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomshumantranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml index f23ef7e29afe2..1074e66c5774d 100644 --- a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomsmousehttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c0aa96cbd5ee7e19296dde5a72232d17 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomsmousehttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml index 900a5fd7c540e..271042584f0fd 100644 --- a/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomsmousetranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 76d0e2204dcbd5d85d8e53d43710aac5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomsmousetranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml index dda97365b309e..326e026ab0521 100644 --- a/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomsrathttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e7c71721f8201bfd1553a98cfbf47458 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomsrathttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml index e1e18af7efc25..15edbc0937e97 100644 --- a/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "clariomsrattranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 72923a3a90f2df27a361b1730cfc0d00 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clariomsrattranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-classifyr/meta.yaml b/recipes/bioconductor-classifyr/meta.yaml index cf51f7b610e65..704f02bfee8e5 100644 --- a/recipes/bioconductor-classifyr/meta.yaml +++ b/recipes/bioconductor-classifyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.7" %} +{% set version = "3.6.2" %} {% set name = "ClassifyR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61d0fa2d28ce2d1a8f3c984f7dc71e4c + md5: 002678b6aeace9d7967b87654547a4f3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-classifyr", max_pin="x.x") }}' # Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-generics - 'r-ggplot2 >=3.0.0' - r-ggpubr + - r-ggupset - r-ranger - r-reshape2 - r-rlang @@ -37,15 +39,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-generics - 'r-ggplot2 >=3.0.0' - r-ggpubr + - r-ggupset - r-ranger - r-reshape2 - r-rlang diff --git a/recipes/bioconductor-cleanupdtseq/meta.yaml b/recipes/bioconductor-cleanupdtseq/meta.yaml index 526d1e356a691..722708178c451 100644 --- a/recipes/bioconductor-cleanupdtseq/meta.yaml +++ b/recipes/bioconductor-cleanupdtseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "cleanUpdTSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fc6f5fd9421004bf9ab234060d7714d + md5: 52f27e948758be1db9d6b003d69a84b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cleanupdtseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-e1071 - r-seqinr - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-e1071 - r-seqinr diff --git a/recipes/bioconductor-cleaver/meta.yaml b/recipes/bioconductor-cleaver/meta.yaml index 817641b020b8e..e69fedb991a3b 100644 --- a/recipes/bioconductor-cleaver/meta.yaml +++ b/recipes/bioconductor-cleaver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "cleaver" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cd859842ff42dc19c2d4356fbb9f65f9 + md5: 978f7bba3eb0dae3a3edee5c5721de7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cleaver", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-clevrvis/meta.yaml b/recipes/bioconductor-clevrvis/meta.yaml index 09cd3712f83bb..4cbdb433898df 100644 --- a/recipes/bioconductor-clevrvis/meta.yaml +++ b/recipes/bioconductor-clevrvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "clevRvis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43c9647c43af55cee12813e91c37f569 + md5: 96fde7a442a2cdb69754ebf1e68ccc65 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clevrvis", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-clippda/meta.yaml b/recipes/bioconductor-clippda/meta.yaml index ee2060d37cffa..4aea5febf6e97 100644 --- a/recipes/bioconductor-clippda/meta.yaml +++ b/recipes/bioconductor-clippda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "clippda" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f31b017726d6b75db0537ae313adc135 + md5: d416c567cfb3615472045bc57c2bce72 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clippda", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-lattice - r-rgl - r-scatterplot3d - r-statmod run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-lattice - r-rgl diff --git a/recipes/bioconductor-clipper/meta.yaml b/recipes/bioconductor-clipper/meta.yaml index d0e6246555f54..63e140182b6f3 100644 --- a/recipes/bioconductor-clipper/meta.yaml +++ b/recipes/bioconductor-clipper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "clipper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 421940d057355924606d4cfe710237d0 + md5: 551f3c6ad3a56f2a70439f48a4aef431 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clipper", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-qpgraph >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-qpgraph >=2.36.0,<2.37.0' - r-base - r-corpcor - 'r-grbase >=1.6.6' @@ -34,11 +34,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-qpgraph >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-qpgraph >=2.36.0,<2.37.0' - r-base - r-corpcor - 'r-grbase >=1.6.6' diff --git a/recipes/bioconductor-cliprofiler/meta.yaml b/recipes/bioconductor-cliprofiler/meta.yaml index a7a37aff8423f..c0910f32ab09f 100644 --- a/recipes/bioconductor-cliprofiler/meta.yaml +++ b/recipes/bioconductor-cliprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "cliProfiler" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54bce2fd9a5c5b30887a3139c0c50301 + md5: 10a33ec5af89503fcb12a8142ec966f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cliprofiler", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-cliquems/meta.yaml b/recipes/bioconductor-cliquems/meta.yaml index a7e4df20a8ce3..0c96850839c51 100644 --- a/recipes/bioconductor-cliquems/meta.yaml +++ b/recipes/bioconductor-cliquems/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.13.0" %} +{% set version = "1.16.0" %} {% set name = "cliqueMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21a77001912e964b72c091a32961b42b + md5: f423e41dd4ca04cefe4bd5be77ceec3a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cliquems", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, CAMERA # SystemRequirements: C++11 requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-bh - r-igraph @@ -33,8 +34,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-bh - r-igraph diff --git a/recipes/bioconductor-cll/meta.yaml b/recipes/bioconductor-cll/meta.yaml index e87436e996e9b..dfeb4ff22d3ea 100644 --- a/recipes/bioconductor-cll/meta.yaml +++ b/recipes/bioconductor-cll/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "CLL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af6541d53d8bb71eb10e661c0a6efde0 + md5: 4f71fa48ba2205b80c098275c866ac1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cll", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cll/post-link.sh b/recipes/bioconductor-cll/post-link.sh index 253975f1a9713..bfc51d8a40c4f 100644 --- a/recipes/bioconductor-cll/post-link.sh +++ b/recipes/bioconductor-cll/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cll-1.40.0" +installBiocDataPackage.sh "cll-1.42.0" diff --git a/recipes/bioconductor-cllmethylation/meta.yaml b/recipes/bioconductor-cllmethylation/meta.yaml index 30437c33b2d02..1ed25ff3378d0 100644 --- a/recipes/bioconductor-cllmethylation/meta.yaml +++ b/recipes/bioconductor-cllmethylation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CLLmethylation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3304bdcdaa207660d51a29e1ad2a4c6 + md5: a8c3768dca1df5bb9e911878b68ad4c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cllmethylation", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cllmethylation/post-link.sh b/recipes/bioconductor-cllmethylation/post-link.sh index e74887d8fb150..24af32275232b 100644 --- a/recipes/bioconductor-cllmethylation/post-link.sh +++ b/recipes/bioconductor-cllmethylation/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cllmethylation-1.20.0" +installBiocDataPackage.sh "cllmethylation-1.22.0" diff --git a/recipes/bioconductor-clomial/meta.yaml b/recipes/bioconductor-clomial/meta.yaml index 966b40e4e4735..280429af62f00 100644 --- a/recipes/bioconductor-clomial/meta.yaml +++ b/recipes/bioconductor-clomial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Clomial" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3b126ecc8f8786eeb190d8a150326562 + md5: 71e609b1bef40cdadcd812f99a5956e8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clomial", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-clst/meta.yaml b/recipes/bioconductor-clst/meta.yaml index 6a88fe2a497e7..40c671b879c52 100644 --- a/recipes/bioconductor-clst/meta.yaml +++ b/recipes/bioconductor-clst/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "clst" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b9c002ff0d92c15fef6fc5abd3c76789 + md5: 5988cf1c0b5207d2f78f75dbe6f2b467 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clst", max_pin="x.x") }}' noarch: generic # Suggests: RUnit requirements: host: - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-lattice run: - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-lattice test: diff --git a/recipes/bioconductor-clstutils/meta.yaml b/recipes/bioconductor-clstutils/meta.yaml index c38910cfda1f3..fbd9437560808 100644 --- a/recipes/bioconductor-clstutils/meta.yaml +++ b/recipes/bioconductor-clstutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "clstutils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 40f1c145c0d85feb28a7935705b389fb + md5: 4343490b2b05bf2e4429f2081b3a82c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clstutils", max_pin="x.x") }}' noarch: generic # Suggests: RUnit requirements: host: - - 'bioconductor-clst >=1.48.0,<1.49.0' + - 'bioconductor-clst >=1.50.0,<1.51.0' - r-ape - r-base - r-lattice - r-rjson - r-rsqlite run: - - 'bioconductor-clst >=1.48.0,<1.49.0' + - 'bioconductor-clst >=1.50.0,<1.51.0' - r-ape - r-base - r-lattice diff --git a/recipes/bioconductor-clumsid/meta.yaml b/recipes/bioconductor-clumsid/meta.yaml index 49ee2d606b139..f845097e08a5c 100644 --- a/recipes/bioconductor-clumsid/meta.yaml +++ b/recipes/bioconductor-clumsid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CluMSID" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b38aa0e170c6aff41ab31e3bcb47ed7 + md5: 0f441929cf30f7ab6c9a035023ef3a20 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clumsid", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-dbscan @@ -36,10 +37,10 @@ requirements: - r-rcolorbrewer - r-sna run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-dbscan diff --git a/recipes/bioconductor-clumsiddata/meta.yaml b/recipes/bioconductor-clumsiddata/meta.yaml index 2176b782a6929..ea06ae2fe5f88 100644 --- a/recipes/bioconductor-clumsiddata/meta.yaml +++ b/recipes/bioconductor-clumsiddata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CluMSIDdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f97c24b60d106fe1285496ace8fad79 + md5: 315da29d9f052e0abfbad59be9606f34 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clumsiddata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clumsiddata/post-link.sh b/recipes/bioconductor-clumsiddata/post-link.sh index 13dcc91868f79..2e82be8661106 100644 --- a/recipes/bioconductor-clumsiddata/post-link.sh +++ b/recipes/bioconductor-clumsiddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "clumsiddata-1.16.0" +installBiocDataPackage.sh "clumsiddata-1.18.0" diff --git a/recipes/bioconductor-clustcomp/meta.yaml b/recipes/bioconductor-clustcomp/meta.yaml index bf6927af6b6c4..b3fc8f1f502a3 100644 --- a/recipes/bioconductor-clustcomp/meta.yaml +++ b/recipes/bioconductor-clustcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "clustComp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d1d219e2545f57d1d323e65497c50ea + md5: c1783d91366b98b4afbe0b0acc49c452 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clustcomp", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, colonCA, RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-clusterexperiment/meta.yaml b/recipes/bioconductor-clusterexperiment/meta.yaml index 8490b0476dbcc..82eb2c72a6339 100644 --- a/recipes/bioconductor-clusterexperiment/meta.yaml +++ b/recipes/bioconductor-clusterexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "clusterExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f32e3bf65cc1997b021722429f34700 + md5: 0a4bac02f2b310d941afe62b329e7eee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clusterexperiment", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mbkmeans >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mbkmeans >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - 'r-ape >=5.0' - r-base - r-cluster @@ -49,17 +50,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mbkmeans >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mbkmeans >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - 'r-ape >=5.0' - r-base - r-cluster diff --git a/recipes/bioconductor-clusterjudge/meta.yaml b/recipes/bioconductor-clusterjudge/meta.yaml index 5ce838aabca2c..6b919674df414 100644 --- a/recipes/bioconductor-clusterjudge/meta.yaml +++ b/recipes/bioconductor-clusterjudge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ClusterJudge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56ecef405e11e333d5c93fe785ba3c8e + md5: 1f1db5b57d83f67f60de690e6f224bde build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clusterjudge", max_pin="x.x") }}' noarch: generic # Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt requirements: diff --git a/recipes/bioconductor-clusterprofiler/meta.yaml b/recipes/bioconductor-clusterprofiler/meta.yaml index fdae3be5aa869..f55cd8017a8be 100644 --- a/recipes/bioconductor-clusterprofiler/meta.yaml +++ b/recipes/bioconductor-clusterprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.8.1" %} +{% set version = "4.10.0" %} {% set name = "clusterProfiler" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,47 +11,52 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ad792319e54d0f39cd6caff54dc1021 + md5: 6eb1c0888849211e04896b3431460048 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clusterprofiler", max_pin="x.x") }}' noarch: generic -# Suggests: AnnotationHub, knitr, rmarkdown, org.Hs.eg.db, prettydoc, ReactomePA, testthat +# Suggests: AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-downloader - r-dplyr - 'r-gson >=0.0.7' + - r-httr + - r-igraph - r-magrittr - r-plyr - r-rlang - r-tidyr - - r-yulab.utils + - 'r-yulab.utils >=0.0.7' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-downloader - r-dplyr - 'r-gson >=0.0.7' + - r-httr + - r-igraph - r-magrittr - r-plyr - r-rlang - r-tidyr - - r-yulab.utils + - 'r-yulab.utils >=0.0.7' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clusterseq/build.sh b/recipes/bioconductor-clusterseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clusterseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clusterseq/meta.yaml b/recipes/bioconductor-clusterseq/meta.yaml new file mode 100644 index 0000000000000..89f709b6c7c02 --- /dev/null +++ b/recipes/bioconductor-clusterseq/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.26.0" %} +{% set name = "clusterSeq" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c0f51fc6b851b707de4f53107c6179f5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clusterseq", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - r-base + run: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Clustering of high-throughput sequencing data by identifying co-expression patterns' + description: 'Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-clustersignificance/meta.yaml b/recipes/bioconductor-clustersignificance/meta.yaml index 578873112c4d8..452ee4190c486 100644 --- a/recipes/bioconductor-clustersignificance/meta.yaml +++ b/recipes/bioconductor-clustersignificance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ClusterSignificance" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2c35b077596b2fe12be5c9baff99047 + md5: 46f8a23ba4910712f2c65ebbb151ad4f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clustersignificance", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr requirements: diff --git a/recipes/bioconductor-clusterstab/meta.yaml b/recipes/bioconductor-clusterstab/meta.yaml index ac9e1a16e147f..0f20cc38a7835 100644 --- a/recipes/bioconductor-clusterstab/meta.yaml +++ b/recipes/bioconductor-clusterstab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "clusterStab" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42577966d771992cbafdf2efdcdda484 + md5: 87f3941fd121e6a60acdefd9a682ba9a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clusterstab", max_pin="x.x") }}' noarch: generic # Suggests: fibroEset, genefilter requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-clustifyr/meta.yaml b/recipes/bioconductor-clustifyr/meta.yaml index 8f891d05b5519..2cb67cd3a2219 100644 --- a/recipes/bioconductor-clustifyr/meta.yaml +++ b/recipes/bioconductor-clustifyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "clustifyr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6744ece04f6b8aacaff4d235cdf1458b + md5: 5fc803262c7a3b4d11d464f30a110802 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clustifyr", max_pin="x.x") }}' noarch: generic -# Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, Seurat, gprofiler2, purrr +# Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, Seurat, gprofiler2, purrr, data.table, R.utils requirements: host: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -34,17 +35,16 @@ requirements: - r-matrix - r-matrixstats - r-proxy - - r-readr - r-rlang - r-scales - r-stringr - r-tibble - r-tidyr run: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -54,7 +54,6 @@ requirements: - r-matrix - r-matrixstats - r-proxy - - r-readr - r-rlang - r-scales - r-stringr diff --git a/recipes/bioconductor-clustifyrdatahub/meta.yaml b/recipes/bioconductor-clustifyrdatahub/meta.yaml index c271419be117c..c910400fc78c8 100644 --- a/recipes/bioconductor-clustifyrdatahub/meta.yaml +++ b/recipes/bioconductor-clustifyrdatahub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "clustifyrdatahub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d1345a885c1b770cd461cf3c69451b39 + md5: aac4529e5c0d71fdc49bda51c3915f61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clustifyrdatahub", max_pin="x.x") }}' noarch: generic # Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr, BiocStyle requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-clustifyrdatahub/post-link.sh b/recipes/bioconductor-clustifyrdatahub/post-link.sh index 6913cf66ffe04..312ed6f9276d2 100644 --- a/recipes/bioconductor-clustifyrdatahub/post-link.sh +++ b/recipes/bioconductor-clustifyrdatahub/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "clustifyrdatahub-1.10.0" +installBiocDataPackage.sh "clustifyrdatahub-1.12.0" diff --git a/recipes/bioconductor-clustirr/build.sh b/recipes/bioconductor-clustirr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clustirr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clustirr/meta.yaml b/recipes/bioconductor-clustirr/meta.yaml new file mode 100644 index 0000000000000..58ca1182b4301 --- /dev/null +++ b/recipes/bioconductor-clustirr/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "ClustIRR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ffd1884844b297c2e593e465a776fb6d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clustirr", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, testthat, ggplot2, patchwork, ggrepel +requirements: + host: + - r-base + - r-future + - r-future.apply + - r-igraph + - r-stringdist + - r-visnetwork + run: + - r-base + - r-future + - r-future.apply + - r-igraph + - r-stringdist + - r-visnetwork +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Clustering of immune receptor repertoires' + description: 'ClustIRR is a quantitative method for clustering of immune receptor repertoires (IRRs). The algorithm identifies groups of T or B cell receptors (TCRs or BCRs) with similar specificity by comparing their sequences. ClustIRR uses graphs to visualize the specificity structures of IRRs.' + license_file: LICENSE + diff --git a/recipes/bioconductor-cma/meta.yaml b/recipes/bioconductor-cma/meta.yaml index 7cf5de809d7e7..7dcc40d917ad9 100644 --- a/recipes/bioconductor-cma/meta.yaml +++ b/recipes/bioconductor-cma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "CMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7b22a1bca581dca052746c3049d15b7 + md5: 6654a3ef8f06edc618b81b8a059b2139 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cma", max_pin="x.x") }}' noarch: generic # Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-cmap/meta.yaml b/recipes/bioconductor-cmap/meta.yaml index 007b0c087943c..d9037cbfaab0a 100644 --- a/recipes/bioconductor-cmap/meta.yaml +++ b/recipes/bioconductor-cmap/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.1" %} {% set name = "cMAP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dbf8df4d4540151936884e1c5d747bcf build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cmap", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cmap2data/meta.yaml b/recipes/bioconductor-cmap2data/meta.yaml index f8cd0f45b31df..7b58d905ef119 100644 --- a/recipes/bioconductor-cmap2data/meta.yaml +++ b/recipes/bioconductor-cmap2data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "cMap2data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd007c68b5fd75539c62081497ab1ee5 + md5: c5ecbc59a690426c6def7feb720e1a7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cmap2data", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cmap2data/post-link.sh b/recipes/bioconductor-cmap2data/post-link.sh index 679c3f090733e..ca70907c04096 100644 --- a/recipes/bioconductor-cmap2data/post-link.sh +++ b/recipes/bioconductor-cmap2data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cmap2data-1.36.0" +installBiocDataPackage.sh "cmap2data-1.38.0" diff --git a/recipes/bioconductor-cmapr/meta.yaml b/recipes/bioconductor-cmapr/meta.yaml index 3b0121b7fb521..03a057ffbe9ef 100644 --- a/recipes/bioconductor-cmapr/meta.yaml +++ b/recipes/bioconductor-cmapr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "cmapR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de47953e61c6df4cd2db9d5551cdcffc + md5: 257c275c11341cac65aae8f0d8cd4e2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cmapr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrixstats run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrixstats diff --git a/recipes/bioconductor-cn.farms/meta.yaml b/recipes/bioconductor-cn.farms/meta.yaml index 3e4bdcf6ffbda..43f61d3317be2 100644 --- a/recipes/bioconductor-cn.farms/meta.yaml +++ b/recipes/bioconductor-cn.farms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "cn.farms" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c8dbca1cbb703358e3e24c5fe1d63ee1 + md5: 8a991cf7fb9deb2d6ed855617dcfb853 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cn.farms", max_pin="x.x") }}' # Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-ff @@ -34,12 +35,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-ff diff --git a/recipes/bioconductor-cn.mops/meta.yaml b/recipes/bioconductor-cn.mops/meta.yaml index 12f2094e41535..d923f5f26fc2d 100644 --- a/recipes/bioconductor-cn.mops/meta.yaml +++ b/recipes/bioconductor-cn.mops/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "cn.mops" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 76e3ef5df3615011d3ba8fbf432ee0d0 + md5: e4e51a7ecd3810464be443ba9a6b6919 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cn.mops", max_pin="x.x") }}' # Suggests: DNAcopy requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cnanorm/meta.yaml b/recipes/bioconductor-cnanorm/meta.yaml index bf9abd406114f..0c80a7be46633 100644 --- a/recipes/bioconductor-cnanorm/meta.yaml +++ b/recipes/bioconductor-cnanorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.1" %} +{% set version = "1.48.0" %} {% set name = "CNAnorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77feee7f1c624b8b4e380198d923e23c + md5: b9d0f995f3466875285a152415863842 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnanorm", max_pin="x.x") }}' requirements: host: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - r-base - libblas - liblapack run: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cner/meta.yaml b/recipes/bioconductor-cner/meta.yaml index 5363c676fcf79..107812a815c75 100644 --- a/recipes/bioconductor-cner/meta.yaml +++ b/recipes/bioconductor-cner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "CNEr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2382aa80af28d00b3f990268bf61bfbf + md5: 56fdc5f3323b1f3efbb8d85584ff75d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cner", max_pin="x.x") }}' # Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-dbi >=0.7' - 'r-ggplot2 >=2.1.0' @@ -43,18 +44,18 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-dbi >=0.7' - 'r-ggplot2 >=2.1.0' diff --git a/recipes/bioconductor-cnordt/meta.yaml b/recipes/bioconductor-cnordt/meta.yaml index 6259262861c0d..b6ac951b76ba2 100644 --- a/recipes/bioconductor-cnordt/meta.yaml +++ b/recipes/bioconductor-cnordt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "CNORdt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd2389f6b262b0bf323ca0e49a20d3f4 + md5: 74b0c2783638f7d5ce872577eb305ad3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnordt", max_pin="x.x") }}' requirements: host: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-abind - r-base - libblas - liblapack run: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-abind - r-base build: diff --git a/recipes/bioconductor-cnorfeeder/meta.yaml b/recipes/bioconductor-cnorfeeder/meta.yaml index 3c97382193da2..5e8b159d1d8a6 100644 --- a/recipes/bioconductor-cnorfeeder/meta.yaml +++ b/recipes/bioconductor-cnorfeeder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "CNORfeeder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ba673e6af1ed038b14678843be82304 + md5: 4dd8271e71505e41edc9509155cb4f9f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnorfeeder", max_pin="x.x") }}' noarch: generic # Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph requirements: host: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-cnorfuzzy/meta.yaml b/recipes/bioconductor-cnorfuzzy/meta.yaml index 3d5879dc204ed..7343bc5ed0dea 100644 --- a/recipes/bioconductor-cnorfuzzy/meta.yaml +++ b/recipes/bioconductor-cnorfuzzy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "CNORfuzzy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c018031c48dc484ad32838a281083afe + md5: c7d388f25498f45c39d8af83c5e14a89 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnorfuzzy", max_pin="x.x") }}' # Suggests: xtable, Rgraphviz, RUnit, BiocGenerics requirements: host: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-base - 'r-nloptr >=0.8.5' - libblas - liblapack run: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-base - 'r-nloptr >=0.8.5' build: diff --git a/recipes/bioconductor-cnorode/meta.yaml b/recipes/bioconductor-cnorode/meta.yaml index 4f2da296035a0..7e2f238c23ba1 100644 --- a/recipes/bioconductor-cnorode/meta.yaml +++ b/recipes/bioconductor-cnorode/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "CNORode" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7b31713feb3c910b5bd09e105cb0a5d + md5: e93b3e3437c26f6cfab6690f78c6a6cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnorode", max_pin="x.x") }}' requirements: host: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-base - r-genalg - r-knitr - libblas - liblapack run: - - 'bioconductor-cellnoptr >=1.46.0,<1.47.0' + - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - r-base - r-genalg - r-knitr diff --git a/recipes/bioconductor-cntools/meta.yaml b/recipes/bioconductor-cntools/meta.yaml index 436548a21c867..f19724490eaa7 100644 --- a/recipes/bioconductor-cntools/meta.yaml +++ b/recipes/bioconductor-cntools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "CNTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f8beb8f9bd3721c978cb42536062279 + md5: e3ce148937711a84dadf67b5f09c5373 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cntools", max_pin="x.x") }}' requirements: host: - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base - libblas - liblapack run: - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-cnvfilter/meta.yaml b/recipes/bioconductor-cnvfilter/meta.yaml index 04e1f13b266fe..3908bc6abda4c 100644 --- a/recipes/bioconductor-cnvfilter/meta.yaml +++ b/recipes/bioconductor-cnvfilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "CNVfilteR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fba99dc7e437235fee4a92960716f34f + md5: dda71463a83db8c7aaf1bbfa79424ba3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvfilter", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown +# Suggests: knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-copynumberplots >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-pracma run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-copynumberplots >=1.16.0,<1.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-pracma diff --git a/recipes/bioconductor-cnvgsa/meta.yaml b/recipes/bioconductor-cnvgsa/meta.yaml index b7846884afed1..b0cf597118eb0 100644 --- a/recipes/bioconductor-cnvgsa/meta.yaml +++ b/recipes/bioconductor-cnvgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "cnvGSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f98d6c70fbf31cfb8cd3282cabffce4f + md5: b3216442e27ff2c602e908aeb6a6f6e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvgsa", max_pin="x.x") }}' noarch: generic # Suggests: cnvGSAdata, org.Hs.eg.db requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-brglm - r-doparallel - r-foreach - r-splitstackshape run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-brglm - r-doparallel diff --git a/recipes/bioconductor-cnvgsadata/meta.yaml b/recipes/bioconductor-cnvgsadata/meta.yaml index 2cd90be972d1f..cea79ff073286 100644 --- a/recipes/bioconductor-cnvgsadata/meta.yaml +++ b/recipes/bioconductor-cnvgsadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "cnvGSAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 706bef72dd4c818adc1295a3f93bd2cf + md5: 1cc86a2066cae55493d710c475cc7112 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvgsadata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-cnvgsa >=1.44.0,<1.45.0' + - 'bioconductor-cnvgsa >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-cnvgsa >=1.44.0,<1.45.0' + - 'bioconductor-cnvgsa >=1.46.0,<1.47.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cnvgsadata/post-link.sh b/recipes/bioconductor-cnvgsadata/post-link.sh index c07e462f3f5e4..068b0cb6fee2b 100644 --- a/recipes/bioconductor-cnvgsadata/post-link.sh +++ b/recipes/bioconductor-cnvgsadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cnvgsadata-1.36.0" +installBiocDataPackage.sh "cnvgsadata-1.38.0" diff --git a/recipes/bioconductor-cnviz/meta.yaml b/recipes/bioconductor-cnviz/meta.yaml index 30708fe0762b3..000ef56911ecf 100644 --- a/recipes/bioconductor-cnviz/meta.yaml +++ b/recipes/bioconductor-cnviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CNViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f269c211d1f940ae3e019441ca4ec85 + md5: e0499b53c29869a1f661e40f4e1f76ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnviz", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-copynumberplots >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' + - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' - r-base - r-dplyr - r-dt @@ -32,9 +33,9 @@ requirements: - r-scales - 'r-shiny >=1.5.0' run: - - 'bioconductor-copynumberplots >=1.16.0,<1.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' + - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-cnvmetrics/meta.yaml b/recipes/bioconductor-cnvmetrics/meta.yaml index 7b477048e9c84..5a6a3e47ff376 100644 --- a/recipes/bioconductor-cnvmetrics/meta.yaml +++ b/recipes/bioconductor-cnvmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "CNVMetrics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d745a88974ac4ec80fced32581c02fe + md5: ebb4f847744aaddcc125d870b1a67154 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvmetrics", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-gridextra - r-magrittr - r-pheatmap + - r-rbeta2009 run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-gridextra - r-magrittr - r-pheatmap + - r-rbeta2009 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cnvpanelizer/meta.yaml b/recipes/bioconductor-cnvpanelizer/meta.yaml index abc49fe1ceaeb..3af7fd5235897 100644 --- a/recipes/bioconductor-cnvpanelizer/meta.yaml +++ b/recipes/bioconductor-cnvpanelizer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "CNVPanelizer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bc8f796d0a9a70d1047059939acaef89 + md5: 1d984f2fa3f3db99f3ccf72b5c9a0890 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvpanelizer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-noiseq >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-foreach - r-ggplot2 @@ -42,14 +43,14 @@ requirements: - r-stringr - r-testthat run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-noiseq >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-foreach - r-ggplot2 diff --git a/recipes/bioconductor-cnvranger/meta.yaml b/recipes/bioconductor-cnvranger/meta.yaml index 816e951bed0f6..cba6dd7a6a6ec 100644 --- a/recipes/bioconductor-cnvranger/meta.yaml +++ b/recipes/bioconductor-cnvranger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.4" %} +{% set version = "1.18.0" %} {% set name = "CNVRanger" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fba593b7facaf4bad0bbd16b64b41830 + md5: 3e68952c47447dfad311d1adf7b971d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvranger", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gdsarray >=1.20.0,<1.21.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gdsarray >=1.22.0,<1.23.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-lattice @@ -42,19 +43,19 @@ requirements: - r-rappdirs - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gdsarray >=1.20.0,<1.21.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gdsarray >=1.22.0,<1.23.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-lattice diff --git a/recipes/bioconductor-cnvrd2/meta.yaml b/recipes/bioconductor-cnvrd2/meta.yaml index 60e0572097bea..85d6f7fae13aa 100644 --- a/recipes/bioconductor-cnvrd2/meta.yaml +++ b/recipes/bioconductor-cnvrd2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CNVrd2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e8eafc38f592bd7322d9f4e8fd12a598 + md5: 9cc2c933a0a521472b5eb6f1382cefd5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cnvrd2", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-gridextra - r-rjags run: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-cocitestats/meta.yaml b/recipes/bioconductor-cocitestats/meta.yaml index 26df6d2a2141c..5c72102058add 100644 --- a/recipes/bioconductor-cocitestats/meta.yaml +++ b/recipes/bioconductor-cocitestats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "CoCiteStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2129b78957087707546562a0934e738a + md5: de358f1bd9429dbedc2e7bc91037373a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cocitestats", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-cocoa/build_failure.linux-64.yaml b/recipes/bioconductor-cocoa/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..65ed04bfcc672 --- /dev/null +++ b/recipes/bioconductor-cocoa/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: dd85fa037d453102ef61e3f47e51564c9d31f479966d88c0b89e752d33f8ea37 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + bioconda/noarch 100% + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gbioconda/noarch + [] 1.5s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 100% + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 + [] 1.6s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/noarch + [] 1.7s + conda-forge/linux-64 + conda-forge/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.8s + conda-forge/linux-64 + conda-forge/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.9s + conda-forge/linux-64 + conda-forge/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 2.0s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 2.1s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gconda-forge/noarch + [] 2.2s + conda-forge/linux-64 + pkgs/r/linux-64 + pkgs/r/noarch 100%[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/r/noarch + pkgs/r/linux-64 + [] 2.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.9s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.3s + [2K[1A[2K[0Gconda-forge/linux-64 + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.2MB/s 0.0s + opt/conda/conda-bld/noarch 1.1kB @ 22.3MB/s 0.0s + [?25hTraceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test + environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, + File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env + display_actions(actions, index) + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions + actions['LINK'] = [index[d] for d in actions['LINK']] + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in + actions['LINK'] = [index[d] for d in actions['LINK']] + KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-cocoa/meta.yaml b/recipes/bioconductor-cocoa/meta.yaml index 2da84c65e4b84..6a4528f450642 100644 --- a/recipes/bioconductor-cocoa/meta.yaml +++ b/recipes/bioconductor-cocoa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "COCOA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 528e8eb1e1a358866292395b64570c61 + md5: 6525a033b4b6ab78aa4ecb8e3f35b6e3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cocoa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mira >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mira >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-fitdistrplus @@ -35,13 +36,13 @@ requirements: - r-simplecache - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mira >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mira >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-fitdistrplus diff --git a/recipes/bioconductor-codelink/meta.yaml b/recipes/bioconductor-codelink/meta.yaml index c83b6b10126cb..5aa4146f8d961 100644 --- a/recipes/bioconductor-codelink/meta.yaml +++ b/recipes/bioconductor-codelink/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "codelink" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 35d35231bf21b1815e02271098872c05 + md5: 7988c997146174710b5faacc70c10328 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-codelink", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, parallel, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-codex/meta.yaml b/recipes/bioconductor-codex/meta.yaml index dd3350d1a11ec..0b4bb41c7a4db 100644 --- a/recipes/bioconductor-codex/meta.yaml +++ b/recipes/bioconductor-codex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "CODEX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee6fc5514b4d8982f0d639c34c589b9f + md5: 5b1f67c5fbf4bbe4a3ee4f6da956a886 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-codex", max_pin="x.x") }}' noarch: generic # Suggests: WES.1KG.WUGSC requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-cogaps/meta.yaml b/recipes/bioconductor-cogaps/meta.yaml index f8b21e0ae36c9..c891b02938f1c 100644 --- a/recipes/bioconductor-cogaps/meta.yaml +++ b/recipes/bioconductor-cogaps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.19.1" %} +{% set version = "3.22.0" %} {% set name = "CoGAPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22a7d6bb9033c0a2d4c1170856b87b06 + md5: d4c9ec9b2be6c77fbb47c632b62c84b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat, knitr, rmarkdown, BiocStyle + run_exports: '{{ pin_subpackage("bioconductor-cogaps", max_pin="x.x") }}' +# Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-cluster @@ -40,13 +41,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-cluster diff --git a/recipes/bioconductor-cogena/meta.yaml b/recipes/bioconductor-cogena/meta.yaml index e57e9a3bcf655..ea4472b90f122 100644 --- a/recipes/bioconductor-cogena/meta.yaml +++ b/recipes/bioconductor-cogena/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "cogena" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6d25c8d1515cc3b06d4337a28819ea16 + md5: 47a50e5f5d62a9b2f6fcd7bf3f5b9cc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cogena", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown (>= 2.1) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-amap - r-apcluster - r-base @@ -43,7 +44,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-amap - r-apcluster - r-base diff --git a/recipes/bioconductor-cogeqc/meta.yaml b/recipes/bioconductor-cogeqc/meta.yaml index b39477688806a..49d2616f6027b 100644 --- a/recipes/bioconductor-cogeqc/meta.yaml +++ b/recipes/bioconductor-cogeqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "cogeqc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2a92798147ae38ee7e618149ffabcdf5 + md5: 751833fc95e416546193b021e0cbfc69 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cogeqc", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr # SystemRequirements: BUSCO (>= 5.1.3) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-ggbeeswarm - r-ggplot2 @@ -34,8 +35,8 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-ggbeeswarm - r-ggplot2 diff --git a/recipes/bioconductor-cogito/meta.yaml b/recipes/bioconductor-cogito/meta.yaml index c2faac70f8f75..85a806043f509 100644 --- a/recipes/bioconductor-cogito/meta.yaml +++ b/recipes/bioconductor-cogito/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "Cogito" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 436e9cbf49b6a9fbe470772048229db3 + md5: 934ceee8a56ab742bbf3c09af96cb2ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cogito", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-biocmanager @@ -35,11 +36,11 @@ requirements: - r-magrittr - r-rmarkdown run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-biocmanager diff --git a/recipes/bioconductor-cogps/meta.yaml b/recipes/bioconductor-cogps/meta.yaml index cef7325cc9a13..558d1ed731974 100644 --- a/recipes/bioconductor-cogps/meta.yaml +++ b/recipes/bioconductor-cogps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "coGPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2836cad04f3b94cbe305cacaaaee6570 + md5: a824d8a41fee47628eb7f369adef4a2c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cogps", max_pin="x.x") }}' noarch: generic # Suggests: limma requirements: diff --git a/recipes/bioconductor-cohcap/meta.yaml b/recipes/bioconductor-cohcap/meta.yaml index 56afd1c45e2a5..eaafa323c174f 100644 --- a/recipes/bioconductor-cohcap/meta.yaml +++ b/recipes/bioconductor-cohcap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "COHCAP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c6563694a4c95720c88bcc4df639f28 + md5: 6c7c601f8c8aee626d2fa1a6dd306dca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cohcap", max_pin="x.x") }}' # SystemRequirements: Perl requirements: host: - - 'bioconductor-cohcapanno >=1.36.0,<1.37.0' + - 'bioconductor-cohcapanno >=1.38.0,<1.39.0' - r-base - r-bh - r-gplots @@ -32,7 +33,7 @@ requirements: - liblapack - 'perl >=5.6.0' run: - - 'bioconductor-cohcapanno >=1.36.0,<1.37.0' + - 'bioconductor-cohcapanno >=1.38.0,<1.39.0' - r-base - r-bh - r-gplots diff --git a/recipes/bioconductor-cohcapanno/meta.yaml b/recipes/bioconductor-cohcapanno/meta.yaml index b42c2e9817598..4c64d0e2c842f 100644 --- a/recipes/bioconductor-cohcapanno/meta.yaml +++ b/recipes/bioconductor-cohcapanno/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "COHCAPanno" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d95f164282852d44cc982e461157b622 + md5: 78fd4891651a8a62779fe402a13ba6b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cohcapanno", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cohcapanno/post-link.sh b/recipes/bioconductor-cohcapanno/post-link.sh index 5ae5b6c9dbbe4..4b2b9b6c06bfa 100644 --- a/recipes/bioconductor-cohcapanno/post-link.sh +++ b/recipes/bioconductor-cohcapanno/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cohcapanno-1.36.0" +installBiocDataPackage.sh "cohcapanno-1.38.0" diff --git a/recipes/bioconductor-cola/meta.yaml b/recipes/bioconductor-cola/meta.yaml index 11f671e63f537..f5913bc74f273 100644 --- a/recipes/bioconductor-cola/meta.yaml +++ b/recipes/bioconductor-cola/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "cola" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 983ec7f83e64be0637f134ca3576c106 + md5: 57e054e12610fb8d62de83c22f6ed1de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cola", max_pin="x.x") }}' # Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-brew - 'r-circlize >=0.4.7' @@ -51,9 +52,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-brew - 'r-circlize >=0.4.7' diff --git a/recipes/bioconductor-colonca/meta.yaml b/recipes/bioconductor-colonca/meta.yaml index 1a0fd696e7055..642bf020f6e11 100644 --- a/recipes/bioconductor-colonca/meta.yaml +++ b/recipes/bioconductor-colonca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "colonCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88a73e6339cf99f42858ddcb073c4e61 + md5: d12f03a7ded676f392dbbb26bbbef174 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-colonca", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-colonca/post-link.sh b/recipes/bioconductor-colonca/post-link.sh index ab2079c657c89..63e3e55b7a7a0 100644 --- a/recipes/bioconductor-colonca/post-link.sh +++ b/recipes/bioconductor-colonca/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "colonca-1.42.0" +installBiocDataPackage.sh "colonca-1.44.0" diff --git a/recipes/bioconductor-comapr/meta.yaml b/recipes/bioconductor-comapr/meta.yaml index a4f6549c9f2c1..130fa29cd2cd1 100644 --- a/recipes/bioconductor-comapr/meta.yaml +++ b/recipes/bioconductor-comapr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.1" %} {% set name = "comapr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eca7d37960ffea05ade6ed24636d08ff + md5: 64dbcfb7f563dc874dc327988ebf8c07 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-comapr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr @@ -43,13 +44,13 @@ requirements: - r-scales - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr diff --git a/recipes/bioconductor-combi/meta.yaml b/recipes/bioconductor-combi/meta.yaml index 7bccb67dc97cd..9998659a07a49 100644 --- a/recipes/bioconductor-combi/meta.yaml +++ b/recipes/bioconductor-combi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "combi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2b81ee7cc0b92f982a363f54d42d62dd + md5: 6fe16559db40b31126eb543abf6819fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-combi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-alabama - r-base - r-bb - r-cobs - r-dbi - r-ggplot2 - - r-matrix + - 'r-matrix >=1.6.0' - r-nleqslv - r-reshape2 - r-tensor - r-vegan run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-alabama - r-base - r-bb - r-cobs - r-dbi - r-ggplot2 - - r-matrix + - 'r-matrix >=1.6.0' - r-nleqslv - r-reshape2 - r-tensor diff --git a/recipes/bioconductor-comet/meta.yaml b/recipes/bioconductor-comet/meta.yaml index 11290e90520bd..8ba6a888a5ef3 100644 --- a/recipes/bioconductor-comet/meta.yaml +++ b/recipes/bioconductor-comet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "coMET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1cbe82dc9eccd6c98d091a7c46516e0 + md5: 34ef806a15489ccd38abd9002fe075ed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-comet", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RUnit, BiocGenerics, showtext requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-corrplot - r-gridextra - r-hash - r-psych run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-corrplot - r-gridextra diff --git a/recipes/bioconductor-comethdmr/meta.yaml b/recipes/bioconductor-comethdmr/meta.yaml index 52616731a8f9d..710278af6f46a 100644 --- a/recipes/bioconductor-comethdmr/meta.yaml +++ b/recipes/bioconductor-comethdmr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "coMethDMR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 625273089317239e835e4d368f579230 + md5: 0a6229d90868a4a60eb0f72c4499d1fc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-comethdmr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-lmertest run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-lmertest test: diff --git a/recipes/bioconductor-compass/meta.yaml b/recipes/bioconductor-compass/meta.yaml index 9919fb7c6de16..2948a0f2be468 100644 --- a/recipes/bioconductor-compass/meta.yaml +++ b/recipes/bioconductor-compass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.1" %} +{% set version = "1.40.0" %} {% set name = "COMPASS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd27c24d1296f22f905ca0533581224a + md5: 6ab4a9ce40637244377f77b7baaecc38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compass", max_pin="x.x") }}' # Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-abind - r-base - r-clue @@ -42,7 +43,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-abind - r-base - r-clue diff --git a/recipes/bioconductor-compcoder/meta.yaml b/recipes/bioconductor-compcoder/meta.yaml index 7c614b91c9c83..5cc77115da02b 100644 --- a/recipes/bioconductor-compcoder/meta.yaml +++ b/recipes/bioconductor-compcoder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.2" %} +{% set version = "1.38.0" %} {% set name = "compcodeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ceef6dc14644528d10b8b0549ddd8cdb + md5: b1ec77496e614cf3399843b8c34e6ab2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compcoder", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), baySeq (>= 2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), rmarkdown, phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva +# Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-ape - r-base - r-catools @@ -37,13 +38,16 @@ requirements: - r-matrixstats - r-modeest - r-phylolm + - r-rmarkdown - r-rocr + - r-shiny + - r-shinydashboard - r-sm - r-stringr - r-vioplot run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-ape - r-base - r-catools @@ -58,7 +62,10 @@ requirements: - r-matrixstats - r-modeest - r-phylolm + - r-rmarkdown - r-rocr + - r-shiny + - r-shinydashboard - r-sm - r-stringr - r-vioplot diff --git a/recipes/bioconductor-compepitools/meta.yaml b/recipes/bioconductor-compepitools/meta.yaml index 10f4dce2ea032..df49a8380538b 100644 --- a/recipes/bioconductor-compepitools/meta.yaml +++ b/recipes/bioconductor-compepitools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "compEpiTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4073e61c47740e5f0c48db76dfb4b91c + md5: 0ccd28b8de6020ae19f303fc7009ce19 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compepitools", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylpipe >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylpipe >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-gplots run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylpipe >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylpipe >=1.36.0,<1.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-gplots test: diff --git a/recipes/bioconductor-complexheatmap/meta.yaml b/recipes/bioconductor-complexheatmap/meta.yaml index 24486629fc4bb..e97a5929f5d7d 100644 --- a/recipes/bioconductor-complexheatmap/meta.yaml +++ b/recipes/bioconductor-complexheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "ComplexHeatmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87feece17236af22e1d3ad35e3fb7efd + md5: f4f19a1339c99471cb23ffc4a7272881 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-complexheatmap", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.14' - r-clue @@ -36,7 +37,7 @@ requirements: - r-png - r-rcolorbrewer run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.14' - r-clue diff --git a/recipes/bioconductor-compounddb/meta.yaml b/recipes/bioconductor-compounddb/meta.yaml index 71c955494be81..6c581d53b553f 100644 --- a/recipes/bioconductor-compounddb/meta.yaml +++ b/recipes/bioconductor-compounddb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "CompoundDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38742446decc04a230b9f43055145158 + md5: 7863bdbb64d2068c22225ece8ed5844c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compounddb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-dbi - r-dbplyr @@ -41,17 +42,17 @@ requirements: - r-tibble - r-xml2 run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-dbi - r-dbplyr diff --git a/recipes/bioconductor-compran/meta.yaml b/recipes/bioconductor-compran/meta.yaml index 1a13f4a07dfb8..487b8ff516290 100644 --- a/recipes/bioconductor-compran/meta.yaml +++ b/recipes/bioconductor-compran/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ComPrAn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41183d8093e3f4a754c7eac6a666993e + md5: 24011dcffe9f6c7b22be8e2de0e855b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compran", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-compspot/build.sh b/recipes/bioconductor-compspot/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-compspot/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-compspot/meta.yaml b/recipes/bioconductor-compspot/meta.yaml new file mode 100644 index 0000000000000..c735ad00891b4 --- /dev/null +++ b/recipes/bioconductor-compspot/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.0" %} +{% set name = "compSPOT" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7aa69c9c3ec0c008ad0fdfb4dbbcac57 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-compspot", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - r-base + - r-data.table + - r-ggplot2 + - r-ggpubr + - r-gridextra + - r-magrittr + - r-plotly + run: + - r-base + - r-data.table + - r-ggplot2 + - r-ggpubr + - r-gridextra + - r-magrittr + - r-plotly +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots' + description: 'Clonal cell groups share common mutations within cancer, precancer, and even clinically normal appearing tissues. The frequency and location of these mutations may predict prognosis and cancer risk. It has also been well established that certain genomic regions have increased sensitivity to acquiring mutations. Mutation-sensitive genomic regions may therefore serve as markers for predicting cancer risk. This package contains multiple functions to establish significantly mutated hotspots, compare hotspot mutation burden between samples, and perform exploratory data analysis of the correlation between hotspot mutation burden and personal risk factors for cancer, such as age, gender, and history of carcinogen exposure. This package allows users to identify robust genomic markers to help establish cancer risk.' + diff --git a/recipes/bioconductor-concordexr/meta.yaml b/recipes/bioconductor-concordexr/meta.yaml index 26925b4bf5159..16a7d13375823 100644 --- a/recipes/bioconductor-concordexr/meta.yaml +++ b/recipes/bioconductor-concordexr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "concordexR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a83636d355e3b226da6f6030c17d84d + md5: 5ffab81582264ccb300c9f937c698adf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-concordexr", max_pin="x.x") }}' noarch: generic # Suggests: BiocNeighbors, BiocStyle, bluster, covr, knitr, patchwork, rmarkdown, scater, TENxPBMCData, testthat (>= 3.0.0), vdiffr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-cli - r-ggplot2 @@ -31,8 +32,8 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-cli - r-ggplot2 diff --git a/recipes/bioconductor-condiments/build_failure.linux-64.yaml b/recipes/bioconductor-condiments/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..64bb7869e9bff --- /dev/null +++ b/recipes/bioconductor-condiments/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d70ad20d6aa8d5ec24cc58bdae0002e9ce657a5241a612189057a31a9a2b5902 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - bioconductor-distinct >=1.14.0,<1.15.0 + - r-ecume >=0.9.1 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-mgcv + - bioconductor-slingshot >=2.10.0,<2.11.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-matrixstats + - r-base 4.3.* + - r-rann + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-distinct >=1.14.0,<1.15.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-pbapply + - r-igraph + - r-magrittr + - r-dplyr >=1.0 + - bioconductor-trajectoryutils >=1.10.0,<1.11.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + - bioconductor-distinct >=1.14.0,<1.15.0 + - r-ecume >=0.9.1 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-mgcv + - bioconductor-slingshot >=2.10.0,<2.11.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-matrixstats + - r-base 4.3.* + - r-rann + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-distinct >=1.14.0,<1.15.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-distinct[version='>=1.14.0,<1.15.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-condiments/meta.yaml b/recipes/bioconductor-condiments/meta.yaml index 752243104b7c8..c6cceadc411f7 100644 --- a/recipes/bioconductor-condiments/meta.yaml +++ b/recipes/bioconductor-condiments/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "condiments" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 34ccc7d55f139c0c225b31f5a4d6d54e + md5: 63b9756275a532e7d38c67402cef7efd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-condiments", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-distinct >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-distinct >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - 'r-dplyr >=1.0' - 'r-ecume >=0.9.1' @@ -37,12 +38,12 @@ requirements: - r-pbapply - r-rann run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-distinct >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-distinct >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - 'r-dplyr >=1.0' - 'r-ecume >=0.9.1' diff --git a/recipes/bioconductor-confess/meta.yaml b/recipes/bioconductor-confess/meta.yaml index bfc0aec5efc7d..6e7de11118b8b 100644 --- a/recipes/bioconductor-confess/meta.yaml +++ b/recipes/bioconductor-confess/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CONFESS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7778073e6c190fe4ce709a28cd0c644e + md5: 67bd1d40551528aab55620fc0a619713 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-confess", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowmeans >=1.60.0,<1.61.0' - - 'bioconductor-flowmerge >=2.48.0,<2.49.0' - - 'bioconductor-flowpeaks >=1.46.0,<1.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-samspectral >=1.54.0,<1.55.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowmeans >=1.62.0,<1.63.0' + - 'bioconductor-flowmerge >=2.50.0,<2.51.0' + - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-samspectral >=1.56.0,<1.57.0' - r-base - r-changepoint - r-cluster @@ -49,14 +50,14 @@ requirements: - r-wavethresh - r-zoo run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowmeans >=1.60.0,<1.61.0' - - 'bioconductor-flowmerge >=2.48.0,<2.49.0' - - 'bioconductor-flowpeaks >=1.46.0,<1.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-samspectral >=1.54.0,<1.55.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowmeans >=1.62.0,<1.63.0' + - 'bioconductor-flowmerge >=2.50.0,<2.51.0' + - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-samspectral >=1.56.0,<1.57.0' - r-base - r-changepoint - r-cluster diff --git a/recipes/bioconductor-confessdata/meta.yaml b/recipes/bioconductor-confessdata/meta.yaml index 4d75f88da25a8..68d94dd254c3a 100644 --- a/recipes/bioconductor-confessdata/meta.yaml +++ b/recipes/bioconductor-confessdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CONFESSdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dde8faa711c55ae0abd4a0b9f8132233 + md5: 07df3f8f783b3e734c4032b3f6ed61bd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-confessdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-confessdata/post-link.sh b/recipes/bioconductor-confessdata/post-link.sh index 83419aae9c66c..bd491dd59a8f3 100644 --- a/recipes/bioconductor-confessdata/post-link.sh +++ b/recipes/bioconductor-confessdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "confessdata-1.28.0" +installBiocDataPackage.sh "confessdata-1.30.0" diff --git a/recipes/bioconductor-connectivitymap/meta.yaml b/recipes/bioconductor-connectivitymap/meta.yaml index 792e086df1b38..ce2ee8169dab4 100644 --- a/recipes/bioconductor-connectivitymap/meta.yaml +++ b/recipes/bioconductor-connectivitymap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ConnectivityMap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c98c66f64c50f8ae262bccdd4cd0bae + md5: bac29780256afebfd49b90f268114eaf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-connectivitymap", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-connectivitymap/post-link.sh b/recipes/bioconductor-connectivitymap/post-link.sh index 937ed494e6c7c..6840e2570ebd7 100644 --- a/recipes/bioconductor-connectivitymap/post-link.sh +++ b/recipes/bioconductor-connectivitymap/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "connectivitymap-1.36.0" +installBiocDataPackage.sh "connectivitymap-1.38.0" diff --git a/recipes/bioconductor-consensus/meta.yaml b/recipes/bioconductor-consensus/meta.yaml index 5f5940f7ad49e..3cfdf91faedfc 100644 --- a/recipes/bioconductor-consensus/meta.yaml +++ b/recipes/bioconductor-consensus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "consensus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bd7bce9ef0825d845f3b7db038974ab7 + md5: f930fc9b058bce80ccbb112082cf3dc7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consensus", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, rmarkdown, BiocGenerics requirements: diff --git a/recipes/bioconductor-consensusclusterplus/meta.yaml b/recipes/bioconductor-consensusclusterplus/meta.yaml index e9500b459fbd0..03b92e32b0a1c 100644 --- a/recipes/bioconductor-consensusclusterplus/meta.yaml +++ b/recipes/bioconductor-consensusclusterplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "ConsensusClusterPlus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56f8a569c9a014296b658e520f1993d2 + md5: 0943cc2a0d1dff314f384e65b8d71897 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consensusclusterplus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-all >=1.42.0,<1.43.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-all >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster run: - - 'bioconductor-all >=1.42.0,<1.43.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-all >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster test: diff --git a/recipes/bioconductor-consensusde/meta.yaml b/recipes/bioconductor-consensusde/meta.yaml index f31966944b1c0..303d9bae79e62 100644 --- a/recipes/bioconductor-consensusde/meta.yaml +++ b/recipes/bioconductor-consensusde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "consensusDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,62 +11,63 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef7863253b783fe015aee65395b9c453 + md5: f4aedcdf9823551d0ea0cc2ae64ac475 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consensusde", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-airway >=1.20.0,<1.21.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-airway >=1.22.0,<1.23.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - r-base - r-data.table - r-dendextend - r-rcolorbrewer run: - - 'bioconductor-airway >=1.20.0,<1.21.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-airway >=1.22.0,<1.23.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - r-base - r-data.table diff --git a/recipes/bioconductor-consensusov/meta.yaml b/recipes/bioconductor-consensusov/meta.yaml index ebb65e08d7703..10d4991a9294a 100644 --- a/recipes/bioconductor-consensusov/meta.yaml +++ b/recipes/bioconductor-consensusov/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "consensusOV" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd71f79b5fac603f87f16319580f65ff + md5: 54a03e3c6775a27643ffbf5192967ac2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consensusov", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefu >=2.32.0,<2.33.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefu >=2.34.0,<2.35.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gdata - r-matrixstats - r-randomforest run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefu >=2.32.0,<2.33.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefu >=2.34.0,<2.35.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gdata - r-matrixstats diff --git a/recipes/bioconductor-consensusseeker/meta.yaml b/recipes/bioconductor-consensusseeker/meta.yaml index b9a4044f33479..55d0281d77d27 100644 --- a/recipes/bioconductor-consensusseeker/meta.yaml +++ b/recipes/bioconductor-consensusseeker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "consensusSeekeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 60e0fda93cad54f7882cba52186783eb + md5: e752cec43fa487cd071a27a1f955b17e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consensusseeker", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-stringr test: diff --git a/recipes/bioconductor-consica/meta.yaml b/recipes/bioconductor-consica/meta.yaml index 1f06a4b25d807..cfe5f1bd4e8c0 100644 --- a/recipes/bioconductor-consica/meta.yaml +++ b/recipes/bioconductor-consica/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "2.0.0" %} {% set name = "consICA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5063262bd3705a643f8fada1e509fce4 + md5: b64f871ca062dc65d6a883b000c761d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-consica", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, BiocStyle, rmarkdown, testthat +# Suggests: knitr, BiocStyle, rmarkdown, testthat, Seurat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - 'r-fastica >=1.2.1' + - r-ggplot2 - r-pheatmap + - r-rfast - r-sm - r-survival run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - 'r-fastica >=1.2.1' + - r-ggplot2 - r-pheatmap + - r-rfast - r-sm - r-survival test: diff --git a/recipes/bioconductor-constand/meta.yaml b/recipes/bioconductor-constand/meta.yaml index b730f63f0843f..f4242d0e9f6d5 100644 --- a/recipes/bioconductor-constand/meta.yaml +++ b/recipes/bioconductor-constand/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CONSTANd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd346235e5d208c081a80054f0c3d00f + md5: 6337f6a248f820600a99fa9ef9fc1571 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-constand", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma requirements: diff --git a/recipes/bioconductor-contibait/meta.yaml b/recipes/bioconductor-contibait/meta.yaml index 168269e1a26ab..71415b965efc6 100644 --- a/recipes/bioconductor-contibait/meta.yaml +++ b/recipes/bioconductor-contibait/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "contiBAIT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bc21baae59dc116f62b237e1690ac8ec + md5: 8297fd66bbfcd997be0f23cf31fcd644 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-contibait", max_pin="x.x") }}' # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.51.0.3' - r-clue @@ -47,17 +48,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-exomecopy >=1.46.0,<1.47.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-exomecopy >=1.48.0,<1.49.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.51.0.3' - r-clue diff --git a/recipes/bioconductor-conumee/meta.yaml b/recipes/bioconductor-conumee/meta.yaml index 9d3c9cffbc336..e3dde4f6aeff4 100644 --- a/recipes/bioconductor-conumee/meta.yaml +++ b/recipes/bioconductor-conumee/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "conumee" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2e8642efe6cfe74f1856bae5c4b5ec7d + md5: f7eab6e95ed82f050ef52895ef178ba0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-conumee", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl requirements: host: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-convert/meta.yaml b/recipes/bioconductor-convert/meta.yaml index 5ed7bfd042ff8..82edc223b9c80 100644 --- a/recipes/bioconductor-convert/meta.yaml +++ b/recipes/bioconductor-convert/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "convert" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bd45e86f579302d2cc0e0418ba7ee45b + md5: 828a21b5a554d63faeb6cc2af0784394 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-convert", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-copa/meta.yaml b/recipes/bioconductor-copa/meta.yaml index ce007cd183029..a06e57133a675 100644 --- a/recipes/bioconductor-copa/meta.yaml +++ b/recipes/bioconductor-copa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "copa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7eceebde920ee2cdba8ff709c51b0607 + md5: bd372714a4dd7e70b90d9232fcba322d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-copa", max_pin="x.x") }}' # Suggests: colonCA requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml b/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml index 9f08845e78458..2239bacb44612 100644 --- a/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml +++ b/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "COPDSexualDimorphism.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ae2601608f8b3f711b73d24734e7d7c + md5: d7cf1990679c90cbaf5250c4761effec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-copdsexualdimorphism.data", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh b/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh index a3394d9c9cada..646f2cfcfb63e 100644 --- a/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh +++ b/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "copdsexualdimorphism.data-1.36.0" +installBiocDataPackage.sh "copdsexualdimorphism.data-1.38.0" diff --git a/recipes/bioconductor-copyhelper/meta.yaml b/recipes/bioconductor-copyhelper/meta.yaml index 87f295b8ca1a0..7b020ea9f183e 100644 --- a/recipes/bioconductor-copyhelper/meta.yaml +++ b/recipes/bioconductor-copyhelper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "CopyhelpeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c38e2379228446d4d94e5ced48633a54 + md5: bb8d3e8cba0c27898e43cbdcfcac6c62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-copyhelper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-copyhelper/post-link.sh b/recipes/bioconductor-copyhelper/post-link.sh index ae2a9b3ec6ac2..e5749ce2fa85f 100644 --- a/recipes/bioconductor-copyhelper/post-link.sh +++ b/recipes/bioconductor-copyhelper/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "copyhelper-1.32.0" +installBiocDataPackage.sh "copyhelper-1.34.0" diff --git a/recipes/bioconductor-copyneutralima/meta.yaml b/recipes/bioconductor-copyneutralima/meta.yaml index 6fa32af26bdfe..ded511225ae06 100644 --- a/recipes/bioconductor-copyneutralima/meta.yaml +++ b/recipes/bioconductor-copyneutralima/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "CopyNeutralIMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8707f36701c11a45e25e92a63cb81f20 + md5: 5f1921b0aff4c3f39b662cc1ae70bf28 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-copyneutralima", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - 'r-rdpack >=0.8' run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - 'r-rdpack >=0.8' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-copyneutralima/post-link.sh b/recipes/bioconductor-copyneutralima/post-link.sh index 70533c31c5401..4ee3bca445581 100644 --- a/recipes/bioconductor-copyneutralima/post-link.sh +++ b/recipes/bioconductor-copyneutralima/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "copyneutralima-1.18.0" +installBiocDataPackage.sh "copyneutralima-1.20.0" diff --git a/recipes/bioconductor-copynumberplots/meta.yaml b/recipes/bioconductor-copynumberplots/meta.yaml index f7bdde352d85c..cd504f81494c7 100644 --- a/recipes/bioconductor-copynumberplots/meta.yaml +++ b/recipes/bioconductor-copynumberplots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "CopyNumberPlots" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72aa4e93152130ecf6edd5f80955c1a2 + md5: d35c96c521087a1183dd2ae465b3d2a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-copynumberplots", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat requirements: host: - - 'bioconductor-cn.mops >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-cn.mops >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-cn.mops >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-cn.mops >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-cordon/meta.yaml b/recipes/bioconductor-cordon/meta.yaml index 2e22b546b679c..5733faeb89818 100644 --- a/recipes/bioconductor-cordon/meta.yaml +++ b/recipes/bioconductor-cordon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "coRdon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e0567325e9913078d8dfec839b8bf7ae + md5: 19e0e0e91d3cccd4c277710c9273275e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cordon", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-data.table - r-dplyr @@ -30,8 +31,8 @@ requirements: - r-purrr - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-coregx/meta.yaml b/recipes/bioconductor-coregx/meta.yaml index eae9d496887ff..42ac17580c6ed 100644 --- a/recipes/bioconductor-coregx/meta.yaml +++ b/recipes/bioconductor-coregx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "CoreGx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcab6de8de5c96329785558051193dbe + md5: 3556f412bd014d5294b15feb8342d78e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-coregx", max_pin="x.x") }}' noarch: generic # Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-piano >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-piano >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bench - r-checkmate @@ -39,15 +40,15 @@ requirements: - r-lsa - r-rlang run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-piano >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-piano >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bench - r-checkmate @@ -65,4 +66,3 @@ about: summary: 'Classes and Functions to Serve as the Basis for Other ''Gx'' Packages' description: 'A collection of functions and classes which serve as the foundation for our lab''s suite of R packages, such as ''PharmacoGx'' and ''RadioGx''. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future ''Gx'' suite programs. Major features include a ''CoreSet'' class, from which ''RadioSet'' and ''PharmacoSet'' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) . Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) .' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - diff --git a/recipes/bioconductor-cormotif/meta.yaml b/recipes/bioconductor-cormotif/meta.yaml index fa6bd5bd21c2c..55b5aa549ab64 100644 --- a/recipes/bioconductor-cormotif/meta.yaml +++ b/recipes/bioconductor-cormotif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "Cormotif" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f673c43aae08a2209f46845b805650dc + md5: 6e65ec2460aecf6004e416d7c61c4c1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cormotif", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-corral/meta.yaml b/recipes/bioconductor-corral/meta.yaml index ff154a3ace1c2..9086ae8658de5 100644 --- a/recipes/bioconductor-corral/meta.yaml +++ b/recipes/bioconductor-corral/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "corral" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 41cabd6e030f01ca76f98c551ec32287 + md5: 7f1ebb217a695452605bd8aa94f8a5a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-corral", max_pin="x.x") }}' noarch: generic # Suggests: ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggthemes @@ -34,9 +35,9 @@ requirements: - r-reshape2 - r-transport run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggthemes diff --git a/recipes/bioconductor-correp/meta.yaml b/recipes/bioconductor-correp/meta.yaml index e56b7ed84b106..948f984973f67 100644 --- a/recipes/bioconductor-correp/meta.yaml +++ b/recipes/bioconductor-correp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "CORREP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f8c70e08f9fea69ce64ede0fa0d2f65 + md5: 2cf1b0a377be4fec857415e908e2d8d2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-correp", max_pin="x.x") }}' noarch: generic # Suggests: cluster, MASS requirements: diff --git a/recipes/bioconductor-coseq/meta.yaml b/recipes/bioconductor-coseq/meta.yaml index 11ee5916f621e..6d453975c5710 100644 --- a/recipes/bioconductor-coseq/meta.yaml +++ b/recipes/bioconductor-coseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "coseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 17d095c8ad593a4b879ea4056758ce0c + md5: 1e4bea8d520a2554f8f1095d6912074b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-coseq", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-htsfilter >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-htsfilter >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-capushe - r-compositions @@ -38,12 +39,12 @@ requirements: - r-rmixmod - r-scales run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-htsfilter >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-htsfilter >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-capushe - r-compositions diff --git a/recipes/bioconductor-cosia/meta.yaml b/recipes/bioconductor-cosia/meta.yaml index 26d86569f0b09..9db22300f331c 100644 --- a/recipes/bioconductor-cosia/meta.yaml +++ b/recipes/bioconductor-cosia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "CoSIA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f8ef5bd89e113c1bf68ce002bd54140 + md5: 217ff53ed0aac2ca3c2d91ce5237c111 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosia", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.22.0), tidyverse (>= 1.3.1), knitr (>= 1.42), rmarkdown (>= 2.20), testthat (>= 3.1.6), qpdf (>= 1.3.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationtools >=1.74.0,<1.75.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-org.ce.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationtools >=1.76.0,<1.77.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - 'r-dplyr >=1.0.7' - 'r-ggplot2 >=3.3.5' @@ -44,16 +45,16 @@ requirements: - 'r-tidyr >=1.2.0' - 'r-tidyselect >=1.1.2' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationtools >=1.74.0,<1.75.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-org.ce.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationtools >=1.76.0,<1.77.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - 'r-dplyr >=1.0.7' - 'r-ggplot2 >=3.3.5' diff --git a/recipes/bioconductor-cosiadata/meta.yaml b/recipes/bioconductor-cosiadata/meta.yaml index 184f0cea9bd1b..22efff4627359 100644 --- a/recipes/bioconductor-cosiadata/meta.yaml +++ b/recipes/bioconductor-cosiadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "CoSIAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a1d517d2c097ad8abf9c8298f4ab46d + md5: f0ec9d5ca01647ec3d52e264c0828273 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosiadata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.26.0), utils (>= 4.3.0), AnnotationHub (>= 3.7.3), knitr (>= 1.42) requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cosiadata/post-link.sh b/recipes/bioconductor-cosiadata/post-link.sh index 372312c2627c9..1ec63202a4c96 100644 --- a/recipes/bioconductor-cosiadata/post-link.sh +++ b/recipes/bioconductor-cosiadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cosiadata-1.0.0" +installBiocDataPackage.sh "cosiadata-1.2.0" diff --git a/recipes/bioconductor-cosmic.67/meta.yaml b/recipes/bioconductor-cosmic.67/meta.yaml index 805c769c75dc5..4782b2a7ffb93 100644 --- a/recipes/bioconductor-cosmic.67/meta.yaml +++ b/recipes/bioconductor-cosmic.67/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "COSMIC.67" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5242999a8b93e384ab8c05a2950ccde + md5: 392f31ffd7e95a7558d248d36dcc37fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosmic.67", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cosmic.67/post-link.sh b/recipes/bioconductor-cosmic.67/post-link.sh index 7ceb0e5a939f6..fe6c437614e15 100644 --- a/recipes/bioconductor-cosmic.67/post-link.sh +++ b/recipes/bioconductor-cosmic.67/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cosmic.67-1.36.0" +installBiocDataPackage.sh "cosmic.67-1.38.0" diff --git a/recipes/bioconductor-cosmiq/meta.yaml b/recipes/bioconductor-cosmiq/meta.yaml index 304d635d26040..9b3100477fa33 100644 --- a/recipes/bioconductor-cosmiq/meta.yaml +++ b/recipes/bioconductor-cosmiq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "cosmiq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d8f08cd3b2fd8da501b6f24cc86edbe0 + md5: ae02870f3759e09bb2c8f86d38306f01 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosmiq", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-faahko >=1.40.0,<1.41.0' - - 'bioconductor-massspecwavelet >=1.66.0,<1.67.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-faahko >=1.42.0,<1.43.0' + - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-pracma - r-rcpp - libblas - liblapack run: - - 'bioconductor-faahko >=1.40.0,<1.41.0' - - 'bioconductor-massspecwavelet >=1.66.0,<1.67.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-faahko >=1.42.0,<1.43.0' + - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-pracma - r-rcpp diff --git a/recipes/bioconductor-cosmosr/meta.yaml b/recipes/bioconductor-cosmosr/meta.yaml index 6fc21c8828f62..3e3679704e138 100644 --- a/recipes/bioconductor-cosmosr/meta.yaml +++ b/recipes/bioconductor-cosmosr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "cosmosR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f18bfd17d55bd1b64aa31eb80aa19126 + md5: f1e0ed65fc63cbdf3a7936bf45e73f3e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosmosr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, piano, ggplot2 requirements: host: - - 'bioconductor-carnival >=2.10.0,<2.11.0' - - 'bioconductor-dorothea >=1.12.0,<1.13.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-carnival >=2.12.0,<2.13.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - 'bioconductor-dorothea >=1.14.0,<1.15.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-dplyr - r-igraph @@ -33,9 +35,10 @@ requirements: - r-stringr - r-visnetwork run: - - 'bioconductor-carnival >=2.10.0,<2.11.0' - - 'bioconductor-dorothea >=1.12.0,<1.13.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-carnival >=2.12.0,<2.13.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - 'bioconductor-dorothea >=1.14.0,<1.15.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-dplyr - r-igraph diff --git a/recipes/bioconductor-cosnet/meta.yaml b/recipes/bioconductor-cosnet/meta.yaml index 4ff74fc3d6a72..83ab3129d7fd1 100644 --- a/recipes/bioconductor-cosnet/meta.yaml +++ b/recipes/bioconductor-cosnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "COSNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed1d625a532916dc04b50ff346f6aedd + md5: 6648998ac68e41642f1a7bad77e0bb7f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cosnet", max_pin="x.x") }}' # Suggests: bionetdata, PerfMeas, RUnit, BiocGenerics requirements: host: diff --git a/recipes/bioconductor-cotan/meta.yaml b/recipes/bioconductor-cotan/meta.yaml index b712c8dc4228b..7b8cee0e472ab 100644 --- a/recipes/bioconductor-cotan/meta.yaml +++ b/recipes/bioconductor-cotan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.4" %} +{% set version = "2.2.1" %} {% set name = "COTAN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 186328978b156456a4490ce7eb44361a + md5: ec3bbfe10c1ede4ae12398534ab5395b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cotan", max_pin="x.x") }}' noarch: generic -# Suggests: testthat (>= 3.0.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery +# Suggests: testthat (>= 3.0.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - r-assertthat - r-base - r-circlize @@ -33,6 +34,7 @@ requirements: - r-ggthemes - r-irlba - r-matrix + - r-paralleldist - r-parallelly - r-plyr - r-rcolorbrewer @@ -47,7 +49,7 @@ requirements: - r-withr - r-zeallot run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - r-assertthat - r-base - r-circlize @@ -59,6 +61,7 @@ requirements: - r-ggthemes - r-irlba - r-matrix + - r-paralleldist - r-parallelly - r-plyr - r-rcolorbrewer diff --git a/recipes/bioconductor-cottoncdf/meta.yaml b/recipes/bioconductor-cottoncdf/meta.yaml index 1d7edd68e7f91..c8d58aec1b26b 100644 --- a/recipes/bioconductor-cottoncdf/meta.yaml +++ b/recipes/bioconductor-cottoncdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "cottoncdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b9d2a4b43235c6e531b78cca006e84b2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cottoncdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cottonprobe/meta.yaml b/recipes/bioconductor-cottonprobe/meta.yaml index 6c4575d866433..6b4cc385024ae 100644 --- a/recipes/bioconductor-cottonprobe/meta.yaml +++ b/recipes/bioconductor-cottonprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "cottonprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 032fa94876685820d94526fd56dd0b65 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cottonprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-countsimqc/meta.yaml b/recipes/bioconductor-countsimqc/meta.yaml index 38c8cb7b77e2f..718397f70710d 100644 --- a/recipes/bioconductor-countsimqc/meta.yaml +++ b/recipes/bioconductor-countsimqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "countsimQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a076a7246b7f4037ccd8660860a160a + md5: a44b69f7c0a9b3f5f822df61a6fcef73 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-countsimqc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-catools - r-dplyr @@ -36,11 +37,11 @@ requirements: - 'r-rmarkdown >=2.5' - r-tidyr run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-catools - r-dplyr diff --git a/recipes/bioconductor-coveb/meta.yaml b/recipes/bioconductor-coveb/meta.yaml index 34665cfe61e9a..df6fb540d4b0b 100644 --- a/recipes/bioconductor-coveb/meta.yaml +++ b/recipes/bioconductor-coveb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "covEB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67dcc92152292212d430f023d1cca9b5 + md5: 5469ab09a3d502902dc4d698abd1cbae build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-coveb", max_pin="x.x") }}' noarch: generic # Suggests: curatedBladderData requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gsl - r-igraph @@ -29,7 +30,7 @@ requirements: - r-matrix - r-mvtnorm run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gsl - r-igraph diff --git a/recipes/bioconductor-coverageview/meta.yaml b/recipes/bioconductor-coverageview/meta.yaml index eaccfd23cd371..c5783d123cbb9 100644 --- a/recipes/bioconductor-coverageview/meta.yaml +++ b/recipes/bioconductor-coverageview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CoverageView" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec25cb60624d5cf284f2f41a60abf969 + md5: 27821acd2787d95d95532f71d22378df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-coverageview", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-covrna/meta.yaml b/recipes/bioconductor-covrna/meta.yaml index 07bd860be2a35..43b8f2d3c5e2f 100644 --- a/recipes/bioconductor-covrna/meta.yaml +++ b/recipes/bioconductor-covrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "covRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae2b33f4b58cbd6d9f42bb5ba444b717 + md5: dd8405538f8c54345579ee7d0d5dc63f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-covrna", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-ade4 - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-ade4 - r-base test: diff --git a/recipes/bioconductor-cpvsnp/meta.yaml b/recipes/bioconductor-cpvsnp/meta.yaml index d15cd5ea861d9..c4c3bdc69a5f3 100644 --- a/recipes/bioconductor-cpvsnp/meta.yaml +++ b/recipes/bioconductor-cpvsnp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "cpvSNP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 064f756a6ebeb3d9944e85a45b99e032 + md5: 2edb50570eb609c9962e57d36d70ceba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cpvsnp", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-corpcor - r-ggplot2 - r-plyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-corpcor - r-ggplot2 diff --git a/recipes/bioconductor-cqn/meta.yaml b/recipes/bioconductor-cqn/meta.yaml index 9559ff98266f3..267b7af6d65ba 100644 --- a/recipes/bioconductor-cqn/meta.yaml +++ b/recipes/bioconductor-cqn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "cqn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d0d1324320136000b8b75056cdc3bf78 + md5: a72eb9ae5c393dec7ecc4f992d11328f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cqn", max_pin="x.x") }}' noarch: generic # Suggests: scales, edgeR requirements: host: - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-mclust - r-nor1mix - r-quantreg run: - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-mclust - r-nor1mix diff --git a/recipes/bioconductor-crcl18/meta.yaml b/recipes/bioconductor-crcl18/meta.yaml index 6849b5e08730f..7a7776d0bfc5d 100644 --- a/recipes/bioconductor-crcl18/meta.yaml +++ b/recipes/bioconductor-crcl18/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CRCL18" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df8b3bf91d7c7ac39d0fee78b65c1da0 + md5: 176bd921f08e717ec49e4e3eb4a5e5e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crcl18", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-crcl18/post-link.sh b/recipes/bioconductor-crcl18/post-link.sh index afb5adf88878a..841a4c62b2bb7 100644 --- a/recipes/bioconductor-crcl18/post-link.sh +++ b/recipes/bioconductor-crcl18/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "crcl18-1.20.0" +installBiocDataPackage.sh "crcl18-1.22.0" diff --git a/recipes/bioconductor-crimage/meta.yaml b/recipes/bioconductor-crimage/meta.yaml index bba214a251f5f..42e7d5fc48fd8 100644 --- a/recipes/bioconductor-crimage/meta.yaml +++ b/recipes/bioconductor-crimage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "CRImage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67f3739d67a92f8e46b27e2b3ff83d55 + md5: 84d9bedefc25b08b7e6d86c47bf233f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crimage", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base - r-e1071 - r-foreach - r-mass - r-sgeostat run: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base - r-e1071 - r-foreach diff --git a/recipes/bioconductor-crisprbase/meta.yaml b/recipes/bioconductor-crisprbase/meta.yaml index e75426f262fca..92d843a59a6cf 100644 --- a/recipes/bioconductor-crisprbase/meta.yaml +++ b/recipes/bioconductor-crisprbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "crisprBase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5fc52160cd713801b9499ed277ebcec9 + md5: 20cc1254ee7d33a966bb795f09f8be44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprbase", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-stringr test: diff --git a/recipes/bioconductor-crisprbowtie/meta.yaml b/recipes/bioconductor-crisprbowtie/meta.yaml index 152de6564d4a3..c2923cdfff081 100644 --- a/recipes/bioconductor-crisprbowtie/meta.yaml +++ b/recipes/bioconductor-crisprbowtie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "crisprBowtie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f84e8a18573b68f4d70067e3180b08a3 + md5: eabea0206c16b87d8acaa65245390d30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprbowtie", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' - r-base - r-readr - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' - r-base - r-readr - r-stringr diff --git a/recipes/bioconductor-crisprbwa/meta.yaml b/recipes/bioconductor-crisprbwa/meta.yaml index 1f433fa15b865..58f4eece924b8 100644 --- a/recipes/bioconductor-crisprbwa/meta.yaml +++ b/recipes/bioconductor-crisprbwa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "crisprBwa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a42166c3ec58a55aeec7eda3e512eae + md5: d77734ef6cfa03fb7b08c21c59155518 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprbwa", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-rbwa >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-rbwa >=1.6.0,<1.7.0' - r-base - r-readr - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-rbwa >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-rbwa >=1.6.0,<1.7.0' - r-base - r-readr - r-stringr diff --git a/recipes/bioconductor-crisprdesign/meta.yaml b/recipes/bioconductor-crisprdesign/meta.yaml index ee30ed17f1f52..ead19116d4702 100644 --- a/recipes/bioconductor-crisprdesign/meta.yaml +++ b/recipes/bioconductor-crisprdesign/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "crisprDesign" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,49 +11,50 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84860ded55e114a288c8d4b22b90f7da + md5: f4efe77ba4d8f440af21a1e80f0e1f5d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprdesign", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprbowtie >=1.4.0,<1.5.0' - - 'bioconductor-crisprscore >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' + - 'bioconductor-crisprscore >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrix run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprbowtie >=1.4.0,<1.5.0' - - 'bioconductor-crisprscore >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' + - 'bioconductor-crisprscore >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-crisprscore/meta.yaml b/recipes/bioconductor-crisprscore/meta.yaml index e7547701a84ed..2ac786f7e1988 100644 --- a/recipes/bioconductor-crisprscore/meta.yaml +++ b/recipes/bioconductor-crisprscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "crisprScore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2652f2da85d86eb913f4c5dc403ae5be + md5: c83f7928b03ce0308175835556dfcb54 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprscore", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-basilisk.utils >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-crisprscoredata >=1.4.0,<1.5.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-randomforest - r-reticulate - r-stringr run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-basilisk.utils >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-crisprscoredata >=1.4.0,<1.5.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-randomforest - r-reticulate diff --git a/recipes/bioconductor-crisprscoredata/meta.yaml b/recipes/bioconductor-crisprscoredata/meta.yaml index 385f8db75cbd4..56963b7b20d4a 100644 --- a/recipes/bioconductor-crisprscoredata/meta.yaml +++ b/recipes/bioconductor-crisprscoredata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "crisprScoreData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: feb17485db66f6e86d92b42af3731f4a + md5: 1f4d86404f045ec36cf7d1b1c64373fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprscoredata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-crisprscoredata/post-link.sh b/recipes/bioconductor-crisprscoredata/post-link.sh index 3e7804e70fdcb..4fd2ecb7ae14e 100644 --- a/recipes/bioconductor-crisprscoredata/post-link.sh +++ b/recipes/bioconductor-crisprscoredata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "crisprscoredata-1.4.0" +installBiocDataPackage.sh "crisprscoredata-1.6.0" diff --git a/recipes/bioconductor-crisprseek/meta.yaml b/recipes/bioconductor-crisprseek/meta.yaml index cd254e810c69b..56325695ce330 100644 --- a/recipes/bioconductor-crisprseek/meta.yaml +++ b/recipes/bioconductor-crisprseek/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "CRISPRseek" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f820f2bad907afb0a89e75f3923152d0 + md5: b14c3c52470140b9c7bc85b9ca4044a5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprseek", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-data.table - r-dplyr @@ -40,16 +41,16 @@ requirements: - r-reticulate - r-seqinr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-crisprvariants/meta.yaml b/recipes/bioconductor-crisprvariants/meta.yaml index 9750f1f3a78e8..a820551578ab1 100644 --- a/recipes/bioconductor-crisprvariants/meta.yaml +++ b/recipes/bioconductor-crisprvariants/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CrispRVariants" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f6121ca35c8ed2e06bd42111ac2aeea + md5: ede7cabcf986e2494f2e7b489621dd09 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprvariants", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown, rtracklayer, sangerseqR, testthat, VariantAnnotation +# Suggests: BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ggplot2 >=2.2.0' - r-gridextra - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ggplot2 >=2.2.0' - r-gridextra diff --git a/recipes/bioconductor-crisprverse/meta.yaml b/recipes/bioconductor-crisprverse/meta.yaml index 49c16fe8000ba..112545aadf561 100644 --- a/recipes/bioconductor-crisprverse/meta.yaml +++ b/recipes/bioconductor-crisprverse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "crisprVerse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc5f98e715c08356e21bd39d54ca812e + md5: dff359d1f63b8a58289ef0914c9260c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprverse", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprbowtie >=1.4.0,<1.5.0' - - 'bioconductor-crisprdesign >=1.2.0,<1.3.0' - - 'bioconductor-crisprscore >=1.4.0,<1.5.0' - - 'bioconductor-crisprscoredata >=1.4.0,<1.5.0' - - 'bioconductor-crisprviz >=1.2.0,<1.3.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' + - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' + - 'bioconductor-crisprscore >=1.6.0,<1.7.0' + - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' + - 'bioconductor-crisprviz >=1.4.0,<1.5.0' - r-base - r-biocmanager - r-cli - r-rlang run: - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprbowtie >=1.4.0,<1.5.0' - - 'bioconductor-crisprdesign >=1.2.0,<1.3.0' - - 'bioconductor-crisprscore >=1.4.0,<1.5.0' - - 'bioconductor-crisprscoredata >=1.4.0,<1.5.0' - - 'bioconductor-crisprviz >=1.2.0,<1.3.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' + - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' + - 'bioconductor-crisprscore >=1.6.0,<1.7.0' + - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' + - 'bioconductor-crisprviz >=1.4.0,<1.5.0' - r-base - r-biocmanager - r-cli diff --git a/recipes/bioconductor-crisprviz/meta.yaml b/recipes/bioconductor-crisprviz/meta.yaml index a32e148c6aea0..1c835bd954fd8 100644 --- a/recipes/bioconductor-crisprviz/meta.yaml +++ b/recipes/bioconductor-crisprviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "crisprViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 418a29f193e424f19794de01c36412ec + md5: a95c0cc87c7934da1e9bbfeb1e27bd3a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprviz", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprdesign >=1.2.0,<1.3.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprbase >=1.4.0,<1.5.0' - - 'bioconductor-crisprdesign >=1.2.0,<1.3.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprbase >=1.6.0,<1.7.0' + - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-crlmm/meta.yaml b/recipes/bioconductor-crlmm/meta.yaml index f433b5954fc87..6e0ee3be271f6 100644 --- a/recipes/bioconductor-crlmm/meta.yaml +++ b/recipes/bioconductor-crlmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "crlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c77b15041b77a1679d307900099a79a9 + md5: d047359287ee832d97e95c0945dff8cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crlmm", max_pin="x.x") }}' # Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit requirements: host: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-beanplot - r-ellipse @@ -40,13 +41,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-beanplot - r-ellipse diff --git a/recipes/bioconductor-crossmeta/meta.yaml b/recipes/bioconductor-crossmeta/meta.yaml index 75049a5143101..2175cb526022a 100644 --- a/recipes/bioconductor-crossmeta/meta.yaml +++ b/recipes/bioconductor-crossmeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "crossmeta" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eb215cbcc990a0a74352342c1c952885 + md5: 5bc5c865fba1a04864f9a0643adf041f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crossmeta", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat # SystemRequirements: libxml2: libxml2-dev (deb), libxml2-devel (rpm) libcurl: libcurl4-openssl-dev (deb), libcurl-devel (rpm) openssl: libssl-dev (deb), openssl-devel (rpm), libssl_dev (csw), openssl@1.1 (brew) requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - 'r-biocmanager >=1.30.4' - 'r-data.table >=1.10.4' @@ -54,16 +55,16 @@ requirements: - r-tibble - 'r-xml >=3.98.1.17' run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - 'r-biocmanager >=1.30.4' - 'r-data.table >=1.10.4' diff --git a/recipes/bioconductor-csar/meta.yaml b/recipes/bioconductor-csar/meta.yaml index 9b25df6a1a1a3..4767cf2e78ac2 100644 --- a/recipes/bioconductor-csar/meta.yaml +++ b/recipes/bioconductor-csar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "CSAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 796d8b24ecf0424a0227ec54124628fa + md5: cf22689abca527406f9f2b333739d7bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-csar", max_pin="x.x") }}' # Suggests: ShortRead, Biostrings requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-csaw/meta.yaml b/recipes/bioconductor-csaw/meta.yaml index ae24e0b28d739..257d3e9ac5aca 100644 --- a/recipes/bioconductor-csaw/meta.yaml +++ b/recipes/bioconductor-csaw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "csaw" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,48 +11,49 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2303363515d9358462fa8670bddbb041 + md5: 07ad4af3be8e5e799b06826cc97a449e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-csaw", max_pin="x.x") }}' # Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-csdr/meta.yaml b/recipes/bioconductor-csdr/meta.yaml index 58600b6179b91..8f28df3937931 100644 --- a/recipes/bioconductor-csdr/meta.yaml +++ b/recipes/bioconductor-csdr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "csdR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a19cb2405a198584f25a03df4b0569d + md5: 02132c2d953434d0bb7de9b58e8b5769 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-csdr", max_pin="x.x") }}' # Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr requirements: host: diff --git a/recipes/bioconductor-cssq/meta.yaml b/recipes/bioconductor-cssq/meta.yaml index 411139143feae..52270a9d7e002 100644 --- a/recipes/bioconductor-cssq/meta.yaml +++ b/recipes/bioconductor-cssq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "CSSQ" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b33aa7496759ea3e7af2e4670956254 + md5: d9a6f6200f67cc06173c30dcd6775e5a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cssq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown requirements: host: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 run: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-ctc/meta.yaml b/recipes/bioconductor-ctc/meta.yaml index 00893b46b8267..67bcc2e93f176 100644 --- a/recipes/bioconductor-ctc/meta.yaml +++ b/recipes/bioconductor-ctc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "ctc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 56004c787150f55f1ae6b3c5b1452c3a + md5: ea94b8b636b26d4f827ecd4569804d1e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctc", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-ctcf/meta.yaml b/recipes/bioconductor-ctcf/meta.yaml index eed0fcb6af070..1c4437ce61d37 100644 --- a/recipes/bioconductor-ctcf/meta.yaml +++ b/recipes/bioconductor-ctcf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.11" %} {% set name = "CTCF" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5ec44245864395de390e68fa56e465af build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctcf", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, AnnotationHub, GenomicRanges, plyranges, sessioninfo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ctdata/meta.yaml b/recipes/bioconductor-ctdata/meta.yaml index 03168c81f245e..051c707054ba5 100644 --- a/recipes/bioconductor-ctdata/meta.yaml +++ b/recipes/bioconductor-ctdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "CTdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5666dc0fc962f452b36e1469947dd28 + md5: d130308cf078329f4cc6a1cc8055475d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctdata", max_pin="x.x") }}' noarch: generic -# Suggests: testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown, SummarizedExperiment +# Suggests: testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown, SummarizedExperiment, SingleCellExperiment requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base test: commands: diff --git a/recipes/bioconductor-ctdquerier/meta.yaml b/recipes/bioconductor-ctdquerier/meta.yaml index a66cbb012eee3..9cfc17e349b4e 100644 --- a/recipes/bioconductor-ctdquerier/meta.yaml +++ b/recipes/bioconductor-ctdquerier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "CTDquerier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ae71eaec9c380d827d4ba3f6c6034be + md5: 42c5654d014714b22e5c1c2c2e7a2118 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctdquerier", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gridextra @@ -31,8 +32,8 @@ requirements: - r-stringdist - r-stringr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-ctrap/meta.yaml b/recipes/bioconductor-ctrap/meta.yaml index a589d5f0d98b3..07edfeb916d8a 100644 --- a/recipes/bioconductor-ctrap/meta.yaml +++ b/recipes/bioconductor-ctrap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "cTRAP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 69a1a37a36696d321c04734075ec6802 + md5: 049de878508ce8d8031d7d93f6a1fd01 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctrap", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-binr - r-cowplot @@ -50,11 +51,11 @@ requirements: - r-shinycssloaders - r-tibble run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-binr - r-cowplot diff --git a/recipes/bioconductor-ctsge/meta.yaml b/recipes/bioconductor-ctsge/meta.yaml index 8af0af8538976..44c7878302301 100644 --- a/recipes/bioconductor-ctsge/meta.yaml +++ b/recipes/bioconductor-ctsge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ctsGE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb8561fe9bd7f3b4eccbbb40f8573ede + md5: 31cfbfb8002cbb54747b9a4a41fb17d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctsge", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ccapp - r-ggplot2 @@ -29,7 +30,7 @@ requirements: - r-shiny - r-stringr run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ccapp - r-ggplot2 diff --git a/recipes/bioconductor-ctsv/meta.yaml b/recipes/bioconductor-ctsv/meta.yaml index bf775fa227b23..209549d623061 100644 --- a/recipes/bioconductor-ctsv/meta.yaml +++ b/recipes/bioconductor-ctsv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "CTSV" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 343c9934a4e4ad3ea145927cb7605bad + md5: 4a3f8c7b5398449ea01b312ed7da1f43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctsv", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-knitr - r-pscl run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-knitr - r-pscl diff --git a/recipes/bioconductor-cummerbund/meta.yaml b/recipes/bioconductor-cummerbund/meta.yaml index e56d26fdc5b6b..b02fb64575016 100644 --- a/recipes/bioconductor-cummerbund/meta.yaml +++ b/recipes/bioconductor-cummerbund/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "cummeRbund" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5221eb3a427c7a29beb2404715794561 + md5: 367d124a098eca55a6da149e35621c65 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cummerbund", max_pin="x.x") }}' noarch: generic # Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fastcluster - r-ggplot2 @@ -33,11 +34,11 @@ requirements: - r-reshape2 - r-rsqlite run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fastcluster - r-ggplot2 diff --git a/recipes/bioconductor-curatedadipoarray/meta.yaml b/recipes/bioconductor-curatedadipoarray/meta.yaml index 43353cd4929d2..771e50a148b5c 100644 --- a/recipes/bioconductor-curatedadipoarray/meta.yaml +++ b/recipes/bioconductor-curatedadipoarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "curatedAdipoArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84600c36847d6fff69d646f1ff65dcbd + md5: 109be77c099e9d7b6da437577f619a54 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedadipoarray", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedadipoarray/post-link.sh b/recipes/bioconductor-curatedadipoarray/post-link.sh index 2720124804a73..7471a605b14e7 100644 --- a/recipes/bioconductor-curatedadipoarray/post-link.sh +++ b/recipes/bioconductor-curatedadipoarray/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedadipoarray-1.12.0" +installBiocDataPackage.sh "curatedadipoarray-1.14.0" diff --git a/recipes/bioconductor-curatedadipochip/meta.yaml b/recipes/bioconductor-curatedadipochip/meta.yaml index 11bfe0d9b2e9f..5c312a510e921 100644 --- a/recipes/bioconductor-curatedadipochip/meta.yaml +++ b/recipes/bioconductor-curatedadipochip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "curatedAdipoChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c5ffe38c97500d4fadfdd2c6af165b4 + md5: 0074cb63250ac197dad12e4138d47463 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedadipochip", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, GenomicFeatures, ChIPseeker, AnnotationDbi, S4Vectors, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2 requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedadipochip/post-link.sh b/recipes/bioconductor-curatedadipochip/post-link.sh index c018890261d24..452dbadac0268 100644 --- a/recipes/bioconductor-curatedadipochip/post-link.sh +++ b/recipes/bioconductor-curatedadipochip/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedadipochip-1.16.0" +installBiocDataPackage.sh "curatedadipochip-1.18.0" diff --git a/recipes/bioconductor-curatedadiporna/meta.yaml b/recipes/bioconductor-curatedadiporna/meta.yaml index 3ac6e6b4b45b8..b7c5d9884fddc 100644 --- a/recipes/bioconductor-curatedadiporna/meta.yaml +++ b/recipes/bioconductor-curatedadiporna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "curatedAdipoRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81535f56828fc6043a8461b0f9e09ca7 + md5: 61c2e750fc2cf09a6bde6c0bf46e6b8b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedadiporna", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedadiporna/post-link.sh b/recipes/bioconductor-curatedadiporna/post-link.sh index cf9b4d8383a8c..71d70dbe2607b 100644 --- a/recipes/bioconductor-curatedadiporna/post-link.sh +++ b/recipes/bioconductor-curatedadiporna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedadiporna-1.16.0" +installBiocDataPackage.sh "curatedadiporna-1.18.0" diff --git a/recipes/bioconductor-curatedatlasqueryr/build.sh b/recipes/bioconductor-curatedatlasqueryr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-curatedatlasqueryr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-curatedatlasqueryr/meta.yaml b/recipes/bioconductor-curatedatlasqueryr/meta.yaml new file mode 100644 index 0000000000000..4599ae6b3e273 --- /dev/null +++ b/recipes/bioconductor-curatedatlasqueryr/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.0.0" %} +{% set name = "CuratedAtlasQueryR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 21e5bf1d5aa58d59098176dca867c42c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedatlasqueryr", max_pin="x.x") }}' + noarch: generic +# Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-assertthat + - r-base + - r-cli + - r-dbi + - 'r-dbplyr >=2.3.0' + - r-dplyr + - r-duckdb + - r-glue + - r-httr + - 'r-purrr >=1.0.0' + - r-rlang + - r-seurat + - r-seuratobject + - r-stringr + - r-tibble + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-assertthat + - r-base + - r-cli + - r-dbi + - 'r-dbplyr >=2.3.0' + - r-dplyr + - r-duckdb + - r-glue + - r-httr + - 'r-purrr >=1.0.0' + - r-rlang + - r-seurat + - r-seuratobject + - r-stringr + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Queries the Human Cell Atlas' + description: 'Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-curatedbladderdata/meta.yaml b/recipes/bioconductor-curatedbladderdata/meta.yaml index f911f00d9dc99..a19912b009d71 100644 --- a/recipes/bioconductor-curatedbladderdata/meta.yaml +++ b/recipes/bioconductor-curatedbladderdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "curatedBladderData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7db958b1758a3b7bc3f2b552962ed51a + md5: bd8965c4ad49840b4985f90f3dc5a441 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedbladderdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, survival, xtable, sva, genefilter, logging requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedbladderdata/post-link.sh b/recipes/bioconductor-curatedbladderdata/post-link.sh index 72edc5f4d75d6..a5a74357ee58b 100644 --- a/recipes/bioconductor-curatedbladderdata/post-link.sh +++ b/recipes/bioconductor-curatedbladderdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedbladderdata-1.36.0" +installBiocDataPackage.sh "curatedbladderdata-1.38.0" diff --git a/recipes/bioconductor-curatedbreastdata/meta.yaml b/recipes/bioconductor-curatedbreastdata/meta.yaml index 24984a5870644..147d8dbd24191 100644 --- a/recipes/bioconductor-curatedbreastdata/meta.yaml +++ b/recipes/bioconductor-curatedbreastdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "curatedBreastData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e53cc4c883e3b3c94842727f34ad6a6 + md5: 41383ff9e1295448ec0e8004789ab9d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedbreastdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-ggplot2 - r-xml run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-ggplot2 - r-xml - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedbreastdata/post-link.sh b/recipes/bioconductor-curatedbreastdata/post-link.sh index 08d6436b4b509..58788177cdca3 100644 --- a/recipes/bioconductor-curatedbreastdata/post-link.sh +++ b/recipes/bioconductor-curatedbreastdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedbreastdata-2.28.0" +installBiocDataPackage.sh "curatedbreastdata-2.30.0" diff --git a/recipes/bioconductor-curatedcrcdata/meta.yaml b/recipes/bioconductor-curatedcrcdata/meta.yaml index 9e1ade1a1bcd2..56546d4ac282f 100644 --- a/recipes/bioconductor-curatedcrcdata/meta.yaml +++ b/recipes/bioconductor-curatedcrcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "curatedCRCData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c88686b133a9f30f4904dc4e706ef5c8 + md5: c36bf5dbc0970503f4137b55e8c65534 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedcrcdata", max_pin="x.x") }}' noarch: generic # Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-nlme run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-nlme - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedcrcdata/post-link.sh b/recipes/bioconductor-curatedcrcdata/post-link.sh index a684c9f7a3324..fd84280190a21 100644 --- a/recipes/bioconductor-curatedcrcdata/post-link.sh +++ b/recipes/bioconductor-curatedcrcdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedcrcdata-2.32.0" +installBiocDataPackage.sh "curatedcrcdata-2.34.0" diff --git a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml index fd3c6cc2e1a5c..8f7bf4f49af2c 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml +++ b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "curatedMetagenomicData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f24faacda7b263f1bcde098dbffa5f8f + md5: 39c08149fe4261d4961ff1235825ae97 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedmetagenomicdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat, utils, uwot, vegan requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-dplyr - r-magrittr @@ -37,12 +38,12 @@ requirements: - r-tidyr - r-tidyselect run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-dplyr - r-magrittr @@ -53,7 +54,7 @@ requirements: - r-tidyr - r-tidyselect - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh index 6e0440addbb55..1766abe724ad8 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh +++ b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedmetagenomicdata-3.8.0" +installBiocDataPackage.sh "curatedmetagenomicdata-3.10.0" diff --git a/recipes/bioconductor-curatedovariandata/meta.yaml b/recipes/bioconductor-curatedovariandata/meta.yaml index a204bc966f9f5..ae3f6134fef68 100644 --- a/recipes/bioconductor-curatedovariandata/meta.yaml +++ b/recipes/bioconductor-curatedovariandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.1" %} {% set name = "curatedOvarianData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0cbda3a714637304ffcc38aa91588c86 + md5: 7651ff7abb11057b3ceec8f869e259d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedovariandata", max_pin="x.x") }}' noarch: generic # Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedovariandata/post-link.sh b/recipes/bioconductor-curatedovariandata/post-link.sh index b8688a68dcdc4..2dca151523690 100644 --- a/recipes/bioconductor-curatedovariandata/post-link.sh +++ b/recipes/bioconductor-curatedovariandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedovariandata-1.38.0" +installBiocDataPackage.sh "curatedovariandata-1.40.1" diff --git a/recipes/bioconductor-curatedtbdata/meta.yaml b/recipes/bioconductor-curatedtbdata/meta.yaml index e1559e07a2936..86218926bfa5d 100644 --- a/recipes/bioconductor-curatedtbdata/meta.yaml +++ b/recipes/bioconductor-curatedtbdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "curatedTBData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d09277f807e04495c582052e25930d02 + md5: 190a770c4f5df45cf722b7ee287a2384 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedtbdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, DT, dplyr, HGNChelper, knitr, methods, rmarkdown, SummarizedExperiment, sva, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - r-rlang run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - r-rlang - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedtbdata/post-link.sh b/recipes/bioconductor-curatedtbdata/post-link.sh index e9fe0f3a58674..460b16dba5ca4 100644 --- a/recipes/bioconductor-curatedtbdata/post-link.sh +++ b/recipes/bioconductor-curatedtbdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedtbdata-1.6.0" +installBiocDataPackage.sh "curatedtbdata-1.8.0" diff --git a/recipes/bioconductor-curatedtcgadata/meta.yaml b/recipes/bioconductor-curatedtcgadata/meta.yaml index 30a3fed4b41ae..a2dfc71c781c2 100644 --- a/recipes/bioconductor-curatedtcgadata/meta.yaml +++ b/recipes/bioconductor-curatedtcgadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.2" %} +{% set version = "1.24.0" %} {% set name = "curatedTCGAData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 066107da416bfad28b75ee3488dbdad0 + md5: de450b3bbb137b63a1ca46ae81a96909 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-curatedtcgadata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-curatedtcgadata/post-link.sh b/recipes/bioconductor-curatedtcgadata/post-link.sh index 9431278b28ca6..151fe01e10b62 100644 --- a/recipes/bioconductor-curatedtcgadata/post-link.sh +++ b/recipes/bioconductor-curatedtcgadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedtcgadata-1.22.2" +installBiocDataPackage.sh "curatedtcgadata-1.24.0" diff --git a/recipes/bioconductor-customcmpdb/meta.yaml b/recipes/bioconductor-customcmpdb/meta.yaml index 94ee55331b883..b6f9d4baff3ab 100644 --- a/recipes/bioconductor-customcmpdb/meta.yaml +++ b/recipes/bioconductor-customcmpdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "customCMPdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a2da348c8192136738fff3c390a390b + md5: 1aa1425d87c45ac42f2c7ed808a7a583 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-customcmpdb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-rappdirs - r-rsqlite - r-xml run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-rappdirs - r-rsqlite diff --git a/recipes/bioconductor-customprodb/meta.yaml b/recipes/bioconductor-customprodb/meta.yaml index 422fecfca8d82..a90f2ffde8365 100644 --- a/recipes/bioconductor-customprodb/meta.yaml +++ b/recipes/bioconductor-customprodb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.41.0" %} {% set name = "customProDB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51e83c7af0198e0ac93b5aadb34d50d5 + md5: 08f0eb20ac48a7b8f1e27b45522dd029 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-customprodb", max_pin="x.x") }}' noarch: generic # Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-ahocorasicktrie - r-base - r-dbi @@ -41,18 +42,18 @@ requirements: - r-rsqlite - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-ahocorasicktrie - r-base - r-dbi diff --git a/recipes/bioconductor-cyanofilter/meta.yaml b/recipes/bioconductor-cyanofilter/meta.yaml index 2aeab900d9dd4..35f0db1c71cb4 100644 --- a/recipes/bioconductor-cyanofilter/meta.yaml +++ b/recipes/bioconductor-cyanofilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "cyanoFilter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 368e6b94dab2f6f3e34e633dc2d6a14c + md5: a562257b012ddcf28b78c5cee7e85fa3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cyanofilter", max_pin="x.x") }}' noarch: generic # Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' - r-base - r-cytometree - r-ggally - r-ggplot2 - r-mrfdepth run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' - r-base - r-cytometree - r-ggally diff --git a/recipes/bioconductor-cycle/meta.yaml b/recipes/bioconductor-cycle/meta.yaml index 860242e4bf1b7..f9388f490a65e 100644 --- a/recipes/bioconductor-cycle/meta.yaml +++ b/recipes/bioconductor-cycle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "cycle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 04088083f69f37fd4bf35ad28e0b57ae + md5: 8c659d2ae2fb2b31f4b6dd07d68873be build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cycle", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mfuzz >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mfuzz >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-cydar/meta.yaml b/recipes/bioconductor-cydar/meta.yaml index 9e2835f0bcff6..4f5ab55d02786 100644 --- a/recipes/bioconductor-cydar/meta.yaml +++ b/recipes/bioconductor-cydar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "cydar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7b8dbb3a9113d2bba4b2a9f656e8edb1 + md5: b804632cc0742b1e2f9910353a6ed75d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cydar", max_pin="x.x") }}' # Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcpp - r-shiny @@ -36,14 +37,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcpp - r-shiny diff --git a/recipes/bioconductor-cyp450cdf/meta.yaml b/recipes/bioconductor-cyp450cdf/meta.yaml index 24e5aa29562cf..278e2ac3086d0 100644 --- a/recipes/bioconductor-cyp450cdf/meta.yaml +++ b/recipes/bioconductor-cyp450cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "cyp450cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7923c4d24b7b654d0f59d52ed2258eb9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cyp450cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-cytodx/meta.yaml b/recipes/bioconductor-cytodx/meta.yaml index b7755fcbf70b2..fa2f5ec95a63d 100644 --- a/recipes/bioconductor-cytodx/meta.yaml +++ b/recipes/bioconductor-cytodx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CytoDx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34c6cd6a96a62551f4ca24cb91b76842 + md5: 86d2f225be6ebdaecd3aa4960e443796 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytodx", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-doparallel - r-dplyr @@ -29,7 +30,7 @@ requirements: - r-rpart - r-rpart.plot run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-cytofpower/meta.yaml b/recipes/bioconductor-cytofpower/meta.yaml index a2083e7d3ff5b..981d052fa8067 100644 --- a/recipes/bioconductor-cytofpower/meta.yaml +++ b/recipes/bioconductor-cytofpower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "CyTOFpower" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b01cc449a6fe4426458624c5705bcec9 + md5: ea70d698bf8ba363250de04f634c5f74 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytofpower", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, knitr requirements: host: - - 'bioconductor-cytoglmm >=1.8.0,<1.9.0' - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-cytoglmm >=1.10.0,<1.11.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-dt @@ -37,9 +38,9 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-cytoglmm >=1.8.0,<1.9.0' - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-cytoglmm >=1.10.0,<1.11.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-cytofqc/meta.yaml b/recipes/bioconductor-cytofqc/meta.yaml index d21510eafbdd4..47f974c4c82e4 100644 --- a/recipes/bioconductor-cytofqc/meta.yaml +++ b/recipes/bioconductor-cytofqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "cytofQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0505813678c5c80055b22702fd6efc1 + md5: 7a4e866c0e57f639b41828c211aff31f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytofqc", max_pin="x.x") }}' noarch: generic # Suggests: gridExtra, knitr, RColorBrewer, testthat, uwot requirements: host: - - 'bioconductor-catalyst >=1.24.0,<1.25.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-catalyst >=1.26.0,<1.27.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-eztune @@ -37,11 +38,11 @@ requirements: - r-rmarkdown - r-ssc run: - - 'bioconductor-catalyst >=1.24.0,<1.25.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-catalyst >=1.26.0,<1.27.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-eztune diff --git a/recipes/bioconductor-cytoglmm/meta.yaml b/recipes/bioconductor-cytoglmm/meta.yaml index f4c4346d39a43..7c2e9656c33dc 100644 --- a/recipes/bioconductor-cytoglmm/meta.yaml +++ b/recipes/bioconductor-cytoglmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CytoGLMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5784f488db9c90aee9aaef89bb2979f + md5: 3a4b95062a82da6afe217f20ef905460 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytoglmm", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-caret - r-cowplot @@ -44,7 +45,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-caret - r-cowplot diff --git a/recipes/bioconductor-cytokernel/meta.yaml b/recipes/bioconductor-cytokernel/meta.yaml index 07981eccb8167..e78587f65500f 100644 --- a/recipes/bioconductor-cytokernel/meta.yaml +++ b/recipes/bioconductor-cytokernel/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "cytoKernel" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5a4d7c512bf35c94d3ff2ba67915455 + md5: 2e1e2b8d2c545a69a0cec180964f2fd9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytokernel", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ashr - r-base - r-circlize @@ -35,10 +36,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ashr - r-base - r-circlize diff --git a/recipes/bioconductor-cytolib/meta.yaml b/recipes/bioconductor-cytolib/meta.yaml index fab17798770e4..9c473184d4d42 100644 --- a/recipes/bioconductor-cytolib/meta.yaml +++ b/recipes/bioconductor-cytolib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "cytolib" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9f90833841459092d549952e5d99124e + md5: f06a976c84ae2adf3c08d07cd90af7f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytolib", max_pin="x.x") }}' # Suggests: knitr, rmarkdown # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - r-base - - 'r-bh >=1.75.0.0' + - 'r-bh >=1.81.0.0' - libblas - liblapack run: - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - r-base - - 'r-bh >=1.75.0.0' + - 'r-bh >=1.81.0.0' build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-cytomapper/meta.yaml b/recipes/bioconductor-cytomapper/meta.yaml index c120d00160aca..cd40bb5f75e8b 100644 --- a/recipes/bioconductor-cytomapper/meta.yaml +++ b/recipes/bioconductor-cytomapper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "cytomapper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a792c54688d69d44dbf91fd86d900a08 + md5: 140e57707c43aeb7bd3b2e48b634464a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytomapper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggbeeswarm - r-ggplot2 @@ -43,15 +44,15 @@ requirements: - r-svgpanzoom - r-viridis run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggbeeswarm - r-ggplot2 diff --git a/recipes/bioconductor-cytomem/meta.yaml b/recipes/bioconductor-cytomem/meta.yaml index abdb5dec2f33b..5c3bb8333f7b3 100644 --- a/recipes/bioconductor-cytomem/meta.yaml +++ b/recipes/bioconductor-cytomem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "cytoMEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5727668f7e144170c6b66ed00a1fce77 + md5: 4a407b89f327c4c88301e81f982598f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytomem", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-gplots - r-matrixstats run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-gplots - r-matrixstats diff --git a/recipes/bioconductor-cytoml/meta.yaml b/recipes/bioconductor-cytoml/meta.yaml index fb7b3b6300c72..ee27b56fde053 100644 --- a/recipes/bioconductor-cytoml/meta.yaml +++ b/recipes/bioconductor-cytoml/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "CytoML" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5118f217fc4d383753ddb7c749b5c949 + md5: 4b0060416cdeef7876cb9aaeb81dbaf7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytoml", max_pin="x.x") }}' # Suggests: testthat, flowWorkspaceData , knitr, rmarkdown, parallel # SystemRequirements: xml2, GNU make, C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-opencyto >=2.12.0,<2.13.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-opencyto >=2.14.0,<2.15.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - r-base - 'r-bh >=1.62.0-1' - r-cpp11 @@ -45,17 +46,17 @@ requirements: - liblapack - libxml2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-opencyto >=2.12.0,<2.13.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-opencyto >=2.14.0,<2.15.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - r-base - 'r-bh >=1.62.0-1' - r-cpp11 diff --git a/recipes/bioconductor-cytopipeline/meta.yaml b/recipes/bioconductor-cytopipeline/meta.yaml index 5fbad5f102509..7e23057f3914e 100644 --- a/recipes/bioconductor-cytopipeline/meta.yaml +++ b/recipes/bioconductor-cytopipeline/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "CytoPipeline" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03008ccf1f86b39cc48a5f9fa82ae3a2 + md5: a4ed3b88553c7115d7dce368a0fda5a5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytopipeline", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowai >=1.30.0,<1.31.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' - - 'bioconductor-peacoqc >=1.10.0,<1.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowai >=1.32.0,<1.33.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' + - 'bioconductor-peacoqc >=1.12.0,<1.13.0' - r-base - r-diagram - 'r-ggplot2 >=3.4.1' @@ -35,12 +36,12 @@ requirements: - r-scales - r-withr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowai >=1.30.0,<1.31.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' - - 'bioconductor-peacoqc >=1.10.0,<1.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowai >=1.32.0,<1.33.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' + - 'bioconductor-peacoqc >=1.12.0,<1.13.0' - r-base - r-diagram - 'r-ggplot2 >=3.4.1' diff --git a/recipes/bioconductor-cytopipelinegui/build.sh b/recipes/bioconductor-cytopipelinegui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cytopipelinegui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cytopipelinegui/meta.yaml b/recipes/bioconductor-cytopipelinegui/meta.yaml new file mode 100644 index 0000000000000..de5a7ec5baba2 --- /dev/null +++ b/recipes/bioconductor-cytopipelinegui/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "CytoPipelineGUI" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fb6a6a7aad638be11919a144f3d9907a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytopipelinegui", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork +requirements: + host: + - 'bioconductor-cytopipeline >=1.2.0,<1.3.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - r-base + - r-ggplot2 + - r-plotly + - r-shiny + run: + - 'bioconductor-cytopipeline >=1.2.0,<1.3.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - r-base + - r-ggplot2 + - r-plotly + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3) | file LICENSE' + summary: 'GUI''s for visualization of flow cytometry data analysis pipelines' + description: 'This package is the companion of the `CytoPipeline` package. It provides GUI''s (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with `CytoPipeline`. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool.' + license_file: LICENSE + diff --git a/recipes/bioconductor-cytoviewer/meta.yaml b/recipes/bioconductor-cytoviewer/meta.yaml index be640d04c0d65..dbf9da026b8dd 100644 --- a/recipes/bioconductor-cytoviewer/meta.yaml +++ b/recipes/bioconductor-cytoviewer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "cytoviewer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: def4b0774e3872eb4cca490bd369318e + md5: dc34f69f53490911e6f621d76db69f4c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytoviewer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat requirements: host: - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-archive - r-base - r-colourpicker @@ -37,11 +38,11 @@ requirements: - r-svgpanzoom - r-viridis run: - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-archive - r-base - r-colourpicker diff --git a/recipes/bioconductor-dada2/meta.yaml b/recipes/bioconductor-dada2/meta.yaml index 34e6608a6fe44..6e500493c1345 100644 --- a/recipes/bioconductor-dada2/meta.yaml +++ b/recipes/bioconductor-dada2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "dada2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8825d2a5c14a5d9ad3482743da42a215 + md5: 096baf34b4618af27b1b430945d3a189 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dada2", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-ggplot2 >=2.1.0' - 'r-rcpp >=0.12.0' @@ -34,11 +35,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-ggplot2 >=2.1.0' - 'r-rcpp >=0.12.0' diff --git a/recipes/bioconductor-daglogo/meta.yaml b/recipes/bioconductor-daglogo/meta.yaml index cba07b792c916..0e97dccda1777 100644 --- a/recipes/bioconductor-daglogo/meta.yaml +++ b/recipes/bioconductor-daglogo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "dagLogo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 143a623abf782e42e9c0ddf40f058e0d + md5: cb8662ee04599fa0076e344d2bf933d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-daglogo", max_pin="x.x") }}' noarch: generic # Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-uniprot.ws >=2.40.0,<2.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' - r-base - r-httr - r-pheatmap run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-uniprot.ws >=2.40.0,<2.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' - r-base - r-httr - r-pheatmap diff --git a/recipes/bioconductor-dama/meta.yaml b/recipes/bioconductor-dama/meta.yaml index 94240cd993003..6f827bb23d349 100644 --- a/recipes/bioconductor-dama/meta.yaml +++ b/recipes/bioconductor-dama/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "daMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 491bcd2f0f98f6fae9a9914a1d9f39cd + md5: ec7e80e81b9d6eb5a76ce06c761bb7da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dama", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-damefinder/meta.yaml b/recipes/bioconductor-damefinder/meta.yaml index 393440433602d..070f5d8dc6e1a 100644 --- a/recipes/bioconductor-damefinder/meta.yaml +++ b/recipes/bioconductor-damefinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "DAMEfinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90d7b5746b798073b831599c1f17dddc + md5: 0f99003a20995ebd0c15fce1a407765f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-damefinder", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-cowplot - r-ggplot2 @@ -41,18 +42,18 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-cowplot - r-ggplot2 diff --git a/recipes/bioconductor-damirseq/meta.yaml b/recipes/bioconductor-damirseq/meta.yaml index ddfdd6adad361..8f31010215ab8 100644 --- a/recipes/bioconductor-damirseq/meta.yaml +++ b/recipes/bioconductor-damirseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "DaMiRseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40d2de748f89528f9be59dff14696cdb + md5: 64986e7db314ddba69d156b35f974680 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-damirseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-arm - r-base - r-caret @@ -49,12 +50,12 @@ requirements: - r-reshape2 - r-rsnns run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-arm - r-base - r-caret @@ -85,8 +86,7 @@ about: summary: 'Data Mining for RNA-seq data: normalization, feature selection and classification' description: 'The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for both binary and multi-class classification purposes. The package accepts any kind of data presented as a table of raw counts and allows including both continous and factorial variables that occur with the experimental setting. A series of functions enable the user to clean up the data by filtering genomic features and samples, to adjust data by identifying and removing the unwanted source of variation (i.e. batches and confounding factors) and to select the best predictors for modeling. Finally, a "stacking" ensemble learning technique is applied to build a robust classification model. Every step includes a checkpoint that the user may exploit to assess the effects of data management by looking at diagnostic plots, such as clustering and heatmaps, RLE boxplots, MDS or correlation plot.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - extra: container: - extended-base: True + extended-base: true diff --git a/recipes/bioconductor-dapar/meta.yaml b/recipes/bioconductor-dapar/meta.yaml index bcc1f3cc45b40..3e5c822b5adaa 100644 --- a/recipes/bioconductor-dapar/meta.yaml +++ b/recipes/bioconductor-dapar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.2" %} +{% set version = "1.34.2" %} {% set name = "DAPAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,110 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 795af5225e1256f97f94864c8002aae6 + md5: 98c2672a3b694f6d1989cdd4f00cd8e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dapar", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db +# Suggests: testthat, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dapardata >=1.30.0,<1.31.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dapardata >=1.32.0,<1.33.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' + - r-apcluster - r-base + - r-cluster + - r-cp4p + - r-dendextend + - r-diptest + - r-doparallel + - r-dplyr + - r-factoextra + - r-factominer + - r-forcats - r-foreach + - r-ggplot2 + - r-gplots - r-highcharter + - r-igraph + - r-imp4p + - r-knitr + - r-lme4 + - r-matrix + - r-multcomp + - r-norm + - r-openxlsx + - r-purrr + - r-rcolorbrewer + - r-readxl + - r-reshape2 + - r-scales + - r-stringr + - r-tibble + - r-tidyr + - r-tidyverse + - r-vioplot + - r-visnetwork run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dapardata >=1.30.0,<1.31.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dapardata >=1.32.0,<1.33.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' + - r-apcluster - r-base + - r-cluster + - r-cp4p + - r-dendextend + - r-diptest + - r-doparallel + - r-dplyr + - r-factoextra + - r-factominer + - r-forcats - r-foreach + - r-ggplot2 + - r-gplots - r-highcharter + - r-igraph + - r-imp4p + - r-knitr + - r-lme4 + - r-matrix + - r-multcomp + - r-norm + - r-openxlsx + - r-purrr + - r-rcolorbrewer + - r-readxl + - r-reshape2 + - r-scales + - r-stringr + - r-tibble + - r-tidyr + - r-tidyverse + - r-vioplot + - r-visnetwork test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dapardata/meta.yaml b/recipes/bioconductor-dapardata/meta.yaml index c7ff1c8be6f2d..a88aae6c229f6 100644 --- a/recipes/bioconductor-dapardata/meta.yaml +++ b/recipes/bioconductor-dapardata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "DAPARdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d730f1b7ef4aab628882f7b9355c7b5 + md5: 5906f180d2e824affe9f2850424c7612 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dapardata", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, DAPAR +# Suggests: knitr, DAPAR, BiocStyle requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dapardata/post-link.sh b/recipes/bioconductor-dapardata/post-link.sh index 0aa7a2b9ed549..3788427c5fce2 100644 --- a/recipes/bioconductor-dapardata/post-link.sh +++ b/recipes/bioconductor-dapardata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dapardata-1.30.0" +installBiocDataPackage.sh "dapardata-1.32.0" diff --git a/recipes/bioconductor-dart/meta.yaml b/recipes/bioconductor-dart/meta.yaml index 16e9a3deaa689..a29f5a06cb466 100644 --- a/recipes/bioconductor-dart/meta.yaml +++ b/recipes/bioconductor-dart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "DART" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54c28a2ba5064bfed75a4e9e631a65c7 + md5: cc7bd6015b08890ec53f8004091c3bb5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dart", max_pin="x.x") }}' noarch: generic # Suggests: breastCancerVDX, breastCancerMAINZ, Biobase requirements: diff --git a/recipes/bioconductor-data-packages/dataURLs.json b/recipes/bioconductor-data-packages/dataURLs.json index 2c6d28f61bbda..2b5d690d1d314 100644 --- a/recipes/bioconductor-data-packages/dataURLs.json +++ b/recipes/bioconductor-data-packages/dataURLs.json @@ -1 +1 @@ -{"ritandata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.15/data/experiment/src/contrib/RITANdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.20.0_src_all.tar.gz"], "md5": "4a9a65c5312893ef3bf279efd32d53f8", "fn": "RITANdata_1.20.0.tar.gz"}, "bioplex-1.3.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BioPlex_1.3.4.tar.gz", "https://bioarchive.galaxyproject.org/BioPlex_1.3.4.tar.gz", 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"https://depot.galaxyproject.org/software/bioconductor-ahlrbasedbs/bioconductor-ahlrbasedbs_1.5.0_src_all.tar.gz"], "md5": "b1266d2bab652542d6f7289898c3e781", "fn": "AHLRBaseDbs_1.5.0.tar.gz"}, "ahmeshdbs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/AHMeSHDbs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/AHMeSHDbs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahmeshdbs/bioconductor-ahmeshdbs_1.5.0_src_all.tar.gz"], "md5": "87c396d15191843ec3cdced73bf504f8", "fn": "AHMeSHDbs_1.5.0.tar.gz"}, "ahpathbankdbs-0.99.5": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/AHPathbankDbs_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/AHPathbankDbs_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpathbankdbs/bioconductor-ahpathbankdbs_0.99.5_src_all.tar.gz", 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"WES.1KG.WUGSC_1.34.0.tar.gz"}, "wgsmapp-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/WGSmapp_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/WGSmapp_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wgsmapp/bioconductor-wgsmapp_1.14.0_src_all.tar.gz"], "md5": "dfc3f5a82d532551e2d6c21b11c99566", "fn": "WGSmapp_1.14.0.tar.gz"}, "xcoredata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/xcoredata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/xcoredata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xcoredata/bioconductor-xcoredata_1.6.0_src_all.tar.gz"], "md5": "214626bfcbb5d66445324f6e367142c7", "fn": "xcoredata_1.6.0.tar.gz"}, "xhybcasneuf-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/XhybCasneuf_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/XhybCasneuf_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.40.0_src_all.tar.gz"], "md5": "f3e6306b5c05fb026e36e4c60656e25a", "fn": "XhybCasneuf_1.40.0.tar.gz"}, "yeastcc-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastCC_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastCC_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.42.0_src_all.tar.gz"], "md5": "847d9bba73cb25f458f608c2cd6bf0e8", "fn": "yeastCC_1.42.0.tar.gz"}, "yeastexpdata-0.48.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastExpData_0.48.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastExpData_0.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.48.0_src_all.tar.gz"], "md5": "7cd63808a957defe831bf3e9d3ef4789", "fn": "yeastExpData_0.48.0.tar.gz"}, "yeastgsdata-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastGSData_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastGSData_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.40.0_src_all.tar.gz"], "md5": "bc455a9ecd3eb2652f887026841b3c69", "fn": "yeastGSData_0.40.0.tar.gz"}, "yeastnagalakshmi-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastNagalakshmi_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.38.0_src_all.tar.gz"], "md5": "ea5068bf2b4053452f416c56ab32736a", "fn": "yeastNagalakshmi_1.38.0.tar.gz"}, "yeastrnaseq-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastRNASeq_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastRNASeq_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.40.0_src_all.tar.gz"], "md5": "2344deacf993b96e1709ad96b710471f", "fn": "yeastRNASeq_0.40.0.tar.gz"}, "zebrafishrnaseq-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/zebrafishRNASeq_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.22.0_src_all.tar.gz"], "md5": "c1fcbadec1b25e4b28483c015f7ab35c", "fn": "zebrafishRNASeq_1.22.0.tar.gz"}} \ No newline at end of file diff --git a/recipes/bioconductor-data-packages/meta.yaml b/recipes/bioconductor-data-packages/meta.yaml index e1e4b22d3f8b8..9a5e1a2092398 100644 --- a/recipes/bioconductor-data-packages/meta.yaml +++ b/recipes/bioconductor-data-packages/meta.yaml @@ -1,10 +1,12 @@ package: name: 'bioconductor-data-packages' - version: '20230718' + version: '20231203' source: build: - number: 1 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage("bioconductor-data-packages", max_pin=None) }} requirements: run: - r-base diff --git a/recipes/bioconductor-davidtiling/meta.yaml b/recipes/bioconductor-davidtiling/meta.yaml index c60799926ebfa..35f0720944fec 100644 --- a/recipes/bioconductor-davidtiling/meta.yaml +++ b/recipes/bioconductor-davidtiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "davidTiling" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa55aaed3cb0a0e29db8c538c636b447 + md5: dace46d6f640014aff544e0faf355b5e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-davidtiling", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-davidtiling/post-link.sh b/recipes/bioconductor-davidtiling/post-link.sh index 2c0cdbe1d7e3e..ebb07a26801fe 100644 --- a/recipes/bioconductor-davidtiling/post-link.sh +++ b/recipes/bioconductor-davidtiling/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "davidtiling-1.40.0" +installBiocDataPackage.sh "davidtiling-1.42.0" diff --git a/recipes/bioconductor-dcanr/meta.yaml b/recipes/bioconductor-dcanr/meta.yaml index d01daf020a69d..839e3b308764b 100644 --- a/recipes/bioconductor-dcanr/meta.yaml +++ b/recipes/bioconductor-dcanr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "dcanr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d2c15eccd56d9265e4b6d81fa4ab3653 + md5: 1a30832879c85ae9430a463d581ba978 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dcanr", max_pin="x.x") }}' noarch: generic # Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR requirements: diff --git a/recipes/bioconductor-dcats/build.sh b/recipes/bioconductor-dcats/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dcats/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dcats/meta.yaml b/recipes/bioconductor-dcats/meta.yaml new file mode 100644 index 0000000000000..121d93a21050b --- /dev/null +++ b/recipes/bioconductor-dcats/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "DCATS" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8a6002426027bd88d05a2b8759d5a12e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dcats", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle +requirements: + host: + - r-aod + - r-base + - r-e1071 + - r-matrixstats + - r-mcmcpack + - r-robustbase + run: + - r-aod + - r-base + - r-e1071 + - r-matrixstats + - r-mcmcpack + - r-robustbase +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Differential Composition Analysis Transformed by a Similarity matrix' + description: 'Methods to detect the differential composition abundances between conditions in singel-cell RNA-seq experiments, with or without replicates. It aims to correct bias introduced by missclaisification and enable controlling of confounding covariates. To avoid the influence of proportion change from big cell types, DCATS can use either total cell number or specific reference group as normalization term.' + license_file: LICENSE + diff --git a/recipes/bioconductor-dce/meta.yaml b/recipes/bioconductor-dce/meta.yaml index d2b9af554e2c9..82addc1e3b3ab 100644 --- a/recipes/bioconductor-dce/meta.yaml +++ b/recipes/bioconductor-dce/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.7.0" %} +{% set version = "1.10.0" %} {% set name = "dce" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43a65a2d1518138f7f6a6984e025fcde + md5: dbebdd246ea193f92c1a466a84617876 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dce", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-assertthat - r-base - r-dplyr @@ -53,13 +54,13 @@ requirements: - r-tidygraph - r-tidyverse run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-dcgsa/meta.yaml b/recipes/bioconductor-dcgsa/meta.yaml index 77f6314b8fb7d..81d2701989b49 100644 --- a/recipes/bioconductor-dcgsa/meta.yaml +++ b/recipes/bioconductor-dcgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "dcGSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c250b2149d2ecfe5fa7b22d305b6753 + md5: f824cffdf3d7c4f41b44d2cc46b69998 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dcgsa", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-matrix run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-ddct/meta.yaml b/recipes/bioconductor-ddct/meta.yaml index 2d4d457b53232..88e86641ae0b3 100644 --- a/recipes/bioconductor-ddct/meta.yaml +++ b/recipes/bioconductor-ddct/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "ddCt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e9800430fe0d1654a624db09b883e2c + md5: 560588380b356d55a4e11811ae9100e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ddct", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-lattice - 'r-rcolorbrewer >=0.1-3' - r-xtable run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-lattice - 'r-rcolorbrewer >=0.1-3' diff --git a/recipes/bioconductor-ddpcrclust/meta.yaml b/recipes/bioconductor-ddpcrclust/meta.yaml index f01a2b33e6d6e..342aec460ad83 100644 --- a/recipes/bioconductor-ddpcrclust/meta.yaml +++ b/recipes/bioconductor-ddpcrclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ddPCRclust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04448bd253195b441eabc6f2f17b208e + md5: 63c29b24786957fcb604e73a61066e47 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ddpcrclust", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' - - 'bioconductor-flowpeaks >=1.46.0,<1.47.0' - - 'bioconductor-samspectral >=1.54.0,<1.55.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' + - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' + - 'bioconductor-samspectral >=1.56.0,<1.57.0' - r-base - r-clue - r-ggplot2 @@ -32,10 +33,10 @@ requirements: - r-plotrix - r-r.utils run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' - - 'bioconductor-flowpeaks >=1.46.0,<1.47.0' - - 'bioconductor-samspectral >=1.54.0,<1.55.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' + - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' + - 'bioconductor-samspectral >=1.56.0,<1.57.0' - r-base - r-clue - r-ggplot2 diff --git a/recipes/bioconductor-dearseq/meta.yaml b/recipes/bioconductor-dearseq/meta.yaml index b67e37a6861c6..d73ece4475cbb 100644 --- a/recipes/bioconductor-dearseq/meta.yaml +++ b/recipes/bioconductor-dearseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "dearseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 544bd47d884e994f11d6b49f331a4915 + md5: 40f5669b310e7d2142836e3b1592bdd6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dearseq", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr requirements: diff --git a/recipes/bioconductor-debcam/meta.yaml b/recipes/bioconductor-debcam/meta.yaml index 14ea154da7e6e..0af1f12365332 100644 --- a/recipes/bioconductor-debcam/meta.yaml +++ b/recipes/bioconductor-debcam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "debCAM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 777e6f50d5b0121ba5cc208d1697512b + md5: 87d118edcaf90e70fd6aafc865ac5c6a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-debcam", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl # SystemRequirements: Java (>= 1.8) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-apcluster - r-base - r-corpcor @@ -36,9 +37,9 @@ requirements: - r-rjava - openjdk run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-apcluster - r-base - r-corpcor diff --git a/recipes/bioconductor-debrowser/meta.yaml b/recipes/bioconductor-debrowser/meta.yaml index 6c96afb5dbe75..ba6472bfcdadd 100644 --- a/recipes/bioconductor-debrowser/meta.yaml +++ b/recipes/bioconductor-debrowser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.2" %} +{% set version = "1.30.0" %} {% set name = "debrowser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6deaca84c5d4d7f700e23ab0887b4567 + md5: dc51add531d95b1e7a924062aa773018 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-debrowser", max_pin="x.x") }}' noarch: generic # Suggests: testthat, rmarkdown, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-harman >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-harman >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-ashr - r-base - r-colourpicker @@ -58,24 +59,24 @@ requirements: - r-shinyjs - r-stringi run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-harman >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-harman >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-ashr - r-base - r-colourpicker diff --git a/recipes/bioconductor-decipher/meta.yaml b/recipes/bioconductor-decipher/meta.yaml index 4ce9ee8807ab5..257e0cf8b5364 100644 --- a/recipes/bioconductor-decipher/meta.yaml +++ b/recipes/bioconductor-decipher/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "DECIPHER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9396595ebcedf5d570edb11acc6198e0 + md5: 0a32c782d61a604dc3594c684daa8c75 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-decipher", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - 'r-rsqlite >=1.1' - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - 'r-rsqlite >=1.1' diff --git a/recipes/bioconductor-decomptumor2sig/meta.yaml b/recipes/bioconductor-decomptumor2sig/meta.yaml index fc0d87e519d65..a220fbdc707c4 100644 --- a/recipes/bioconductor-decomptumor2sig/meta.yaml +++ b/recipes/bioconductor-decomptumor2sig/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "decompTumor2Sig" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e5ef097fd6a7f21bc4d0aea7cb72a00 + md5: efd7bdadb25752241823124b560e9214 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-decomptumor2sig", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-ggplot2 @@ -41,16 +42,16 @@ requirements: - 'r-quadprog >=1.5-5' - r-readxl run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-deconrnaseq/meta.yaml b/recipes/bioconductor-deconrnaseq/meta.yaml index dc799c1ab8852..a32a24d5aab35 100644 --- a/recipes/bioconductor-deconrnaseq/meta.yaml +++ b/recipes/bioconductor-deconrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "DeconRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe6899279ea73a5b02aee2addc34f38d + md5: d38af67b8408b66b85fbb4061442b953 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deconrnaseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - r-base - r-ggplot2 - r-limsolve run: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - r-base - r-ggplot2 - r-limsolve diff --git a/recipes/bioconductor-decontam/meta.yaml b/recipes/bioconductor-decontam/meta.yaml index c451e14479b93..92c3bba5ab045 100644 --- a/recipes/bioconductor-decontam/meta.yaml +++ b/recipes/bioconductor-decontam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "decontam" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 549a965f3aa9c02b7c4533c81acd2252 + md5: 0e6be1cbff9c4396692e39aadc0a5b9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-decontam", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, phyloseq requirements: diff --git a/recipes/bioconductor-decontx/build.sh b/recipes/bioconductor-decontx/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-decontx/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-decontx/meta.yaml b/recipes/bioconductor-decontx/meta.yaml new file mode 100644 index 0000000000000..4a08a6867b10a --- /dev/null +++ b/recipes/bioconductor-decontx/meta.yaml @@ -0,0 +1,88 @@ +{% set version = "1.0.0" %} +{% set name = "decontX" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1e2f4af9204397b8104543dd954bb390 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-decontx", max_pin="x.x") }}' +# Suggests: BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0) +# SystemRequirements: GNU make +requirements: + host: + - 'bioconductor-celda >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - 'r-bh >=1.66.0' + - r-dbscan + - r-ggplot2 + - 'r-matrix >=1.5.3' + - r-mcmcprecision + - r-patchwork + - r-plyr + - 'r-rcpp >=0.12.0' + - 'r-rcppeigen >=0.3.3.3.0' + - 'r-rcppparallel >=5.0.1' + - r-reshape2 + - 'r-rstan >=2.18.1' + - 'r-rstantools >=2.2.0' + - r-seurat + - 'r-stanheaders >=2.18.0' + - r-withr + - libblas + - liblapack + run: + - 'bioconductor-celda >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - 'r-bh >=1.66.0' + - r-dbscan + - r-ggplot2 + - 'r-matrix >=1.5.3' + - r-mcmcprecision + - r-patchwork + - r-plyr + - 'r-rcpp >=0.12.0' + - 'r-rcppeigen >=0.3.3.3.0' + - 'r-rcppparallel >=5.0.1' + - r-reshape2 + - 'r-rstan >=2.18.1' + - 'r-rstantools >=2.2.0' + - r-seurat + - 'r-stanheaders >=2.18.0' + - r-withr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Decontamination of single cell genomics data' + description: 'This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.' + license_file: LICENSE + diff --git a/recipes/bioconductor-deconvr/meta.yaml b/recipes/bioconductor-deconvr/meta.yaml index ddfd91252440c..ea453fe8601db 100644 --- a/recipes/bioconductor-deconvr/meta.yaml +++ b/recipes/bioconductor-deconvr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "deconvR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 378b68def947127eaecc6e0f16231a81 + md5: 77963b41f8655665f3aac5e2cb1d529c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deconvr", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator, RefManageR requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - 'r-data.table >=1.14.0' @@ -41,12 +42,12 @@ requirements: - 'r-rsq >=2.2' - 'r-tidyr >=1.1.3' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - 'r-data.table >=1.14.0' diff --git a/recipes/bioconductor-decoupler/meta.yaml b/recipes/bioconductor-decoupler/meta.yaml index ff57fa682a15e..5694c36e329e4 100644 --- a/recipes/bioconductor-decoupler/meta.yaml +++ b/recipes/bioconductor-decoupler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "decoupleR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46b97475fd42e3633fb5c40d26c88d4e + md5: de2a391693476223ec54521aa77ba121 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-decoupler", max_pin="x.x") }}' noarch: generic # Suggests: glmnet (>= 4.1.0), GSVA, viper, fgsea (>= 1.15.4), AUCell, SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel, patchwork requirements: diff --git a/recipes/bioconductor-deepbluer/build_failure.linux-64.yaml b/recipes/bioconductor-deepbluer/build_failure.linux-64.yaml index 32a64afe45536..4cd5b4a0d4f6b 100644 --- a/recipes/bioconductor-deepbluer/build_failure.linux-64.yaml +++ b/recipes/bioconductor-deepbluer/build_failure.linux-64.yaml @@ -1,72 +1,72 @@ -recipe_sha: b09c118bdb9ad88319ef992ea639cfc1161541201e802900f905d1027c7fcdcc # The commit at which this recipe failed to build. +recipe_sha: 298dc02b6321425f565f394b84e67a916cb488fbfb52ae216e284b9f02ba71ce # The commit at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - r-withr: 2.5.0-r43hc72bb7e_2 conda-forge - r-xfun: 0.39-r43ha503ecb_1 conda-forge - r-xml: 3.99_0.14-r43hc38eee6_2 conda-forge - r-yaml: 2.3.7-r43h57805ef_1 conda-forge - readline: 8.2-h8228510_1 conda-forge - sed: 4.8-he412f7d_0 conda-forge - setuptools: 68.0.0-pyhd8ed1ab_0 conda-forge sysroot_linux-64: 2.12-he073ed8_16 conda-forge - tk: 8.6.12-h27826a3_0 conda-forge - tktable: 2.10-hb7b940f_3 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h0c5db8f_5 conda-forge toml: 0.10.2-pyhd8ed1ab_0 conda-forge - tomlkit: 0.11.8-pyha770c72_0 conda-forge - tzdata: 2023c-h71feb2d_0 conda-forge - wheel: 0.40.0-pyhd8ed1ab_1 conda-forge + tomlkit: 0.12.3-pyha770c72_0 conda-forge + tzdata: 2023d-h0c530f3_0 conda-forge + wheel: 0.42.0-pyhd8ed1ab_0 conda-forge xmltodict: 0.13.0-pyhd8ed1ab_0 conda-forge xorg-kbproto: 1.0.7-h7f98852_1002 conda-forge - xorg-libice: 1.0.10-h7f98852_0 conda-forge - xorg-libsm: 1.2.3-hd9c2040_1000 conda-forge - xorg-libx11: 1.8.6-h8ee46fc_0 conda-forge + xorg-libice: 1.1.1-hd590300_0 conda-forge + xorg-libsm: 1.2.4-h7391055_0 conda-forge + xorg-libx11: 1.8.7-h8ee46fc_0 conda-forge xorg-libxau: 1.0.11-hd590300_0 conda-forge xorg-libxdmcp: 1.1.3-h7f98852_0 conda-forge xorg-libxext: 1.3.4-h0b41bf4_2 conda-forge xorg-libxrender: 0.9.11-hd590300_0 conda-forge - xorg-libxt: 1.3.0-hd590300_0 conda-forge + xorg-libxt: 1.3.0-hd590300_1 conda-forge xorg-renderproto: 0.11.1-h7f98852_1002 conda-forge xorg-xextproto: 7.3.0-h0b41bf4_1003 conda-forge xorg-xproto: 7.0.31-h7f98852_1007 conda-forge xz: 5.2.6-h166bdaf_0 conda-forge yaml: 0.2.5-h7f98852_2 conda-forge - yq: 3.2.2-pyhd8ed1ab_0 conda-forge + yq: 3.2.3-pyhd8ed1ab_0 conda-forge zlib: 1.2.13-hd590300_5 conda-forge - zstd: 1.5.2-hfc55251_7 conda-forge + zstd: 1.5.5-hfc55251_0 conda-forge Preparing transaction: ...working... done Verifying transaction: ...working... done - Executing transaction: ...working... done + Executing transaction: ...working... + To install TinyTeX with tinytex::install_tinytex() the system must have a functional Perl + installation with a File::Find module. Most end-user systems will already satisfy this + requirement; however, some minimal contexts (e.g., containers) may not. Perl is available + via Conda Forge as the package perl. See https://github.com/rstudio/tinytex/issues/419 + + + done [34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 533.1kB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 756.0kB/s 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 1.8MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.4MB/s 0.0s [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 1.3MB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 4.1MB/s 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.0MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.4MB/s 0.0s [?25h ## Package Plan ## - environment location: /opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/_build_env + environment location: /opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/_build_env Source cache directory is: /opt/conda/conda-bld/src_cache INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache - Downloading source to cache: DeepBlueR_1.26.0_6b686d18b4.tar.gz - INFO:conda_build.source:Downloading source to cache: DeepBlueR_1.26.0_6b686d18b4.tar.gz - Downloading https://bioconductor.org/packages/3.17/bioc/src/contrib/DeepBlueR_1.26.0.tar.gz - INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.17/bioc/src/contrib/DeepBlueR_1.26.0.tar.gz + Downloading source to cache: DeepBlueR_1.27.0_2217f4325c.tar.gz + INFO:conda_build.source:Downloading source to cache: DeepBlueR_1.27.0_2217f4325c.tar.gz + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/DeepBlueR_1.27.0.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/DeepBlueR_1.27.0.tar.gz Success INFO:conda_build.source:Success Extracting download - source tree in: /opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/work - export PREFIX=/opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ - export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/_build_env - export SRC_DIR=/opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/work + source tree in: /opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/work + export PREFIX=/opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/work During startup - Warning message: Setting LC_TIME failed, using "C" - * installing to library /opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library + * installing to library /opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library * installing *source* package DeepBlueR ... ** using staged installation ** R @@ -79,10 +79,10 @@ log: |2- "503" Error in xml.rpc(deepblue_options("url"), "list_column_types", user_key) : Problems + ERROR: lazy loading failed for package DeepBlueR Error: unable to load R code in package DeepBlueR Execution halted - ERROR: lazy loading failed for package DeepBlueR - * removing /opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/DeepBlueR + * removing /opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/DeepBlueR Traceback (most recent call last): File "/opt/conda/bin/conda-mambabuild", line 10, in sys.exit(main()) @@ -100,5 +100,5 @@ log: |2- return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-deepbluer_1689835533309/work/conda_build.sh']' returned non-zero exit status 1. + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-deepbluer_1703295180448/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. diff --git a/recipes/bioconductor-deepbluer/meta.yaml b/recipes/bioconductor-deepbluer/meta.yaml index 973fe509bbb9a..05c2f44656ae9 100644 --- a/recipes/bioconductor-deepbluer/meta.yaml +++ b/recipes/bioconductor-deepbluer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.27.0" %} {% set name = "DeepBlueR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b686d18b4c2c51cad4976f4187303fa + md5: 2217f4325cc72c3e22c330fa3a8dd25b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deepbluer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr, RColorBrewer, matrixStats requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-diffr @@ -38,9 +39,9 @@ requirements: - r-withr - r-xml run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-diffr diff --git a/recipes/bioconductor-deeppincs/meta.yaml b/recipes/bioconductor-deeppincs/meta.yaml index 9551fe7cc35c7..9e15f3e125853 100644 --- a/recipes/bioconductor-deeppincs/meta.yaml +++ b/recipes/bioconductor-deeppincs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DeepPINCS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b2ad842adfd8cdc86a4e7fb8e1dad8d + md5: cc5fbdd874a89f88ffed9c215f1e3d74 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deeppincs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-ttgsea >=1.8.0,<1.9.0' + - 'bioconductor-ttgsea >=1.10.0,<1.11.0' - r-base - r-catencoders - r-keras @@ -35,7 +36,7 @@ requirements: - r-tokenizers - r-webchem run: - - 'bioconductor-ttgsea >=1.8.0,<1.9.0' + - 'bioconductor-ttgsea >=1.10.0,<1.11.0' - r-base - r-catencoders - r-keras diff --git a/recipes/bioconductor-deepsnv/meta.yaml b/recipes/bioconductor-deepsnv/meta.yaml index e24a3b3c16087..66edfae750ac9 100644 --- a/recipes/bioconductor-deepsnv/meta.yaml +++ b/recipes/bioconductor-deepsnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "deepSNV" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1b8f9884aafbf5492ce90f19486c2ec + md5: 4df42adbe4997ad401a7d2505ee2b227 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deepsnv", max_pin="x.x") }}' # Suggests: RColorBrewer, knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-vgam - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-vgam build: diff --git a/recipes/bioconductor-deformats/meta.yaml b/recipes/bioconductor-deformats/meta.yaml index 58f77e127633a..e9aaba108780e 100644 --- a/recipes/bioconductor-deformats/meta.yaml +++ b/recipes/bioconductor-deformats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "DEFormats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61f1496fd145226998b44613f7b0e4b2 + md5: d4fd53366cc3ead5959b9af782ff6790 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deformats", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-data.table run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-degnorm/meta.yaml b/recipes/bioconductor-degnorm/meta.yaml index 115a4a3d466b8..a0f2b8bb9bca8 100644 --- a/recipes/bioconductor-degnorm/meta.yaml +++ b/recipes/bioconductor-degnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "DegNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1de83a750bfb953d4984c3fed01730c2 + md5: 45dbc8183e1e18f3027b7880d3b5ef5a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-degnorm", max_pin="x.x") }}' # Suggests: knitr,rmarkdown,formatR requirements: host: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel @@ -40,12 +41,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-degraph/meta.yaml b/recipes/bioconductor-degraph/meta.yaml index bb3c122bcd32c..d8a23d376a3ec 100644 --- a/recipes/bioconductor-degraph/meta.yaml +++ b/recipes/bioconductor-degraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "DEGraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73c561cbb1e5f175b84a1f0837c002e8 + md5: c61fb687376b321b9a52dfd15375e0b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-degraph", max_pin="x.x") }}' noarch: generic # Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-ncigraph >=1.48.0,<1.49.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-ncigraph >=1.50.0,<1.51.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-lattice - r-mvtnorm @@ -33,11 +34,11 @@ requirements: - r-r.utils - r-rrcov run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-ncigraph >=1.48.0,<1.49.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-ncigraph >=1.50.0,<1.51.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-lattice - r-mvtnorm diff --git a/recipes/bioconductor-degreport/meta.yaml b/recipes/bioconductor-degreport/meta.yaml index 104ec171f847c..73f13f7830437 100644 --- a/recipes/bioconductor-degreport/meta.yaml +++ b/recipes/bioconductor-degreport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.4" %} {% set name = "DEGreport" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d7a33c4f6e46476e1130b27b0a34dc2 + md5: d7c43c419f87827c0a116e3ae905ead7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-degreport", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-circlize - r-cluster - r-cowplot + - r-dendextend - r-dplyr - r-ggdendro - r-ggplot2 @@ -46,23 +48,25 @@ requirements: - r-reshape - r-rlang - r-scales + - r-stringi - r-stringr - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-circlize - r-cluster - r-cowplot + - r-dendextend - r-dplyr - r-ggdendro - r-ggplot2 @@ -75,6 +79,7 @@ requirements: - r-reshape - r-rlang - r-scales + - r-stringi - r-stringr - r-tibble - r-tidyr diff --git a/recipes/bioconductor-degseq/meta.yaml b/recipes/bioconductor-degseq/meta.yaml index 1b1c385fc5d8f..1fd5c9056f400 100644 --- a/recipes/bioconductor-degseq/meta.yaml +++ b/recipes/bioconductor-degseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.1" %} {% set name = "DEGseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: befdaa80e6df3dba5b23aba158858b45 + md5: cc89e25cb7e9afc38b5fb2bba34722b5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-degseq", max_pin="x.x") }}' requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - libblas - liblapack run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-delayedarray/meta.yaml b/recipes/bioconductor-delayedarray/meta.yaml index b26889d89e854..164a7bfd3c0bc 100644 --- a/recipes/bioconductor-delayedarray/meta.yaml +++ b/recipes/bioconductor-delayedarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.26.6" %} +{% set version = "0.28.0" %} {% set name = "DelayedArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d15ca54caa5e28aa00c97dd61db886b + md5: 812e7575d6eaa61f5b68364cdf1da3d9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delayedarray", max_pin="x.x") }}' # Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsearray >=1.2.0,<1.3.0' - r-base - r-matrix build: diff --git a/recipes/bioconductor-delayeddataframe/meta.yaml b/recipes/bioconductor-delayeddataframe/meta.yaml index 6534ae371b8b5..986a848355d4e 100644 --- a/recipes/bioconductor-delayeddataframe/meta.yaml +++ b/recipes/bioconductor-delayeddataframe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DelayedDataFrame" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 348557d31d23d725601581912e43e2ea + md5: dd12410d16a2e6cf7bb022d2aa334bf7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delayeddataframe", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, rmarkdown, SeqArray, GDSArray +# Suggests: testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-delayedmatrixstats/meta.yaml b/recipes/bioconductor-delayedmatrixstats/meta.yaml index 5bb1eb58c256d..f3b73711617f5 100644 --- a/recipes/bioconductor-delayedmatrixstats/meta.yaml +++ b/recipes/bioconductor-delayedmatrixstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "DelayedMatrixStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88739eb294c38fc717e77987455a1d58 + md5: 890845d8c80a2b64cd02b3ff7f1e504d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delayedmatrixstats", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem, HDF5Array +# Suggests: testthat, knitr, rmarkdown, BiocStyle, microbenchmark, profmem, HDF5Array, matrixStats (>= 1.0.0) requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' - r-base - 'r-matrix >=1.5-0' - - 'r-matrixstats >=1.0.0' run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' - r-base - 'r-matrix >=1.5-0' - - 'r-matrixstats >=1.0.0' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-delayedrandomarray/meta.yaml b/recipes/bioconductor-delayedrandomarray/meta.yaml index 435ccc7188e36..084a5e1dbc8b2 100644 --- a/recipes/bioconductor-delayedrandomarray/meta.yaml +++ b/recipes/bioconductor-delayedrandomarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DelayedRandomArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4147f1b05d871632f2549d95a775883 + md5: 2f583ab177fd333cf626827fc28a6faf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delayedrandomarray", max_pin="x.x") }}' # Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix # SystemRequirements: C++11 requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-bh - r-dqrng @@ -29,7 +30,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-bh - r-dqrng diff --git a/recipes/bioconductor-delayedtensor/meta.yaml b/recipes/bioconductor-delayedtensor/meta.yaml index ed7c95961bdc5..be01c68df53e5 100644 --- a/recipes/bioconductor-delayedtensor/meta.yaml +++ b/recipes/bioconductor-delayedtensor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "DelayedTensor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4651a15b7f778aefab7307d6fd600631 + md5: ee3e89ac7a0b9f3ca79f744edfdc69b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delayedtensor", max_pin="x.x") }}' noarch: generic # Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate requirements: host: - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedrandomarray >=1.8.0,<1.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedrandomarray >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - r-base - r-einsum - r-irlba - r-matrix - r-rtensor run: - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedrandomarray >=1.8.0,<1.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedrandomarray >=1.10.0,<1.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - r-base - r-einsum - r-irlba diff --git a/recipes/bioconductor-delocal/meta.yaml b/recipes/bioconductor-delocal/meta.yaml index 6dc88c6c7f306..f9361e910db48 100644 --- a/recipes/bioconductor-delocal/meta.yaml +++ b/recipes/bioconductor-delocal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "DELocal" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f595f5306f040c92e53f70db5fb4d81 + md5: 40f2eac89260ff4692fb02047990d048 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-delocal", max_pin="x.x") }}' noarch: generic -# Suggests: biomaRt, knitr, PCRedux, rmarkdown, stringr +# Suggests: biomaRt, knitr, PCRedux, rmarkdown, stringr, BiocStyle requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 - r-matrixstats - r-reshape2 run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-deltacapturec/meta.yaml b/recipes/bioconductor-deltacapturec/meta.yaml index fc51052ee4e7c..16b711e2ce632 100644 --- a/recipes/bioconductor-deltacapturec/meta.yaml +++ b/recipes/bioconductor-deltacapturec/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "deltaCaptureC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac0f8754bd5250993302876e3b443615 + md5: e70cf57b6d22164dd5712a3441b0a788 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deltacapturec", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-tictoc run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-tictoc diff --git a/recipes/bioconductor-deltagseg/meta.yaml b/recipes/bioconductor-deltagseg/meta.yaml index d4b20475cbb57..a0a6ce76a69a8 100644 --- a/recipes/bioconductor-deltagseg/meta.yaml +++ b/recipes/bioconductor-deltagseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "deltaGseg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84ea9181363b1231227685b65a28ca13 + md5: e92ca25a67a9250f26c6263043c60ee2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deltagseg", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: diff --git a/recipes/bioconductor-demand/meta.yaml b/recipes/bioconductor-demand/meta.yaml index 36e5b90b870e2..b56d0286db48a 100644 --- a/recipes/bioconductor-demand/meta.yaml +++ b/recipes/bioconductor-demand/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "DeMAND" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbc37106827433bc654a90a4ac7e6701 + md5: ccb354bddebbebda6c42453810f10e70 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-demand", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-demuxmix/meta.yaml b/recipes/bioconductor-demuxmix/meta.yaml index 2c905657b4e60..252585cebc11f 100644 --- a/recipes/bioconductor-demuxmix/meta.yaml +++ b/recipes/bioconductor-demuxmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "demuxmix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 146120afb774a862ecfb93ec5fb970b0 + md5: 9bbdcc634e542fe151a50a2511206140 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-demuxmix", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0) requirements: diff --git a/recipes/bioconductor-demuxsnp/build.sh b/recipes/bioconductor-demuxsnp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-demuxsnp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-demuxsnp/meta.yaml b/recipes/bioconductor-demuxsnp/meta.yaml new file mode 100644 index 0000000000000..ad5982ba15810 --- /dev/null +++ b/recipes/bioconductor-demuxsnp/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.0.0" %} +{% set name = "demuxSNP" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 66a0ed302acbc18c7a106d99bf645133 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-demuxsnp", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, Seurat, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-demuxmix >=1.4.0,<1.5.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-class + - r-combinat + - r-matrix + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-demuxmix >=1.4.0,<1.5.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-class + - r-combinat + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'scRNAseq demultiplexing using cell hashing and SNPs' + description: 'This package assists in demultiplexing scRNAseq data using both cell hashing and SNPs data. The SNP profile of each group os learned using high confidence assignments from the cell hashing data. Cells which cannot be assigned with high confidence from the cell hashing data are assigned to their most similar group based on their SNPs. We also provide some helper function to optimise SNP selection, create training data and merge SNP data into the SingleCellExperiment framework.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-densvis/meta.yaml b/recipes/bioconductor-densvis/meta.yaml index aaa52a0863d1a..936a9b9557490 100644 --- a/recipes/bioconductor-densvis/meta.yaml +++ b/recipes/bioconductor-densvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.2" %} +{% set version = "1.12.0" %} {% set name = "densvis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a6a87938d3267e5f4ba279e1c0c91533 + md5: cf3ee330c8c9f0b396feb398e342cf8d build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, rmarkdown, BiocStyle, ggplot2, Rtsne, uwot, testthat + run_exports: '{{ pin_subpackage("bioconductor-densvis", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-assertthat - r-base - r-irlba - r-rcpp - r-reticulate + - r-rtsne - libblas - liblapack run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-assertthat - r-base - r-irlba - r-rcpp - r-reticulate + - r-rtsne build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-dep/meta.yaml b/recipes/bioconductor-dep/meta.yaml index a44133258ced4..6f0664c7a0333 100644 --- a/recipes/bioconductor-dep/meta.yaml +++ b/recipes/bioconductor-dep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "DEP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://{{ name|lower }}ot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d020fdba2ecaec00e6f17559a2a7454 + md5: 2bfaf5d5bfd3f05c7a7a80742bd43f7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dep", max_pin="x.x") }}' noarch: generic # Suggests: testthat, enrichR, knitr, BiocStyle requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-assertthat - r-base - r-circlize @@ -46,11 +47,11 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-assertthat - r-base - r-circlize diff --git a/recipes/bioconductor-depecher/meta.yaml b/recipes/bioconductor-depecher/meta.yaml index 32b81b60fc458..74da60263ebdb 100644 --- a/recipes/bioconductor-depecher/meta.yaml +++ b/recipes/bioconductor-depecher/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DepecheR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b560cc798d7fb32413c75317b73e45d9 + md5: 201fe937f16e843f49fbe35a4ae1ebb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-depecher", max_pin="x.x") }}' # Suggests: uwot, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - 'r-beanplot >=1.2' + - 'r-collapse >=1.9.2' - 'r-dosnow >=1.0.16' - 'r-dplyr >=0.7.8' - 'r-fnn >=1.1.3' @@ -41,9 +43,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - 'r-beanplot >=1.2' + - 'r-collapse >=1.9.2' - 'r-dosnow >=1.0.16' - 'r-dplyr >=0.7.8' - 'r-fnn >=1.1.3' diff --git a/recipes/bioconductor-depinfer/meta.yaml b/recipes/bioconductor-depinfer/meta.yaml index e735db3795146..94dc1dcdf83ca 100644 --- a/recipes/bioconductor-depinfer/meta.yaml +++ b/recipes/bioconductor-depinfer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "DepInfeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcf243eeb7152508a9beb10faa48f249 + md5: d673a7cc6ac21a4d899238878c09533f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-depinfer", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, BiocStyle, ggbeeswarm requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-glmnet - r-matrixstats run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-glmnet - r-matrixstats diff --git a/recipes/bioconductor-depmap/meta.yaml b/recipes/bioconductor-depmap/meta.yaml index 515f8263f9737..f38b98fd584e6 100644 --- a/recipes/bioconductor-depmap/meta.yaml +++ b/recipes/bioconductor-depmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "depmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d4405c4714a46efd721be9905eddc21f + md5: 7f00d05c7f899e622293767baa04e120 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-depmap", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, tibble, stringr, tidyr requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-depmap/post-link.sh b/recipes/bioconductor-depmap/post-link.sh index 1f90ee9ff67c0..a1ee9c05ab0be 100644 --- a/recipes/bioconductor-depmap/post-link.sh +++ b/recipes/bioconductor-depmap/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "depmap-1.14.0" +installBiocDataPackage.sh "depmap-1.16.0" diff --git a/recipes/bioconductor-deqms/meta.yaml b/recipes/bioconductor-deqms/meta.yaml index b1f046d308f58..7fee72622c3bd 100644 --- a/recipes/bioconductor-deqms/meta.yaml +++ b/recipes/bioconductor-deqms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DEqMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58542439f1c16afe6974fd4ee95852c4 + md5: bc308e6f683ca1bf0dcdb703274575ac build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deqms", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitr,rmarkdown,markdown,plyr,reshape2,farms,utils,ggrepel,ExperimentHub,LSD requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-matrixstats run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-matrixstats diff --git a/recipes/bioconductor-derfinder/meta.yaml b/recipes/bioconductor-derfinder/meta.yaml index 2c8eafb1cfd89..5f1ca01fd980f 100644 --- a/recipes/bioconductor-derfinder/meta.yaml +++ b/recipes/bioconductor-derfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "derfinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,49 +11,50 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ba0d27535c6e19834607cc8aabc4de9f + md5: a3ef629c180b64b0776c880164603c7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-derfinder", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene, covr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinderhelper >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinderhelper >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-hmisc run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinderhelper >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinderhelper >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-hmisc test: @@ -63,7 +64,11 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach' - description: 'This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.' + description: | + This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. + Two implementations of the DER Finder approach are included in this package: (1) single base-level + F-statistics and (2) DER identification at the expressed regions-level. + The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks. extra: identifiers: - biotools:derfinder diff --git a/recipes/bioconductor-derfinderdata/meta.yaml b/recipes/bioconductor-derfinderdata/meta.yaml index c52d8fcd7b912..ab731b2b7adf4 100644 --- a/recipes/bioconductor-derfinderdata/meta.yaml +++ b/recipes/bioconductor-derfinderdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "derfinderData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7787e049bcee25cb354773f1fd2cf27 + md5: 032efff51d29eae3fc1a5e032c0f3c40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-derfinderdata", max_pin="x.x") }}' noarch: generic # Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>= 0.3.3), BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-derfinderdata/post-link.sh b/recipes/bioconductor-derfinderdata/post-link.sh index cfddf0ccc3eeb..07fd8f6c6666d 100644 --- a/recipes/bioconductor-derfinderdata/post-link.sh +++ b/recipes/bioconductor-derfinderdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "derfinderdata-2.18.0" +installBiocDataPackage.sh "derfinderdata-2.20.0" diff --git a/recipes/bioconductor-derfinderhelper/meta.yaml b/recipes/bioconductor-derfinderhelper/meta.yaml index 5b4c926b08b6d..d23d5cb1f7b01 100644 --- a/recipes/bioconductor-derfinderhelper/meta.yaml +++ b/recipes/bioconductor-derfinderhelper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "derfinderHelper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 85b9dc14c66f5aa287e9673f955f65da + md5: 2544077112525d7f25f34270ed365423 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-derfinderhelper", max_pin="x.x") }}' noarch: generic # Suggests: sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), RefManageR, rmarkdown (>= 0.3.3), testthat, covr requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-derfinderplot/meta.yaml b/recipes/bioconductor-derfinderplot/meta.yaml index 77fbfe9a49ff5..2890878efb489 100644 --- a/recipes/bioconductor-derfinderplot/meta.yaml +++ b/recipes/bioconductor-derfinderplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "derfinderPlot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c60bba2ab936a7c037c3d6311a6b18d + md5: c3dbd553554f3b043b8f03e4b05a964a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-derfinderplot", max_pin="x.x") }}' noarch: generic # Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr requirements: host: - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-plyr @@ -36,14 +37,14 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-plyr diff --git a/recipes/bioconductor-descan2/meta.yaml b/recipes/bioconductor-descan2/meta.yaml index 8bfd045281a86..655f19ab5b6b3 100644 --- a/recipes/bioconductor-descan2/meta.yaml +++ b/recipes/bioconductor-descan2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "DEScan2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c5a508823352ccf16d9af41b273a9a5 + md5: 476f052d4a86e27d332812852fd7e0c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-descan2", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-glue @@ -40,17 +41,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-glue diff --git a/recipes/bioconductor-deseq2/meta.yaml b/recipes/bioconductor-deseq2/meta.yaml index bd256801fe5c6..fbad8ff890c69 100644 --- a/recipes/bioconductor-deseq2/meta.yaml +++ b/recipes/bioconductor-deseq2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.2" %} +{% set version = "1.42.0" %} {% set name = "DESeq2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8869279f9f3cd28d15e65ea75f8d8aab + md5: 5eb89526ce9fd4da98b1a5e0b5ba0bf3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deseq2", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10), glmGamPoi, BiocManager requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - - r-ggplot2 + - 'r-ggplot2 >=3.4.0' - r-locfit - r-matrixstats - 'r-rcpp >=0.11.0' @@ -36,15 +38,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - - r-ggplot2 + - 'r-ggplot2 >=3.4.0' - r-locfit - r-matrixstats - 'r-rcpp >=0.11.0' diff --git a/recipes/bioconductor-desingle/meta.yaml b/recipes/bioconductor-desingle/meta.yaml index bde60c8322a09..2f3cbbd1c30a4 100644 --- a/recipes/bioconductor-desingle/meta.yaml +++ b/recipes/bioconductor-desingle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "DEsingle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee4807f0e64627ced9f59afee0b77b5b + md5: 6969e960919434ccd6e5b9bdd926aece build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-desingle", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, SingleCellExperiment requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-bbmle >=1.0.18' - 'r-gamlss >=4.4-0' @@ -31,7 +32,7 @@ requirements: - 'r-pscl >=1.4.9' - 'r-vgam >=1.0-2' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-bbmle >=1.0.18' - 'r-gamlss >=4.4-0' diff --git a/recipes/bioconductor-desousa2013/meta.yaml b/recipes/bioconductor-desousa2013/meta.yaml index 4e0410693b971..ffb817248a4d9 100644 --- a/recipes/bioconductor-desousa2013/meta.yaml +++ b/recipes/bioconductor-desousa2013/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "DeSousa2013" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a12b8cbbcf6b3ccc758dacd1ef01852 + md5: 41a3ca5cba40653eb4be04203aaf60ac build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-desousa2013", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' - - 'bioconductor-frmatools >=1.52.0,<1.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' + - 'bioconductor-frmatools >=1.54.0,<1.55.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-cluster - r-gplots @@ -38,16 +39,16 @@ requirements: - r-rocr - r-survival run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' - - 'bioconductor-frmatools >=1.52.0,<1.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' + - 'bioconductor-frmatools >=1.54.0,<1.55.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-cluster - r-gplots @@ -56,7 +57,7 @@ requirements: - r-rocr - r-survival - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' build: - {{ cdt('mesa-libgl-devel') }} # [linux] - {{ cdt('mesa-dri-drivers') }} # [linux] diff --git a/recipes/bioconductor-desousa2013/post-link.sh b/recipes/bioconductor-desousa2013/post-link.sh index acd6ef56f68c2..4c31f29da3892 100644 --- a/recipes/bioconductor-desousa2013/post-link.sh +++ b/recipes/bioconductor-desousa2013/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "desousa2013-1.36.0" +installBiocDataPackage.sh "desousa2013-1.38.0" diff --git a/recipes/bioconductor-despace/meta.yaml b/recipes/bioconductor-despace/meta.yaml index 1628764112915..6ad56c3815333 100644 --- a/recipes/bioconductor-despace/meta.yaml +++ b/recipes/bioconductor-despace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "DESpace" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ebe4a43a2479a091a19a012ae6db464c + md5: 436915bded5ec94da6e412ccdff80e8e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-despace", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle, ExperimentHub, concaveman, spatialLIBD, purrr, scuttle, utils requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-cowplot @@ -41,13 +42,13 @@ requirements: - r-patchwork - r-scales run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-cowplot diff --git a/recipes/bioconductor-destiny/meta.yaml b/recipes/bioconductor-destiny/meta.yaml index d92ce04f87d79..4bb1c1f0f7225 100644 --- a/recipes/bioconductor-destiny/meta.yaml +++ b/recipes/bioconductor-destiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.14.0" %} +{% set version = "3.16.0" %} {% set name = "destiny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 251c5635adf088e2ee70626a60e1489d + md5: b86a5cbd268832cb7a6da5999e50393b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-destiny", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot.multistats - r-ggplot2 @@ -47,11 +48,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot.multistats - r-ggplot2 diff --git a/recipes/bioconductor-desubs/meta.yaml b/recipes/bioconductor-desubs/meta.yaml index 5840dfa722811..98b6a9306f8b5 100644 --- a/recipes/bioconductor-desubs/meta.yaml +++ b/recipes/bioconductor-desubs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "DEsubs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e37c127e2b3fdfe0613d43ef5c2e949c + md5: 1e2b74c85e35888eab89ac39a363c32c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-desubs", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-circlize - r-ggplot2 @@ -37,12 +38,12 @@ requirements: - r-nbpseq - r-pheatmap run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-dewseq/meta.yaml b/recipes/bioconductor-dewseq/meta.yaml index dc3676bb2df17..035c2b2dbe9ed 100644 --- a/recipes/bioconductor-dewseq/meta.yaml +++ b/recipes/bioconductor-dewseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.2" %} {% set name = "DEWSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02180a59d83e6a2ef88b2bea89104832 + md5: 4164c3c7d4967586861e0c2d40815ec5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dewseq", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat, BiocStyle, IHW +# Suggests: knitr, rmarkdown, tidyverse, testthat, BiocStyle, IHW requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.11.8' - r-r.utils run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.11.8' - r-r.utils diff --git a/recipes/bioconductor-dexma/meta.yaml b/recipes/bioconductor-dexma/meta.yaml index 555a80d3f5b3e..f828df78731c2 100644 --- a/recipes/bioconductor-dexma/meta.yaml +++ b/recipes/bioconductor-dexma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.6" %} {% set name = "DExMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8155bdaa13020bf598c9357286d290cb + md5: 7397f231c7a241e6bfb258ca064ff8b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dexma", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, qpdf, BiocGenerics, RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dexmadata >=1.8.0,<1.9.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dexmadata >=1.10.0,<1.11.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-bnstruct - r-pheatmap @@ -36,13 +37,13 @@ requirements: - r-scales - r-swamp run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dexmadata >=1.8.0,<1.9.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dexmadata >=1.10.0,<1.11.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-bnstruct - r-pheatmap diff --git a/recipes/bioconductor-dexmadata/meta.yaml b/recipes/bioconductor-dexmadata/meta.yaml index 7c093e1e7363b..418aaacbbfa95 100644 --- a/recipes/bioconductor-dexmadata/meta.yaml +++ b/recipes/bioconductor-dexmadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DExMAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bc2fd62dd24eeaee294a624610b75918 + md5: 3d2a9cc7d0044ffc23e572f4c5cc4426 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dexmadata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dexmadata/post-link.sh b/recipes/bioconductor-dexmadata/post-link.sh index 166930720a76a..deb9a0366746c 100644 --- a/recipes/bioconductor-dexmadata/post-link.sh +++ b/recipes/bioconductor-dexmadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dexmadata-1.8.0" +installBiocDataPackage.sh "dexmadata-1.10.0" diff --git a/recipes/bioconductor-dexseq/build.sh b/recipes/bioconductor-dexseq/build.sh index c1d13421f5f1e..a9c2ad544d4dc 100644 --- a/recipes/bioconductor-dexseq/build.sh +++ b/recipes/bioconductor-dexseq/build.sh @@ -8,4 +8,11 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . \ No newline at end of file + +$R CMD INSTALL --build . +python_path=$PREFIX/lib/R/library/DEXSeq/python_scripts +echo python3 ${python_path}/dexseq_prepare_annotation.py '"$@"' > $PREFIX/bin/dexseq_prepare_annotation.py +chmod +x $PREFIX/bin/dexseq_prepare_annotation.py + +echo python3 ${python_path}/dexseq_count.py '"$@"' > $PREFIX/bin/dexseq_count.py +chmod +x $PREFIX/bin/dexseq_count.py diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 0a42a1c1397a8..29b4cbc81fbe4 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "DEXSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,48 +11,49 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 83652c928d49e5ea8c284a5b5d37a46a + md5: 8e5876f927b0b0cdfc4a402bfb4fb3d6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dexseq", max_pin="x.x") }}' noarch: generic -# Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2 +# Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-hwriter - r-rcolorbrewer - r-statmod - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-hwriter - r-rcolorbrewer diff --git a/recipes/bioconductor-dfp/meta.yaml b/recipes/bioconductor-dfp/meta.yaml index 6fbaa70b6753c..846c1dbfc78a7 100644 --- a/recipes/bioconductor-dfp/meta.yaml +++ b/recipes/bioconductor-dfp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "DFP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8f6a4937ae9aaadca48470a41911245 + md5: 5eb14fe67a6dd0599cd24c3473eec349 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dfp", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-dialignr/meta.yaml b/recipes/bioconductor-dialignr/meta.yaml index 4aa8508dc2b67..b0ad1e11855dc 100644 --- a/recipes/bioconductor-dialignr/meta.yaml +++ b/recipes/bioconductor-dialignr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "DIAlignR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64265ce3d538110aac22ed20a151c9b3 + md5: b67387fec7e8a9e5de5189fecd7077aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dialignr", max_pin="x.x") }}' # Suggests: knitr, akima, lattice, scales, gridExtra, latticeExtra, rmarkdown, BiocStyle, BiocParallel, testthat (>= 2.1.0) # SystemRequirements: C++14 requirements: host: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-ape - r-base - r-bit64 @@ -44,7 +45,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-ape - r-base - r-bit64 diff --git a/recipes/bioconductor-diffbind/meta.yaml b/recipes/bioconductor-diffbind/meta.yaml index b1b7a2f20e370..57d109de6119d 100644 --- a/recipes/bioconductor-diffbind/meta.yaml +++ b/recipes/bioconductor-diffbind/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.10.0" %} +{% set version = "3.12.0" %} {% set name = "DiffBind" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9cdbcead719d0c3d268ff9184c2a146e + md5: aa7c15e33713ad0ced01a5b6442e2d3d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffbind", max_pin="x.x") }}' # Suggests: BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid # SystemRequirements: GNU make requirements: host: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-greylistchip >=1.32.0,<1.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-systempiper >=2.6.0,<2.7.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-greylistchip >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-systempiper >=2.8.0,<2.9.0' - r-amap - r-ashr - r-base @@ -48,19 +49,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-greylistchip >=1.32.0,<1.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-systempiper >=2.6.0,<2.7.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-greylistchip >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-systempiper >=2.8.0,<2.9.0' - r-amap - r-ashr - r-base diff --git a/recipes/bioconductor-diffcoexp/meta.yaml b/recipes/bioconductor-diffcoexp/meta.yaml index 5e7d4bebf284e..aa9d59c7e2550 100644 --- a/recipes/bioconductor-diffcoexp/meta.yaml +++ b/recipes/bioconductor-diffcoexp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "diffcoexp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 161074b1baaa04dfba989eb96d6931ac + md5: 0985f656837da53f557041125f7583a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffcoexp", max_pin="x.x") }}' noarch: generic -# Suggests: GEOquery +# Suggests: GEOquery, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-diffcorr - r-igraph - r-psych - r-wgcna run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-diffcorr - r-igraph diff --git a/recipes/bioconductor-diffcyt/meta.yaml b/recipes/bioconductor-diffcyt/meta.yaml index e99566efd27fe..cd7e975c7fa60 100644 --- a/recipes/bioconductor-diffcyt/meta.yaml +++ b/recipes/bioconductor-diffcyt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "diffcyt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4fc1208b2b23cb07450a1b1f9250594b + md5: 8118267e493c2646533a9730a876d340 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffcyt", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr @@ -37,13 +38,13 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dplyr diff --git a/recipes/bioconductor-differentialregulation/meta.yaml b/recipes/bioconductor-differentialregulation/meta.yaml index eff49e2146e20..a4577cc53de1e 100644 --- a/recipes/bioconductor-differentialregulation/meta.yaml +++ b/recipes/bioconductor-differentialregulation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.2" %} +{% set version = "2.0.2" %} {% set name = "DifferentialRegulation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37854686cce5bc0d3bdf3b839ad04d69 + md5: 875793d502c3e521b4faa3eba0d1c2e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-differentialregulation", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle -# SystemRequirements: C++11 +# SystemRequirements: C++17 requirements: host: - - 'bioconductor-bandits >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-bandits >=1.18.0,<1.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-data.table - r-doparallel - r-dorng - r-foreach - r-ggplot2 + - r-gridextra - r-mass - r-matrix - r-rcpp @@ -38,16 +40,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-bandits >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-bandits >=1.18.0,<1.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-data.table - r-doparallel - r-dorng - r-foreach - r-ggplot2 + - r-gridextra - r-mass - r-matrix - r-rcpp diff --git a/recipes/bioconductor-diffgeneanalysis/meta.yaml b/recipes/bioconductor-diffgeneanalysis/meta.yaml index 26231b27f9c7b..2ddba971b2d64 100644 --- a/recipes/bioconductor-diffgeneanalysis/meta.yaml +++ b/recipes/bioconductor-diffgeneanalysis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.82.0" %} +{% set version = "1.84.0" %} {% set name = "diffGeneAnalysis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dd06a23dac4ee41a326424187d4082b + md5: aa3d8c4ce3b83b8a6f02e87384dd649f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffgeneanalysis", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-diffhic/meta.yaml b/recipes/bioconductor-diffhic/meta.yaml index 19abc926ef125..a3b151ea656d1 100644 --- a/recipes/bioconductor-diffhic/meta.yaml +++ b/recipes/bioconductor-diffhic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "diffHic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,56 +11,57 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a1e279c2d1f02340a6cbcc771e64ce3 + md5: ba97084f7b4e4510514df43be6eb9bf8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffhic", max_pin="x.x") }}' # Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-locfit - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-locfit - r-rcpp diff --git a/recipes/bioconductor-difflogo/meta.yaml b/recipes/bioconductor-difflogo/meta.yaml index 7655cc38189e1..7021a22253322 100644 --- a/recipes/bioconductor-difflogo/meta.yaml +++ b/recipes/bioconductor-difflogo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "DiffLogo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37d13c84d12b18ac6a302bd4ed9672fe + md5: f122cc5f6153c8dc4fabe92b33d1e608 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-difflogo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, seqLogo, MotifDb requirements: diff --git a/recipes/bioconductor-diffloopdata/meta.yaml b/recipes/bioconductor-diffloopdata/meta.yaml index fa1e401e6f017..5578e9031bc30 100644 --- a/recipes/bioconductor-diffloopdata/meta.yaml +++ b/recipes/bioconductor-diffloopdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "diffloopdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e004a82f024eb82c188415e8ca65563 + md5: 748ee71ae44999ca2c568619ad5a47eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffloopdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-diffloopdata/post-link.sh b/recipes/bioconductor-diffloopdata/post-link.sh index 73218bbd38264..51e96d69fdede 100644 --- a/recipes/bioconductor-diffloopdata/post-link.sh +++ b/recipes/bioconductor-diffloopdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "diffloopdata-1.28.0" +installBiocDataPackage.sh "diffloopdata-1.30.0" diff --git a/recipes/bioconductor-diffustats/meta.yaml b/recipes/bioconductor-diffustats/meta.yaml index e61fddfc151de..0a7ea0001788f 100644 --- a/recipes/bioconductor-diffustats/meta.yaml +++ b/recipes/bioconductor-diffustats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "diffuStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aafc3aa67189fbbb04b4ac8ea2df5280 + md5: 7c47ae0431034f3de807ad1fa3684530 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffustats", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2, utils # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-diffutr/meta.yaml b/recipes/bioconductor-diffutr/meta.yaml index 59d6828c1d6dc..e43e853baf8f8 100644 --- a/recipes/bioconductor-diffutr/meta.yaml +++ b/recipes/bioconductor-diffutr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "diffUTR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7c06f1c637e763f2dd8ac0209145fa2 + md5: 10b4af48c1a3f5e823c67cf569dcf1c2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diffutr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -41,18 +42,18 @@ requirements: - r-stringi - r-viridislite run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-diggit/meta.yaml b/recipes/bioconductor-diggit/meta.yaml index 4c5fcd80a3b97..43b921f1c6b65 100644 --- a/recipes/bioconductor-diggit/meta.yaml +++ b/recipes/bioconductor-diggit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "diggit" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 51bae1ffaac56dfb95c2a3a0bdc769ec + md5: 8685d9b55ebfad0b44d6ca96d6fb4ab0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diggit", max_pin="x.x") }}' noarch: generic # Suggests: diggitdata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-ks run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-ks test: diff --git a/recipes/bioconductor-diggitdata/meta.yaml b/recipes/bioconductor-diggitdata/meta.yaml index e50de6a3e7821..b4c6cdf57ec45 100644 --- a/recipes/bioconductor-diggitdata/meta.yaml +++ b/recipes/bioconductor-diggitdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "diggitdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d68dbde08e8d4b936a15a73a23a48830 + md5: 48dc6a1a35dae2169279a2766e3b56de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-diggitdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-diggitdata/post-link.sh b/recipes/bioconductor-diggitdata/post-link.sh index d1dfc6fddbbe7..3d3e3107cca47 100644 --- a/recipes/bioconductor-diggitdata/post-link.sh +++ b/recipes/bioconductor-diggitdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "diggitdata-1.32.0" +installBiocDataPackage.sh "diggitdata-1.34.0" diff --git a/recipes/bioconductor-dino/meta.yaml b/recipes/bioconductor-dino/meta.yaml index e7d9e88c73391..f3775ab4fc288 100644 --- a/recipes/bioconductor-dino/meta.yaml +++ b/recipes/bioconductor-dino/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "Dino" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c8e15f69998933ef26099e60db42b92 + md5: cf084f6d83c8245a5c4969849a7e3e82 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dino", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-matrixstats - r-seurat run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-matrixstats diff --git a/recipes/bioconductor-dir.expiry/meta.yaml b/recipes/bioconductor-dir.expiry/meta.yaml index e916f0fbdac8d..77e5aabe1d30e 100644 --- a/recipes/bioconductor-dir.expiry/meta.yaml +++ b/recipes/bioconductor-dir.expiry/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "dir.expiry" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 21f10f90c60b2b127529b1b1028d5756 + md5: ddefb728416ca4283805e19a898e9245 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dir.expiry", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat, BiocStyle requirements: diff --git a/recipes/bioconductor-director/meta.yaml b/recipes/bioconductor-director/meta.yaml index d3f2403c8d18c..8cd98393738e0 100644 --- a/recipes/bioconductor-director/meta.yaml +++ b/recipes/bioconductor-director/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "Director" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41504b173dd3af18b1ee7ba53979e0e5 + md5: 7c6c9d1a4762ffbdf723111273ee0899 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-director", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-dirichletmultinomial/meta.yaml b/recipes/bioconductor-dirichletmultinomial/meta.yaml index 39b57980f9af4..c522f169f7852 100644 --- a/recipes/bioconductor-dirichletmultinomial/meta.yaml +++ b/recipes/bioconductor-dirichletmultinomial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "DirichletMultinomial" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 645e54be0954e16b383584892733e45d + md5: 8527c543b1ada9640d2f434fb516ff4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dirichletmultinomial", max_pin="x.x") }}' # Suggests: lattice, parallel, MASS, RColorBrewer, xtable # SystemRequirements: gsl requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack - gsl run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - gsl build: diff --git a/recipes/bioconductor-discordant/meta.yaml b/recipes/bioconductor-discordant/meta.yaml index 35fbc9e4ae863..8a2f3fd4b1593 100644 --- a/recipes/bioconductor-discordant/meta.yaml +++ b/recipes/bioconductor-discordant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "discordant" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e0656f834cd221da58ba523968b30bc + md5: 78ce10a5d9777c9db9b72fec29688bee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-discordant", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-biwt - r-dplyr @@ -30,7 +31,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-biwt - r-dplyr diff --git a/recipes/bioconductor-discorhythm/meta.yaml b/recipes/bioconductor-discorhythm/meta.yaml index a66ba2d3d9725..f66f116d7b1fa 100644 --- a/recipes/bioconductor-discorhythm/meta.yaml +++ b/recipes/bioconductor-discorhythm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DiscoRhythm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c96324132931c93539174ad49ee1b914 + md5: c502bfa871cb7e3aa322684117a70b2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-discorhythm", max_pin="x.x") }}' noarch: generic # Suggests: testthat # SystemRequirements: To generate html reports pandoc (http://pandoc.org/installing.html) is required. requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-data.table @@ -55,10 +56,10 @@ requirements: - r-zip - pandoc run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-data.table diff --git a/recipes/bioconductor-distinct/build_failure.linux-64.yaml b/recipes/bioconductor-distinct/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b4346b41f3fe8 --- /dev/null +++ b/recipes/bioconductor-distinct/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 4cdee96b11c599d7d86852005b1fcdb8fc168a77b8c4cd0973697dbfc2af519f # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + compiler error +log: |2- + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Archive/distinct/distinct_1.14.0.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Archive/distinct/distinct_1.14.0.tar.gz + Success + INFO:conda_build.source:Success + Extracting download + source tree in: /opt/conda/conda-bld/bioconductor-distinct_1703301470415/work + export PREFIX=/opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-distinct_1703301470415/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-distinct_1703301470415/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library + * installing *source* package distinct ... + ** using staged installation + ** libs + using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 12.3.0-3) 12.3.0 + using C11 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rfast/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1700316003380/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Perm.cpp -o Perm.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rfast/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1700316003380/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Perm_covariates.cpp -o Perm_covariates.o + In file included from /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast/templates.h:10, + from /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast/matrix.hpp:14, + from /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast.h:5, + from Perm_covariates.cpp:2: + /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast/parallel.h:7:10: fatal error: RcppParallel.h: No such file or directory + 7 | #include + | ^~~~~~~~~~~~~~~~ + compilation terminated. + make: *** [/opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/etc/Makeconf:200: Perm_covariates.o] Error 1 + ERROR: compilation failed for package distinct + * removing /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/distinct + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-distinct_1703301470415/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-distinct/build_failure.osx-64.yaml b/recipes/bioconductor-distinct/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..be50a664177f3 --- /dev/null +++ b/recipes/bioconductor-distinct/build_failure.osx-64.yaml @@ -0,0 +1,38 @@ +recipe_sha: 4cdee96b11c599d7d86852005b1fcdb8fc168a77b8c4cd0973697dbfc2af519f # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + parallel.h:7:10: fatal error: 'RcppParallel.h' file not found +category: |- + compiler error +log: |- + 12:17:08 BIOCONDA INFO (ERR) In file included from Perm_covariates.cpp:2: + 12:17:08 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast.h:5: + 12:17:08 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast/matrix.hpp:14: + 12:17:08 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast/templates.h:10: + 12:17:08 BIOCONDA INFO (ERR) /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast/parallel.h:7:10: fatal error: 'RcppParallel.h' file not found + 12:17:08 BIOCONDA INFO (ERR) #include + 12:17:08 BIOCONDA INFO (ERR) ^~~~~~~~~~~~~~~~ + 12:17:08 BIOCONDA INFO (ERR) 1 error generated. + 12:17:08 BIOCONDA INFO (ERR) make: *** [/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/etc/Makeconf:200: Perm_covariates.o] Error 1 + 12:17:08 BIOCONDA INFO (ERR) ERROR: compilation failed for package ‘distinct’ + 12:17:08 BIOCONDA INFO (ERR) * removing ‘/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/distinct’ + 12:17:09 BIOCONDA INFO (ERR) Traceback (most recent call last): + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + 12:17:09 BIOCONDA INFO (ERR) sys.exit(main()) + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 12:17:09 BIOCONDA INFO (ERR) call_conda_build(action, config) + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 12:17:09 BIOCONDA INFO (ERR) result = api.build( + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 12:17:09 BIOCONDA INFO (ERR) return build_tree( + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + 12:17:09 BIOCONDA INFO (ERR) packages_from_this = build(metadata, stats, + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + 12:17:09 BIOCONDA INFO (ERR) utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + 12:17:09 BIOCONDA INFO (ERR) return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + 12:17:09 BIOCONDA INFO (ERR) raise subprocess.CalledProcessError(proc.returncode, _args) + 12:17:09 BIOCONDA INFO (ERR) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/work/conda_build.sh']' returned non-zero exit status 1. + 12:17:18 BIOCONDA ERROR COMMAND FAILED (exited with 1): /opt/mambaforge/envs/bioconda/bin/conda mambabuild --override-channels --no-anaconda-upload -c conda-forge -c bioconda -c defaults -e /opt/mambaforge/envs/bioconda/conda_build_config.yaml -e /opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml recipes/bioconductor-distinct/meta.yaml + diff --git a/recipes/bioconductor-distinct/meta.yaml b/recipes/bioconductor-distinct/meta.yaml index 5d70c56cc8d36..94fd0a58dc596 100644 --- a/recipes/bioconductor-distinct/meta.yaml +++ b/recipes/bioconductor-distinct/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "distinct" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 952be7f89ed08259c89941b312132b35 + md5: b4817384f7f8fad6e30ee01270e31d10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-distinct", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, UpSetR, BiocStyle # SystemRequirements: C++11 requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dorng @@ -37,10 +38,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dorng diff --git a/recipes/bioconductor-dittoseq/meta.yaml b/recipes/bioconductor-dittoseq/meta.yaml index da1c9a0e79891..2c331373afe40 100644 --- a/recipes/bioconductor-dittoseq/meta.yaml +++ b/recipes/bioconductor-dittoseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "dittoSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b2089286b90a1e519b82194f205784c + md5: 6d7e63c0018a57726033bb5862dccf7e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dittoseq", max_pin="x.x") }}' noarch: generic # Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-colorspace >=1.4' - r-cowplot @@ -34,9 +35,9 @@ requirements: - r-pheatmap - r-reshape2 run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-colorspace >=1.4' - r-cowplot diff --git a/recipes/bioconductor-divergence/meta.yaml b/recipes/bioconductor-divergence/meta.yaml index 8405572604541..a322557c552a1 100644 --- a/recipes/bioconductor-divergence/meta.yaml +++ b/recipes/bioconductor-divergence/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "divergence" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0d386fade56d1aefb877693d2d468aca + md5: 0ead0047c69549361f0f86d7207aee2b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-divergence", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-dks/meta.yaml b/recipes/bioconductor-dks/meta.yaml index 54475c9ca8d0f..ea476c6b5f0f4 100644 --- a/recipes/bioconductor-dks/meta.yaml +++ b/recipes/bioconductor-dks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "dks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bda53a4f0f6a746a4f0ade7ecbc9d728 + md5: f15cb2d88222e2936dc9460d69a924ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dks", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-dlbcl/meta.yaml b/recipes/bioconductor-dlbcl/meta.yaml index 826b1990b2a5f..5324572ce48c0 100644 --- a/recipes/bioconductor-dlbcl/meta.yaml +++ b/recipes/bioconductor-dlbcl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.1" %} {% set name = "DLBCL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f22495affaad1066fbe54791486ebd53 + md5: a2906f8e35b0457c1cd8052d2457d40b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dlbcl", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dlbcl/post-link.sh b/recipes/bioconductor-dlbcl/post-link.sh index 4a3925603037e..c17921df4bc39 100644 --- a/recipes/bioconductor-dlbcl/post-link.sh +++ b/recipes/bioconductor-dlbcl/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dlbcl-1.40.0" +installBiocDataPackage.sh "dlbcl-1.42.1" diff --git a/recipes/bioconductor-dmchmm/meta.yaml b/recipes/bioconductor-dmchmm/meta.yaml index 3fbd3d1cd7b03..440303fd576f2 100644 --- a/recipes/bioconductor-dmchmm/meta.yaml +++ b/recipes/bioconductor-dmchmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "DMCHMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1bd9934bf164aae70e6b1eacadbcdae4 + md5: 4a4e52e12df4e699e0e20d13828f25f0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmchmm", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-calibrate - r-fdrtool - r-multcomp run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-calibrate - r-fdrtool diff --git a/recipes/bioconductor-dmelsgi/meta.yaml b/recipes/bioconductor-dmelsgi/meta.yaml index 64e1775ca9de6..6dabf001c9956 100644 --- a/recipes/bioconductor-dmelsgi/meta.yaml +++ b/recipes/bioconductor-dmelsgi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "DmelSGI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 611e89ab1359a4e0283b61e75205878f + md5: c13b3a8f881ca54d5e8ddf52ebe8b86a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmelsgi", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, hwriter, xtable, beeswarm requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-abind - r-base - r-gplots @@ -30,8 +31,8 @@ requirements: - r-knitr - r-tsp run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-abind - r-base - r-gplots @@ -39,7 +40,7 @@ requirements: - r-knitr - r-tsp - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dmelsgi/post-link.sh b/recipes/bioconductor-dmelsgi/post-link.sh index 517c5d22c9e6c..9666ced12ef5f 100644 --- a/recipes/bioconductor-dmelsgi/post-link.sh +++ b/recipes/bioconductor-dmelsgi/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dmelsgi-1.32.0" +installBiocDataPackage.sh "dmelsgi-1.34.0" diff --git a/recipes/bioconductor-dmrcaller/meta.yaml b/recipes/bioconductor-dmrcaller/meta.yaml index 334e3141ab264..877d463affcbd 100644 --- a/recipes/bioconductor-dmrcaller/meta.yaml +++ b/recipes/bioconductor-dmrcaller/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "DMRcaller" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 721451b67d2e53e1d2a76142208c18cb + md5: 1c5b37620b4950eb63e32c3063235e8e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmrcaller", max_pin="x.x") }}' # Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-betareg - r-rcpp @@ -30,9 +31,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-betareg - r-rcpp diff --git a/recipes/bioconductor-dmrcatedata/meta.yaml b/recipes/bioconductor-dmrcatedata/meta.yaml index cff320dcd2e33..06d80da935efd 100644 --- a/recipes/bioconductor-dmrcatedata/meta.yaml +++ b/recipes/bioconductor-dmrcatedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "DMRcatedata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2d0addb7984dadb9a3c0012dcd8c719 + md5: ac938c6259121c4a60ca3c8c5bfdf724 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmrcatedata", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-plyr - r-readxl run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-plyr - r-readxl - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dmrcatedata/post-link.sh b/recipes/bioconductor-dmrcatedata/post-link.sh index eabb638ec0fc9..d4ad6b968cb0a 100644 --- a/recipes/bioconductor-dmrcatedata/post-link.sh +++ b/recipes/bioconductor-dmrcatedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dmrcatedata-2.18.0" +installBiocDataPackage.sh "dmrcatedata-2.20.0" diff --git a/recipes/bioconductor-dmrscan/meta.yaml b/recipes/bioconductor-dmrscan/meta.yaml index 53143408153e9..0b03fd4a53375 100644 --- a/recipes/bioconductor-dmrscan/meta.yaml +++ b/recipes/bioconductor-dmrscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "DMRScan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e05e55e05878903f9d35e30c7bbf3a37 + md5: 698b81baf921ef394adedb8d8ff7ba7f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmrscan", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, BiocManager requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-mass - r-matrix - r-mvtnorm - r-rcpproll run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-mass - r-matrix diff --git a/recipes/bioconductor-dmrseq/meta.yaml b/recipes/bioconductor-dmrseq/meta.yaml index efaa67d94c3ec..505c49b1d0fb8 100644 --- a/recipes/bioconductor-dmrseq/meta.yaml +++ b/recipes/bioconductor-dmrseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "dmrseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 30fbe6664a5ed95ed8cd32e6726fd218 + md5: a8181423ea50609ae16545b9f8bb1895 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dmrseq", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle +# Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotatr >=1.26.0,<1.27.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-locfit @@ -40,17 +41,17 @@ requirements: - r-outliers - r-rcolorbrewer run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotatr >=1.26.0,<1.27.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-locfit diff --git a/recipes/bioconductor-dnabarcodecompatibility/meta.yaml b/recipes/bioconductor-dnabarcodecompatibility/meta.yaml index d8cb8b9e6de09..bc74f779dfa5a 100644 --- a/recipes/bioconductor-dnabarcodecompatibility/meta.yaml +++ b/recipes/bioconductor-dnabarcodecompatibility/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DNABarcodeCompatibility" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 481a9ea651c4ff63152c214b3250677e + md5: b1e2988c254cf089a2f887abf139b7bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnabarcodecompatibility", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-dnabarcodes >=1.30.0,<1.31.0' + - 'bioconductor-dnabarcodes >=1.32.0,<1.33.0' - r-base - r-dplyr - r-numbers @@ -29,7 +30,7 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-dnabarcodes >=1.30.0,<1.31.0' + - 'bioconductor-dnabarcodes >=1.32.0,<1.33.0' - r-base - r-dplyr - r-numbers diff --git a/recipes/bioconductor-dnabarcodes/meta.yaml b/recipes/bioconductor-dnabarcodes/meta.yaml index bb47078fe041c..53c9caad94d27 100644 --- a/recipes/bioconductor-dnabarcodes/meta.yaml +++ b/recipes/bioconductor-dnabarcodes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "DNABarcodes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7922c9dbc0b216fca9de9a18afef465a + md5: 6047e393e89e644fbf9aa4aa5a9faa64 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnabarcodes", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, rmarkdown requirements: host: diff --git a/recipes/bioconductor-dnacopy/meta.yaml b/recipes/bioconductor-dnacopy/meta.yaml index f788a79e19267..11f96aa6d76d5 100644 --- a/recipes/bioconductor-dnacopy/meta.yaml +++ b/recipes/bioconductor-dnacopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.1" %} +{% set version = "1.76.0" %} {% set name = "DNAcopy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41ab8f2ec3f9ee0a4b63eb57e97cdeef + md5: 1b80859f79a39def302664f11b91a98f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnacopy", max_pin="x.x") }}' requirements: host: - r-base @@ -34,7 +35,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'DNA copy number data analysis' + summary: 'DNA Copy Number Data Analysis' description: 'Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: diff --git a/recipes/bioconductor-dnafusion/meta.yaml b/recipes/bioconductor-dnafusion/meta.yaml index 38aeb1d4e0dcc..03be682d7e794 100644 --- a/recipes/bioconductor-dnafusion/meta.yaml +++ b/recipes/bioconductor-dnafusion/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "DNAfusion" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: edd9b9e868337162ddb38fa5eca32876 + md5: b7ef2bb10bea5334d6d159208c284c16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnafusion", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle requirements: host: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-dnashaper/meta.yaml b/recipes/bioconductor-dnashaper/meta.yaml index 05df265da888d..06c57e6991e97 100644 --- a/recipes/bioconductor-dnashaper/meta.yaml +++ b/recipes/bioconductor-dnashaper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "DNAshapeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92308b5f9b7b9ed27d5663313d92f2a2 + md5: f2b90849d52bce75d88a4970f08c2544 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnashaper", max_pin="x.x") }}' # Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-fields - 'r-rcpp >=0.12.1' - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-fields - 'r-rcpp >=0.12.1' diff --git a/recipes/bioconductor-dnazoodata/meta.yaml b/recipes/bioconductor-dnazoodata/meta.yaml index 07a9c8399ec46..6ac0f55444cfb 100644 --- a/recipes/bioconductor-dnazoodata/meta.yaml +++ b/recipes/bioconductor-dnazoodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "DNAZooData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76d7687720d175ca13a1057c22b68b1e + md5: 06c4b9dbbaddc3dd4dcdc51e34150aa7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dnazoodata", max_pin="x.x") }}' noarch: generic # Suggests: dplyr, testthat, methods, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rjson run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rjson - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dnazoodata/post-link.sh b/recipes/bioconductor-dnazoodata/post-link.sh index 99f71e297f7d8..34b10c2512e29 100644 --- a/recipes/bioconductor-dnazoodata/post-link.sh +++ b/recipes/bioconductor-dnazoodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dnazoodata-1.0.0" +installBiocDataPackage.sh "dnazoodata-1.2.0" diff --git a/recipes/bioconductor-do.db/meta.yaml b/recipes/bioconductor-do.db/meta.yaml index b8fcca5ca4089..5c3b17b44eba8 100644 --- a/recipes/bioconductor-do.db/meta.yaml +++ b/recipes/bioconductor-do.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.9" %} {% set name = "DO.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 63dda6d46d2fe40c52a2e79260a7fb9d build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-do.db", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dominoeffect/meta.yaml b/recipes/bioconductor-dominoeffect/meta.yaml index 71dd0a84aba94..eb625150b9ecb 100644 --- a/recipes/bioconductor-dominoeffect/meta.yaml +++ b/recipes/bioconductor-dominoeffect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "DominoEffect" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f620b081e95046b62ef0c8f9081f26e3 + md5: 2e92d099e31b5feaf035b8eb5ad92376 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dominoeffect", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table test: diff --git a/recipes/bioconductor-donapllp2013/meta.yaml b/recipes/bioconductor-donapllp2013/meta.yaml index e2e5d42e94204..abdd5e739d806 100644 --- a/recipes/bioconductor-donapllp2013/meta.yaml +++ b/recipes/bioconductor-donapllp2013/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "DonaPLLP2013" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ef96235e9049d31e27f5e5fff17d1ec + md5: d8dc37afefc52856d520540b07faf545 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-donapllp2013", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-donapllp2013/post-link.sh b/recipes/bioconductor-donapllp2013/post-link.sh index 091fa30e9113d..5921a0116e213 100644 --- a/recipes/bioconductor-donapllp2013/post-link.sh +++ b/recipes/bioconductor-donapllp2013/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "donapllp2013-1.38.0" +installBiocDataPackage.sh "donapllp2013-1.40.0" diff --git a/recipes/bioconductor-doppelgangr/meta.yaml b/recipes/bioconductor-doppelgangr/meta.yaml index fa878f48b7983..8038472db593b 100644 --- a/recipes/bioconductor-doppelgangr/meta.yaml +++ b/recipes/bioconductor-doppelgangr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "doppelgangR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 294c75b10f9555eca7ba92b5d903c3b0 + md5: c50eff7bb5871b545a8199a9b1c4667b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-doppelgangr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-digest - r-mnormt run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-digest - r-mnormt diff --git a/recipes/bioconductor-dorothea/meta.yaml b/recipes/bioconductor-dorothea/meta.yaml index 827105752b8d7..e6eda607d7e68 100644 --- a/recipes/bioconductor-dorothea/meta.yaml +++ b/recipes/bioconductor-dorothea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "dorothea" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 068a6de9744d9d5c7085dfe910968e17 + md5: d1ad1213db5d54f1fc6ef8d195b9bbc0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dorothea", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils requirements: host: - - 'bioconductor-bcellviper >=1.36.0,<1.37.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' + - 'bioconductor-bcellviper >=1.38.0,<1.39.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' - r-base - r-dplyr - r-magrittr run: - - 'bioconductor-bcellviper >=1.36.0,<1.37.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' + - 'bioconductor-bcellviper >=1.38.0,<1.39.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' - r-base - r-dplyr - r-magrittr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dorothea/post-link.sh b/recipes/bioconductor-dorothea/post-link.sh index ed11f25157cc9..b77af7c38dc2e 100644 --- a/recipes/bioconductor-dorothea/post-link.sh +++ b/recipes/bioconductor-dorothea/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dorothea-1.12.0" +installBiocDataPackage.sh "dorothea-1.14.0" diff --git a/recipes/bioconductor-doscheda/meta.yaml b/recipes/bioconductor-doscheda/meta.yaml index 4b32f2f293aaf..896c4140c8007 100644 --- a/recipes/bioconductor-doscheda/meta.yaml +++ b/recipes/bioconductor-doscheda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "Doscheda" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8fc89a023bcd59d4fabf8d485b7826d1 + md5: 3eee0480f798b00860daaf2cb88325ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-doscheda", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-calibrate - r-corrgram @@ -41,9 +42,9 @@ requirements: - r-shinydashboard - r-stringr run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-calibrate - r-corrgram diff --git a/recipes/bioconductor-dose/meta.yaml b/recipes/bioconductor-dose/meta.yaml index 2598bc88fb879..0d10dde0a81d3 100644 --- a/recipes/bioconductor-dose/meta.yaml +++ b/recipes/bioconductor-dose/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.26.1" %} +{% set version = "3.28.1" %} {% set name = "DOSE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1dad84a44c7ce259b0538d452cb7aaf9 + md5: 11096edb2862c8a442f53435082e40b6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dose", max_pin="x.x") }}' noarch: generic -# Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, rmarkdown, org.Hs.eg.db, testthat +# Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, rmarkdown, org.Hs.eg.db, MPO.db, HPO.db, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - 'bioconductor-hdo.db >=0.99.0,<0.100.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-ggplot2 - r-reshape2 + - r-yulab.utils run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - 'bioconductor-hdo.db >=0.99.0,<0.100.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-ggplot2 - r-reshape2 + - r-yulab.utils test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-doser/meta.yaml b/recipes/bioconductor-doser/meta.yaml index 9e43fae39943c..7b6a6fdc3f312 100644 --- a/recipes/bioconductor-doser/meta.yaml +++ b/recipes/bioconductor-doser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "doseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23b8b183287c77bfae54e16a488988d8 + md5: 20251942acb7343859507c138bc2b902 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-doser", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-digest - r-lme4 @@ -31,9 +32,9 @@ requirements: - r-mclust - r-runit run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-digest - r-lme4 diff --git a/recipes/bioconductor-doubletrouble/meta.yaml b/recipes/bioconductor-doubletrouble/meta.yaml index 7536d4a2b14e1..a6b8eb760d0b6 100644 --- a/recipes/bioconductor-doubletrouble/meta.yaml +++ b/recipes/bioconductor-doubletrouble/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.1" %} {% set name = "doubletrouble" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3900ef117b25b1aad217a9953deb4a46 + md5: e494ee8650e6c8a13c7149c68683bea8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-doubletrouble", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), knitr, feature, BiocStyle, rmarkdown, covr, sessioninfo requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-msa2dist >=1.4.0,<1.5.0' - - 'bioconductor-syntenet >=1.2.0,<1.3.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-msa2dist >=1.6.0,<1.7.0' + - 'bioconductor-syntenet >=1.4.0,<1.5.0' - r-base - r-ggplot2 - r-mclust + - r-rlang run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-msa2dist >=1.4.0,<1.5.0' - - 'bioconductor-syntenet >=1.2.0,<1.3.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-msa2dist >=1.6.0,<1.7.0' + - 'bioconductor-syntenet >=1.4.0,<1.5.0' - r-base - r-ggplot2 - r-mclust + - r-rlang test: commands: - '$R -e "library(''{{ name }}'')"' @@ -43,6 +50,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Identification and classification of duplicated genes' - description: 'doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are: i. whole-genome duplication (WGD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). If users want a simpler classification scheme, duplicates can also be classified into WGD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.' + description: 'doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-drawproteins/meta.yaml b/recipes/bioconductor-drawproteins/meta.yaml index cb3cac5120abe..54bccf2331977 100644 --- a/recipes/bioconductor-drawproteins/meta.yaml +++ b/recipes/bioconductor-drawproteins/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "drawProteins" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 309e0805cb162bc9e22e8ad73dd775a9 + md5: 67cbf634b37851946e9cc3885cdda6c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drawproteins", max_pin="x.x") }}' noarch: generic # Suggests: covr, testthat, knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-dreamlet/build.sh b/recipes/bioconductor-dreamlet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dreamlet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dreamlet/build_failure.linux-64.yaml b/recipes/bioconductor-dreamlet/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0e452d24e3b59 --- /dev/null +++ b/recipes/bioconductor-dreamlet/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 9267c92fbfbee2b151933e110f05e516a8f84863f222f244128a2f63b327fcf7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + nothing provides requested r-mashr >=0.2.52 +category: |- + dependency issue diff --git a/recipes/bioconductor-dreamlet/build_failure.osx-64.yaml b/recipes/bioconductor-dreamlet/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0e452d24e3b59 --- /dev/null +++ b/recipes/bioconductor-dreamlet/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 9267c92fbfbee2b151933e110f05e516a8f84863f222f244128a2f63b327fcf7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + nothing provides requested r-mashr >=0.2.52 +category: |- + dependency issue diff --git a/recipes/bioconductor-dreamlet/meta.yaml b/recipes/bioconductor-dreamlet/meta.yaml new file mode 100644 index 0000000000000..14eba535c39a1 --- /dev/null +++ b/recipes/bioconductor-dreamlet/meta.yaml @@ -0,0 +1,106 @@ +{% set version = "1.0.0" %} +{% set name = "dreamlet" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 34ea1ec9e44c635699ed9cf8deed29cd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dreamlet", max_pin="x.x") }}' +# Suggests: BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub, RUnit, scater, scuttle +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' + - 'bioconductor-zenith >=1.4.0,<1.5.0' + - r-ashr + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-gtools + - 'r-lme4 >=1.1-33' + - 'r-mashr >=0.2.52' + - r-mass + - r-matrix + - r-purrr + - r-rcpp + - r-rdpack + - r-reshape2 + - r-scattermore + - r-tidyr + - libblas + - liblapack + run: + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' + - 'bioconductor-zenith >=1.4.0,<1.5.0' + - r-ashr + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-gtools + - 'r-lme4 >=1.1-33' + - 'r-mashr >=0.2.52' + - r-mass + - r-matrix + - r-purrr + - r-rcpp + - r-rdpack + - r-reshape2 + - r-scattermore + - r-tidyr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Cohort-scale differential expression analysis of single cell data using linear (mixed) models' + description: 'Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of these data, complex study designs, and low read count per cell mean that characterizing cell type specific molecular mechanisms requires a user-frieldly, purpose-build analytical framework. We have developed the dreamlet package that applies a pseudobulk approach and fits a regression model for each gene and cell cluster to test differential expression across individuals associated with a trait of interest. Use of precision-weighted linear mixed models enables accounting for repeated measures study designs, high dimensional batch effects, and varying sequencing depth or observed cells per biosample.' + diff --git a/recipes/bioconductor-dresscheck/meta.yaml b/recipes/bioconductor-dresscheck/meta.yaml index 9f7499d0e8bbb..5c21bedf99cda 100644 --- a/recipes/bioconductor-dresscheck/meta.yaml +++ b/recipes/bioconductor-dresscheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "dressCheck" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 27fc1d1485335601b86ab54b8380f1dc + md5: d6fb25eaad39c714024ed855c8c9c87d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dresscheck", max_pin="x.x") }}' noarch: generic # Suggests: survival, chron requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dresscheck/post-link.sh b/recipes/bioconductor-dresscheck/post-link.sh index 6bb9b9ee996f5..307a736efcaa5 100644 --- a/recipes/bioconductor-dresscheck/post-link.sh +++ b/recipes/bioconductor-dresscheck/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dresscheck-0.38.0" +installBiocDataPackage.sh "dresscheck-0.40.0" diff --git a/recipes/bioconductor-drimseq/meta.yaml b/recipes/bioconductor-drimseq/meta.yaml index 036fb1329f664..0900c40f993b6 100644 --- a/recipes/bioconductor-drimseq/meta.yaml +++ b/recipes/bioconductor-drimseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "DRIMSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7145a27da005c65bda5885bf2de31976 + md5: fae7a1b0945b2942ef3f633d68a74fd2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drimseq", max_pin="x.x") }}' noarch: generic # Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-mass - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-mass diff --git a/recipes/bioconductor-drivernet/meta.yaml b/recipes/bioconductor-drivernet/meta.yaml index aa29c546732e6..6b233cd48cc6b 100644 --- a/recipes/bioconductor-drivernet/meta.yaml +++ b/recipes/bioconductor-drivernet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "DriverNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9d229b232a5ee18771af476f9477584 + md5: 78b923b016f6bd8097c1edc43ca0cca4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drivernet", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-droplettestfiles/meta.yaml b/recipes/bioconductor-droplettestfiles/meta.yaml index daca202c76a27..505870f109933 100644 --- a/recipes/bioconductor-droplettestfiles/meta.yaml +++ b/recipes/bioconductor-droplettestfiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "DropletTestFiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: addd41a9a235a4216b4c7067879203d6 + md5: 5a3a3f0d0901c90c6a2b173b976c4868 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-droplettestfiles", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-droplettestfiles/post-link.sh b/recipes/bioconductor-droplettestfiles/post-link.sh index 0d1ccdac66b6c..968fbe466a2dc 100644 --- a/recipes/bioconductor-droplettestfiles/post-link.sh +++ b/recipes/bioconductor-droplettestfiles/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "droplettestfiles-1.10.0" +installBiocDataPackage.sh "droplettestfiles-1.12.0" diff --git a/recipes/bioconductor-dropletutils/meta.yaml b/recipes/bioconductor-dropletutils/meta.yaml index 063be886c2025..211af9c8e5c59 100644 --- a/recipes/bioconductor-dropletutils/meta.yaml +++ b/recipes/bioconductor-dropletutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "DropletUtils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0633d05d7dde6fe7e7c28eba4c5862db + md5: f1fe907e6269e652adc4607fdb335c41 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dropletutils", max_pin="x.x") }}' # Suggests: testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-dqrng @@ -45,21 +46,21 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-dqrng diff --git a/recipes/bioconductor-drosgenome1.db/meta.yaml b/recipes/bioconductor-drosgenome1.db/meta.yaml index 99ab030ba9492..8fc4379c2d8c6 100644 --- a/recipes/bioconductor-drosgenome1.db/meta.yaml +++ b/recipes/bioconductor-drosgenome1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "drosgenome1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6432e2ae22cf58524278a559097bdf3a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosgenome1.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosgenome1cdf/meta.yaml b/recipes/bioconductor-drosgenome1cdf/meta.yaml index 240ef113c68af..a6ce8e5c2a650 100644 --- a/recipes/bioconductor-drosgenome1cdf/meta.yaml +++ b/recipes/bioconductor-drosgenome1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosgenome1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e12983f2148c10ef1faa50f810b6eee3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosgenome1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosgenome1probe/meta.yaml b/recipes/bioconductor-drosgenome1probe/meta.yaml index e944121e7679f..ec78a4874ba4f 100644 --- a/recipes/bioconductor-drosgenome1probe/meta.yaml +++ b/recipes/bioconductor-drosgenome1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosgenome1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1f12abdfeee65e8a6554f57507d86fb3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosgenome1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosophila2.db/meta.yaml b/recipes/bioconductor-drosophila2.db/meta.yaml index aa6cda347819e..93fbb18884cc1 100644 --- a/recipes/bioconductor-drosophila2.db/meta.yaml +++ b/recipes/bioconductor-drosophila2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "drosophila2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c01d0d1b5e17c3b36ad801b44da72b96 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosophila2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosophila2cdf/meta.yaml b/recipes/bioconductor-drosophila2cdf/meta.yaml index f3aa808424b36..1b1e175abbed9 100644 --- a/recipes/bioconductor-drosophila2cdf/meta.yaml +++ b/recipes/bioconductor-drosophila2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosophila2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3323e723c133ff2b6188e22bebf3e20a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosophila2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drosophila2probe/meta.yaml b/recipes/bioconductor-drosophila2probe/meta.yaml index b12a4cb086c88..15be4b2d9a764 100644 --- a/recipes/bioconductor-drosophila2probe/meta.yaml +++ b/recipes/bioconductor-drosophila2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "drosophila2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ba0251902ea0a5f0db61105bdcdc3530 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drosophila2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drugtargetinteractions/meta.yaml b/recipes/bioconductor-drugtargetinteractions/meta.yaml index 0e37c7539a4e0..27b696b08cd54 100644 --- a/recipes/bioconductor-drugtargetinteractions/meta.yaml +++ b/recipes/bioconductor-drugtargetinteractions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.1" %} {% set name = "drugTargetInteractions" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fdf995df89dbce9197ad2577325b409 + md5: c1a702c085df262e0a697b6687ea3ee4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drugtargetinteractions", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86 requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-uniprot.ws >=2.40.0,<2.41.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' - r-base - r-dplyr - r-rappdirs - r-rsqlite run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-uniprot.ws >=2.40.0,<2.41.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' - r-base - r-dplyr - r-rappdirs diff --git a/recipes/bioconductor-drugvsdisease/meta.yaml b/recipes/bioconductor-drugvsdisease/meta.yaml index 5a94487874b41..1189be641777b 100644 --- a/recipes/bioconductor-drugvsdisease/meta.yaml +++ b/recipes/bioconductor-drugvsdisease/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "DrugVsDisease" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cea656c739b76d8bc0c44206d3419ae0 + md5: cfb6f4111b0003213278308c1672e49c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drugvsdisease", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-arrayexpress >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-cmap2data >=1.36.0,<1.37.0' - - 'bioconductor-drugvsdiseasedata >=1.36.0,<1.37.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-arrayexpress >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-cmap2data >=1.38.0,<1.39.0' + - 'bioconductor-drugvsdiseasedata >=1.38.0,<1.39.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133a2.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-runit - r-xtable run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-arrayexpress >=1.60.0,<1.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-cmap2data >=1.36.0,<1.37.0' - - 'bioconductor-drugvsdiseasedata >=1.36.0,<1.37.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-arrayexpress >=1.62.0,<1.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-cmap2data >=1.38.0,<1.39.0' + - 'bioconductor-drugvsdiseasedata >=1.38.0,<1.39.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133a2.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-runit - r-xtable diff --git a/recipes/bioconductor-drugvsdiseasedata/meta.yaml b/recipes/bioconductor-drugvsdiseasedata/meta.yaml index d780758c2d4db..ddef5ea5e9960 100644 --- a/recipes/bioconductor-drugvsdiseasedata/meta.yaml +++ b/recipes/bioconductor-drugvsdiseasedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "DrugVsDiseasedata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64c011debe7f2f876d073b7383502db0 + md5: 40b800653aab57e822a18afe5bd1a2e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-drugvsdiseasedata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-drugvsdiseasedata/post-link.sh b/recipes/bioconductor-drugvsdiseasedata/post-link.sh index 1bea3948414ee..f2a69117547ff 100644 --- a/recipes/bioconductor-drugvsdiseasedata/post-link.sh +++ b/recipes/bioconductor-drugvsdiseasedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "drugvsdiseasedata-1.36.0" +installBiocDataPackage.sh "drugvsdiseasedata-1.38.0" diff --git a/recipes/bioconductor-dstruct/meta.yaml b/recipes/bioconductor-dstruct/meta.yaml index ed2b313366a99..6324f6b91a238 100644 --- a/recipes/bioconductor-dstruct/meta.yaml +++ b/recipes/bioconductor-dstruct/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "dStruct" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de647acd70d0a19a5b1bdf9758a8389c + md5: 294cd694534f0d82a92aaabeea86836f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dstruct", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) +# Suggests: BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-purrr @@ -30,8 +31,8 @@ requirements: - r-rlang - r-zoo run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-purrr @@ -45,6 +46,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Identifying differentially reactive regions from RNA structurome profiling data' - description: 'dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al, Genome Biology, 2019 for the underlying method.' + description: 'dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al., Genome Biology, 2019 for the underlying method.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-dta/meta.yaml b/recipes/bioconductor-dta/meta.yaml index a5da04f2395dc..8ce1f64afc9a8 100644 --- a/recipes/bioconductor-dta/meta.yaml +++ b/recipes/bioconductor-dta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "DTA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d4f0fb0b0ca75c66def75c8a31f6867 + md5: 58705aacdbf08c61d4713273dbd9bc6f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dta", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-dune/meta.yaml b/recipes/bioconductor-dune/meta.yaml index 41c46b2937b8e..5b2e50d6b815b 100644 --- a/recipes/bioconductor-dune/meta.yaml +++ b/recipes/bioconductor-dune/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "Dune" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3842b818ceba7018c1cfa4b89a41347d + md5: afc7d133de0af7ccdc64a9a7a3722ccb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dune", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-aricode - r-base - r-dplyr @@ -33,8 +34,8 @@ requirements: - r-rcolorbrewer - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-aricode - r-base - r-dplyr diff --git a/recipes/bioconductor-duoclustering2018/meta.yaml b/recipes/bioconductor-duoclustering2018/meta.yaml index 1fda672436ba2..4d5c22819da1a 100644 --- a/recipes/bioconductor-duoclustering2018/meta.yaml +++ b/recipes/bioconductor-duoclustering2018/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DuoClustering2018" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 697a0b8aecfb07cb6034d7626001f262 + md5: a2761f4db56025af2eaf8240392d01a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-duoclustering2018", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, iSEE, scater, SingleCellExperiment, SummarizedExperiment, plyr requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr - r-ggplot2 @@ -33,7 +34,7 @@ requirements: - r-tidyr - r-viridis run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr - r-ggplot2 @@ -45,7 +46,7 @@ requirements: - r-tidyr - r-viridis - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-duoclustering2018/post-link.sh b/recipes/bioconductor-duoclustering2018/post-link.sh index 1b85c5cdaacd6..25113c1241a25 100644 --- a/recipes/bioconductor-duoclustering2018/post-link.sh +++ b/recipes/bioconductor-duoclustering2018/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "duoclustering2018-1.18.0" +installBiocDataPackage.sh "duoclustering2018-1.20.0" diff --git a/recipes/bioconductor-dupradar/meta.yaml b/recipes/bioconductor-dupradar/meta.yaml index 6fc83d6d9e27d..c628243cfea17 100644 --- a/recipes/bioconductor-dupradar/meta.yaml +++ b/recipes/bioconductor-dupradar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "dupRadar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25020f4fc2033e3cb25d8fbc428219a6 + md5: 306ba6ddb1786eb7ec5e6cb4bc15562e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dupradar", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, AnnotationHub requirements: host: - - 'bioconductor-rsubread >=2.14.0,<2.15.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' - r-base - r-kernsmooth run: - - 'bioconductor-rsubread >=2.14.0,<2.15.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' - r-base - r-kernsmooth test: diff --git a/recipes/bioconductor-dvddata/meta.yaml b/recipes/bioconductor-dvddata/meta.yaml index 5f230dac04d9c..2ab2b9dc07a65 100644 --- a/recipes/bioconductor-dvddata/meta.yaml +++ b/recipes/bioconductor-dvddata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "DvDdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c21d1ca3b1808272b1d90004201512b2 + md5: d07387219229c006ba96b9ab43ddf4ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dvddata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dvddata/post-link.sh b/recipes/bioconductor-dvddata/post-link.sh index d1a8b4afcd138..650d586b47f90 100644 --- a/recipes/bioconductor-dvddata/post-link.sh +++ b/recipes/bioconductor-dvddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dvddata-1.36.0" +installBiocDataPackage.sh "dvddata-1.38.0" diff --git a/recipes/bioconductor-dyebias/meta.yaml b/recipes/bioconductor-dyebias/meta.yaml index b95f864f1361d..fbbc05f23ec24 100644 --- a/recipes/bioconductor-dyebias/meta.yaml +++ b/recipes/bioconductor-dyebias/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "dyebias" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3103ff75b1717ba43653c272fec9c73f + md5: 2b3e10379a29b0cb931514e06fe7259f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dyebias", max_pin="x.x") }}' noarch: generic # Suggests: limma, convert, GEOquery, dyebiasexamples, methods requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-dyebiasexamples/meta.yaml b/recipes/bioconductor-dyebiasexamples/meta.yaml index 587748a9d2149..060513470d522 100644 --- a/recipes/bioconductor-dyebiasexamples/meta.yaml +++ b/recipes/bioconductor-dyebiasexamples/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "dyebiasexamples" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8ba42215153001f0334b098938eacf9c + md5: b73aa6c0c98150b2bccba7802dda8c86 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dyebiasexamples", max_pin="x.x") }}' noarch: generic # Suggests: dyebias, convert, Biobase requirements: host: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-dyebiasexamples/post-link.sh b/recipes/bioconductor-dyebiasexamples/post-link.sh index b8db735360a71..15ba43db540e5 100644 --- a/recipes/bioconductor-dyebiasexamples/post-link.sh +++ b/recipes/bioconductor-dyebiasexamples/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dyebiasexamples-1.40.0" +installBiocDataPackage.sh "dyebiasexamples-1.42.0" diff --git a/recipes/bioconductor-dyndoc/meta.yaml b/recipes/bioconductor-dyndoc/meta.yaml index fe9c210847aff..e987221cef2d7 100644 --- a/recipes/bioconductor-dyndoc/meta.yaml +++ b/recipes/bioconductor-dyndoc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "DynDoc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec7f41041d851001acdf1c2c0b3b3626 + md5: 1d5ea2c0b36289466bdb8095b39634fd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dyndoc", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-easier/meta.yaml b/recipes/bioconductor-easier/meta.yaml index 2cedf31d5992c..340d682ef186c 100644 --- a/recipes/bioconductor-easier/meta.yaml +++ b/recipes/bioconductor-easier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.3" %} +{% set version = "1.8.0" %} {% set name = "easier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 722dd22a32a8bc541b0ead14b639594d + md5: 65f72a669a157fdf57501fb32d1c0333 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-easier", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment, viper requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dorothea >=1.12.0,<1.13.0' - - 'bioconductor-easierdata >=1.6.0,<1.7.0' - - 'bioconductor-progeny >=1.22.0,<1.23.0' - - 'bioconductor-quantiseqr >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dorothea >=1.14.0,<1.15.0' + - 'bioconductor-easierdata >=1.8.0,<1.9.0' + - 'bioconductor-progeny >=1.24.0,<1.25.0' + - 'bioconductor-quantiseqr >=1.10.0,<1.11.0' - r-base - r-coin - r-dplyr @@ -43,13 +44,13 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dorothea >=1.12.0,<1.13.0' - - 'bioconductor-easierdata >=1.6.0,<1.7.0' - - 'bioconductor-progeny >=1.22.0,<1.23.0' - - 'bioconductor-quantiseqr >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dorothea >=1.14.0,<1.15.0' + - 'bioconductor-easierdata >=1.8.0,<1.9.0' + - 'bioconductor-progeny >=1.24.0,<1.25.0' + - 'bioconductor-quantiseqr >=1.10.0,<1.11.0' - r-base - r-coin - r-dplyr diff --git a/recipes/bioconductor-easierdata/meta.yaml b/recipes/bioconductor-easierdata/meta.yaml index 7c385d3a4d023..b7b3eb87fc60f 100644 --- a/recipes/bioconductor-easierdata/meta.yaml +++ b/recipes/bioconductor-easierdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "easierData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8cdf9119aa80107e2d8d6853c2a6fde + md5: 5092649863b833021ff8593731571183 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-easierdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-easierdata/post-link.sh b/recipes/bioconductor-easierdata/post-link.sh index f734c14187602..c4e73343e9661 100644 --- a/recipes/bioconductor-easierdata/post-link.sh +++ b/recipes/bioconductor-easierdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "easierdata-1.6.0" +installBiocDataPackage.sh "easierdata-1.8.0" diff --git a/recipes/bioconductor-easylift/build.sh b/recipes/bioconductor-easylift/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-easylift/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-easylift/meta.yaml b/recipes/bioconductor-easylift/meta.yaml new file mode 100644 index 0000000000000..61eabc651b5e0 --- /dev/null +++ b/recipes/bioconductor-easylift/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "easylift" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 86d8c0188c35ab56732fd5cc55475e8c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-easylift", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown +requirements: + host: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-r.utils + run: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-r.utils +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'An R package to perform genomic liftover' + description: 'The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with Bioconductor''s GRanges objects and chain files from the UCSC Genome Browser, allowing for straightforward handling of genomic ranges across various genome versions. One noteworthy feature of easylift is its integration with the BiocFileCache package. This integration automates the management and caching of chain files necessary for liftover operations. Users no longer need to manually specify chain file paths in their function calls, reducing the complexity of the liftover process.' + license_file: LICENSE + diff --git a/recipes/bioconductor-easyreporting/meta.yaml b/recipes/bioconductor-easyreporting/meta.yaml index 5f278d52db552..aa88366c1a868 100644 --- a/recipes/bioconductor-easyreporting/meta.yaml +++ b/recipes/bioconductor-easyreporting/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "easyreporting" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fa8f5e752448cad38c4a14242247ad60 + md5: cffad8bbd7df1cd9ac54b4605a0c555e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-easyreporting", max_pin="x.x") }}' noarch: generic # Suggests: distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq, statmod requirements: diff --git a/recipes/bioconductor-easyrnaseq/meta.yaml b/recipes/bioconductor-easyrnaseq/meta.yaml index 18fe1382616eb..4f704725ab89e 100644 --- a/recipes/bioconductor-easyrnaseq/meta.yaml +++ b/recipes/bioconductor-easyrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "easyRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,53 +11,54 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5ce1f716e811ef9d2a9aad791b33253 + md5: c763a083ce852695593a183ff7f9edcb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-easyrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.18.0), BSgenome (>= 1.58.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.32) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-locfit - 'r-lsd >=4.1-0' - 'r-rappdirs >=0.3.1' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-locfit - 'r-lsd >=4.1-0' diff --git a/recipes/bioconductor-eatonetalchipseq/meta.yaml b/recipes/bioconductor-eatonetalchipseq/meta.yaml index 8841323159b09..54fe87b9b4f10 100644 --- a/recipes/bioconductor-eatonetalchipseq/meta.yaml +++ b/recipes/bioconductor-eatonetalchipseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "EatonEtAlChIPseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa5225647fa5b852a38635bb2ba759ef + md5: e7695c3761d5f3d41dec21b0c8b50947 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eatonetalchipseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-eatonetalchipseq/post-link.sh b/recipes/bioconductor-eatonetalchipseq/post-link.sh index d230394725d2d..346813c7b54e0 100644 --- a/recipes/bioconductor-eatonetalchipseq/post-link.sh +++ b/recipes/bioconductor-eatonetalchipseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "eatonetalchipseq-0.38.0" +installBiocDataPackage.sh "eatonetalchipseq-0.40.0" diff --git a/recipes/bioconductor-ebarrays/meta.yaml b/recipes/bioconductor-ebarrays/meta.yaml index ab564f3bdf108..c4b790998b5de 100644 --- a/recipes/bioconductor-ebarrays/meta.yaml +++ b/recipes/bioconductor-ebarrays/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.64.0" %} +{% set version = "2.66.0" %} {% set name = "EBarrays" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 877a76dfa9d767cfc95b8073ddf7e45e + md5: d273e2e9411207653d4e079e14484026 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ebarrays", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster - r-lattice - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster - r-lattice diff --git a/recipes/bioconductor-ebcoexpress/meta.yaml b/recipes/bioconductor-ebcoexpress/meta.yaml index fce53590dbdff..f22be4d02c7b7 100644 --- a/recipes/bioconductor-ebcoexpress/meta.yaml +++ b/recipes/bioconductor-ebcoexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "EBcoexpress" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a279447b6ebe095682a46c302d2759f3 + md5: 66fa4257fbd0222064b30f6c15e74ab1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ebcoexpress", max_pin="x.x") }}' # Suggests: graph, igraph, colorspace requirements: host: - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - r-base - r-mclust - r-minqa - libblas - liblapack run: - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - r-base - r-mclust - r-minqa diff --git a/recipes/bioconductor-ebimage/meta.yaml b/recipes/bioconductor-ebimage/meta.yaml index 4eb7975ed1018..e8b8c950d28d8 100644 --- a/recipes/bioconductor-ebimage/meta.yaml +++ b/recipes/bioconductor-ebimage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.42.0" %} +{% set version = "4.44.0" %} {% set name = "EBImage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9cd9c206c813cac474584a16c247946b + md5: 22e920a81ab633cdbf753daf3e128d64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ebimage", max_pin="x.x") }}' # Suggests: BiocStyle, digest, knitr, rmarkdown, shiny requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-abind - r-base - 'r-fftwtools >=0.9-7' @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-abind - r-base - 'r-fftwtools >=0.9-7' diff --git a/recipes/bioconductor-ebsea/meta.yaml b/recipes/bioconductor-ebsea/meta.yaml index db931d1204df1..d16b40144208f 100644 --- a/recipes/bioconductor-ebsea/meta.yaml +++ b/recipes/bioconductor-ebsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "EBSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a127e02c2d643195ec73bfa7668f9301 + md5: d016b1e83c4b885565a573db1b134fbd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ebsea", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-empiricalbrownsmethod >=1.28.0,<1.29.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-empiricalbrownsmethod >=1.28.0,<1.29.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' - r-base test: commands: diff --git a/recipes/bioconductor-ebseq/meta.yaml b/recipes/bioconductor-ebseq/meta.yaml index 6254ef104cf0e..056e0f895151f 100644 --- a/recipes/bioconductor-ebseq/meta.yaml +++ b/recipes/bioconductor-ebseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "2.0.0" %} {% set name = "EBSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fa9347689a45799ec669c47880beec7 + md5: e64aabb38197aba0ee5985a1558cce60 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-ebseq", max_pin="x.x") }}' +# SystemRequirements: c++11 requirements: host: - r-base + - r-bh - r-blockmodeling - r-gplots + - 'r-rcpp >=0.12.11' + - 'r-rcppeigen >=0.3.2.9.0' - r-testthat + - libblas + - liblapack run: - r-base + - r-bh - r-blockmodeling - r-gplots + - 'r-rcpp >=0.12.11' + - 'r-rcppeigen >=0.3.2.9.0' - r-testthat + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ebseqhmm/meta.yaml b/recipes/bioconductor-ebseqhmm/meta.yaml index 6995a1ad16d64..54ba10633450f 100644 --- a/recipes/bioconductor-ebseqhmm/meta.yaml +++ b/recipes/bioconductor-ebseqhmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.35.0" %} {% set name = "EBSeqHMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c727c482e89c11143c38785c3fa9570 + md5: d63f173eea402bf0e63ed7018c66d4d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ebseqhmm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ebseq >=1.40.0,<1.41.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' - r-base run: - - 'bioconductor-ebseq >=1.40.0,<1.41.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' - r-base test: commands: diff --git a/recipes/bioconductor-ecoli2.db/meta.yaml b/recipes/bioconductor-ecoli2.db/meta.yaml index a8c18503deeef..50e6af2815625 100644 --- a/recipes/bioconductor-ecoli2.db/meta.yaml +++ b/recipes/bioconductor-ecoli2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "ecoli2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 110d6549b1d105fdff31ab8f45b08d65 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoli2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.eck12.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.eck12.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.eck12.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.eck12.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoli2cdf/meta.yaml b/recipes/bioconductor-ecoli2cdf/meta.yaml index abb629a424e72..12b93a0ff9c58 100644 --- a/recipes/bioconductor-ecoli2cdf/meta.yaml +++ b/recipes/bioconductor-ecoli2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoli2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b5cd1f05322ce494132ff649de9806c6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoli2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoli2probe/meta.yaml b/recipes/bioconductor-ecoli2probe/meta.yaml index f1c2ebe9bc3c1..1d0e8f7b2081f 100644 --- a/recipes/bioconductor-ecoli2probe/meta.yaml +++ b/recipes/bioconductor-ecoli2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoli2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 061fcb782ee9da3aa5108881677a4531 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoli2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoliasv2cdf/meta.yaml b/recipes/bioconductor-ecoliasv2cdf/meta.yaml index 5ca8789b939ab..dda890ce3dddf 100644 --- a/recipes/bioconductor-ecoliasv2cdf/meta.yaml +++ b/recipes/bioconductor-ecoliasv2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoliasv2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d7771ca1648b26a6af5bfb7582c6c778 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoliasv2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecoliasv2probe/meta.yaml b/recipes/bioconductor-ecoliasv2probe/meta.yaml index 9d840d05475b1..189c801a32b21 100644 --- a/recipes/bioconductor-ecoliasv2probe/meta.yaml +++ b/recipes/bioconductor-ecoliasv2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoliasv2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b3e4332266184576279c3a478f286dc9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoliasv2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolicdf/meta.yaml b/recipes/bioconductor-ecolicdf/meta.yaml index 57e2bf50c9017..ae5dec1242d25 100644 --- a/recipes/bioconductor-ecolicdf/meta.yaml +++ b/recipes/bioconductor-ecolicdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecolicdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4e664c1ac41a8ab68ef22f8a889b916c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecolicdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolik12.db0/meta.yaml b/recipes/bioconductor-ecolik12.db0/meta.yaml index af7c68888e039..5fe013dc64149 100644 --- a/recipes/bioconductor-ecolik12.db0/meta.yaml +++ b/recipes/bioconductor-ecolik12.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "ecoliK12.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acf1faa22de4e8b535baf0d7403acbe0 + md5: dd303204595a25bc730695462e930247 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecolik12.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolik12.db0/post-link.sh b/recipes/bioconductor-ecolik12.db0/post-link.sh index 3ac028b892847..1ea1a96c05c6f 100644 --- a/recipes/bioconductor-ecolik12.db0/post-link.sh +++ b/recipes/bioconductor-ecolik12.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ecolik12.db0-3.17.0" +installBiocDataPackage.sh "ecolik12.db0-3.18.0" diff --git a/recipes/bioconductor-ecolileucine/meta.yaml b/recipes/bioconductor-ecolileucine/meta.yaml index 8292b62611e44..d735e051bbdef 100644 --- a/recipes/bioconductor-ecolileucine/meta.yaml +++ b/recipes/bioconductor-ecolileucine/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "ecoliLeucine" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f29571bdbf113fe17eb2a91638acf1a + md5: 30af71114480d851f4dad806e7f8e0d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecolileucine", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - 'bioconductor-ecolicdf >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - 'bioconductor-ecolicdf >=2.18.0,<2.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolileucine/post-link.sh b/recipes/bioconductor-ecolileucine/post-link.sh index c8c483bd70916..069ee49494795 100644 --- a/recipes/bioconductor-ecolileucine/post-link.sh +++ b/recipes/bioconductor-ecolileucine/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ecolileucine-1.40.0" +installBiocDataPackage.sh "ecolileucine-1.42.0" diff --git a/recipes/bioconductor-ecoliprobe/meta.yaml b/recipes/bioconductor-ecoliprobe/meta.yaml index d5bea7a7e2d95..fc9b2941ec792 100644 --- a/recipes/bioconductor-ecoliprobe/meta.yaml +++ b/recipes/bioconductor-ecoliprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ecoliprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 09586f9907bdbc43ba5ea4ce07c1f756 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecoliprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolisakai.db0/meta.yaml b/recipes/bioconductor-ecolisakai.db0/meta.yaml index 4673684e174f2..f4a33593ee350 100644 --- a/recipes/bioconductor-ecolisakai.db0/meta.yaml +++ b/recipes/bioconductor-ecolisakai.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "ecoliSakai.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f49e4fe2806f14f78db0de22d37a7e7 + md5: 2afd28e9062d869d37e3d65dbe410bcb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecolisakai.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ecolisakai.db0/post-link.sh b/recipes/bioconductor-ecolisakai.db0/post-link.sh index 818939129b685..5a26a1ced0260 100644 --- a/recipes/bioconductor-ecolisakai.db0/post-link.sh +++ b/recipes/bioconductor-ecolisakai.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ecolisakai.db0-3.17.0" +installBiocDataPackage.sh "ecolisakai.db0-3.18.0" diff --git a/recipes/bioconductor-ecolitk/meta.yaml b/recipes/bioconductor-ecolitk/meta.yaml index 512663e7315e7..eb82d060744b5 100644 --- a/recipes/bioconductor-ecolitk/meta.yaml +++ b/recipes/bioconductor-ecolitk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "ecolitk" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8867acb9dd27e581f696ec0afd77be79 + md5: 58667dc1f403986935c98a97f2e0b9e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ecolitk", max_pin="x.x") }}' noarch: generic # Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-edaseq/meta.yaml b/recipes/bioconductor-edaseq/meta.yaml index d9ee0fb7067a8..4e0352c7939f4 100644 --- a/recipes/bioconductor-edaseq/meta.yaml +++ b/recipes/bioconductor-edaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "EDASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1bedbd7d1b319ddeb8eff7fc5d2d9bb7 + md5: b2d28fdad31e8c56f68873b599ffc235 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-edaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-aroma.light >=3.30.0,<3.31.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-aroma.light >=3.32.0,<3.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-biocmanager run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-aroma.light >=3.30.0,<3.31.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-aroma.light >=3.32.0,<3.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-biocmanager test: diff --git a/recipes/bioconductor-edge/meta.yaml b/recipes/bioconductor-edge/meta.yaml index 2b0e02ce3cdcb..fc6de808fba13 100644 --- a/recipes/bioconductor-edge/meta.yaml +++ b/recipes/bioconductor-edge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "edge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ce7aff708078e2ddba0b00c919a67429 + md5: 89d1683b6b4f9723b4c4fcef6972d543 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-edge", max_pin="x.x") }}' # Suggests: testthat, knitr, ggplot2, reshape2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-snm >=1.48.0,<1.49.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-snm >=1.50.0,<1.51.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-mass - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-snm >=1.48.0,<1.49.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-snm >=1.50.0,<1.51.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-mass build: diff --git a/recipes/bioconductor-edger/meta.yaml b/recipes/bioconductor-edger/meta.yaml index 5a3493060c73a..0884137cf6b49 100644 --- a/recipes/bioconductor-edger/meta.yaml +++ b/recipes/bioconductor-edger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.42.4" %} +{% set version = "4.0.2" %} {% set name = "edgeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad81660fe783c10b69e06fdab6130dc8 + md5: 0ba48556be0c95b929db5bbed32923f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: jsonlite, readr, rhdf5, splines, statmod, Biobase, AnnotationDbi, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject + run_exports: '{{ pin_subpackage("bioconductor-edger", max_pin="x.x") }}' +# Suggests: jsonlite, readr, rhdf5, splines, knitr, AnnotationDbi, Biobase, BiocStyle, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit - r-rcpp - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit - r-rcpp diff --git a/recipes/bioconductor-edirquery/meta.yaml b/recipes/bioconductor-edirquery/meta.yaml index eeb40850533ac..2adef6a882208 100644 --- a/recipes/bioconductor-edirquery/meta.yaml +++ b/recipes/bioconductor-edirquery/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "EDIRquery" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ef6b7ba141cd7778c7d5bf31d138af2 + md5: ff19937af17cf0a7a874b986192d6b1c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-edirquery", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' - r-base - 'r-readr >=2.1.2' - 'r-tibble >=3.1.6' - 'r-tictoc >=1.0.1' run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' - r-base - 'r-readr >=2.1.2' - 'r-tibble >=3.1.6' diff --git a/recipes/bioconductor-eds/meta.yaml b/recipes/bioconductor-eds/meta.yaml index fc15dbcda7029..de545d756c8e0 100644 --- a/recipes/bioconductor-eds/meta.yaml +++ b/recipes/bioconductor-eds/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "eds" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0250c849115fe963572ba6669f5377a3 + md5: 5992ff2692afb665a65bc9755175de5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eds", max_pin="x.x") }}' # Suggests: knitr, tximportData, testthat (>= 3.0.0) # SystemRequirements: C++11 requirements: diff --git a/recipes/bioconductor-egad/meta.yaml b/recipes/bioconductor-egad/meta.yaml index 9413400986988..d7cb742f73393 100644 --- a/recipes/bioconductor-egad/meta.yaml +++ b/recipes/bioconductor-egad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "EGAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f46e429f7ee3c80517e8fa46e1819e18 + md5: 9a76ae26d942a1e8b8c8764b80c69927 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-egad", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-igraph @@ -34,10 +35,10 @@ requirements: - r-rcurl - r-zoo run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-igraph diff --git a/recipes/bioconductor-egseadata/meta.yaml b/recipes/bioconductor-egseadata/meta.yaml index bf8e5346a6f45..aab5bfb3fdc69 100644 --- a/recipes/bioconductor-egseadata/meta.yaml +++ b/recipes/bioconductor-egseadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "EGSEAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ccaaafd4866fa1cf07e06b6370739a3 + md5: 838b30ae6caf7c3cbb854e0404b52cda build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-egseadata", max_pin="x.x") }}' noarch: generic # Suggests: EGSEA requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-egseadata/post-link.sh b/recipes/bioconductor-egseadata/post-link.sh index d17c19a3933ce..4969b6b51c98a 100644 --- a/recipes/bioconductor-egseadata/post-link.sh +++ b/recipes/bioconductor-egseadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "egseadata-1.28.0" +installBiocDataPackage.sh "egseadata-1.30.0" diff --git a/recipes/bioconductor-eir/meta.yaml b/recipes/bioconductor-eir/meta.yaml index 6a9d27cf785b5..882112a2aaeb1 100644 --- a/recipes/bioconductor-eir/meta.yaml +++ b/recipes/bioconductor-eir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "eiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23f3e513756302dbc768aa836d474f0f + md5: 71e5c96821411e053b417fb15618e1cb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eir", max_pin="x.x") }}' # Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap,rmarkdown,RSQLite requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-dbi - r-digest @@ -33,8 +34,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-dbi - r-digest diff --git a/recipes/bioconductor-eisar/meta.yaml b/recipes/bioconductor-eisar/meta.yaml index c06ab9d062533..5daa7b7fcd320 100644 --- a/recipes/bioconductor-eisar/meta.yaml +++ b/recipes/bioconductor-eisar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "eisaR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3338687a24a33d16373c1033c2150c7f + md5: 0a81a6727f2514ce8e2836cc170bdb19 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eisar", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, rtracklayer requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-elmer.data/meta.yaml b/recipes/bioconductor-elmer.data/meta.yaml index 7d864ee0ec783..46a704674c673 100644 --- a/recipes/bioconductor-elmer.data/meta.yaml +++ b/recipes/bioconductor-elmer.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "ELMER.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bb614a1bd1fd96f91af883bad29c914 + md5: 565ea1aa52f3f61d16b7560859ed7a3a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-elmer.data", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, dplyr, devtools, DT, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-elmer.data/post-link.sh b/recipes/bioconductor-elmer.data/post-link.sh index e9acc598f0002..f070b978224f7 100644 --- a/recipes/bioconductor-elmer.data/post-link.sh +++ b/recipes/bioconductor-elmer.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "elmer.data-2.24.0" +installBiocDataPackage.sh "elmer.data-2.26.0" diff --git a/recipes/bioconductor-elmer/meta.yaml b/recipes/bioconductor-elmer/meta.yaml index f306c2e69897e..680af36125772 100644 --- a/recipes/bioconductor-elmer/meta.yaml +++ b/recipes/bioconductor-elmer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.1" %} +{% set version = "2.26.0" %} {% set name = "ELMER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d6a247672fe62e4bedb7b72a56af020e + md5: 528e6779b95faafbb8ff2e32e0b28ca5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-elmer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-elmer.data >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-elmer.data >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-circlize - r-doparallel @@ -62,20 +63,20 @@ requirements: - r-tidyr - r-xml2 run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-elmer.data >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-elmer.data >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-circlize - r-doparallel diff --git a/recipes/bioconductor-emdomics/meta.yaml b/recipes/bioconductor-emdomics/meta.yaml index d592a8cc531b5..f0657e63a91b6 100644 --- a/recipes/bioconductor-emdomics/meta.yaml +++ b/recipes/bioconductor-emdomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "EMDomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23c951e5766c53a07cc1946335b4e06c + md5: 3ac097828648747f0be1ed4d956ecfa7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-emdomics", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-cdft - r-emdist - r-ggplot2 - r-matrixstats run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-cdft - r-emdist diff --git a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml index 04d10e3cba9a4..e73e26279321b 100644 --- a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml +++ b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "EmpiricalBrownsMethod" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7c4a27f1986e21a7bf4a447305fb916 + md5: cde2165928019f9c13982d640a1303c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-empiricalbrownsmethod", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-emtdata/meta.yaml b/recipes/bioconductor-emtdata/meta.yaml index c94df7781a194..7dbe179742d90 100644 --- a/recipes/bioconductor-emtdata/meta.yaml +++ b/recipes/bioconductor-emtdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "emtdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e4c17e43c1d50287179f7fb2f594d6c3 + md5: 4f861584cce979edd6d7bdce3624e916 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-emtdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle, Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-emtdata/post-link.sh b/recipes/bioconductor-emtdata/post-link.sh index 414a9037e8614..93baa8560da53 100644 --- a/recipes/bioconductor-emtdata/post-link.sh +++ b/recipes/bioconductor-emtdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "emtdata-1.8.0" +installBiocDataPackage.sh "emtdata-1.10.0" diff --git a/recipes/bioconductor-encodexplorerdata/meta.yaml b/recipes/bioconductor-encodexplorerdata/meta.yaml index 4777d7613ad5e..5eb72ebf61053 100644 --- a/recipes/bioconductor-encodexplorerdata/meta.yaml +++ b/recipes/bioconductor-encodexplorerdata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.5" %} {% set name = "ENCODExplorerData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c6d9b491548529db0739b79c98adacd7 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-encodexplorerdata", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, RUnit, BiocGenerics, knitr, curl, httr requirements: @@ -31,7 +32,7 @@ requirements: - r-jsonlite - r-rcurl - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-enhancedvolcano/meta.yaml b/recipes/bioconductor-enhancedvolcano/meta.yaml index 6940df17b140d..717cd7a75281d 100644 --- a/recipes/bioconductor-enhancedvolcano/meta.yaml +++ b/recipes/bioconductor-enhancedvolcano/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "EnhancedVolcano" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32e59ff1c6981c80fcfef699efbe2798 + md5: b8224be72afe86d3d951a6a8fdc6788e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enhancedvolcano", max_pin="x.x") }}' noarch: generic # Suggests: ggalt, ggrastr, RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, org.Hs.eg.db, gridExtra, magrittr, rmarkdown requirements: diff --git a/recipes/bioconductor-enhancerhomologsearch/meta.yaml b/recipes/bioconductor-enhancerhomologsearch/meta.yaml index 8ce3dff69f64b..2d0d66cd9e7d2 100644 --- a/recipes/bioconductor-enhancerhomologsearch/meta.yaml +++ b/recipes/bioconductor-enhancerhomologsearch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.2" %} {% set name = "enhancerHomologSearch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72963b28ae430436bea374d01e6158da - patches: - - infinity.patch + md5: ce4ad762be83b367c02fc926bf67c383 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enhancerhomologsearch", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb, testthat, TFBSTools requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-httr - r-jsonlite @@ -41,17 +40,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-enmcb/meta.yaml b/recipes/bioconductor-enmcb/meta.yaml index bcf851b6a4481..137714b151321 100644 --- a/recipes/bioconductor-enmcb/meta.yaml +++ b/recipes/bioconductor-enmcb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "EnMCB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc2bd872fb5b7e28ec799d122512d7ab + md5: f9fee363d9285ffdf2895062fc0cf26b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enmcb", max_pin="x.x") }}' noarch: generic # Suggests: SummarizedExperiment, testthat, Biobase, survminer, affycoretools, knitr, plotROC, limma, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-boot - r-e1071 @@ -35,7 +36,7 @@ requirements: - r-survivalroc - r-survivalsvm run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-boot - r-e1071 diff --git a/recipes/bioconductor-enmix/meta.yaml b/recipes/bioconductor-enmix/meta.yaml index 7d2844fd82aa5..d38d91df9f69a 100644 --- a/recipes/bioconductor-enmix/meta.yaml +++ b/recipes/bioconductor-enmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.01" %} +{% set version = "1.38.01" %} {% set name = "ENmix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,56 +11,57 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 581b13b091573a2925d86004487ed0c3 + md5: 3ac8861e8c3ad067b1baa266958227cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enmix", max_pin="x.x") }}' noarch: generic # Suggests: minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dynamictreecut - r-foreach - r-gplots - r-gtools + - r-irlba - r-matrixstats - r-quadprog - r-rpmm run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dynamictreecut - r-foreach - r-gplots - r-gtools + - r-irlba - r-matrixstats - r-quadprog - r-rpmm diff --git a/recipes/bioconductor-enrichedheatmap/build_failure.osx-64.yaml b/recipes/bioconductor-enrichedheatmap/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..a339ea97f8532 --- /dev/null +++ b/recipes/bioconductor-enrichedheatmap/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 9a6c8d621c8da5f9299d5af966645abebfcfa7fd1cab2bbd703ca5e6f763fec7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + 11:47:03 BIOCONDA INFO (ERR) dyld[20647]: Library not loaded: '@rpath/libtapi.dylib' 11:47:03 BIOCONDA INFO (ERR) Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/x86_64-apple-darwin13.4.0-ld' 11:47:03 BIOCONDA INFO (ERR) Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/../lib/libtapi.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/../lib/libtapi.dylib' (no such file), '/usr/local/lib/libtapi.dylib' (no such file), '/usr/lib/libtapi.dylib' (no such file) 11:47:03 BIOCONDA INFO (ERR) clang-15: error: unable to execute command: Abort trap: 6 11:47:03 BIOCONDA INFO (ERR) clang-15: error: linker command failed due to signal (use -v to see invocation) +category: |- + compiler error diff --git a/recipes/bioconductor-enrichedheatmap/meta.yaml b/recipes/bioconductor-enrichedheatmap/meta.yaml index e7ffabb3dd518..87efa37d244c1 100644 --- a/recipes/bioconductor-enrichedheatmap/meta.yaml +++ b/recipes/bioconductor-enrichedheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "EnrichedHeatmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3adcecb7cb7b60fb2dd0266052d697b + md5: 269aeb6d749072508069805663216dc4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enrichedheatmap", max_pin="x.x") }}' # Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.5' - r-getoptlong @@ -32,9 +33,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.5' - r-getoptlong diff --git a/recipes/bioconductor-enrichmentbrowser/meta.yaml b/recipes/bioconductor-enrichmentbrowser/meta.yaml index e2505a9c37c89..b55ecad92a7c4 100644 --- a/recipes/bioconductor-enrichmentbrowser/meta.yaml +++ b/recipes/bioconductor-enrichmentbrowser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.1" %} +{% set version = "2.32.0" %} {% set name = "EnrichmentBrowser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,52 +11,53 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c543e0cbb1ba98aa022dbfaf08c537ee + md5: fa4ec5a19513178896d60057a26ec6ce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enrichmentbrowser", max_pin="x.x") }}' noarch: generic # Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-safe >=3.40.0,<3.41.0' - - 'bioconductor-spia >=2.52.0,<2.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-safe >=3.42.0,<3.43.0' + - 'bioconductor-spia >=2.54.0,<2.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-hwriter run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-safe >=3.40.0,<3.41.0' - - 'bioconductor-spia >=2.52.0,<2.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-safe >=3.42.0,<3.43.0' + - 'bioconductor-spia >=2.54.0,<2.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-hwriter diff --git a/recipes/bioconductor-enrichplot/meta.yaml b/recipes/bioconductor-enrichplot/meta.yaml index 57d62b1537dd7..60ac7b0cc9d3b 100644 --- a/recipes/bioconductor-enrichplot/meta.yaml +++ b/recipes/bioconductor-enrichplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "enrichplot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d76d773c796cc76d486af2e796b6dca3 + md5: 4accfec43292c11ec0165092f3266ac2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enrichplot", max_pin="x.x") }}' noarch: generic -# Suggests: clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggrepel (>= 0.9.0), ggstar, treeio, scales, tidytree, ggtreeExtra, tidydr +# Suggests: clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggrepel (>= 0.9.0), ggstar, scales, ggtreeExtra, tidydr requirements: host: - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'r-aplot >=0.1.4' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'r-aplot >=0.2.1' - r-base + - 'r-ggfun >=0.1.3' - r-ggnewscale - r-ggplot2 - r-ggraph @@ -38,13 +40,14 @@ requirements: - r-rlang - r-scatterpie - r-shadowtext - - 'r-yulab.utils >=0.0.4' + - 'r-yulab.utils >=0.0.8' run: - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'r-aplot >=0.1.4' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'r-aplot >=0.2.1' - r-base + - 'r-ggfun >=0.1.3' - r-ggnewscale - r-ggplot2 - r-ggraph @@ -57,7 +60,7 @@ requirements: - r-rlang - r-scatterpie - r-shadowtext - - 'r-yulab.utils >=0.0.4' + - 'r-yulab.utils >=0.0.8' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-enrichtf/build_failure.linux-64.yaml b/recipes/bioconductor-enrichtf/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0885f7bb52630 --- /dev/null +++ b/recipes/bioconductor-enrichtf/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1c991de1bbfe0824a102700e267a7f4665d9ce725d1b2ee87b87e8ec4ccbd588 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.5s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 100% + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.6s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 100% + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 + [] 1.7s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.8s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/noarch + pkgs/r/noarch + [] 1.9s + conda-forge/linux-64 + conda-forge/noarch + pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0G[] 2.0s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0G[] 2.1s + conda-forge/linux-64 + pkgs/r/linux-64 [2K[1A[2K[1A[2K[0Gconda-forge/noarch + pkgs/r/linux-64 + [] 2.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 5.0s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.3s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.4s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.5s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.6s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.7s + [2K[1A[2K[0Gconda-forge/linux-64 + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.1MB/s 0.0s + opt/conda/conda-bld/noarch 1.4kB @ 28.7MB/s 0.0s + [?25hTraceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test + environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, + File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env + display_actions(actions, index) + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions + actions['LINK'] = [index[d] for d in actions['LINK']] + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in + actions['LINK'] = [index[d] for d in actions['LINK']] + KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-enrichtf/meta.yaml b/recipes/bioconductor-enrichtf/meta.yaml index 497ae6659c32d..942370c55322c 100644 --- a/recipes/bioconductor-enrichtf/meta.yaml +++ b/recipes/bioconductor-enrichtf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "enrichTF" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3b22db2a149bf9e4cbe916173849722 + md5: a88296c9418e41a8e66fccc276925471 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enrichtf", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, webshot requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-pipeframe >=1.16.0,<1.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-pipeframe >=1.18.0,<1.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-ggpubr @@ -41,18 +42,18 @@ requirements: - r-r.utils - r-rmarkdown run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-pipeframe >=1.16.0,<1.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-pipeframe >=1.18.0,<1.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-ggpubr diff --git a/recipes/bioconductor-enrichviewnet/build.sh b/recipes/bioconductor-enrichviewnet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-enrichviewnet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-enrichviewnet/meta.yaml b/recipes/bioconductor-enrichviewnet/meta.yaml new file mode 100644 index 0000000000000..853b3336dc8e7 --- /dev/null +++ b/recipes/bioconductor-enrichviewnet/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.0" %} +{% set name = "enrichViewNet" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5b2eb51ee4f57abd3b77da182e7e5d1a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enrichviewnet", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - r-base + - r-gprofiler2 + - r-jsonlite + - r-strex + - r-stringr + run: + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - r-base + - r-gprofiler2 + - r-jsonlite + - r-strex + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'From functional enrichment results to biological networks' + description: 'This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes.' + diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml index 035e577d1b943..e9d78eb695b76 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v75" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6c896475252903972bfc6c0eb0d8f334 build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.hsapiens.v75", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml index 4c52d38262581..1ba0892011aad 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v79" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 16b5629805c07649b2aa501d34fcc588 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.hsapiens.v79", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml index a94e97097dfe1..f91361ab9fb38 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v86" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0c9e52512ff6dbbbdb754c4d41149939 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.hsapiens.v86", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml b/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml index 14ba8a094c45b..53552d68e3b42 100644 --- a/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Mmusculus.v75" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 081bf6f90ff77031b634b4fe32e00be8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.mmusculus.v75", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml b/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml index 1035f94d66e52..b07f2e2eb5bd1 100644 --- a/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Mmusculus.v79" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 28bbab743b0d2d550dbfa0bcd3274fad build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.mmusculus.v79", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml b/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml index ac9b5f465e9cf..a89441fa23d47 100644 --- a/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Rnorvegicus.v75" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 40ff53b41aa6fad0d5bd15f9c6f3bad8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.rnorvegicus.v75", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml b/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml index 711cbb93749c5..5646d093a9d17 100644 --- a/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Rnorvegicus.v79" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7d305bd0d1a073bd8c60063ae210a7a9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensdb.rnorvegicus.v79", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ensembldb/meta.yaml b/recipes/bioconductor-ensembldb/meta.yaml index 137ffef63ab7e..c421d63cd8558 100644 --- a/recipes/bioconductor-ensembldb/meta.yaml +++ b/recipes/bioconductor-ensembldb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "ensembldb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,47 +11,48 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4d1be7f0e9d2ff9e4c473b891eec62de + md5: 0ad7a33ad9592f54e39d647195aa4c91 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensembldb", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-dbi - 'r-rsqlite >=1.1' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-dbi diff --git a/recipes/bioconductor-ensemblvep/meta.yaml b/recipes/bioconductor-ensemblvep/meta.yaml index 0d0f14c7c5142..537285ab0b96e 100644 --- a/recipes/bioconductor-ensemblvep/meta.yaml +++ b/recipes/bioconductor-ensemblvep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "ensemblVEP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad5be46f89b6fb698603bf2caa25bc19 + md5: 378569d68f5d4973a7b16eb7cc2b9327 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ensemblvep", max_pin="x.x") }}' noarch: generic # Suggests: RUnit # SystemRequirements: Ensembl VEP (API version 105) and the Perl modules DBI and DBD::mysql must be installed. See the package README and Ensembl installation instructions: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-epialleler/build.sh b/recipes/bioconductor-epialleler/build.sh index 5ea71a1203cac..c1d13421f5f1e 100644 --- a/recipes/bioconductor-epialleler/build.sh +++ b/recipes/bioconductor-epialleler/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epialleler/meta.yaml b/recipes/bioconductor-epialleler/meta.yaml index ab584ae6edd1f..c3950d568d811 100644 --- a/recipes/bioconductor-epialleler/meta.yaml +++ b/recipes/bioconductor-epialleler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "epialleleR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e242bf8aa9a114b4eeebd2e7cd57c096 + md5: cbe73c32dc61dac41266279db72e4bee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epialleler", max_pin="x.x") }}' # Suggests: RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra # SystemRequirements: C++17, GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-data.table - r-rcpp - - r-stringi - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-data.table - r-rcpp - - r-stringi build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -58,6 +57,6 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Fast, Epiallele-Aware Methylation Reporter' - description: 'Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls hypermethylated epiallele frequencies at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Other functionality includes extracting methylation patterns, computing the empirical cumulative distribution function for per-read beta values, and testing the significance of the association between epiallele methylation status and base frequencies at particular genomic positions (SNPs).' + summary: 'Fast, Epiallele-Aware Methylation Caller and Reporter' + description: 'Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract methylation patterns and assess allele specificity of methylation.' diff --git a/recipes/bioconductor-epidecoder/meta.yaml b/recipes/bioconductor-epidecoder/meta.yaml index bd29b9981ab70..c322d6f121c8b 100644 --- a/recipes/bioconductor-epidecoder/meta.yaml +++ b/recipes/bioconductor-epidecoder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "epidecodeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06413f62d44e93ed0fa687a6d81e00ff + md5: 409ed7c959818b7400944e1d20653f68 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epidecoder", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-envstats @@ -31,9 +32,9 @@ requirements: - r-ggpubr - r-rstatix run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-envstats diff --git a/recipes/bioconductor-epidish/meta.yaml b/recipes/bioconductor-epidish/meta.yaml index ecb9046de608f..5ae9b8411ac2a 100644 --- a/recipes/bioconductor-epidish/meta.yaml +++ b/recipes/bioconductor-epidish/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "EpiDISH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: facabe437e4fd3e9c6e8a7545bfc2c55 + md5: db7b5d2165fad653dabc1bfd8faeab83 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epidish", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat requirements: diff --git a/recipes/bioconductor-epigenomix/meta.yaml b/recipes/bioconductor-epigenomix/meta.yaml index cf59745b01a7e..44a46bcbbb2a0 100644 --- a/recipes/bioconductor-epigenomix/meta.yaml +++ b/recipes/bioconductor-epigenomix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "epigenomix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3bf32e589c4fc3ea302d75a821ce29e1 + md5: eef6318b8b342675c1fdd4c99ed541e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epigenomix", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mcmcpack run: - - 'bioconductor-beadarray >=2.50.0,<2.51.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beadarray >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mcmcpack test: diff --git a/recipes/bioconductor-epigrahmm/meta.yaml b/recipes/bioconductor-epigrahmm/meta.yaml index ccf466c267dbc..6ac28075e8219 100644 --- a/recipes/bioconductor-epigrahmm/meta.yaml +++ b/recipes/bioconductor-epigrahmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.2" %} +{% set version = "1.10.0" %} {% set name = "epigraHMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a095bb8f775608ebfc7ca1a8ea4e165e + md5: 1c86fa9edec93550acae520d84420b88 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epigrahmm", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData # SystemRequirements: GNU make requirements: host: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-greylistchip >=1.32.0,<1.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-greylistchip >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-ggplot2 @@ -48,19 +49,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-greylistchip >=1.32.0,<1.33.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-greylistchip >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-epimix.data/meta.yaml b/recipes/bioconductor-epimix.data/meta.yaml index 508d3fb34bbbc..38d41a4d5a840 100644 --- a/recipes/bioconductor-epimix.data/meta.yaml +++ b/recipes/bioconductor-epimix.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.2" %} +{% set version = "1.4.0" %} {% set name = "EpiMix.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3234766b0bc549ab200604206a9ba5b8 + md5: 52c386f6828945121acfca44eabb7827 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epimix.data", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-epimix.data/post-link.sh b/recipes/bioconductor-epimix.data/post-link.sh index 0bd1b17c93d35..62d257d916df8 100644 --- a/recipes/bioconductor-epimix.data/post-link.sh +++ b/recipes/bioconductor-epimix.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "epimix.data-1.2.2" +installBiocDataPackage.sh "epimix.data-1.4.0" diff --git a/recipes/bioconductor-epimix/meta.yaml b/recipes/bioconductor-epimix/meta.yaml index 6630fa2901172..2f933593dc46b 100644 --- a/recipes/bioconductor-epimix/meta.yaml +++ b/recipes/bioconductor-epimix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.2" %} +{% set version = "1.4.0" %} {% set name = "EpiMix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f068a8ea3b2cd23bac159f19320d455 + md5: d86305c56618b7f327d0068e09ad6558 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epimix", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, clusterProfiler, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics +# Suggests: BiocStyle, clusterProfiler, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-elmer.data >=2.24.0,<2.25.0' - - 'bioconductor-epimix.data >=1.2.0,<1.3.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-elmer.data >=2.26.0,<2.27.0' + - 'bioconductor-epimix.data >=1.4.0,<1.5.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-doparallel @@ -55,22 +55,21 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-elmer.data >=2.24.0,<2.25.0' - - 'bioconductor-epimix.data >=1.2.0,<1.3.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-elmer.data >=2.26.0,<2.27.0' + - 'bioconductor-epimix.data >=1.4.0,<1.5.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-epimutacions/meta.yaml b/recipes/bioconductor-epimutacions/meta.yaml index 2009149f65299..dec1d85892e1b 100644 --- a/recipes/bioconductor-epimutacions/meta.yaml +++ b/recipes/bioconductor-epimutacions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.1" %} {% set name = "epimutacions" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: df7b334f2a1aa9a8ad23679c25578eda + md5: 73fdaf9db5e5d035601282d6e5d832fd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epimutacions", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-epimutacionsdata >=1.4.0,<1.5.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-epimutacionsdata >=1.6.0,<1.7.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-ggrepel @@ -59,32 +60,32 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-epimutacionsdata >=1.4.0,<1.5.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-epimutacionsdata >=1.6.0,<1.7.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-epimutacionsdata/meta.yaml b/recipes/bioconductor-epimutacionsdata/meta.yaml index 9fe6ecbb04437..761c0fbdf4067 100644 --- a/recipes/bioconductor-epimutacionsdata/meta.yaml +++ b/recipes/bioconductor-epimutacionsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "epimutacionsData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 162b5aaa6a5f6df2528dce4285efdea4 + md5: e2681ab8096fd0f2b7e5d8ed68928280 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epimutacionsdata", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, BiocStyle, knitr, ExperimentHub, minfi requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-epimutacionsdata/post-link.sh b/recipes/bioconductor-epimutacionsdata/post-link.sh index 0989eb175b6ad..04b4600843e28 100644 --- a/recipes/bioconductor-epimutacionsdata/post-link.sh +++ b/recipes/bioconductor-epimutacionsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "epimutacionsdata-1.4.0" +installBiocDataPackage.sh "epimutacionsdata-1.6.0" diff --git a/recipes/bioconductor-epinem/meta.yaml b/recipes/bioconductor-epinem/meta.yaml index dfbe44e395c46..704d6f0117daf 100644 --- a/recipes/bioconductor-epinem/meta.yaml +++ b/recipes/bioconductor-epinem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "epiNEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d3c178dac61b79d58666db49073ead75 + md5: 03702ef94f047496994ebaf19f750787 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epinem", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' - r-base - r-boolnet - r-e1071 @@ -35,9 +36,9 @@ requirements: - r-pcalg - r-rcolorbrewer run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' - r-base - r-boolnet - r-e1071 diff --git a/recipes/bioconductor-epistack/meta.yaml b/recipes/bioconductor-epistack/meta.yaml index 2765821eb8517..3dab4be583771 100644 --- a/recipes/bioconductor-epistack/meta.yaml +++ b/recipes/bioconductor-epistack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "epistack" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c555b4279771d26c7cfe9334d694fcbb + md5: 7d06dbae71f93e2c3cb91ba3d16fa916 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epistack", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-plotrix run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-plotrix test: diff --git a/recipes/bioconductor-epistasisga/meta.yaml b/recipes/bioconductor-epistasisga/meta.yaml index fa6e9e8a58c30..f7bb792a8c68a 100644 --- a/recipes/bioconductor-epistasisga/meta.yaml +++ b/recipes/bioconductor-epistasisga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "epistasisGA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62ed9886878fc33fd72be12e391cccee + md5: 79635d9683f002813e51fa3c17e49b39 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epistasisga", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-batchtools - r-bh @@ -36,7 +37,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-batchtools - r-bh diff --git a/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml b/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml index a8255a97fe06e..9edb215bfcecc 100644 --- a/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml +++ b/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.7" %} {% set name = "EpiTxDb.Hs.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e30af95f285788a9777a8207a8ef73a9 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epitxdb.hs.hg38", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, Modstrings, rtracklayer requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml b/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml index fe37e709b6bc8..526e3d97d4b4e 100644 --- a/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml +++ b/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.6" %} {% set name = "EpiTxDb.Mm.mm10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 518e4967f7f038e3cbf2865b74dc4f1b build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epitxdb.mm.mm10", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml b/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml index f0df4cc359c84..69da19dba72fc 100644 --- a/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml +++ b/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.5" %} {% set name = "EpiTxDb.Sc.sacCer3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6d9e5f37e5dcb60e890d99d80fddda00 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epitxdb.sc.saccer3", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, Modstrings, rtracklayer requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-epitxdb >=1.12.0,<1.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-epitxdb >=1.14.0,<1.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-epitxdb/meta.yaml b/recipes/bioconductor-epitxdb/meta.yaml index faa034bbfa391..9120d238c9984 100644 --- a/recipes/bioconductor-epitxdb/meta.yaml +++ b/recipes/bioconductor-epitxdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "EpiTxDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55ab42b455431e070e058b65a43784da + md5: a693697bcccd27be6e57c304438d94a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epitxdb", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-trnadbimport >=1.18.0,<1.19.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-trnadbimport >=1.20.0,<1.21.0' - r-base - r-curl - r-dbi @@ -39,17 +40,17 @@ requirements: - r-rsqlite - r-xml2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-trnadbimport >=1.18.0,<1.19.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-trnadbimport >=1.20.0,<1.21.0' - r-base - r-curl - r-dbi diff --git a/recipes/bioconductor-epivizr/meta.yaml b/recipes/bioconductor-epivizr/meta.yaml index 556f6962606bd..51bbf203d8997 100644 --- a/recipes/bioconductor-epivizr/meta.yaml +++ b/recipes/bioconductor-epivizr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "epivizr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 710f534004dc7cbf1364255f3b42ad0d + md5: aaf997f0c4eccf72d795d79a3ebd7bfe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epivizr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown requirements: host: - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-epivizrchart/meta.yaml b/recipes/bioconductor-epivizrchart/meta.yaml index 6cc148b0b6716..f66a753816ffa 100644 --- a/recipes/bioconductor-epivizrchart/meta.yaml +++ b/recipes/bioconductor-epivizrchart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "epivizrChart" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: baf134b11bf7e3f3957f76f35091b317 + md5: 076ebf7f9141cb71df0867f480ff960c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epivizrchart", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - r-base - r-htmltools - r-rjson run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - r-base - r-htmltools - r-rjson diff --git a/recipes/bioconductor-epivizrdata/meta.yaml b/recipes/bioconductor-epivizrdata/meta.yaml index 67c2c1574e7d4..412409f2896f3 100644 --- a/recipes/bioconductor-epivizrdata/meta.yaml +++ b/recipes/bioconductor-epivizrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "epivizrData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d8c2385e4c9f9a37c1f8314bf817a2f + md5: aa9cf42fdbb0ad293964de33fc62e27a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epivizrdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-epivizrserver/meta.yaml b/recipes/bioconductor-epivizrserver/meta.yaml index 52893be238b8b..7b384efc68bd6 100644 --- a/recipes/bioconductor-epivizrserver/meta.yaml +++ b/recipes/bioconductor-epivizrserver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "epivizrServer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d78bdc9e29069b92d87d127c49608c8 + md5: 4bc67106aa169616232174c422fb6e2b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epivizrserver", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-epivizrstandalone/meta.yaml b/recipes/bioconductor-epivizrstandalone/meta.yaml index 71477decd623c..fba6c056e868e 100644 --- a/recipes/bioconductor-epivizrstandalone/meta.yaml +++ b/recipes/bioconductor-epivizrstandalone/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "epivizrStandalone" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1948048074aed3f5221e8cdaa4ea1fbb + md5: aa34f18a7a4f4340f2e4a0ecc46af0a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epivizrstandalone", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-epivizr >=2.30.0,<2.31.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-epivizr >=2.32.0,<2.33.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-git2r run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-epivizr >=2.30.0,<2.31.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-epivizr >=2.32.0,<2.33.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-git2r test: diff --git a/recipes/bioconductor-erccdashboard/meta.yaml b/recipes/bioconductor-erccdashboard/meta.yaml index fb60c3517521d..f0d714a1af896 100644 --- a/recipes/bioconductor-erccdashboard/meta.yaml +++ b/recipes/bioconductor-erccdashboard/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "erccdashboard" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b74db4e015a32aea7a4a5b691d79b6d3 + md5: fa211269012a775dcdc114f3eb0282bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-erccdashboard", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.1.0' - r-gplots @@ -36,9 +37,9 @@ requirements: - r-scales - r-stringr run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.1.0' - r-gplots diff --git a/recipes/bioconductor-erma/meta.yaml b/recipes/bioconductor-erma/meta.yaml index a57e31ec5e0c0..18cea096ef670 100644 --- a/recipes/bioconductor-erma/meta.yaml +++ b/recipes/bioconductor-erma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "erma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5ec82c451352c22d4b909caab6002683 + md5: 38679c439fbeb31db81c90c90ba4f79d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-erma", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-shiny run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-shiny diff --git a/recipes/bioconductor-erssa/meta.yaml b/recipes/bioconductor-erssa/meta.yaml index 047e3402fbd51..aa706e6ec05ae 100644 --- a/recipes/bioconductor-erssa/meta.yaml +++ b/recipes/bioconductor-erssa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ERSSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1388c9ab46a0d5d765a0a8871bcd5387 + md5: 160e82bdb1b7af9f6452d4767a7e8a1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-erssa", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - 'r-ggplot2 >=3.0.0' - 'r-plyr >=1.8.4' - 'r-rcolorbrewer >=1.1-2' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - 'r-ggplot2 >=3.0.0' - 'r-plyr >=1.8.4' diff --git a/recipes/bioconductor-esatac/meta.yaml b/recipes/bioconductor-esatac/meta.yaml index 8ae1df64adff7..6959b5764686a 100644 --- a/recipes/bioconductor-esatac/meta.yaml +++ b/recipes/bioconductor-esatac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "esATAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4672f9eba4a66406890a4cfdf9f552dd + md5: 6ea63da6e75365243df878d55d6b39f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-esatac", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat, webshot, prettydoc # SystemRequirements: C++11 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-pipeframe >=1.16.0,<1.17.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-pipeframe >=1.18.0,<1.19.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-biocmanager - r-corrplot @@ -57,26 +58,26 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-pipeframe >=1.16.0,<1.17.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-pipeframe >=1.18.0,<1.19.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-biocmanager - r-corrplot diff --git a/recipes/bioconductor-escape/meta.yaml b/recipes/bioconductor-escape/meta.yaml index 48b004148c4b3..86ec8bba522ff 100644 --- a/recipes/bioconductor-escape/meta.yaml +++ b/recipes/bioconductor-escape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "escape" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 52dc55acb0a04f9030f1aae725e57af8 + md5: e3dc22e072190e21938689fc0f3ab112 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-escape", max_pin="x.x") }}' noarch: generic # Suggests: Seurat, SeuratObject, knitr, rmarkdown, markdown, BiocStyle, testthat, dittoSeq (>= 1.1.2) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-ucell >=2.4.0,<2.5.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-ucell >=2.6.0,<2.7.0' - r-base - r-broom - r-data.table @@ -41,13 +42,13 @@ requirements: - r-rlang - r-stringr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-ucell >=2.4.0,<2.5.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-ucell >=2.6.0,<2.7.0' - r-base - r-broom - r-data.table diff --git a/recipes/bioconductor-escher/meta.yaml b/recipes/bioconductor-escher/meta.yaml index 758e49c0a1c5d..e8649e5391cf2 100644 --- a/recipes/bioconductor-escher/meta.yaml +++ b/recipes/bioconductor-escher/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "escheR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df1ed86f7963992371c853e9b05284b7 + md5: ed2586d2e42f89db85790889863421b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-escher", max_pin="x.x") }}' noarch: generic -# Suggests: STexampleData, knitr, rmarkdown, BiocStyle +# Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat requirements: host: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spatiallibd >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-rlang run: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spatiallibd >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-rlang diff --git a/recipes/bioconductor-esetvis/meta.yaml b/recipes/bioconductor-esetvis/meta.yaml index 119e0e8661341..7ce7e35074dd0 100644 --- a/recipes/bioconductor-esetvis/meta.yaml +++ b/recipes/bioconductor-esetvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.0" %} {% set name = "esetVis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6f18d6b3474a5018f138bafe1324542 + md5: 2edbf6b1764a5ebfdcefaf7a8b6c247d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-esetvis", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mlp >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mlp >=1.50.0,<1.51.0' - r-base - r-hexbin - r-mass - r-mpm - r-rtsne run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mlp >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mlp >=1.50.0,<1.51.0' - r-base - r-hexbin - r-mass diff --git a/recipes/bioconductor-estrogen/meta.yaml b/recipes/bioconductor-estrogen/meta.yaml index c188aec2e2eb2..cd11513496376 100644 --- a/recipes/bioconductor-estrogen/meta.yaml +++ b/recipes/bioconductor-estrogen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "estrogen" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c7f687b7e46c1e224e9008143926f12e + md5: 41a3321678d1a9cb057e979d675f0cee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-estrogen", max_pin="x.x") }}' noarch: generic -# Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr +# Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr, genefilter requirements: host: - r-base run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-estrogen/post-link.sh b/recipes/bioconductor-estrogen/post-link.sh index 422fccdd666d7..92a917b9ef078 100644 --- a/recipes/bioconductor-estrogen/post-link.sh +++ b/recipes/bioconductor-estrogen/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "estrogen-1.46.0" +installBiocDataPackage.sh "estrogen-1.48.0" diff --git a/recipes/bioconductor-etec16s/meta.yaml b/recipes/bioconductor-etec16s/meta.yaml index bfe9834af0a45..e4180b711643d 100644 --- a/recipes/bioconductor-etec16s/meta.yaml +++ b/recipes/bioconductor-etec16s/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "etec16s" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b2540d5e5287458a7fbec76b5656d3c6 + md5: 86353b5f2f77274b883120dc043f8ce5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-etec16s", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-etec16s/post-link.sh b/recipes/bioconductor-etec16s/post-link.sh index d48158fae1247..7ab2be62ab9c5 100644 --- a/recipes/bioconductor-etec16s/post-link.sh +++ b/recipes/bioconductor-etec16s/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "etec16s-1.28.0" +installBiocDataPackage.sh "etec16s-1.30.0" diff --git a/recipes/bioconductor-eudysbiome/meta.yaml b/recipes/bioconductor-eudysbiome/meta.yaml index bfc0c4700fa42..c4d7c109e3260 100644 --- a/recipes/bioconductor-eudysbiome/meta.yaml +++ b/recipes/bioconductor-eudysbiome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "eudysbiome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 491deafab7090ce11e0eaac79537dc15 + md5: 76023a8328d58f7d5b783679a08c7ea8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eudysbiome", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-plyr - r-r.utils run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-plyr - r-r.utils diff --git a/recipes/bioconductor-eupathdb/meta.yaml b/recipes/bioconductor-eupathdb/meta.yaml index 0a9428b37d14f..c302fc335cb08 100644 --- a/recipes/bioconductor-eupathdb/meta.yaml +++ b/recipes/bioconductor-eupathdb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "EuPathDB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,33 +13,34 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1451c3ab6c224d9a4cfbdf27dc5c2680 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eupathdb", max_pin="x.x") }}' noarch: generic # Suggests: dplyr, knitr, BiocStyle, rmarkdown, jsonlite requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-biocmanager run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-biocmanager - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-evaluomer/meta.yaml b/recipes/bioconductor-evaluomer/meta.yaml index 66d0c27267921..d60206052a04d 100644 --- a/recipes/bioconductor-evaluomer/meta.yaml +++ b/recipes/bioconductor-evaluomer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "evaluomeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e64f5dc7c769522b12dff9613a3c0e65 + md5: 2cee372b9bb28916d6ab543be8eca9b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-evaluomer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, magrittr requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-class - 'r-cluster >=2.0.9' @@ -41,8 +42,8 @@ requirements: - r-rdpack - r-reshape2 run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-class - 'r-cluster >=2.0.9' diff --git a/recipes/bioconductor-eventpointer/meta.yaml b/recipes/bioconductor-eventpointer/meta.yaml index 2077e89eacca9..5bf12d43a71a1 100644 --- a/recipes/bioconductor-eventpointer/meta.yaml +++ b/recipes/bioconductor-eventpointer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "EventPointer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f97dd94868c28a966269c717e4cfccff + md5: d25561e0288a54ed43c823b371941972 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eventpointer", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sgseq >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sgseq >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-abind - r-base - r-cobs @@ -57,23 +58,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sgseq >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sgseq >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-abind - r-base - r-cobs diff --git a/recipes/bioconductor-ewce/meta.yaml b/recipes/bioconductor-ewce/meta.yaml index e63814309ad73..f085f9b01d230 100644 --- a/recipes/bioconductor-ewce/meta.yaml +++ b/recipes/bioconductor-ewce/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.2" %} +{% set version = "1.10.2" %} {% set name = "EWCE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c8b7db118292d3cbd6c01c1fd6e15d7 + md5: b00b3feb36956603c46e6de1f03e9c09 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ewce", max_pin="x.x") }}' noarch: generic # Suggests: rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ewcedata >=1.8.0,<1.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-orthogene >=1.6.0,<1.7.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ewcedata >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-orthogene >=1.8.0,<1.9.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -38,13 +39,13 @@ requirements: - 'r-rnomni >=1.0' - r-stringr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ewcedata >=1.8.0,<1.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-orthogene >=1.6.0,<1.7.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ewcedata >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-orthogene >=1.8.0,<1.9.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-ewcedata/meta.yaml b/recipes/bioconductor-ewcedata/meta.yaml index fe81c8bb10775..e46f489867173 100644 --- a/recipes/bioconductor-ewcedata/meta.yaml +++ b/recipes/bioconductor-ewcedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ewceData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3107bac6cd0fb07a4cba3ad59cabb665 + md5: d2ee91be35e2c5433ce16e94717c50e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ewcedata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ewcedata/post-link.sh b/recipes/bioconductor-ewcedata/post-link.sh index c5cd6c05609bd..16e7f83675a3c 100644 --- a/recipes/bioconductor-ewcedata/post-link.sh +++ b/recipes/bioconductor-ewcedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ewcedata-1.8.0" +installBiocDataPackage.sh "ewcedata-1.10.0" diff --git a/recipes/bioconductor-excluderanges/meta.yaml b/recipes/bioconductor-excluderanges/meta.yaml index 29c4ecd94fd1e..01959646c16da 100644 --- a/recipes/bioconductor-excluderanges/meta.yaml +++ b/recipes/bioconductor-excluderanges/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.8" %} {% set name = "excluderanges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2ec19df8a51df1900a339f7f505cd5fa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-excluderanges", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RefManageR, rmarkdown, ggridges, httr, readr, pheatmap, rtracklayer, AnnotationHub requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-excluster/meta.yaml b/recipes/bioconductor-excluster/meta.yaml index e77fe8a171463..d71771d5759d4 100644 --- a/recipes/bioconductor-excluster/meta.yaml +++ b/recipes/bioconductor-excluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ExCluster" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8cf0ecfe19ff1a9a9a461ff9d9738cfb + md5: 2f60d612945a7f431831ce690d01d042 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-excluster", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-matrixstats run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-matrixstats test: diff --git a/recipes/bioconductor-eximir/meta.yaml b/recipes/bioconductor-eximir/meta.yaml index a78f2e6588bfa..5aea5abeb29f4 100644 --- a/recipes/bioconductor-eximir/meta.yaml +++ b/recipes/bioconductor-eximir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "ExiMiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5339767954f9bdc5eb05a5e62529d80f + md5: a68c067ab91567287317a760f9e4c738 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-eximir", max_pin="x.x") }}' noarch: generic # Suggests: mirna10cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-exomecopy/meta.yaml b/recipes/bioconductor-exomecopy/meta.yaml index f6a9d1547655d..f7971f0ae0e21 100644 --- a/recipes/bioconductor-exomecopy/meta.yaml +++ b/recipes/bioconductor-exomecopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "exomeCopy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 589525e05086f9d2387c287beb8c35e7 + md5: 068f1f0cb675297a1b7940330fae0cbe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-exomecopy", max_pin="x.x") }}' # Suggests: Biostrings requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-exomepeak2/meta.yaml b/recipes/bioconductor-exomepeak2/meta.yaml index 7c62eee295e28..c86fb924cebde 100644 --- a/recipes/bioconductor-exomepeak2/meta.yaml +++ b/recipes/bioconductor-exomepeak2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.3" %} {% set name = "exomePeak2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,50 +11,51 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0281b3cf39ab0e2dd661c6b95b899a9a + md5: 078608012fb7c2dc3a60d02a4e2fcbbc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-exomepeak2", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown +# Suggests: knitr, rmarkdown, BiocManager, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-magrittr - r-mclust - r-speedglm run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-magrittr @@ -67,5 +68,5 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Peak Calling and differential analysis for MeRIP-Seq' - description: 'exomePeak2 provides peak detection and differential methylation for Methylated RNA Immunoprecipitation Sequencing (MeRIP-Seq) data. MeRIP-Seq is a commonly applied sequencing assay that measures the location and abundance of RNA modification sites under specific cellular conditions. In practice, the technique is sensitive to PCR amplification biases commonly found in NGS data. In addition, the efficiency of immunoprecipitation often varies between different IP samples. exomePeak2 can perform peak calling and differential analysis independent of GC content bias and IP efficiency changes.' + description: 'exomePeak2 provides peak detection and differential methylation for Methylated RNA Immunoprecipitation Sequencing (MeRIP-Seq) data. MeRIP-Seq is a commonly applied sequencing assay that measures the location and abundance of RNA modification sites under specific cellular conditions. The technique is sensitive to PCR amplification biases commonly found in NGS data. In addition, the efficiency of immunoprecipitation often varies between different IP samples. exomePeak2 can perform peak calling and differential analysis independent of GC content bias and IP efficiency changes.' diff --git a/recipes/bioconductor-experimenthub/meta.yaml b/recipes/bioconductor-experimenthub/meta.yaml index 09bc1a50ca50b..931b307d36148 100644 --- a/recipes/bioconductor-experimenthub/meta.yaml +++ b/recipes/bioconductor-experimenthub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "ExperimentHub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7f87d5d1ab426cae3083029b6d345f5 + md5: bea896eadb8eb999e48d1cf5974dfe9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-experimenthub", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, BiocStyle, rmarkdown, HubPub +# Suggests: knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-rappdirs run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-rappdirs diff --git a/recipes/bioconductor-experimenthubdata/meta.yaml b/recipes/bioconductor-experimenthubdata/meta.yaml index 48f5e4a1939f5..67fe9eb4addd6 100644 --- a/recipes/bioconductor-experimenthubdata/meta.yaml +++ b/recipes/bioconductor-experimenthubdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ExperimentHubData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55726da02a14f0b5b2805153bbb0fbe7 + md5: 9e36d1a7958213cce85feccfd46fd7d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-experimenthubdata", max_pin="x.x") }}' noarch: generic # Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub requirements: host: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-curl - r-dbi - r-httr run: - - 'bioconductor-annotationhubdata >=1.30.0,<1.31.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-curl diff --git a/recipes/bioconductor-experimentsubset/meta.yaml b/recipes/bioconductor-experimentsubset/meta.yaml index 747fd0314fe40..b3c0f29e6a81f 100644 --- a/recipes/bioconductor-experimentsubset/meta.yaml +++ b/recipes/bioconductor-experimentsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ExperimentSubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae8e83b163d8d2394af49d2c3c2a333c + md5: fc52b3d67f7f9641a3851f987af7cdee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-experimentsubset", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-matrix run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-exploremodelmatrix/meta.yaml b/recipes/bioconductor-exploremodelmatrix/meta.yaml index 73eb8daa5103a..810de26338c61 100644 --- a/recipes/bioconductor-exploremodelmatrix/meta.yaml +++ b/recipes/bioconductor-exploremodelmatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ExploreModelMatrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5317164fd3206c56c7e566b8a7ef102 + md5: 86f96045b0ae6877428f28466b113097 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-exploremodelmatrix", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-dplyr @@ -38,8 +39,8 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-dplyr diff --git a/recipes/bioconductor-expressionatlas/meta.yaml b/recipes/bioconductor-expressionatlas/meta.yaml index c61896e634c13..07e7c2df9194b 100644 --- a/recipes/bioconductor-expressionatlas/meta.yaml +++ b/recipes/bioconductor-expressionatlas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ExpressionAtlas" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7abccba2bf2c9ebfd1ed02b907fb05b5 + md5: eb11568a0a2a81e1bf636eaa24e45906 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-expressionatlas", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-httr - r-jsonlite @@ -33,11 +34,11 @@ requirements: - r-xml - r-xml2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-extrachips/build_failure.osx-64.yaml b/recipes/bioconductor-extrachips/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4061ce0faf29f --- /dev/null +++ b/recipes/bioconductor-extrachips/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: cd6c654642b58a1ae021676e3516975dbc01a6ba6e27b668bc181e21ad457739 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + /opt/mambaforge/envs/bioconda/conda-bld/work + Test: + /opt/mambaforge/envs/bioconda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + Build: + source activate /opt/mambaforge/envs/bioconda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-ggside >=0.2.2 + - r-glue + - libblas 3.9.* *netlib + - r-ggplot2 >=3.4.0 + - bioconductor-interactionset >=1.30.0,<1.31.0 + - r-dplyr >=1.1.1 + - liblapack 3.9.* *netlib + - bioconductor-enrichedheatmap >=1.32.0,<1.33.0 + - bioconductor-limma >=3.58.0,<3.59.0 + - bioconductor-rtracklayer >=1.62.0,<1.63.0 + - r-tidyr + - r-ggforce + - bioconductor-genomicranges >=1.54.0,<1.55.0 + - bioconductor-genomicinteractions >=1.36.0,<1.37.0 + - r-stringr + - r-scales + - r-tidyselect + - r-ggrepel + - r-base 4.3.* + - r-rlang + - bioconductor-iranges >=2.36.0,<2.37.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - bioconductor-edger >=4.0.0,<4.1.0 + - r-vctrs + - r-broom + - r-complexupset + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - bioconductor-genomeinfodb >=1.38.0,<1.39.0 + - r-matrixstats + - r-patchwork + - bioconductor-csaw >=1.36.0,<1.37.0 + - r-forcats + - r-venndiagram + - bioconductor-biocio >=1.12.0,<1.13.0 + - bioconductor-gviz >=1.46.0,<1.47.0 + - r-rcolorbrewer + - r-tibble + - bioconductor-rsamtools >=2.18.0,<2.19.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-enrichedheatmap >=1.32.0,<1.33.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-enrichedheatmap[version='>=1.32.0,<1.33.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-extrachips/meta.yaml b/recipes/bioconductor-extrachips/meta.yaml index 6a323e02d4b8a..678c82cbb0c55 100644 --- a/recipes/bioconductor-extrachips/meta.yaml +++ b/recipes/bioconductor-extrachips/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.5" %} +{% set version = "1.6.0" %} {% set name = "extraChIPs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c26b5ce1303129efe33efebc2fa60dd5 + md5: 462672c12f16f912b7e3d4b30a07162f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-extrachips", max_pin="x.x") }}' # Suggests: BiocStyle, covr, cqn, harmonicmeanp, here, knitr, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse requirements: host: - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichedheatmap >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-complexupset - - 'r-dplyr >=1.1.0' + - 'r-dplyr >=1.1.1' - r-forcats - r-ggforce - 'r-ggplot2 >=3.4.0' - r-ggrepel - - r-ggside + - 'r-ggside >=0.2.2' - r-glue - r-matrixstats - r-patchwork @@ -60,31 +61,31 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichedheatmap >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-complexupset - - 'r-dplyr >=1.1.0' + - 'r-dplyr >=1.1.1' - r-forcats - r-ggforce - 'r-ggplot2 >=3.4.0' - r-ggrepel - - r-ggside + - 'r-ggside >=0.2.2' - r-glue - r-matrixstats - r-patchwork diff --git a/recipes/bioconductor-faahko/meta.yaml b/recipes/bioconductor-faahko/meta.yaml index 5b4d091c85cb5..16959e9059ddd 100644 --- a/recipes/bioconductor-faahko/meta.yaml +++ b/recipes/bioconductor-faahko/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "faahKO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29697c16b4e90b21fd8515dfdfea7fde + md5: 3525f525973323d33955a68ca38b5cd7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-faahko", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-faahko/post-link.sh b/recipes/bioconductor-faahko/post-link.sh index 091dc51972ffa..8d50d83771269 100644 --- a/recipes/bioconductor-faahko/post-link.sh +++ b/recipes/bioconductor-faahko/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "faahko-1.40.0" +installBiocDataPackage.sh "faahko-1.42.0" diff --git a/recipes/bioconductor-fabia/meta.yaml b/recipes/bioconductor-fabia/meta.yaml index 2371256f1c4b2..aadcaa307b6c8 100644 --- a/recipes/bioconductor-fabia/meta.yaml +++ b/recipes/bioconductor-fabia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "fabia" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9920fe1cb40cc35e9c53a0b15e4f56e5 + md5: 9d336b3c9a97aca0a6b062ec137f5566 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fabia", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-fabiadata/meta.yaml b/recipes/bioconductor-fabiadata/meta.yaml index 343950c36eaed..8de5e015973e7 100644 --- a/recipes/bioconductor-fabiadata/meta.yaml +++ b/recipes/bioconductor-fabiadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "fabiaData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 970fc1894222fe7eac67b8c94d9a2eab + md5: 7fd64db4d15610a66c609e60624bbff9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fabiadata", max_pin="x.x") }}' noarch: generic # Suggests: fabia requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fabiadata/post-link.sh b/recipes/bioconductor-fabiadata/post-link.sh index 77a1795a9f905..561c4ec71758f 100644 --- a/recipes/bioconductor-fabiadata/post-link.sh +++ b/recipes/bioconductor-fabiadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fabiadata-1.38.0" +installBiocDataPackage.sh "fabiadata-1.40.0" diff --git a/recipes/bioconductor-factdesign/meta.yaml b/recipes/bioconductor-factdesign/meta.yaml index df24a022421cc..695bb48686cab 100644 --- a/recipes/bioconductor-factdesign/meta.yaml +++ b/recipes/bioconductor-factdesign/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "factDesign" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb6bfbecf160000664037c0bf51f9953 + md5: 774d444f3227bbac6bc13e48d3974b20 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-factdesign", max_pin="x.x") }}' noarch: generic # Suggests: affy, genefilter, multtest requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-factr/meta.yaml b/recipes/bioconductor-factr/meta.yaml index 98f77eee10aa2..a9c19a5db30aa 100644 --- a/recipes/bioconductor-factr/meta.yaml +++ b/recipes/bioconductor-factr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "factR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,64 +11,65 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4494ae41081395fd86e88600af5d4ada + md5: 55b088d84e382a7068b40062151e4bec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-factr", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub (>= 2.22), BSgenome (>= 1.58), BSgenome.Mmusculus.UCSC.mm10, testthat, knitr, rmarkdown, markdown, zeallot, rmdformats, bio3d (>= 2.4), signalHsmm (>= 1.5), tidyverse (>= 1.3), covr, patchwork requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-drawproteins >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-wiggleplotr >=1.24.0,<1.25.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-drawproteins >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-wiggleplotr >=1.26.0,<1.27.0' - r-base - - r-crayon + - 'r-crayon >=1.5' - 'r-data.table >=1.14' - - 'r-dplyr >=1.0' - - 'r-ggplot2 >=3.3' - - 'r-pbapply >=1.5' - - 'r-purrr >=0.3' + - 'r-dplyr >=1.1' + - 'r-ggplot2 >=3.4' + - 'r-pbapply >=1.7' + - 'r-purrr >=1.0' - 'r-rcurl >=1.98' - - 'r-rlang >=1.0' - - 'r-stringr >=1.4' - - 'r-tibble >=3.1' - - 'r-tidyr >=1.1' + - 'r-rlang >=1.1' + - 'r-stringr >=1.5' + - 'r-tibble >=3.2' + - 'r-tidyr >=1.3' - 'r-xml >=3.99' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-drawproteins >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-wiggleplotr >=1.24.0,<1.25.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-drawproteins >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-wiggleplotr >=1.26.0,<1.27.0' - r-base - - r-crayon + - 'r-crayon >=1.5' - 'r-data.table >=1.14' - - 'r-dplyr >=1.0' - - 'r-ggplot2 >=3.3' - - 'r-pbapply >=1.5' - - 'r-purrr >=0.3' + - 'r-dplyr >=1.1' + - 'r-ggplot2 >=3.4' + - 'r-pbapply >=1.7' + - 'r-purrr >=1.0' - 'r-rcurl >=1.98' - - 'r-rlang >=1.0' - - 'r-stringr >=1.4' - - 'r-tibble >=3.1' - - 'r-tidyr >=1.1' + - 'r-rlang >=1.1' + - 'r-stringr >=1.5' + - 'r-tibble >=3.2' + - 'r-tidyr >=1.3' - 'r-xml >=3.99' test: commands: diff --git a/recipes/bioconductor-famagg/meta.yaml b/recipes/bioconductor-famagg/meta.yaml index d524237b721d7..b68b0c8f34645 100644 --- a/recipes/bioconductor-famagg/meta.yaml +++ b/recipes/bioconductor-famagg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "FamAgg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62218f2a42b754c17175ce542c0850fc + md5: 0169ebe9c05d0b540946e2d111fe6437 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-famagg", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RUnit, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-gap >=1.1-17' - r-igraph @@ -29,7 +30,7 @@ requirements: - r-matrix - r-survey run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - 'r-gap >=1.1-17' - r-igraph diff --git a/recipes/bioconductor-famat/meta.yaml b/recipes/bioconductor-famat/meta.yaml index ccdc6dda84ad4..425dee5ad0e88 100644 --- a/recipes/bioconductor-famat/meta.yaml +++ b/recipes/bioconductor-famat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "famat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e59deb7c41a3ecec355312a5db76f4cf + md5: 12883ce4989ed35758a8902493e2bb07 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-famat", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, BiocManager requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' - r-base - r-biasedurn - r-dplyr @@ -42,12 +43,12 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' - r-base - r-biasedurn - r-dplyr diff --git a/recipes/bioconductor-fantom3and4cage/meta.yaml b/recipes/bioconductor-fantom3and4cage/meta.yaml index ffd1135dc5f77..bffc9cb885992 100644 --- a/recipes/bioconductor-fantom3and4cage/meta.yaml +++ b/recipes/bioconductor-fantom3and4cage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "FANTOM3and4CAGE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 049d0b3978f16771bd7e48aa80e8fb93 + md5: 5d964e7a085d6a7b00e2b2215b765861 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fantom3and4cage", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fantom3and4cage/post-link.sh b/recipes/bioconductor-fantom3and4cage/post-link.sh index 7ad71e3469da9..53f3c97e37d5f 100644 --- a/recipes/bioconductor-fantom3and4cage/post-link.sh +++ b/recipes/bioconductor-fantom3and4cage/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fantom3and4cage-1.36.0" +installBiocDataPackage.sh "fantom3and4cage-1.38.0" diff --git a/recipes/bioconductor-fastliquidassociation/meta.yaml b/recipes/bioconductor-fastliquidassociation/meta.yaml index cd2ac541108b7..c8a5f515cdf33 100644 --- a/recipes/bioconductor-fastliquidassociation/meta.yaml +++ b/recipes/bioconductor-fastliquidassociation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "fastLiquidAssociation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19cd90ee83e1fe666279d7656fb9cb78 + md5: b57e0af4700d6a6872d88ca0d2eda5d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fastliquidassociation", max_pin="x.x") }}' noarch: generic # Suggests: GOstats, yeastCC, org.Sc.sgd.db requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-liquidassociation >=1.54.0,<1.55.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-liquidassociation >=1.56.0,<1.57.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-doparallel - r-hmisc - r-wgcna run: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-liquidassociation >=1.54.0,<1.55.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-liquidassociation >=1.56.0,<1.57.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-doparallel - r-hmisc diff --git a/recipes/bioconductor-fastqcleaner/meta.yaml b/recipes/bioconductor-fastqcleaner/meta.yaml index ed4e50ec8a0b8..d19fbfc3143e2 100644 --- a/recipes/bioconductor-fastqcleaner/meta.yaml +++ b/recipes/bioconductor-fastqcleaner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "FastqCleaner" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f5a185e44c2e087d9cd502343839a20 + md5: bace77f4e33bd7fe58cbbadaefd896d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fastqcleaner", max_pin="x.x") }}' # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dt - r-htmltools @@ -33,10 +34,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dt - r-htmltools diff --git a/recipes/bioconductor-fastreer/meta.yaml b/recipes/bioconductor-fastreer/meta.yaml index 43941e0d8973d..cf391745726da 100644 --- a/recipes/bioconductor-fastreer/meta.yaml +++ b/recipes/bioconductor-fastreer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "fastreeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8992e9982a96e461d83174b1e401637c + md5: e2b7164aeaa305f819536d9b85e4de12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fastreer", max_pin="x.x") }}' noarch: generic # Suggests: BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0) # SystemRequirements: Java (>= 8) diff --git a/recipes/bioconductor-fastseg/meta.yaml b/recipes/bioconductor-fastseg/meta.yaml index 868ab493238d2..2a67786842c05 100644 --- a/recipes/bioconductor-fastseg/meta.yaml +++ b/recipes/bioconductor-fastseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "fastseg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 742f51d390453aca568b16001d3d674f + md5: ca8ead071a9b881b19dea7b71e0e73b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: DNAcopy, oligo + run_exports: '{{ pin_subpackage("bioconductor-fastseg", max_pin="x.x") }}' +# Suggests: DNAcopy, oligo, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-fccac/meta.yaml b/recipes/bioconductor-fccac/meta.yaml index 4f60ddf7d6845..e2b8cff1c58c2 100644 --- a/recipes/bioconductor-fccac/meta.yaml +++ b/recipes/bioconductor-fccac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "fCCAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 78d5504a05fdc9fe1b993a0244a06ace + md5: f4152105666120b6529f55983c4e2aa3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fccac", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda - r-ggplot2 - r-rcolorbrewer run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda - r-ggplot2 diff --git a/recipes/bioconductor-fci/meta.yaml b/recipes/bioconductor-fci/meta.yaml index 22d517c7944cd..de6bb8839434c 100644 --- a/recipes/bioconductor-fci/meta.yaml +++ b/recipes/bioconductor-fci/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "fCI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c5f500670ac386e7cb2318b3f93891b + md5: 5a6ec7dcf6303ef44018924283b87586 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fci", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-fcscan/meta.yaml b/recipes/bioconductor-fcscan/meta.yaml index 57a171acf4588..bcf4f078fb8c9 100644 --- a/recipes/bioconductor-fcscan/meta.yaml +++ b/recipes/bioconductor-fcscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "fcScan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 497ff22cdc8e837d2a49fa931c6aa162 + md5: a23eab38b0106852ecca920f1f1db0bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fcscan", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-doparallel - r-foreach - r-plyr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml b/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml index 9c850222c2153..3a5d0aac46574 100644 --- a/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "FDb.FANTOM4.promoters.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,25 +13,26 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 99a610eb895470e3d945acc5cfb3ebe6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.fantom4.promoters.hg19", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer, matrixStats requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml index fe8afec3ab01b..66990d70a99d3 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml +++ b/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.2.0" %} {% set name = "FDb.InfiniumMethylation.hg18" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,28 +13,29 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 95ceab50d0a7c3d417cee12fbe3defb3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.infiniummethylation.hg18", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml index 9a89db96412bf..3f4a764d09a61 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.2.0" %} {% set name = "FDb.InfiniumMethylation.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,29 +13,30 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b8b1abc599b9556b9fe9c6e824cb2697 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.infiniummethylation.hg19", max_pin="x.x") }}' noarch: generic # Suggests: FDb.UCSC.snp135common.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml index f54c865e42788..76eab4357415e 100644 --- a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "FDb.UCSC.snp135common.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0cdca5fa595bb69464016ceb97635f78 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.ucsc.snp135common.hg19", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20111119 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml index a1ff83de10f2b..0fd1755b911dc 100644 --- a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "FDb.UCSC.snp137common.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dac83f2d2f9ea9f033e50beac5c44838 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.ucsc.snp137common.hg19", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml b/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml index f007f80703caa..c95a592d717ad 100644 --- a/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "FDb.UCSC.tRNAs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 77bfdadd4d9f995a72b001e4e41792fa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdb.ucsc.trnas", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fdrame/meta.yaml b/recipes/bioconductor-fdrame/meta.yaml index 03ae4ceea9649..37166d2fd75f6 100644 --- a/recipes/bioconductor-fdrame/meta.yaml +++ b/recipes/bioconductor-fdrame/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "fdrame" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4ed3cd1054bb77ea566bc89e8fe00285 + md5: d7fafba89f784f421a43b4b4d9a10000 build: number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fdrame", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-feast/meta.yaml b/recipes/bioconductor-feast/meta.yaml index 68598a4aa23b0..1ba80d9f1fc73 100644 --- a/recipes/bioconductor-feast/meta.yaml +++ b/recipes/bioconductor-feast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "FEAST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1337d86557f7c377f5a80484bff003f4 + md5: 5b32fdf869bc97368c62f50ccd8fe9f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-feast", max_pin="x.x") }}' # Suggests: rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-sc3 >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tscan >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-sc3 >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tscan >=1.40.0,<1.41.0' - r-base - r-irlba - r-matrixstats @@ -32,11 +33,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-sc3 >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tscan >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-sc3 >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tscan >=1.40.0,<1.41.0' - r-base - r-irlba - r-matrixstats diff --git a/recipes/bioconductor-featseekr/meta.yaml b/recipes/bioconductor-featseekr/meta.yaml index cd2969666b135..b13b10cada5f1 100644 --- a/recipes/bioconductor-featseekr/meta.yaml +++ b/recipes/bioconductor-featseekr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "FeatSeekR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14bd43f9ea1a98d7c049f34d20c1a66d + md5: 9792a703c1ec0b4a58c759274c2cb571 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-featseekr", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, DmelSGI, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass - r-pheatmap - r-pracma run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass - r-pheatmap diff --git a/recipes/bioconductor-fedup/meta.yaml b/recipes/bioconductor-fedup/meta.yaml index 9fadc2a2d359a..ab157eb4d27ac 100644 --- a/recipes/bioconductor-fedup/meta.yaml +++ b/recipes/bioconductor-fedup/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "fedup" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1264d858aa93e0c49dd71e11c6215848 + md5: a5ac34da42c1a460ab50e307c73f8116 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fedup", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr requirements: host: - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-data.table - r-dplyr @@ -32,7 +33,7 @@ requirements: - r-rcolorbrewer - r-tibble run: - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-fella/meta.yaml b/recipes/bioconductor-fella/meta.yaml index c282fc3e1af17..0b00c88027e81 100644 --- a/recipes/bioconductor-fella/meta.yaml +++ b/recipes/bioconductor-fella/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "FELLA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b1bee53b4cef474ce91c2920b8ca4dd + md5: 106f8558197df891cfb6e28e406363e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fella", max_pin="x.x") }}' noarch: generic # Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim requirements: host: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - r-base - r-igraph - r-matrix - r-plyr run: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - r-base - r-igraph - r-matrix diff --git a/recipes/bioconductor-fenr/build.sh b/recipes/bioconductor-fenr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fenr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fenr/meta.yaml b/recipes/bioconductor-fenr/meta.yaml new file mode 100644 index 0000000000000..1c2c8d0c43996 --- /dev/null +++ b/recipes/bioconductor-fenr/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.0" %} +{% set name = "fenr" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f908fa38bd91672d7d0567d6232d2214 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fenr", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, testthat, knitr, rmarkdown, topGO, org.Hs.eg.db +requirements: + host: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - r-assertthat + - r-base + - r-dplyr + - r-ggplot2 + - r-httr + - r-jsonlite + - r-progress + - r-purrr + - r-readr + - r-rlang + - r-shiny + - r-stringr + - r-tibble + - r-tidyr + - r-tidyselect + - r-xml + run: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - r-assertthat + - r-base + - r-dplyr + - r-ggplot2 + - r-httr + - r-jsonlite + - r-progress + - r-purrr + - r-readr + - r-rlang + - r-shiny + - r-stringr + - r-tibble + - r-tidyr + - r-tidyselect + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Fast functional enrichment for interactive applications' + description: 'Perform fast functional enrichment on feature lists (like genes or proteins) using the hypergeometric distribution. Tailored for speed, this package is ideal for interactive platforms such as Shiny. It supports the retrieval of functional data from sources like GO, KEGG, Reactome, and WikiPathways. By downloading and preparing data first, it allows for rapid successive tests on various feature selections without the need for repetitive, time-consuming preparatory steps typical of other packages.' + license_file: LICENSE + diff --git a/recipes/bioconductor-ffpe/meta.yaml b/recipes/bioconductor-ffpe/meta.yaml index f9e56c7cab696..0a41ce9b5dabf 100644 --- a/recipes/bioconductor-ffpe/meta.yaml +++ b/recipes/bioconductor-ffpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "ffpe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2cb6393fc9ed1d1286a10016f95d8b56 + md5: c2a3dbd53e85caf82d7c8f91a8277454 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ffpe", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, ffpeExampleData requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' - r-base - r-sfsmisc - r-ttr run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' - r-base - r-sfsmisc - r-ttr diff --git a/recipes/bioconductor-ffpeexampledata/meta.yaml b/recipes/bioconductor-ffpeexampledata/meta.yaml index 5affb00b25589..e47fc10975fe9 100644 --- a/recipes/bioconductor-ffpeexampledata/meta.yaml +++ b/recipes/bioconductor-ffpeexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ffpeExampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5b4c1bcd2467b0b82973b2e70243ef0 + md5: 6ea474bdf448ff6026ec4f1f376b7d69 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ffpeexampledata", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, affy requirements: host: - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ffpeexampledata/post-link.sh b/recipes/bioconductor-ffpeexampledata/post-link.sh index bb74729fed1f2..8070c5cbda31e 100644 --- a/recipes/bioconductor-ffpeexampledata/post-link.sh +++ b/recipes/bioconductor-ffpeexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ffpeexampledata-1.38.0" +installBiocDataPackage.sh "ffpeexampledata-1.40.0" diff --git a/recipes/bioconductor-fgga/meta.yaml b/recipes/bioconductor-fgga/meta.yaml index 0a9b21b325fc1..5988b466d1305 100644 --- a/recipes/bioconductor-fgga/meta.yaml +++ b/recipes/bioconductor-fgga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.9.0" %} {% set name = "fgga" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47ae70169f23e0631cd50fc840dd2973 + md5: eaa84557f2fd00490bb5f9f12e8ca1d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fgga", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-curl - r-e1071 - r-grbase - r-jsonlite run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-curl - r-e1071 diff --git a/recipes/bioconductor-fgnet/meta.yaml b/recipes/bioconductor-fgnet/meta.yaml index ffe2941c90507..c90b268edfc43 100644 --- a/recipes/bioconductor-fgnet/meta.yaml +++ b/recipes/bioconductor-fgnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.34.0" %} +{% set version = "3.36.0" %} {% set name = "FGNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46da20768d223011b2691e3f8575addb + md5: 00da241d84bdc16ec9a8b1e27a3db509 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fgnet", max_pin="x.x") }}' noarch: generic # Suggests: RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager requirements: diff --git a/recipes/bioconductor-fgsea/meta.yaml b/recipes/bioconductor-fgsea/meta.yaml index b9ff9dc799c78..1d179f86b50b2 100644 --- a/recipes/bioconductor-fgsea/meta.yaml +++ b/recipes/bioconductor-fgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "fgsea" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3b02276027800535421f38bbe5e83921 + md5: 53b8ab8a13390a0920bc13eeba3aa1b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fgsea", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation, Seurat # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-bh - r-cowplot @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-bh - r-cowplot diff --git a/recipes/bioconductor-fibroeset/meta.yaml b/recipes/bioconductor-fibroeset/meta.yaml index 1a3674c445420..8f520b8b38f59 100644 --- a/recipes/bioconductor-fibroeset/meta.yaml +++ b/recipes/bioconductor-fibroeset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "fibroEset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42efffdc75032b3305ebdceb55f3754f + md5: cbc13cc5c4ac4f6445dc69383ad183ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fibroeset", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fibroeset/post-link.sh b/recipes/bioconductor-fibroeset/post-link.sh index 646fd7df45ff7..bee7497a33fcb 100644 --- a/recipes/bioconductor-fibroeset/post-link.sh +++ b/recipes/bioconductor-fibroeset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fibroeset-1.42.0" +installBiocDataPackage.sh "fibroeset-1.44.0" diff --git a/recipes/bioconductor-fieldeffectcrc/meta.yaml b/recipes/bioconductor-fieldeffectcrc/meta.yaml index 6221d1d18f340..a75f40d2d0445 100644 --- a/recipes/bioconductor-fieldeffectcrc/meta.yaml +++ b/recipes/bioconductor-fieldeffectcrc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "FieldEffectCrc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b20c0c45eec814e077d124b45d6589a6 + md5: 73fa4e8649f3c4a523764d35afd421f2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fieldeffectcrc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-runit run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-runit - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fieldeffectcrc/post-link.sh b/recipes/bioconductor-fieldeffectcrc/post-link.sh index b9e9fdb703e71..dca22c34d2083 100644 --- a/recipes/bioconductor-fieldeffectcrc/post-link.sh +++ b/recipes/bioconductor-fieldeffectcrc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fieldeffectcrc-1.10.0" +installBiocDataPackage.sh "fieldeffectcrc-1.12.0" diff --git a/recipes/bioconductor-filterffpe/meta.yaml b/recipes/bioconductor-filterffpe/meta.yaml index 2348708871e68..94d1f62824669 100644 --- a/recipes/bioconductor-filterffpe/meta.yaml +++ b/recipes/bioconductor-filterffpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "FilterFFPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 596fa16e66e1e46fdf0776b50b4b0ae2 + md5: e2aabe533af9d2779d1ffc2f76017ecd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-filterffpe", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-findit2/meta.yaml b/recipes/bioconductor-findit2/meta.yaml index 06bf8a8711aeb..62b26bed34e95 100644 --- a/recipes/bioconductor-findit2/meta.yaml +++ b/recipes/bioconductor-findit2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "FindIT2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d09d40b53c0d856a804d4735d816fae8 + md5: d48fffebc5ff34ec3276d3f4675d6c71 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-findit2", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -46,17 +47,17 @@ requirements: - r-tidyr - r-withr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-fis/meta.yaml b/recipes/bioconductor-fis/meta.yaml index 7cc084d4f9fbb..bc6ce25a237ce 100644 --- a/recipes/bioconductor-fis/meta.yaml +++ b/recipes/bioconductor-fis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "FIs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a79abe38c53faa7176cd1dc4189351b + md5: ef807b75136742a1dcb5ea70993d5c38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fis", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fis/post-link.sh b/recipes/bioconductor-fis/post-link.sh index b6c6f347761a8..081f3868dae51 100644 --- a/recipes/bioconductor-fis/post-link.sh +++ b/recipes/bioconductor-fis/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fis-1.28.0" +installBiocDataPackage.sh "fis-1.30.0" diff --git a/recipes/bioconductor-fishalyser/meta.yaml b/recipes/bioconductor-fishalyser/meta.yaml index a65b079aeaf85..54a8f41dc04b4 100644 --- a/recipes/bioconductor-fishalyser/meta.yaml +++ b/recipes/bioconductor-fishalyser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "FISHalyseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8263bd2ee43d6c8e6c05aedd5901b81f + md5: fea17ba4629a7d53c62eef47a3cdfab2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fishalyser", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base test: diff --git a/recipes/bioconductor-fishpond/meta.yaml b/recipes/bioconductor-fishpond/meta.yaml index a2589b18d6606..92bd84c80a051 100644 --- a/recipes/bioconductor-fishpond/meta.yaml +++ b/recipes/bioconductor-fishpond/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.2" %} +{% set version = "2.8.0" %} {% set name = "fishpond" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fb2d9b6d5b1ec1938baca42fd8936fbc + md5: 407bd027d801c207371750eba2c9d735 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fishpond", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi, pheatmap, Gviz, GenomeInfoDb, data.table requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-gtools @@ -35,12 +36,12 @@ requirements: - r-matrixstats - r-svmisc run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-gtools diff --git a/recipes/bioconductor-fission/meta.yaml b/recipes/bioconductor-fission/meta.yaml index 3dc988c615684..113cdd94fae1d 100644 --- a/recipes/bioconductor-fission/meta.yaml +++ b/recipes/bioconductor-fission/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "fission" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf744d1be1f95417b4379e55aadfcef3 + md5: 7d404509808bfc439270093b647ccd80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fission", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fission/post-link.sh b/recipes/bioconductor-fission/post-link.sh index e8b0b2176a5b1..e0380f99e57cd 100644 --- a/recipes/bioconductor-fission/post-link.sh +++ b/recipes/bioconductor-fission/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fission-1.20.0" +installBiocDataPackage.sh "fission-1.22.0" diff --git a/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml b/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml index 9e954926a6341..8d3045a648c6b 100644 --- a/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.1" %} {% set name = "fitCons.UCSC.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 53d954890ec9b91084664a10161ce391 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fitcons.ucsc.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fithic/meta.yaml b/recipes/bioconductor-fithic/meta.yaml index bc8693d7cc3d1..adf18559a5108 100644 --- a/recipes/bioconductor-fithic/meta.yaml +++ b/recipes/bioconductor-fithic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "FitHiC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2333d06cb1378d9cd9301db5988bb7c + md5: ee894d402d0c5567935ade4f8dc75c29 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fithic", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: diff --git a/recipes/bioconductor-flagme/meta.yaml b/recipes/bioconductor-flagme/meta.yaml index 8f1e4e65d55c1..90086340aa522 100644 --- a/recipes/bioconductor-flagme/meta.yaml +++ b/recipes/bioconductor-flagme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "flagme" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 59bf39feefe5d755928a32e05016cf6b + md5: ada68435478c0172b282919125008b1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flagme", max_pin="x.x") }}' requirements: host: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-gcspikelite >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-gcspikelite >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-gplots - r-mass @@ -29,9 +30,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-gcspikelite >=1.38.0,<1.39.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-gcspikelite >=1.40.0,<1.41.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-gplots - r-mass diff --git a/recipes/bioconductor-flames/meta.yaml b/recipes/bioconductor-flames/meta.yaml index 133956e55a0ca..05cea2c22df0e 100644 --- a/recipes/bioconductor-flames/meta.yaml +++ b/recipes/bioconductor-flames/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "FLAMES" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94fd7ed1565fc08d6f858123b0aa23b3 + md5: ecfe856c54464ffd2c27f8e10063d494 build: - skip: true # [osx] + skip: True # [osx] number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flames", max_pin="x.x") }}' # Suggests: BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0) -# SystemRequirements: GNU make, C++11 +# SystemRequirements: GNU make, C++17 requirements: host: - - 'bioconductor-bambu >=3.2.0,<3.3.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-bambu >=3.4.0,<3.5.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-circlize - r-cowplot - r-dplyr + - r-future - r-ggplot2 - r-gridextra - r-igraph @@ -62,31 +65,33 @@ requirements: - libblas - liblapack run: - - 'bioconductor-bambu >=3.2.0,<3.3.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-bambu >=3.4.0,<3.5.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-circlize - r-cowplot - r-dplyr + - r-future - r-ggplot2 - r-gridextra - r-igraph diff --git a/recipes/bioconductor-fletcher2013a/meta.yaml b/recipes/bioconductor-fletcher2013a/meta.yaml index ba4901cef0bb8..e4bd34e45937a 100644 --- a/recipes/bioconductor-fletcher2013a/meta.yaml +++ b/recipes/bioconductor-fletcher2013a/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Fletcher2013a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 69ea86d2f1e6aa8e8716c4db65f81cf0 + md5: e4c4f9a4e8b24a7a72f9c63337a0eef9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fletcher2013a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-venndiagram run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-venndiagram - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fletcher2013a/post-link.sh b/recipes/bioconductor-fletcher2013a/post-link.sh index 76947f653f606..36042cfbda031 100644 --- a/recipes/bioconductor-fletcher2013a/post-link.sh +++ b/recipes/bioconductor-fletcher2013a/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fletcher2013a-1.36.0" +installBiocDataPackage.sh "fletcher2013a-1.38.0" diff --git a/recipes/bioconductor-fletcher2013b/meta.yaml b/recipes/bioconductor-fletcher2013b/meta.yaml index 278b7c8f0bb5a..5c2e191438443 100644 --- a/recipes/bioconductor-fletcher2013b/meta.yaml +++ b/recipes/bioconductor-fletcher2013b/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Fletcher2013b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd7177b33cc525534e80c197f4a14b0b + md5: cf656c92425c8a63ef584be08e8b742e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fletcher2013b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-fletcher2013a >=1.36.0,<1.37.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-rtn >=2.24.0,<2.25.0' + - 'bioconductor-fletcher2013a >=1.38.0,<1.39.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' - r-base - r-igraph - r-rcolorbrewer run: - - 'bioconductor-fletcher2013a >=1.36.0,<1.37.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-rtn >=2.24.0,<2.25.0' + - 'bioconductor-fletcher2013a >=1.38.0,<1.39.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' - r-base - r-igraph - r-rcolorbrewer - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fletcher2013b/post-link.sh b/recipes/bioconductor-fletcher2013b/post-link.sh index d9bf248107be3..94b06ce4f03df 100644 --- a/recipes/bioconductor-fletcher2013b/post-link.sh +++ b/recipes/bioconductor-fletcher2013b/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fletcher2013b-1.36.0" +installBiocDataPackage.sh "fletcher2013b-1.38.0" diff --git a/recipes/bioconductor-flowai/meta.yaml b/recipes/bioconductor-flowai/meta.yaml index 7a54cd4064d1c..2a294b9332201 100644 --- a/recipes/bioconductor-flowai/meta.yaml +++ b/recipes/bioconductor-flowai/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "flowAI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d59cf6bed0f7b6837d83b2e9fd90573b + md5: 714cb015ac01ee026e02fc24536770e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowai", max_pin="x.x") }}' noarch: generic # Suggests: testthat, shiny, BiocStyle requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-changepoint - r-ggplot2 @@ -32,7 +33,7 @@ requirements: - r-rmarkdown - r-scales run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-changepoint - r-ggplot2 diff --git a/recipes/bioconductor-flowbeads/meta.yaml b/recipes/bioconductor-flowbeads/meta.yaml index 19e782c06a121..275b1e5c29f2b 100644 --- a/recipes/bioconductor-flowbeads/meta.yaml +++ b/recipes/bioconductor-flowbeads/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "flowBeads" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e744c88fbbc189754bb9e3006333355 + md5: 3c9aa4f78c8b1b2397d6004773311174 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowbeads", max_pin="x.x") }}' noarch: generic # Suggests: flowViz requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-knitr - r-rrcov - r-xtable run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-knitr - r-rrcov diff --git a/recipes/bioconductor-flowbin/meta.yaml b/recipes/bioconductor-flowbin/meta.yaml index b202a7db84c28..50962c3a7aee2 100644 --- a/recipes/bioconductor-flowbin/meta.yaml +++ b/recipes/bioconductor-flowbin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "flowBin" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 60f858355d66f8ee8f09f2968d82a440 + md5: 3d761d597ff6b4f6929e9f68ea83b366 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowbin", max_pin="x.x") }}' noarch: generic # Suggests: parallel requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowfp >=1.58.0,<1.59.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowfp >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-class - r-snow run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowfp >=1.58.0,<1.59.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowfp >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-class - r-snow diff --git a/recipes/bioconductor-flowcatchr/meta.yaml b/recipes/bioconductor-flowcatchr/meta.yaml index 538ea1b9f3d0c..5f47ecd63335c 100644 --- a/recipes/bioconductor-flowcatchr/meta.yaml +++ b/recipes/bioconductor-flowcatchr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "flowcatchR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91c941bf107a4f973859adcd584d0ac2 + md5: a823367e5e1e432980ca41c1516c97f2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowcatchr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown # SystemRequirements: ImageMagick requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base - r-colorramps @@ -31,8 +32,8 @@ requirements: - r-shiny - imagemagick run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base - r-colorramps diff --git a/recipes/bioconductor-flowchic/meta.yaml b/recipes/bioconductor-flowchic/meta.yaml index a6bad36cb85d0..2aaf6235bb116 100644 --- a/recipes/bioconductor-flowchic/meta.yaml +++ b/recipes/bioconductor-flowchic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "flowCHIC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72229b8e073b7f7beaab5d3718dfdc2e + md5: 72e50628c116c31eebd78d620514dca1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowchic", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-ggplot2 - r-hexbin - r-vegan run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-ggplot2 - r-hexbin diff --git a/recipes/bioconductor-flowclean/meta.yaml b/recipes/bioconductor-flowclean/meta.yaml index 6fe89720fe2ee..02be800eea903 100644 --- a/recipes/bioconductor-flowclean/meta.yaml +++ b/recipes/bioconductor-flowclean/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "flowClean" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd29baeeed9e6883aeb1dd592ec63e82 + md5: 77f86a84c8ed6dbd2df24d9458765205 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowclean", max_pin="x.x") }}' noarch: generic # Suggests: flowViz, grid, gridExtra requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-bit - r-changepoint - r-sfsmisc run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-bit - r-changepoint diff --git a/recipes/bioconductor-flowclust/meta.yaml b/recipes/bioconductor-flowclust/meta.yaml index 1c81b8b9cc239..946cfdb1cd414 100644 --- a/recipes/bioconductor-flowclust/meta.yaml +++ b/recipes/bioconductor-flowclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.38.0" %} +{% set version = "3.40.0" %} {% set name = "flowClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 843149c02cec1b6eedac82c6faf3ecd0 + md5: 50e5d774ae44b8aaca69069733c175e3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowclust", max_pin="x.x") }}' # Suggests: testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown, openCyto, flowStats(>= 4.7.1) # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-flowcore/meta.yaml b/recipes/bioconductor-flowcore/meta.yaml index 5c0b25e087f4f..bb31c70c0c63a 100644 --- a/recipes/bioconductor-flowcore/meta.yaml +++ b/recipes/bioconductor-flowcore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "flowCore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46283d4ef07328f5a7824471bbd6e2ef + md5: 3b0696fd3fc45a87531ab3503be00277 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowcore", max_pin="x.x") }}' # Suggests: Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat, flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - - 'r-bh >=1.65.0.1' + - 'r-bh >=1.81.0.0' - r-cpp11 - r-matrixstats - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - - 'r-bh >=1.65.0.1' + - 'r-bh >=1.81.0.0' - r-cpp11 - r-matrixstats - r-rcpp diff --git a/recipes/bioconductor-flowcut/meta.yaml b/recipes/bioconductor-flowcut/meta.yaml index a9b4ed4154841..f60fa58a8ac7a 100644 --- a/recipes/bioconductor-flowcut/meta.yaml +++ b/recipes/bioconductor-flowcut/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "flowCut" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a879badc8fb1ccd7f4bd8b7fdf560255 + md5: b79bc38dd887cef19040c2d7178311d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowcut", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, markdown, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' - r-base - r-cairo - r-e1071 run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowdensity >=1.34.0,<1.35.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowdensity >=1.36.0,<1.37.0' - r-base - r-cairo - r-e1071 diff --git a/recipes/bioconductor-flowcybar/meta.yaml b/recipes/bioconductor-flowcybar/meta.yaml index f0290c51cd3ae..cf71a394b6ac8 100644 --- a/recipes/bioconductor-flowcybar/meta.yaml +++ b/recipes/bioconductor-flowcybar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "flowCyBar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5666ea536602365882d54be550274877 + md5: 9236c02598960d4536906fb7449a7dd4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowcybar", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-flowdensity/meta.yaml b/recipes/bioconductor-flowdensity/meta.yaml index f4be69a59e827..7a7978ac58c3d 100644 --- a/recipes/bioconductor-flowdensity/meta.yaml +++ b/recipes/bioconductor-flowdensity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.1" %} {% set name = "flowDensity" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9582e24db40a4754b375f0ee675bf635 + md5: 30c661d010484bff6c2eb427a7056aa1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowdensity", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown # SystemRequirements: xml2, GNU make, C++11 requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base - r-car - r-gplots - - r-rfoc - - r-rgeos - - r-sp + - r-polyclip - libxml2 run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base - r-car - r-gplots - - r-rfoc - - r-rgeos - - r-sp + - r-polyclip - libxml2 test: commands: diff --git a/recipes/bioconductor-flowfp/meta.yaml b/recipes/bioconductor-flowfp/meta.yaml index 447cd63812bb6..680a77375956c 100644 --- a/recipes/bioconductor-flowfp/meta.yaml +++ b/recipes/bioconductor-flowfp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "flowFP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a826a5cf4c655b5f0fc9d5f80655f30 + md5: 5f0424d8a662d2d65bacbcff080d9c7a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowfp", max_pin="x.x") }}' # Suggests: RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-flowgate/meta.yaml b/recipes/bioconductor-flowgate/meta.yaml index b9a3005511cce..c565637710606 100644 --- a/recipes/bioconductor-flowgate/meta.yaml +++ b/recipes/bioconductor-flowgate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "flowGate" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06253e3ee0f40cfd6446ec6aba2a4562 + md5: d5b19dee6139d26306d14563f445a64f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowgate", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, stringr, tidyverse, testthat requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' - r-base - 'r-biocmanager >=1.30.10' - 'r-dplyr >=1.0.0' @@ -33,9 +34,9 @@ requirements: - 'r-shiny >=1.5.0' - r-tibble run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ggcyto >=1.28.0,<1.29.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ggcyto >=1.30.0,<1.31.0' - r-base - 'r-biocmanager >=1.30.10' - 'r-dplyr >=1.0.0' diff --git a/recipes/bioconductor-flowgraph/meta.yaml b/recipes/bioconductor-flowgraph/meta.yaml index 0cb0ad7fa10fe..a0e5db9f2c1f9 100644 --- a/recipes/bioconductor-flowgraph/meta.yaml +++ b/recipes/bioconductor-flowgraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "flowGraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae032bd4f1c462d1643902facf008dd6 + md5: 68abd457f6a200f435ebbf41183c0e94 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowgraph", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, dplyr, knitr, rmarkdown, testthat (>= 2.1.0) requirements: diff --git a/recipes/bioconductor-flowmatch/meta.yaml b/recipes/bioconductor-flowmatch/meta.yaml index cfb3a59262ef2..fbbc71e016972 100644 --- a/recipes/bioconductor-flowmatch/meta.yaml +++ b/recipes/bioconductor-flowmatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "flowMatch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2642ae3123f2b7fa6715d5f23a1d76bc + md5: 78b2b9dc87eec35dbc65c59dadb1ffd9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowmatch", max_pin="x.x") }}' # Suggests: healthyFlowData requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-rcpp >=0.11.0' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-rcpp >=0.11.0' build: diff --git a/recipes/bioconductor-flowmeans/meta.yaml b/recipes/bioconductor-flowmeans/meta.yaml index c33e164d34bfd..4830d38e0f6a9 100644 --- a/recipes/bioconductor-flowmeans/meta.yaml +++ b/recipes/bioconductor-flowmeans/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "flowMeans" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 907da9157eecd2bcf4ff53536254bbc9 + md5: 5cbb796502f09bf65cae60e4f0f53c1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowmeans", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-feature - r-rrcov run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-feature - r-rrcov diff --git a/recipes/bioconductor-flowmerge/meta.yaml b/recipes/bioconductor-flowmerge/meta.yaml index 63020aae225c2..cb220a14afbac 100644 --- a/recipes/bioconductor-flowmerge/meta.yaml +++ b/recipes/bioconductor-flowmerge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.48.0" %} +{% set version = "2.50.0" %} {% set name = "flowMerge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f0c37b4e9c43ab26edaae92dd9b1fb2e + md5: c0d4d124e3d94a0eab8fc138f9044d2c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowmerge", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-feature - r-foreach - r-rrcov - r-snow run: - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-feature - r-foreach diff --git a/recipes/bioconductor-flowpeaks/meta.yaml b/recipes/bioconductor-flowpeaks/meta.yaml index 4965ed48624d1..ac3d20f1f9a9d 100644 --- a/recipes/bioconductor-flowpeaks/meta.yaml +++ b/recipes/bioconductor-flowpeaks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "flowPeaks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d8481859adf962408c139342e9eac893 + md5: f68db373a0d053a7eabd112df80a25f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowpeaks", max_pin="x.x") }}' # SystemRequirements: gsl requirements: host: diff --git a/recipes/bioconductor-flowploidy/meta.yaml b/recipes/bioconductor-flowploidy/meta.yaml index b71d6983cf655..c1569c3b88b46 100644 --- a/recipes/bioconductor-flowploidy/meta.yaml +++ b/recipes/bioconductor-flowploidy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "flowPloidy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14afd95deaa59263b9e2ccc3140cb5a0 + md5: 1020981a0f645d2dcbf1a38a3e42b7e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowploidy", max_pin="x.x") }}' noarch: generic # Suggests: flowPloidyData, testthat requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-car - r-catools @@ -30,7 +31,7 @@ requirements: - r-rmarkdown - r-shiny run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-car - r-catools diff --git a/recipes/bioconductor-flowploidydata/meta.yaml b/recipes/bioconductor-flowploidydata/meta.yaml index 29f71f910219a..1df2c16869432 100644 --- a/recipes/bioconductor-flowploidydata/meta.yaml +++ b/recipes/bioconductor-flowploidydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "flowPloidyData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10d8e5d5d636d7a78c7dd5aa79ba41a4 + md5: 993a663f6d1cdc791c3f4e88d5b3b047 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowploidydata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, flowCore requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowploidydata/post-link.sh b/recipes/bioconductor-flowploidydata/post-link.sh index d1acd28276c1f..dbb4d93fd487f 100644 --- a/recipes/bioconductor-flowploidydata/post-link.sh +++ b/recipes/bioconductor-flowploidydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowploidydata-1.26.0" +installBiocDataPackage.sh "flowploidydata-1.28.0" diff --git a/recipes/bioconductor-flowplots/meta.yaml b/recipes/bioconductor-flowplots/meta.yaml index da76dc7f6737a..e7893a2db7cac 100644 --- a/recipes/bioconductor-flowplots/meta.yaml +++ b/recipes/bioconductor-flowplots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "flowPlots" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6960c2567067f71bab67d0de646533ad + md5: 523b0d79646813f56d711d3e0f38a5e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowplots", max_pin="x.x") }}' noarch: generic # Suggests: vcd requirements: diff --git a/recipes/bioconductor-flowsom/meta.yaml b/recipes/bioconductor-flowsom/meta.yaml index 69e70f2f2330d..e8708a748755e 100644 --- a/recipes/bioconductor-flowsom/meta.yaml +++ b/recipes/bioconductor-flowsom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "FlowSOM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c801e147f4137a9b7c5157f8536e44c3 + md5: 9bc309cc9948473d101d91ba6f1a37f2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsom", max_pin="x.x") }}' # Suggests: BiocStyle, testthat, CytoML, flowWorkspace, ggrepel, scattermore, pheatmap, ggpointdensity requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-colorramps - r-dplyr @@ -39,9 +40,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-colorramps - r-dplyr diff --git a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml index 828f4aae39fba..9c9dcba953274 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "FlowSorted.Blood.450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68977c1bf508dda29bc067929aecc006 + md5: f88422c2d8a2f7ce4ca968292adfc8ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.blood.450k", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh index c04ffe255ad90..291888eff33cc 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.blood.450k-1.38.0" +installBiocDataPackage.sh "flowsorted.blood.450k-1.40.0" diff --git a/recipes/bioconductor-flowsorted.blood.epic/meta.yaml b/recipes/bioconductor-flowsorted.blood.epic/meta.yaml index a4e32da09fc49..90ba4f67f6423 100644 --- a/recipes/bioconductor-flowsorted.blood.epic/meta.yaml +++ b/recipes/bioconductor-flowsorted.blood.epic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.2" %} +{% set version = "2.6.0" %} {% set name = "FlowSorted.Blood.EPIC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d9d98db39792aac4fe1ec1db0b0366b + md5: e94cbb0480a032595cdb5d9714065bed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.blood.epic", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown, FlowSorted.CordBlood.450k, FlowSorted.Blood.450k(>= 1.0.1), EpiDISH,FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19 requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-nlme - r-quadprog run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-nlme - r-quadprog - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.blood.epic/post-link.sh b/recipes/bioconductor-flowsorted.blood.epic/post-link.sh index 7d84a33bceaaf..82feccd703411 100644 --- a/recipes/bioconductor-flowsorted.blood.epic/post-link.sh +++ b/recipes/bioconductor-flowsorted.blood.epic/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.blood.epic-2.4.2" +installBiocDataPackage.sh "flowsorted.blood.epic-2.6.0" diff --git a/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml index 26dde86b085e7..20523ec1de672 100644 --- a/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "FlowSorted.CordBlood.450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbef432e31c78c82fe4498a341d3a5a8 + md5: fca81b7412af68100d7aed4d57d5fc59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.cordblood.450k", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh index 3d72e98279d82..0b82dabf176d0 100644 --- a/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.cordblood.450k-1.28.0" +installBiocDataPackage.sh "flowsorted.cordblood.450k-1.30.0" diff --git a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml index 57947ff21176b..6aef7e141a811 100644 --- a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "FlowSorted.CordBloodCombined.450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0579c0d8bcb50c77d579b082a7bf4158 + md5: 769113b80606820ab2918dcacf1076b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.cordbloodcombined.450k", max_pin="x.x") }}' noarch: generic # Suggests: FlowSorted.Blood.EPIC, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh index b4b08defd7136..c540b53ecf269 100644 --- a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.cordbloodcombined.450k-1.16.0" +installBiocDataPackage.sh "flowsorted.cordbloodcombined.450k-1.18.0" diff --git a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml index 90c84b67f76c8..13471afc01d9a 100644 --- a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "FlowSorted.CordBloodNorway.450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a399952bf229258fe47964a8d3db910 + md5: 40016224becf643102bc3054f4e2508d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.cordbloodnorway.450k", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh index 504978723041e..142aa56ecf3a3 100644 --- a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.cordbloodnorway.450k-1.26.0" +installBiocDataPackage.sh "flowsorted.cordbloodnorway.450k-1.28.0" diff --git a/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml b/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml index f0f6ed40e091e..b9bfdbe04b88e 100644 --- a/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "FlowSorted.DLPFC.450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb70a712a95eaa879d62d7751567aed5 + md5: ad95a51f7e8bcf7c0bec6dda80eb0a92 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowsorted.dlpfc.450k", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh b/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh index dc693b027192e..bdd7e31f4b074 100644 --- a/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.dlpfc.450k-1.36.0" +installBiocDataPackage.sh "flowsorted.dlpfc.450k-1.38.0" diff --git a/recipes/bioconductor-flowspecs/meta.yaml b/recipes/bioconductor-flowspecs/meta.yaml index a695590b17669..f3dea0389b41d 100644 --- a/recipes/bioconductor-flowspecs/meta.yaml +++ b/recipes/bioconductor-flowspecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "flowSpecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84af2116cc90cb4c1df4b384ab9a232c + md5: 502f1e04027fab8076745a5386401f2e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowspecs", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, DepecheR requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-ggplot2 >=3.1.0' - 'r-reshape2 >=1.4.3' - 'r-zoo >=1.8.6' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-ggplot2 >=3.1.0' - 'r-reshape2 >=1.4.3' diff --git a/recipes/bioconductor-flowstats/meta.yaml b/recipes/bioconductor-flowstats/meta.yaml index f9909cc9d27de..6ea2f22d7384f 100644 --- a/recipes/bioconductor-flowstats/meta.yaml +++ b/recipes/bioconductor-flowstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.12.0" %} +{% set version = "4.14.0" %} {% set name = "flowStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 730df788ab11668488ede56d8c65362c + md5: 2817bb2cbd74b07bb948d0988be2a57e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowstats", max_pin="x.x") }}' noarch: generic # Suggests: xtable, testthat, openCyto, ggcyto, ggridges requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - r-base + - r-clue - r-cluster - r-corpcor - 'r-fda >=2.2.6' @@ -39,13 +41,14 @@ requirements: - r-rcolorbrewer - r-rrcov run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - r-base + - r-clue - r-cluster - r-corpcor - 'r-fda >=2.2.6' diff --git a/recipes/bioconductor-flowtime/meta.yaml b/recipes/bioconductor-flowtime/meta.yaml index b684b98a569de..eb87ab80635af 100644 --- a/recipes/bioconductor-flowtime/meta.yaml +++ b/recipes/bioconductor-flowtime/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "flowTime" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00a06c20b516ba2a70acecd10b8c73cc + md5: 04ca452b54e7309493c814844fc1b772 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowtime", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats, flowClust, openCyto, flowStats, ggcyto requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-dplyr >=1.0.0' - r-magrittr @@ -29,7 +30,7 @@ requirements: - r-rlang - r-tibble run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - 'r-dplyr >=1.0.0' - r-magrittr diff --git a/recipes/bioconductor-flowtrans/meta.yaml b/recipes/bioconductor-flowtrans/meta.yaml index e5cc7f9552b92..ebddba32b3bfd 100644 --- a/recipes/bioconductor-flowtrans/meta.yaml +++ b/recipes/bioconductor-flowtrans/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "flowTrans" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 362e389a46df4c08fbdacebb047a0b88 + md5: d98daa4177e5f6b8cda8d8475e34c09a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowtrans", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base run: - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base test: commands: diff --git a/recipes/bioconductor-flowviz/meta.yaml b/recipes/bioconductor-flowviz/meta.yaml index dd1d975d2d390..46eab38ac8366 100644 --- a/recipes/bioconductor-flowviz/meta.yaml +++ b/recipes/bioconductor-flowviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "flowViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c581bc7787fdf9bb136087fb6f966f5 + md5: 320d8392618efe06e6c2a8923b3c6652 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowviz", max_pin="x.x") }}' noarch: generic # Suggests: colorspace, flowStats, knitr, rmarkdown, markdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-hexbin - r-idpmisc @@ -32,8 +33,8 @@ requirements: - r-mass - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-hexbin - r-idpmisc diff --git a/recipes/bioconductor-flowvs/meta.yaml b/recipes/bioconductor-flowvs/meta.yaml index 10f2837f82420..9469254038a37 100644 --- a/recipes/bioconductor-flowvs/meta.yaml +++ b/recipes/bioconductor-flowvs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "flowVS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a44cf1a01b17b9a3a28422aca0ac438 + md5: 43fc57f2be5ccbfcff9ac9b9bc0bb857 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowvs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, vsn, requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowstats >=4.12.0,<4.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowstats >=4.14.0,<4.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowstats >=4.12.0,<4.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowstats >=4.14.0,<4.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' - r-base test: commands: diff --git a/recipes/bioconductor-flowworkspace/meta.yaml b/recipes/bioconductor-flowworkspace/meta.yaml index 85970ddc4fd59..5df796f644a70 100644 --- a/recipes/bioconductor-flowworkspace/meta.yaml +++ b/recipes/bioconductor-flowworkspace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.12.0" %} +{% set version = "4.14.0" %} {% set name = "flowWorkspace" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8f80cf16553cc9099512c1c86c6f60d + md5: e97cd561c6a61ae778261cb55f29af90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowworkspace", max_pin="x.x") }}' # Suggests: testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown, ggcyto, parallel, CytoML, openCyto # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.62.0-1' - r-cpp11 @@ -45,18 +46,18 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-cytolib >=2.12.0,<2.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-rprotobuflib >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-cytolib >=2.14.0,<2.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.62.0-1' - r-cpp11 diff --git a/recipes/bioconductor-flowworkspacedata/meta.yaml b/recipes/bioconductor-flowworkspacedata/meta.yaml index c9a33f5504dfb..ec95026f5f295 100644 --- a/recipes/bioconductor-flowworkspacedata/meta.yaml +++ b/recipes/bioconductor-flowworkspacedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.12.0" %} +{% set version = "3.14.0" %} {% set name = "flowWorkspaceData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d91993dd5a5c5b561a8063ec91046d3 + md5: 96655cef2a21f1b9d303ec775597a2dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-flowworkspacedata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-flowworkspacedata/post-link.sh b/recipes/bioconductor-flowworkspacedata/post-link.sh index 4f4de031dce66..f0331f23198c7 100644 --- a/recipes/bioconductor-flowworkspacedata/post-link.sh +++ b/recipes/bioconductor-flowworkspacedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowworkspacedata-3.12.0" +installBiocDataPackage.sh "flowworkspacedata-3.14.0" diff --git a/recipes/bioconductor-fly.db0/meta.yaml b/recipes/bioconductor-fly.db0/meta.yaml index 58fee2b2ea22c..0ed06aa0d7e48 100644 --- a/recipes/bioconductor-fly.db0/meta.yaml +++ b/recipes/bioconductor-fly.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "fly.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 04b3d22c5825c9a31f5253746df5c4e0 + md5: 49722b8a538d02f71631a418b92c44d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fly.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fly.db0/post-link.sh b/recipes/bioconductor-fly.db0/post-link.sh index 213a32552081d..3fab31db8f277 100644 --- a/recipes/bioconductor-fly.db0/post-link.sh +++ b/recipes/bioconductor-fly.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fly.db0-3.17.0" +installBiocDataPackage.sh "fly.db0-3.18.0" diff --git a/recipes/bioconductor-fmcsr/meta.yaml b/recipes/bioconductor-fmcsr/meta.yaml index f86bf2cd4b73e..d62cc7de82aea 100644 --- a/recipes/bioconductor-fmcsr/meta.yaml +++ b/recipes/bioconductor-fmcsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "fmcsR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2687c7aa47141346582b5b6dac68e906 + md5: 21a6242a61cba8dd537bf846af3260c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fmcsr", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-runit - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - r-runit build: diff --git a/recipes/bioconductor-fmrs/meta.yaml b/recipes/bioconductor-fmrs/meta.yaml index f858ab078409a..667e0c6c78dac 100644 --- a/recipes/bioconductor-fmrs/meta.yaml +++ b/recipes/bioconductor-fmrs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "fmrs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1f73155e7e3d066f5e59fedeb0dcd725 + md5: ccf41504ab27d93464e555b363ef406a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fmrs", max_pin="x.x") }}' # Suggests: BiocGenerics, testthat, knitr, utils requirements: host: diff --git a/recipes/bioconductor-fobitools/meta.yaml b/recipes/bioconductor-fobitools/meta.yaml index 0d734261bb591..d9b0d175e64b0 100644 --- a/recipes/bioconductor-fobitools/meta.yaml +++ b/recipes/bioconductor-fobitools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "fobitools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fe95da3fe13e9bb17165048bbe6f4799 + md5: 24ebda3aed06055ab55d7cdf88a7c2a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fobitools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, ggrepel, kableExtra, knitr, metabolomicsWorkbenchR, POMA, rmarkdown, rvest, SummarizedExperiment, testthat (>= 2.3.2), tidyverse requirements: host: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - r-clisymbols - r-crayon @@ -39,7 +40,7 @@ requirements: - r-tidyr - r-vroom run: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - r-clisymbols - r-crayon diff --git a/recipes/bioconductor-fourdndata/meta.yaml b/recipes/bioconductor-fourdndata/meta.yaml index fe82086bd827c..4b1339af9b5b5 100644 --- a/recipes/bioconductor-fourdndata/meta.yaml +++ b/recipes/bioconductor-fourdndata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "fourDNData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2bea3be8c2abed679fc99cf6bdaee98f + md5: bca623e919f7c17a40ffb4eae27cfe59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fourdndata", max_pin="x.x") }}' noarch: generic # Suggests: rtracklayer, dplyr, testthat, methods, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-fourdndata/post-link.sh b/recipes/bioconductor-fourdndata/post-link.sh index b46b9ff5f46a2..f062b27931ef6 100644 --- a/recipes/bioconductor-fourdndata/post-link.sh +++ b/recipes/bioconductor-fourdndata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fourdndata-1.0.0" +installBiocDataPackage.sh "fourdndata-1.2.0" diff --git a/recipes/bioconductor-fraser/meta.yaml b/recipes/bioconductor-fraser/meta.yaml index f5696e6fec261..e2d50e16fbc6a 100644 --- a/recipes/bioconductor-fraser/meta.yaml +++ b/recipes/bioconductor-fraser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "FRASER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f569aff29dbec9bc4d7797b30d05e593 + md5: 07e7f6a03b43d2111015d4fc051f3a00 build: skip: True # [osx] number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fraser", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-outrider >=1.18.0,<1.19.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-outrider >=1.20.0,<1.21.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bbmisc - r-cowplot @@ -63,27 +64,27 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-outrider >=1.18.0,<1.19.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-outrider >=1.20.0,<1.21.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bbmisc - r-cowplot diff --git a/recipes/bioconductor-frenchfish/meta.yaml b/recipes/bioconductor-frenchfish/meta.yaml index 9a694f3d1d414..3b703c9f03fda 100644 --- a/recipes/bioconductor-frenchfish/meta.yaml +++ b/recipes/bioconductor-frenchfish/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "frenchFISH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a5cd6ee3dcf999336cd1dfc10c583ec + md5: 170f9e757e12e766a8a455d6d3ca9f81 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-frenchfish", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-frgepistasis/meta.yaml b/recipes/bioconductor-frgepistasis/meta.yaml index 6bd5277ce9f25..18dcf4c202ea4 100644 --- a/recipes/bioconductor-frgepistasis/meta.yaml +++ b/recipes/bioconductor-frgepistasis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "FRGEpistasis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0726b7195c31f91dbf12b46ea0514d0d + md5: a5804d62a4e375df7706ebc0573929f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-frgepistasis", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-frma/meta.yaml b/recipes/bioconductor-frma/meta.yaml index f28bc4bae5195..6e27095a3ca5a 100644 --- a/recipes/bioconductor-frma/meta.yaml +++ b/recipes/bioconductor-frma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "frma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f74abf15385619ab89738bc0aeee913c + md5: 4892707c54a5698c48151bd630feb0e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-frma", max_pin="x.x") }}' noarch: generic # Suggests: hgu133afrmavecs, frmaExampleData requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-mass run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-mass diff --git a/recipes/bioconductor-frmaexampledata/meta.yaml b/recipes/bioconductor-frmaexampledata/meta.yaml index c28effa9ce690..9f29cd6e5963e 100644 --- a/recipes/bioconductor-frmaexampledata/meta.yaml +++ b/recipes/bioconductor-frmaexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "frmaExampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 057a53ead8fde2bab4ee0cb71a4faaf6 + md5: 9713801ffd08145323ca4d31a3631995 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-frmaexampledata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-frmaexampledata/post-link.sh b/recipes/bioconductor-frmaexampledata/post-link.sh index ab1764237f9ab..11252f324dcf4 100644 --- a/recipes/bioconductor-frmaexampledata/post-link.sh +++ b/recipes/bioconductor-frmaexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "frmaexampledata-1.36.0" +installBiocDataPackage.sh "frmaexampledata-1.38.0" diff --git a/recipes/bioconductor-frmatools/meta.yaml b/recipes/bioconductor-frmatools/meta.yaml index 6cdde49420424..113507f7441f4 100644 --- a/recipes/bioconductor-frmatools/meta.yaml +++ b/recipes/bioconductor-frmatools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "frmaTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fc17910da8e1a1f2b006edd1c122156 + md5: 270e71dc903bb77add1154782cf17342 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-frmatools", max_pin="x.x") }}' noarch: generic # Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi test: diff --git a/recipes/bioconductor-funchip/meta.yaml b/recipes/bioconductor-funchip/meta.yaml index 80163f7e1dedd..d78b00121ddb0 100644 --- a/recipes/bioconductor-funchip/meta.yaml +++ b/recipes/bioconductor-funchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "FunChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d4be7e4b7194e6c6baf5aa80d938b4a + md5: 93a91487d2e6b0841094c9eb7c997be2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-funchip", max_pin="x.x") }}' requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-doparallel - r-fda @@ -33,10 +34,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-doparallel - r-fda diff --git a/recipes/bioconductor-funtoonorm/meta.yaml b/recipes/bioconductor-funtoonorm/meta.yaml index db61dccd9c11f..ecdc54d66593c 100644 --- a/recipes/bioconductor-funtoonorm/meta.yaml +++ b/recipes/bioconductor-funtoonorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "funtooNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50104886edef68e9248446c34efcb714 + md5: 32208fd7734fe0fcfb1278b80a98c28e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-funtoonorm", max_pin="x.x") }}' noarch: generic # Suggests: prettydoc, minfiData, knitr, rmarkdown requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-pls run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-pls diff --git a/recipes/bioconductor-furrowseg/meta.yaml b/recipes/bioconductor-furrowseg/meta.yaml index f5835bbc9cb5e..19e3d0d33ddfd 100644 --- a/recipes/bioconductor-furrowseg/meta.yaml +++ b/recipes/bioconductor-furrowseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "furrowSeg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ee1d6bc3d7fe7c1855a6b96b429190b + md5: f41e88a4d47949b3b8b126b0fc7852eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-furrowseg", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, knitr requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base - r-dplyr - r-locfit - r-tiff run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-abind - r-base - r-dplyr - r-locfit - r-tiff - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-furrowseg/post-link.sh b/recipes/bioconductor-furrowseg/post-link.sh index f6edea536462d..1cf285a2cc4fd 100644 --- a/recipes/bioconductor-furrowseg/post-link.sh +++ b/recipes/bioconductor-furrowseg/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "furrowseg-1.28.0" +installBiocDataPackage.sh "furrowseg-1.30.0" diff --git a/recipes/bioconductor-fusesom/meta.yaml b/recipes/bioconductor-fusesom/meta.yaml index 9000fbe7a3415..972591b6661df 100644 --- a/recipes/bioconductor-fusesom/meta.yaml +++ b/recipes/bioconductor-fusesom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "FuseSOM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c90411cb119ef9c54cf54f49b909d5a + md5: 8f53b251d77ea648cb8e56bb5eb72b18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-fusesom", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, rmarkdown, SingleCellExperiment requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-analogue - r-base - r-cluster @@ -41,8 +42,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-analogue - r-base - r-cluster diff --git a/recipes/bioconductor-ga4ghclient/meta.yaml b/recipes/bioconductor-ga4ghclient/meta.yaml index 8591a0b9dc674..aef75f3842b74 100644 --- a/recipes/bioconductor-ga4ghclient/meta.yaml +++ b/recipes/bioconductor-ga4ghclient/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "GA4GHclient" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da57780acaf8f06eb3efdd6aeff4446c + md5: d0e8b9a21eda6320d15642c12fcb8392 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ga4ghclient", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-httr - r-jsonlite run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-httr diff --git a/recipes/bioconductor-ga4ghshiny/meta.yaml b/recipes/bioconductor-ga4ghshiny/meta.yaml index cc143cb834480..ae26ca82d7726 100644 --- a/recipes/bioconductor-ga4ghshiny/meta.yaml +++ b/recipes/bioconductor-ga4ghshiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "GA4GHshiny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2e537faaa9cbb451eaf972f495c6de06 + md5: 629ca5d338b8435b238169892016d447 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ga4ghshiny", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ga4ghclient >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ga4ghclient >=1.26.0,<1.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-dt @@ -37,12 +38,12 @@ requirements: - r-shinythemes - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ga4ghclient >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ga4ghclient >=1.26.0,<1.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-gaga/meta.yaml b/recipes/bioconductor-gaga/meta.yaml index 2c252a1df70a7..e96e988b0e664 100644 --- a/recipes/bioconductor-gaga/meta.yaml +++ b/recipes/bioconductor-gaga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "gaga" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a616f28ab9876f7725629d62946aadd + md5: d1b404912b9a23365c9085dc91e20a10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gaga", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - r-base - r-coda - r-mgcv - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - r-base - r-coda - r-mgcv diff --git a/recipes/bioconductor-gage/meta.yaml b/recipes/bioconductor-gage/meta.yaml index 792d38f878e67..4724a254b4280 100644 --- a/recipes/bioconductor-gage/meta.yaml +++ b/recipes/bioconductor-gage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.50.0" %} +{% set version = "2.52.0" %} {% set name = "gage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7981df2c7c9c8bb91d12f0b207f3b380 + md5: ffb5ec419d5e08f9b31154202e0e04c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gage", max_pin="x.x") }}' noarch: generic # Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - r-base test: commands: diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index b5c3d7c318906..eeef14a1c426c 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "gageData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04f7869c72f70f6726372af0a4688d5d + md5: 889e4b6ceda6c2a80f61ad4e867c3b59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gagedata", max_pin="x.x") }}' noarch: generic # Suggests: gage, pathview, genefilter requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gagedata/post-link.sh b/recipes/bioconductor-gagedata/post-link.sh index ae7f71a1154ae..1e6ddee3415bd 100644 --- a/recipes/bioconductor-gagedata/post-link.sh +++ b/recipes/bioconductor-gagedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gagedata-2.38.0" +installBiocDataPackage.sh "gagedata-2.40.0" diff --git a/recipes/bioconductor-gaggle/meta.yaml b/recipes/bioconductor-gaggle/meta.yaml index b5cfe52719523..10757fa0844f0 100644 --- a/recipes/bioconductor-gaggle/meta.yaml +++ b/recipes/bioconductor-gaggle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "gaggle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c86f7ecb5db49b11939c8d9f6077c976 + md5: 3dc385e959f454cd56dec418800c33a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gaggle", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - 'r-rjava >=0.4' - 'r-runit >=0.4.17' run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - 'r-rjava >=0.4' - 'r-runit >=0.4.17' diff --git a/recipes/bioconductor-gaprediction/meta.yaml b/recipes/bioconductor-gaprediction/meta.yaml index 71297ee496db1..04d4db4123a5b 100644 --- a/recipes/bioconductor-gaprediction/meta.yaml +++ b/recipes/bioconductor-gaprediction/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GAprediction" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28fd8f9a1b37806405ac3a5aed4d64fe + md5: 5aceb1005e134eeeb2fc6a77941d8348 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gaprediction", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-garfield/meta.yaml b/recipes/bioconductor-garfield/meta.yaml index bf5fef693a02b..0f71b3e382829 100644 --- a/recipes/bioconductor-garfield/meta.yaml +++ b/recipes/bioconductor-garfield/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "garfield" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 269dabdfcc22cb722db4cdf8fb78ad6c + md5: bf1974925a6c10b95ada01ff6d46bf15 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-garfield", max_pin="x.x") }}' # Suggests: knitr requirements: host: diff --git a/recipes/bioconductor-gars/meta.yaml b/recipes/bioconductor-gars/meta.yaml index 6fab0879d810b..aadcd040d41db 100644 --- a/recipes/bioconductor-gars/meta.yaml +++ b/recipes/bioconductor-gars/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GARS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67cee7307c638973430218e416e4ae01 + md5: 205eceff8f152fa6ac308b7830ef2876 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gars", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-damirseq >=2.12.0,<2.13.0' - - 'bioconductor-mlseq >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-damirseq >=2.14.0,<2.15.0' + - 'bioconductor-mlseq >=2.20.0,<2.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-ggplot2 run: - - 'bioconductor-damirseq >=2.12.0,<2.13.0' - - 'bioconductor-mlseq >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-damirseq >=2.14.0,<2.15.0' + - 'bioconductor-mlseq >=2.20.0,<2.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-ggplot2 @@ -43,7 +44,7 @@ about: summary: 'GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets' description: 'Feature selection aims to identify and remove redundant, irrelevant and noisy variables from high-dimensional datasets. Selecting informative features affects the subsequent classification and regression analyses by improving their overall performances. Several methods have been proposed to perform feature selection: most of them relies on univariate statistics, correlation, entropy measurements or the usage of backward/forward regressions. Herein, we propose an efficient, robust and fast method that adopts stochastic optimization approaches for high-dimensional. GARS is an innovative implementation of a genetic algorithm that selects robust features in high-dimensional and challenging datasets.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - extra: container: - extended-base: True + extended-base: true + diff --git a/recipes/bioconductor-gaschyhs/meta.yaml b/recipes/bioconductor-gaschyhs/meta.yaml index 924b406a8798c..0bbd7d13201a1 100644 --- a/recipes/bioconductor-gaschyhs/meta.yaml +++ b/recipes/bioconductor-gaschyhs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "gaschYHS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: adb36d86b4890c4f4c714d99aa3b3f93 + md5: 29983eadb2a2a20f7c5475206367d641 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gaschyhs", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gaschyhs/post-link.sh b/recipes/bioconductor-gaschyhs/post-link.sh index a0d77e2feb121..51ff00a4819a6 100644 --- a/recipes/bioconductor-gaschyhs/post-link.sh +++ b/recipes/bioconductor-gaschyhs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gaschyhs-1.38.0" +installBiocDataPackage.sh "gaschyhs-1.40.0" diff --git a/recipes/bioconductor-gatefinder/meta.yaml b/recipes/bioconductor-gatefinder/meta.yaml index fead106644f34..ac9a8afe6eacc 100644 --- a/recipes/bioconductor-gatefinder/meta.yaml +++ b/recipes/bioconductor-gatefinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GateFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b893327eec1564d4da0596cc6822b44b + md5: 4fcb13ba6ee293d3ffb30122b652df12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gatefinder", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowfp >=1.58.0,<1.59.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowfp >=1.60.0,<1.61.0' - r-base - r-diptest - r-mvoutlier - r-splancs run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowfp >=1.58.0,<1.59.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowfp >=1.60.0,<1.61.0' - r-base - r-diptest - r-mvoutlier diff --git a/recipes/bioconductor-gatom/build.sh b/recipes/bioconductor-gatom/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gatom/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cancer/build_failure.linux-64.yaml b/recipes/bioconductor-gatom/build_failure.linux-64.yaml similarity index 81% rename from recipes/bioconductor-cancer/build_failure.linux-64.yaml rename to recipes/bioconductor-gatom/build_failure.linux-64.yaml index e0fc6e1bb323f..253ed0b0d61b5 100644 --- a/recipes/bioconductor-cancer/build_failure.linux-64.yaml +++ b/recipes/bioconductor-gatom/build_failure.linux-64.yaml @@ -1,26 +1,25 @@ -recipe_sha: c8371d76491173a2c71d6f48bd4a6acaa34dccfc9e093843f1f28fd72dac3536 # The commit at which this recipe failed to build. +recipe_sha: 7ebb01aa7b6769d098059934bddb98ded4a89c60a59b8400436d8a3a28fb92c1 # The commit at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue log: |2- - - bioconductor-gseabase >=1.62.0,<1.63.0 - - r-circlize - - r-httr - - r-r.oo - - r-survival - - bioconductor-phenotest >=1.48.0,<1.49.0 + - r-mwcsr + - r-pryr + - r-data.table + - r-plyr + - r-shinycyjs >=1.0.0 - r-base 4.3.* - - r-r.methodss3 - - r-rpart - - r-runit - - bioconductor-genetclassifier >=1.40.0,<1.41.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - nothing provides icu 54.* needed by r-base-3.3.2-0 + - - nothing provides requested r-mwcsr + - - nothing provides requested r-shinycyjs >=1.0.0 - Leaving build/test directories: @@ -43,30 +42,33 @@ log: |2- File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve raise RuntimeError("Solver could not find solution." error_string) RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-ggally + - r-xml + - r-sna + - r-htmltools + - r-htmlwidgets + - r-intergraph + - r-ggplot2 + - bioconductor-bionet >=1.62.0,<1.63.0 + - r-network + - r-igraph + - r-mwcsr + - r-pryr + - r-data.table - r-plyr - - r-formula - - r-tkrplot - - bioconductor-biobase >=2.60.0,<2.61.0 - - bioconductor-gseabase >=1.62.0,<1.63.0 - - r-circlize - - r-httr - - r-r.oo - - r-survival - - bioconductor-phenotest >=1.48.0,<1.49.0 + - r-shinycyjs >=1.0.0 - r-base 4.3.* - - r-r.methodss3 - - r-rpart - - r-runit - - bioconductor-genetclassifier >=1.40.0,<1.41.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - nothing provides icu 54.* needed by r-base-3.3.2-0 + - - nothing provides requested r-mwcsr + - - nothing provides requested r-shinycyjs >=1.0.0 - During handling of the above exception, another exception occurred: @@ -100,5 +102,5 @@ log: |2- actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("icu=54"), MatchSpec("r-base==3.3.2=0")} + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-mwcsr"), MatchSpec("r-shinycyjs[version='>=1.0.0']")} # Last 100 lines of the build log. diff --git a/recipes/bioconductor-gatom/meta.yaml b/recipes/bioconductor-gatom/meta.yaml new file mode 100644 index 0000000000000..e51c528dd385d --- /dev/null +++ b/recipes/bioconductor-gatom/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.0.0" %} +{% set name = "gatom" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0e86773c5bafed3a4c13b7db82015463 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gatom", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils +requirements: + host: + - 'bioconductor-bionet >=1.62.0,<1.63.0' + - r-base + - r-data.table + - r-ggally + - r-ggplot2 + - r-htmltools + - r-htmlwidgets + - r-igraph + - r-intergraph + - r-mwcsr + - r-network + - r-plyr + - r-pryr + - 'r-shinycyjs >=1.0.0' + - r-sna + - r-xml + run: + - 'bioconductor-bionet >=1.62.0,<1.63.0' + - r-base + - r-data.table + - r-ggally + - r-ggplot2 + - r-htmltools + - r-htmlwidgets + - r-igraph + - r-intergraph + - r-mwcsr + - r-network + - r-plyr + - r-pryr + - 'r-shinycyjs >=1.0.0' + - r-sna + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENCE' + summary: 'Finding an Active Metabolic Module in Atom Transition Network' + description: 'This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.' + diff --git a/recipes/bioconductor-gbscleanr/meta.yaml b/recipes/bioconductor-gbscleanr/meta.yaml index 9f9a3b75a8f5e..7b565ff74bd52 100644 --- a/recipes/bioconductor-gbscleanr/meta.yaml +++ b/recipes/bioconductor-gbscleanr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.4" %} +{% set version = "1.6.0" %} {% set name = "GBScleanR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1a99a09d42d9cf271d30f570835d9d8 + md5: f54a8356b8931c5c6dd6150a021c56cf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gbscleanr", max_pin="x.x") }}' # Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-expm - r-ggplot2 @@ -32,8 +33,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-expm - r-ggplot2 diff --git a/recipes/bioconductor-gcapc/meta.yaml b/recipes/bioconductor-gcapc/meta.yaml index 3c3a16a0c8b79..9270c58bf5303 100644 --- a/recipes/bioconductor-gcapc/meta.yaml +++ b/recipes/bioconductor-gcapc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "gcapc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9974c87d810bf0e80de4672cdee15c6e + md5: 16c0a9ac78843641871680c0e0d48dfc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gcapc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass - r-matrixstats diff --git a/recipes/bioconductor-gcatest/meta.yaml b/recipes/bioconductor-gcatest/meta.yaml index 9cfd490a3165d..82f540b32e039 100644 --- a/recipes/bioconductor-gcatest/meta.yaml +++ b/recipes/bioconductor-gcatest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.7" %} +{% set version = "2.2.0" %} {% set name = "gcatest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e0cfb7c0ad56c72aaf703b153456d091 + md5: ddfda402a2332e9c16ecfaa035b689a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gcatest", max_pin="x.x") }}' noarch: generic # Suggests: knitr, ggplot2, testthat, BEDMatrix, genio requirements: host: - - 'bioconductor-lfa >=2.0.0,<2.1.0' + - 'bioconductor-lfa >=2.2.0,<2.3.0' - r-base run: - - 'bioconductor-lfa >=2.0.0,<2.1.0' + - 'bioconductor-lfa >=2.2.0,<2.3.0' - r-base test: commands: diff --git a/recipes/bioconductor-gcrisprtools/meta.yaml b/recipes/bioconductor-gcrisprtools/meta.yaml index d07f2c85d5031..421388b058ba2 100644 --- a/recipes/bioconductor-gcrisprtools/meta.yaml +++ b/recipes/bioconductor-gcrisprtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "gCrisprTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a1ff3be1f85750ef41124d7768602df + md5: 113ef693d51de0459865934e9a16d90a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gcrisprtools", max_pin="x.x") }}' noarch: generic # Suggests: edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-rmarkdown - r-robustrankaggreg run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-rmarkdown diff --git a/recipes/bioconductor-gcrma/meta.yaml b/recipes/bioconductor-gcrma/meta.yaml index ba148e347ab47..c742e33709f8f 100644 --- a/recipes/bioconductor-gcrma/meta.yaml +++ b/recipes/bioconductor-gcrma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.72.0" %} +{% set version = "2.74.0" %} {% set name = "gcrma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 78807a1c603b84cf1f0a1eed3ea140a4 + md5: d28b6c225b2677e476da8d0348af4695 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gcrma", max_pin="x.x") }}' # Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-biocmanager - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-biocmanager build: diff --git a/recipes/bioconductor-gcspikelite/meta.yaml b/recipes/bioconductor-gcspikelite/meta.yaml index bcda48ebb7fc7..c6c53cd0af3c6 100644 --- a/recipes/bioconductor-gcspikelite/meta.yaml +++ b/recipes/bioconductor-gcspikelite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "gcspikelite" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 721566ac21590bc7f1e56dd1c716d30c + md5: 91b995753732f0d5508fdc2d7dcb998f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gcspikelite", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gcspikelite/post-link.sh b/recipes/bioconductor-gcspikelite/post-link.sh index e77ece496b3d2..56da58607707c 100644 --- a/recipes/bioconductor-gcspikelite/post-link.sh +++ b/recipes/bioconductor-gcspikelite/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gcspikelite-1.38.0" +installBiocDataPackage.sh "gcspikelite-1.40.0" diff --git a/recipes/bioconductor-gdcrnatools/meta.yaml b/recipes/bioconductor-gdcrnatools/meta.yaml index 75681a20e8676..4ce47ee1d8f08 100644 --- a/recipes/bioconductor-gdcrnatools/meta.yaml +++ b/recipes/bioconductor-gdcrnatools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GDCRNATools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a375e07fa500196928c1c10daf6585ac + md5: bf97cefce864ca1443cb0b0d53601799 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdcrnatools", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, testthat, rmarkdown +# Suggests: knitr, testthat, prettydoc, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicdatacommons >=1.24.0,<1.25.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-dt - r-ggplot2 @@ -42,16 +43,16 @@ requirements: - r-survminer - r-xml run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicdatacommons >=1.24.0,<1.25.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-dt - r-ggplot2 diff --git a/recipes/bioconductor-gdnainrnaseqdata/meta.yaml b/recipes/bioconductor-gdnainrnaseqdata/meta.yaml index 9f347cd9c4adc..bb3142cbcf0d4 100644 --- a/recipes/bioconductor-gdnainrnaseqdata/meta.yaml +++ b/recipes/bioconductor-gdnainrnaseqdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "gDNAinRNAseqData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de757712c6890eb225ad26790e2a23f6 + md5: 52e275ca255493684657a091667f987f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdnainrnaseqdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-rcurl - r-xml run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-rcurl - r-xml - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gdnainrnaseqdata/post-link.sh b/recipes/bioconductor-gdnainrnaseqdata/post-link.sh index 828d3fe116d3a..4daf109d60fca 100644 --- a/recipes/bioconductor-gdnainrnaseqdata/post-link.sh +++ b/recipes/bioconductor-gdnainrnaseqdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gdnainrnaseqdata-1.0.0" +installBiocDataPackage.sh "gdnainrnaseqdata-1.2.0" diff --git a/recipes/bioconductor-gdnax/build.sh b/recipes/bioconductor-gdnax/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdnax/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdnax/meta.yaml b/recipes/bioconductor-gdnax/meta.yaml new file mode 100644 index 0000000000000..d582e28ee690b --- /dev/null +++ b/recipes/bioconductor-gdnax/meta.yaml @@ -0,0 +1,70 @@ +{% set version = "1.0.0" %} +{% set name = "gDNAx" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ca3a7370388bf64ba5ccae7161c64ebd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdnax", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-bitops + - r-plotrix + - r-rcolorbrewer + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-bitops + - r-plotrix + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Diagnostics for assessing genomic DNA contamination in RNA-seq data' + description: 'Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.' + diff --git a/recipes/bioconductor-gdr/build.sh b/recipes/bioconductor-gdr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdr/meta.yaml b/recipes/bioconductor-gdr/meta.yaml new file mode 100644 index 0000000000000..8b311b353ff7d --- /dev/null +++ b/recipes/bioconductor-gdr/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.0.0" %} +{% set name = "gDR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: abefb906e5c9ec014a443b0367844ac9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdr", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 0.99.11), gDRtestData (>= 0.99.11), kableExtra, knitr, markdown, purrr, rmarkdown, SummarizedExperiment, testthat, yaml +requirements: + host: + - 'bioconductor-gdrcore >=1.0.0,<1.1.0' + - 'bioconductor-gdrimport >=1.0.0,<1.1.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - r-base + run: + - 'bioconductor-gdrcore >=1.0.0,<1.1.0' + - 'bioconductor-gdrimport >=1.0.0,<1.1.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Umbrella package for R packages in the gDR suite' + description: 'Package is a part of the gDR suite. It reexports functions from other packages in the gDR suite that contain critical processing functions and utilities. The vignette walks through the full processing pipeline for drug response analyses that the gDR suite offers.' + diff --git a/recipes/bioconductor-gdrcore/build.sh b/recipes/bioconductor-gdrcore/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdrcore/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdrcore/meta.yaml b/recipes/bioconductor-gdrcore/meta.yaml new file mode 100644 index 0000000000000..91fd6a2760db8 --- /dev/null +++ b/recipes/bioconductor-gdrcore/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.0" %} +{% set name = "gDRcore" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 76f729e9fce669107120d0ec73c32bfc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdrcore", max_pin="x.x") }}' +# Suggests: BiocStyle, gDRstyle (>= 0.99.15), gDRimport (>= 0.99.10), gDRtestData (>= 0.99.20), IRanges, knitr, pkgbuild, qs, testthat, yaml +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-checkmate + - r-data.table + - r-futile.logger + - r-purrr + - r-stringr + - libblas + - liblapack + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-checkmate + - r-data.table + - r-futile.logger + - r-purrr + - r-stringr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Processing functions and interface to process and analyze drug dose-response data' + description: 'This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way.' + diff --git a/recipes/bioconductor-gdrimport/build.sh b/recipes/bioconductor-gdrimport/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdrimport/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdrimport/meta.yaml b/recipes/bioconductor-gdrimport/meta.yaml new file mode 100644 index 0000000000000..2b32dd59962bc --- /dev/null +++ b/recipes/bioconductor-gdrimport/meta.yaml @@ -0,0 +1,74 @@ +{% set version = "1.0.0" %} +{% set name = "gDRimport" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0390ee6a16f21624044bc509ebdbabd1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdrimport", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, gDRtestData (>= 0.99.10), gDRstyle (>= 0.99.11), knitr, purrr, qs, testthat +requirements: + host: + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-assertthat + - r-base + - r-checkmate + - r-data.table + - r-futile.logger + - r-magrittr + - r-openxlsx + - r-readxl + - r-rio + - r-stringi + - r-tibble + - r-xml + - r-yaml + run: + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-assertthat + - r-base + - r-checkmate + - r-data.table + - r-futile.logger + - r-magrittr + - r-openxlsx + - r-readxl + - r-rio + - r-stringi + - r-tibble + - r-xml + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package for handling the import of dose-response data' + description: 'The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats.' + diff --git a/recipes/bioconductor-gdrstyle/build.sh b/recipes/bioconductor-gdrstyle/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdrstyle/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdrstyle/meta.yaml b/recipes/bioconductor-gdrstyle/meta.yaml new file mode 100644 index 0000000000000..e8ec2ff8fdf2a --- /dev/null +++ b/recipes/bioconductor-gdrstyle/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.0.0" %} +{% set name = "gDRstyle" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 473f3c2e73e05f50ec3af2b72bb18a55 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdrstyle", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-bioccheck >=1.38.0,<1.39.0' + - r-base + - r-biocmanager + - r-desc + - r-git2r + - 'r-lintr >=3.0.0' + - r-pkgbuild + - r-rcmdcheck + - r-remotes + - r-rjson + - r-withr + - r-yaml + run: + - 'bioconductor-bioccheck >=1.38.0,<1.39.0' + - r-base + - r-biocmanager + - r-desc + - r-git2r + - 'r-lintr >=3.0.0' + - r-pkgbuild + - r-rcmdcheck + - r-remotes + - r-rjson + - r-withr + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A package with style requirements for the gDR suite' + description: 'Package fills a helper package role for whole gDR suite. It helps to support good development practices by keeping style requirements and style tests for other packages. It also contains build helpers to make all package requirements met.' + diff --git a/recipes/bioconductor-gdrtestdata/meta.yaml b/recipes/bioconductor-gdrtestdata/meta.yaml new file mode 100644 index 0000000000000..0118da30f9290 --- /dev/null +++ b/recipes/bioconductor-gdrtestdata/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.0" %} +{% set name = "gDRtestData" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8de3dea2673f0e7dc9412e36da2c4f9d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdrtestdata", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, data.table, gDRstyle (>= 0.99.16), knitr, qs, reshape2, rmarkdown, SummarizedExperiment, testthat +requirements: + host: + - r-base + - r-checkmate + run: + - r-base + - r-checkmate + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'gDRtestData - R data package with testing dose reponse data' + description: 'R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains RDS files with MAE data processed by gDR.' + diff --git a/recipes/bioconductor-gdrtestdata/post-link.sh b/recipes/bioconductor-gdrtestdata/post-link.sh new file mode 100644 index 0000000000000..1e1afaeb5de88 --- /dev/null +++ b/recipes/bioconductor-gdrtestdata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "gdrtestdata-1.0.0" diff --git a/recipes/bioconductor-gdrtestdata/pre-unlink.sh b/recipes/bioconductor-gdrtestdata/pre-unlink.sh new file mode 100644 index 0000000000000..d04affb324053 --- /dev/null +++ b/recipes/bioconductor-gdrtestdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ gDRtestData diff --git a/recipes/bioconductor-gdrutils/build.sh b/recipes/bioconductor-gdrutils/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdrutils/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdrutils/meta.yaml b/recipes/bioconductor-gdrutils/meta.yaml new file mode 100644 index 0000000000000..ea940ee0ab23d --- /dev/null +++ b/recipes/bioconductor-gdrutils/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.0.0" %} +{% set name = "gDRutils" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fdf71802bbd5967b163447eda2fe37ef +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdrutils", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocManager, BiocStyle, futile.logger, gDRstyle (>= 0.99.15), gDRtestData (>= 0.99.12), IRanges, knitr, lintr, purrr, qs, rcmdcheck, rmarkdown, testthat, tools, yaml +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-checkmate + - r-data.table + - r-drc + - r-jsonlite + - r-jsonvalidate + - r-magrittr + - r-stringr + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-checkmate + - r-data.table + - r-drc + - r-jsonlite + - r-jsonvalidate + - r-magrittr + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A package with helper functions for processing drug response data' + description: 'This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many of the functions are utilized by the gDRcore package.' + diff --git a/recipes/bioconductor-gdsarray/meta.yaml b/recipes/bioconductor-gdsarray/meta.yaml index 25d7d2c956c81..66ec184fb02c7 100644 --- a/recipes/bioconductor-gdsarray/meta.yaml +++ b/recipes/bioconductor-gdsarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GDSArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bbc6fe4ba9fe9379724590bb868e6332 + md5: 3ae99d95017d67dd67e17f47436f0301 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdsarray", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-gdsfmt/meta.yaml b/recipes/bioconductor-gdsfmt/meta.yaml index eb66ba4b7c045..e69a5c33b929e 100644 --- a/recipes/bioconductor-gdsfmt/meta.yaml +++ b/recipes/bioconductor-gdsfmt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "gdsfmt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7e54216f1539f908f188665986552ab5 + md5: 8851c188356c12f7e99488ceb4daeca8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gdsfmt", max_pin="x.x") }}' # Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics requirements: host: diff --git a/recipes/bioconductor-gem/meta.yaml b/recipes/bioconductor-gem/meta.yaml index 72cf2fdcff018..3cb07be59e5e2 100644 --- a/recipes/bioconductor-gem/meta.yaml +++ b/recipes/bioconductor-gem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3380a1e025f9cae67a0d51dba6afa7a + md5: 2c2c8e79fda151dee0060411c9610ff4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gem", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown requirements: diff --git a/recipes/bioconductor-gemini/meta.yaml b/recipes/bioconductor-gemini/meta.yaml index 67a4b1e9adcb7..974ee79f5a978 100644 --- a/recipes/bioconductor-gemini/meta.yaml +++ b/recipes/bioconductor-gemini/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "gemini" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a753f3c9edcc5daa937e60bdf51defa6 + md5: e8c26d0e8208f56017c8c83a17582f37 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gemini", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-gemma.r/meta.yaml b/recipes/bioconductor-gemma.r/meta.yaml index ad53496689310..d15d66baff3ab 100644 --- a/recipes/bioconductor-gemma.r/meta.yaml +++ b/recipes/bioconductor-gemma.r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "2.0.0" %} {% set name = "gemma.R" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a3bb3ba1d43da242f629d1fbe0025fd + md5: 404ce4fa50032ebf727cfdccece32ba2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gemma.r", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, digest requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-bit64 - r-data.table + - r-digest - r-glue - r-httr - r-jsonlite @@ -39,15 +41,15 @@ requirements: - r-stringr - r-tibble - r-tidyr - - r-digest run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-bit64 - r-data.table + - r-digest - r-glue - r-httr - r-jsonlite @@ -59,7 +61,6 @@ requirements: - r-stringr - r-tibble - r-tidyr - - r-digest test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genarise/meta.yaml b/recipes/bioconductor-genarise/meta.yaml index 4ab4cff3db280..ade2b312fe4f8 100644 --- a/recipes/bioconductor-genarise/meta.yaml +++ b/recipes/bioconductor-genarise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "genArise" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ae9d863347d759aeac2262402b9ba2f + md5: d81489147ccfe688c07c228b7fcfcf7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genarise", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-geneattribution/meta.yaml b/recipes/bioconductor-geneattribution/meta.yaml index c548dc31b64f9..e0e87d633ea5f 100644 --- a/recipes/bioconductor-geneattribution/meta.yaml +++ b/recipes/bioconductor-geneattribution/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "geneAttribution" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dfe81a4044fe2d88cdef174a85cb7b8 + md5: 62d05af7aabb146fb41a5d91fa460dff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneattribution", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-genebreak/meta.yaml b/recipes/bioconductor-genebreak/meta.yaml index b137ef0843179..fded2e8fdf46a 100644 --- a/recipes/bioconductor-genebreak/meta.yaml +++ b/recipes/bioconductor-genebreak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "GeneBreak" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba0252965f6f22957eb6ecbd57e8fb32 + md5: 32b69bf4150c25c908235217dc805ed3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genebreak", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base test: commands: diff --git a/recipes/bioconductor-geneclassifiers/meta.yaml b/recipes/bioconductor-geneclassifiers/meta.yaml index 9e957638335a5..1bbd879fd921b 100644 --- a/recipes/bioconductor-geneclassifiers/meta.yaml +++ b/recipes/bioconductor-geneclassifiers/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "geneClassifiers" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1718d2e4ca0d91d6d292acb46a3c712a + md5: 79b7de2354913e5a91e6026f3f815a46 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneclassifiers", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-geneexpressionsignature/meta.yaml b/recipes/bioconductor-geneexpressionsignature/meta.yaml index 8a88f5ad130c6..784b7d4b4cc8a 100644 --- a/recipes/bioconductor-geneexpressionsignature/meta.yaml +++ b/recipes/bioconductor-geneexpressionsignature/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "GeneExpressionSignature" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13984cbd32793c3241e81ab4ca1fa33e + md5: ee82254ee781e3cd6657c89d94e052b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneexpressionsignature", max_pin="x.x") }}' noarch: generic # Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-genefilter/meta.yaml b/recipes/bioconductor-genefilter/meta.yaml index c39b2d22d053c..1e6cb5b05ad13 100644 --- a/recipes/bioconductor-genefilter/meta.yaml +++ b/recipes/bioconductor-genefilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.82.1" %} +{% set version = "1.84.0" %} {% set name = "genefilter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 06f347aaeeb8cb036bb7df7dfe1c67fb + md5: 15011d1662a58967aeb3e89f1f660e40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genefilter", max_pin="x.x") }}' # Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - r-base - r-survival - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - r-base - r-survival build: diff --git a/recipes/bioconductor-genefu/meta.yaml b/recipes/bioconductor-genefu/meta.yaml index 6480c3e1fad27..c9f8b815ed663 100644 --- a/recipes/bioconductor-genefu/meta.yaml +++ b/recipes/bioconductor-genefu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "genefu" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c0fe8ccf39d5090209936c71224c2301 + md5: cfaef57b66d09a355ae7df0db21c107d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genefu", max_pin="x.x") }}' noarch: generic # Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown requirements: host: - - 'bioconductor-aims >=1.32.0,<1.33.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-survcomp >=1.50.0,<1.51.0' + - 'bioconductor-aims >=1.34.0,<1.35.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-survcomp >=1.52.0,<1.53.0' - r-amap - r-base - r-ic10 - r-mclust run: - - 'bioconductor-aims >=1.32.0,<1.33.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-survcomp >=1.50.0,<1.51.0' + - 'bioconductor-aims >=1.34.0,<1.35.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-survcomp >=1.52.0,<1.53.0' - r-amap - r-base - r-ic10 diff --git a/recipes/bioconductor-genega/build.sh b/recipes/bioconductor-genega/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genega/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genega/meta.yaml b/recipes/bioconductor-genega/meta.yaml new file mode 100644 index 0000000000000..296123222ca7a --- /dev/null +++ b/recipes/bioconductor-genega/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.52.0" %} +{% set name = "GeneGA" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3047f864af1845ce91869fc2560733c4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genega", max_pin="x.x") }}' + noarch: generic +requirements: + host: + - r-base + - r-hash + - r-seqinr + run: + - r-base + - r-hash + - r-seqinr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL version 2' + summary: 'Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm' + description: 'R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + diff --git a/recipes/bioconductor-genegeneinter/meta.yaml b/recipes/bioconductor-genegeneinter/meta.yaml index 03f30e758faf8..666e48ad08da2 100644 --- a/recipes/bioconductor-genegeneinter/meta.yaml +++ b/recipes/bioconductor-genegeneinter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GeneGeneInteR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4764cc9239b96f79d0dd56ad6774ec44 + md5: 119efde24626155c173e9b24b5f2c9e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genegeneinter", max_pin="x.x") }}' requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - r-data.table - r-factominer @@ -32,10 +33,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - r-data.table - r-factominer diff --git a/recipes/bioconductor-genelendatabase/meta.yaml b/recipes/bioconductor-genelendatabase/meta.yaml index af599c18cb481..7619efdaf2175 100644 --- a/recipes/bioconductor-genelendatabase/meta.yaml +++ b/recipes/bioconductor-genelendatabase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "geneLenDataBase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3063a75a94ecd65185c3490a1baba601 + md5: c29099d3142aad07590e22ce37c6acf3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genelendatabase", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genelendatabase/post-link.sh b/recipes/bioconductor-genelendatabase/post-link.sh index 70d73fa6e2f73..5423b1add506e 100644 --- a/recipes/bioconductor-genelendatabase/post-link.sh +++ b/recipes/bioconductor-genelendatabase/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genelendatabase-1.36.0" +installBiocDataPackage.sh "genelendatabase-1.38.0" diff --git a/recipes/bioconductor-genemeta/meta.yaml b/recipes/bioconductor-genemeta/meta.yaml index 79f0a57e7e661..46829e4dab0d2 100644 --- a/recipes/bioconductor-genemeta/meta.yaml +++ b/recipes/bioconductor-genemeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "GeneMeta" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa838d8d2428d4d9337732db43dc84f8 + md5: 9d9d2d3dff0ee8a497ac86b5ef8ddac7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genemeta", max_pin="x.x") }}' noarch: generic # Suggests: RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' - r-base test: commands: diff --git a/recipes/bioconductor-genenetworkbuilder/meta.yaml b/recipes/bioconductor-genenetworkbuilder/meta.yaml index 2ef96e766b715..40e22076b24fd 100644 --- a/recipes/bioconductor-genenetworkbuilder/meta.yaml +++ b/recipes/bioconductor-genenetworkbuilder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "GeneNetworkBuilder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17f9146e215456d82474c6afd253cbcd + md5: aedb0b143d59865acfad5ce4d635ff77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genenetworkbuilder", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-htmlwidgets - r-plyr @@ -31,8 +32,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-htmlwidgets - r-plyr diff --git a/recipes/bioconductor-geneoverlap/meta.yaml b/recipes/bioconductor-geneoverlap/meta.yaml index f2da503615aa5..3912599cb2a10 100644 --- a/recipes/bioconductor-geneoverlap/meta.yaml +++ b/recipes/bioconductor-geneoverlap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "GeneOverlap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ddbc52b3f7cb42b24e0563c3d1039181 + md5: 0b5179a1183a82869935ca6c2c55aab3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneoverlap", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle requirements: diff --git a/recipes/bioconductor-geneplast.data.string.v91/meta.yaml b/recipes/bioconductor-geneplast.data.string.v91/meta.yaml index 8e04e55589622..db3e08458d885 100644 --- a/recipes/bioconductor-geneplast.data.string.v91/meta.yaml +++ b/recipes/bioconductor-geneplast.data.string.v91/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.6" %} {% set name = "geneplast.data.string.v91" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 86433f8489d9228c5ed73e2b75a55398 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneplast.data.string.v91", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-geneplast.data/meta.yaml b/recipes/bioconductor-geneplast.data/meta.yaml index a7873a0336455..20f45bdf6867b 100644 --- a/recipes/bioconductor-geneplast.data/meta.yaml +++ b/recipes/bioconductor-geneplast.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.99.6" %} +{% set version = "0.99.7" %} {% set name = "geneplast.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 08ddcdb9b1cf56dab5fe358c85fe1526 + md5: ef658e131138d87033fcd985c38cf45f build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneplast.data", max_pin="x.x") }}' noarch: generic # Suggests: geneplast, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-geneplast >=1.28.0,<1.29.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' + - r-ape - r-base + - r-dplyr + - r-igraph + - r-purrr + - r-readr + - r-tibble run: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-geneplast >=1.28.0,<1.29.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' + - r-ape - r-base + - r-dplyr + - r-igraph + - r-purrr + - r-readr + - r-tibble - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-geneplast.data/post-link.sh b/recipes/bioconductor-geneplast.data/post-link.sh index 970dff7551c64..879df13431c7f 100644 --- a/recipes/bioconductor-geneplast.data/post-link.sh +++ b/recipes/bioconductor-geneplast.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "geneplast.data-0.99.6" +installBiocDataPackage.sh "geneplast.data-0.99.7" diff --git a/recipes/bioconductor-geneplast/meta.yaml b/recipes/bioconductor-geneplast/meta.yaml index 5f40829a0c17c..c78eca2385118 100644 --- a/recipes/bioconductor-geneplast/meta.yaml +++ b/recipes/bioconductor-geneplast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "geneplast" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 38d4e706cda6dee7ef9ca9e3bf4e7c23 + md5: 2cb6b3ec6dbd0978146ea5139cc06e60 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneplast", max_pin="x.x") }}' noarch: generic # Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr requirements: diff --git a/recipes/bioconductor-geneplotter/meta.yaml b/recipes/bioconductor-geneplotter/meta.yaml index e1dd4c0c5091a..67627719ca339 100644 --- a/recipes/bioconductor-geneplotter/meta.yaml +++ b/recipes/bioconductor-geneplotter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "geneplotter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 58bd98605be308d6dd876b6d9fcb10b5 + md5: 29d4ec34db2e953fc9b7306f4d3b7733 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneplotter", max_pin="x.x") }}' noarch: generic -# Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db +# Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-lattice - r-rcolorbrewer run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-lattice - r-rcolorbrewer diff --git a/recipes/bioconductor-generecommender/meta.yaml b/recipes/bioconductor-generecommender/meta.yaml index fa96fc46b2655..55b5c7e1ae759 100644 --- a/recipes/bioconductor-generecommender/meta.yaml +++ b/recipes/bioconductor-generecommender/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "geneRecommender" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cafc0026010c2cd8bbe5b81fe0957e46 + md5: cd697c11912a8f48b5ceaf0abfbb206e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-generecommender", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-generegionscan/meta.yaml b/recipes/bioconductor-generegionscan/meta.yaml index a6525458e7681..c81ed957e93b0 100644 --- a/recipes/bioconductor-generegionscan/meta.yaml +++ b/recipes/bioconductor-generegionscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "GeneRegionScan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c4b75b0cc7beb7f8b3ad6a3e52a93a5 + md5: 9b3e0cfd305d2db2aae5cfd4003e56a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-generegionscan", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome, affy, AnnotationDbi requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-generxcluster/meta.yaml b/recipes/bioconductor-generxcluster/meta.yaml index fac45bf16a238..47294fc1e4560 100644 --- a/recipes/bioconductor-generxcluster/meta.yaml +++ b/recipes/bioconductor-generxcluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "geneRxCluster" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ec6aade79eab7d5be66b90c84b9588e + md5: 61f7d4c5cd314cf84f8648b3097f65b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-generxcluster", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-geneselectmmd/meta.yaml b/recipes/bioconductor-geneselectmmd/meta.yaml index 576bc392a9563..ca85264568320 100644 --- a/recipes/bioconductor-geneselectmmd/meta.yaml +++ b/recipes/bioconductor-geneselectmmd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.1" %} +{% set version = "2.46.0" %} {% set name = "GeneSelectMMD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6552e99f88c6a84d5a34da69b07fb137 + md5: dd6cd07bbe095fca03ce4b134c1507b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneselectmmd", max_pin="x.x") }}' # Suggests: ALL requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-mass - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-mass build: diff --git a/recipes/bioconductor-genesis/meta.yaml b/recipes/bioconductor-genesis/meta.yaml index 7a545c218c54d..49123fdd70790 100644 --- a/recipes/bioconductor-genesis/meta.yaml +++ b/recipes/bioconductor-genesis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "GENESIS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 505a2cf97bef5db3db33657c43937f25 + md5: 909c6b6ea17b2de1716f3a5102caa0df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genesis", max_pin="x.x") }}' # Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-seqvartools >=1.38.0,<1.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-seqvartools >=1.40.0,<1.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base - r-data.table - r-igraph @@ -39,17 +40,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-seqvartools >=1.38.0,<1.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-seqvartools >=1.40.0,<1.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base - r-data.table - r-igraph diff --git a/recipes/bioconductor-genestructuretools/meta.yaml b/recipes/bioconductor-genestructuretools/meta.yaml index bf24c68b375c4..b68d6a11f06d2 100644 --- a/recipes/bioconductor-genestructuretools/meta.yaml +++ b/recipes/bioconductor-genestructuretools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GeneStructureTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 328a3a8ae004e92c4bf515807fe4878c + md5: 513385498b639ea6acc724bb3795de38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genestructuretools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-plyr - r-stringdist - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-plyr diff --git a/recipes/bioconductor-genesummary/meta.yaml b/recipes/bioconductor-genesummary/meta.yaml index 1f56999b19e6c..3f59623599845 100644 --- a/recipes/bioconductor-genesummary/meta.yaml +++ b/recipes/bioconductor-genesummary/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.99.4" %} +{% set version = "0.99.6" %} {% set name = "GeneSummary" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39ee728e42c42ccf200568c9c736b15c + md5: 9df029a96bf0fa5bb76ee8b8923c458c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genesummary", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown, testthat requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genesummary/post-link.sh b/recipes/bioconductor-genesummary/post-link.sh index 536bca09030a3..542c1ac8a9539 100644 --- a/recipes/bioconductor-genesummary/post-link.sh +++ b/recipes/bioconductor-genesummary/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genesummary-0.99.4" +installBiocDataPackage.sh "genesummary-0.99.6" diff --git a/recipes/bioconductor-genetclassifier/meta.yaml b/recipes/bioconductor-genetclassifier/meta.yaml index 4b1142313a1ff..d449d168bddc2 100644 --- a/recipes/bioconductor-genetclassifier/meta.yaml +++ b/recipes/bioconductor-genetclassifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "geNetClassifier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 225d0b3e450c41009734391c48982794 + md5: 7fed3e42e9ec93956b71960e271aa090 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genetclassifier", max_pin="x.x") }}' noarch: generic # Suggests: leukemiasEset, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ebarrays >=2.64.0,<2.65.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' - r-base - r-e1071 test: diff --git a/recipes/bioconductor-geneticsped/meta.yaml b/recipes/bioconductor-geneticsped/meta.yaml index 96bda76dee472..50a50397e73b2 100644 --- a/recipes/bioconductor-geneticsped/meta.yaml +++ b/recipes/bioconductor-geneticsped/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.1" %} +{% set version = "1.64.0" %} {% set name = "GeneticsPed" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 49e37937196a5ec28dafaa5f2c6c0dda + md5: 7d2a79c363e79459dd3edf3b4571f313 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geneticsped", max_pin="x.x") }}' # Suggests: RUnit, gtools requirements: host: diff --git a/recipes/bioconductor-genetonic/meta.yaml b/recipes/bioconductor-genetonic/meta.yaml index 7d83f66968092..4c8e329fd8f3d 100644 --- a/recipes/bioconductor-genetonic/meta.yaml +++ b/recipes/bioconductor-genetonic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "GeneTonic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 012923a30c9d452dd7c826205ecc487d + md5: efbbb39095cb7ff8af87ed47d058d8d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genetonic", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-backbone - r-base - 'r-bs4dash >=2.0.0' @@ -60,12 +61,12 @@ requirements: - r-viridis - r-visnetwork run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-backbone - r-base - 'r-bs4dash >=2.0.0' diff --git a/recipes/bioconductor-genextender/meta.yaml b/recipes/bioconductor-genextender/meta.yaml index 896b13b8fdf81..7676ab9d54672 100644 --- a/recipes/bioconductor-genextender/meta.yaml +++ b/recipes/bioconductor-genextender/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "geneXtendeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39265282123addaf808976a865e308a1 + md5: 63ab36f83aa3d05bf932dc3c0e0c173a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genextender", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr @@ -36,11 +37,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-genie3/meta.yaml b/recipes/bioconductor-genie3/meta.yaml index 9bbb0aef73375..bfc164119e27e 100644 --- a/recipes/bioconductor-genie3/meta.yaml +++ b/recipes/bioconductor-genie3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "GENIE3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,13 +11,14 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37c69218e0e7a1e204d4762de1125c4f + md5: fb7d197e0e34175eba7dd31608aa67d6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods + run_exports: '{{ pin_subpackage("bioconductor-genie3", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle requirements: host: - r-base diff --git a/recipes/bioconductor-genocn/meta.yaml b/recipes/bioconductor-genocn/meta.yaml index e52d58a4e1fff..5e9274f6a5ac2 100644 --- a/recipes/bioconductor-genocn/meta.yaml +++ b/recipes/bioconductor-genocn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "genoCN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b42af5b706f84966e90e5bc11fd129f + md5: ebc7fc5cb3b5c2bcd98718a7bcd95d6a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genocn", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-genomation/meta.yaml b/recipes/bioconductor-genomation/meta.yaml index c1238d45396e5..447d7838acc42 100644 --- a/recipes/bioconductor-genomation/meta.yaml +++ b/recipes/bioconductor-genomation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "genomation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c6f6732f5e75f74f3f27c60de3640e5 + md5: 5453f50009f3f7227025431d4d10f4bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomation", max_pin="x.x") }}' # Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqpattern >=1.32.0,<1.33.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqpattern >=1.34.0,<1.35.0' - r-base - r-data.table - r-ggplot2 @@ -44,17 +45,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqpattern >=1.32.0,<1.33.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqpattern >=1.34.0,<1.35.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-genomationdata/meta.yaml b/recipes/bioconductor-genomationdata/meta.yaml index 0a5f89afe117f..8cb6a2198f75f 100644 --- a/recipes/bioconductor-genomationdata/meta.yaml +++ b/recipes/bioconductor-genomationdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "genomationData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4954915523744efa6d6b3be3feb376eb + md5: dc03eef7730719f7c66f72ca5e9915db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomationdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomationdata/post-link.sh b/recipes/bioconductor-genomationdata/post-link.sh index 8656156c48e81..e092bd607d41b 100644 --- a/recipes/bioconductor-genomationdata/post-link.sh +++ b/recipes/bioconductor-genomationdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genomationdata-1.32.0" +installBiocDataPackage.sh "genomationdata-1.34.0" diff --git a/recipes/bioconductor-genomautomorphism/meta.yaml b/recipes/bioconductor-genomautomorphism/meta.yaml index 89852d60869f8..e16df4a231b76 100644 --- a/recipes/bioconductor-genomautomorphism/meta.yaml +++ b/recipes/bioconductor-genomautomorphism/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "GenomAutomorphism" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53d0988019e357223e35df19cb2da04b + md5: 36ebcd90b454dc7450e875730537811b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomautomorphism", max_pin="x.x") }}' noarch: generic # Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel @@ -35,13 +36,13 @@ requirements: - r-foreach - r-numbers run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-genomeinfodb/meta.yaml b/recipes/bioconductor-genomeinfodb/meta.yaml index 7cbd5ae154ce2..e033652eb641c 100644 --- a/recipes/bioconductor-genomeinfodb/meta.yaml +++ b/recipes/bioconductor-genomeinfodb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.1" %} {% set name = "GenomeInfoDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 635ff12af224e0f7902c35e3dc9166a8 + md5: 4bb1aef4ea2a6422141e3024e11b85e1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomeinfodb", max_pin="x.x") }}' noarch: generic # Suggests: GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcurl run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcurl test: diff --git a/recipes/bioconductor-genomeinfodbdata/meta.yaml b/recipes/bioconductor-genomeinfodbdata/meta.yaml index 4b55d8a8062a3..f4d61f874b1f7 100644 --- a/recipes/bioconductor-genomeinfodbdata/meta.yaml +++ b/recipes/bioconductor-genomeinfodbdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.10" %} +{% set version = "1.2.11" %} {% set name = "GenomeInfoDbData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ebd78c10d672c0eb6c893d6135bdeca9 + md5: 2a4cbfc2031992fed3c9445f450890a2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomeinfodbdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomeinfodbdata/post-link.sh b/recipes/bioconductor-genomeinfodbdata/post-link.sh index af44f56f53dbb..42b37c9d4d1ca 100644 --- a/recipes/bioconductor-genomeinfodbdata/post-link.sh +++ b/recipes/bioconductor-genomeinfodbdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genomeinfodbdata-1.2.10" +installBiocDataPackage.sh "genomeinfodbdata-1.2.11" diff --git a/recipes/bioconductor-genomeintervals/meta.yaml b/recipes/bioconductor-genomeintervals/meta.yaml index c885e2e647ba8..a0b7c1292199a 100644 --- a/recipes/bioconductor-genomeintervals/meta.yaml +++ b/recipes/bioconductor-genomeintervals/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "genomeIntervals" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61b757f3185a04ee582d4dc6e438049d + md5: c47b9bb1293b799a7ac75fef82f45589 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomeintervals", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-intervals >=0.14.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-intervals >=0.14.0' test: diff --git a/recipes/bioconductor-genomes/meta.yaml b/recipes/bioconductor-genomes/meta.yaml index dfc0cd2e55aa1..580bd6df948d1 100644 --- a/recipes/bioconductor-genomes/meta.yaml +++ b/recipes/bioconductor-genomes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.30.0" %} +{% set version = "3.32.0" %} {% set name = "genomes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 09a34e355a35b551f3729d436f8c0c68 + md5: 4c11ca2b7b1d4dfd1ffc178b1d9e87e2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomes", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml b/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml index 3bb6161ae7521..5c85ea0ef7f2e 100644 --- a/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml +++ b/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.6" %} {% set name = "genomewidesnp5Crlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cc24140cd17758b8e09f4fe6c931526a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomewidesnp5crlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml b/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml index 86c00002d3b5a..097994bdee0b6 100644 --- a/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml +++ b/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.7" %} {% set name = "genomewidesnp6Crlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 13dd5aef3d814524896f2f3013beb78b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomewidesnp6crlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomicalignments/meta.yaml b/recipes/bioconductor-genomicalignments/meta.yaml index 3342427f46583..7c60c29965ab8 100644 --- a/recipes/bioconductor-genomicalignments/meta.yaml +++ b/recipes/bioconductor-genomicalignments/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "GenomicAlignments" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a9f56bd93dc00324d09899c195275c0 + md5: a5b7669b8ef7444527c2e43c49840014 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicalignments", max_pin="x.x") }}' # Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-genomicdatacommons/meta.yaml b/recipes/bioconductor-genomicdatacommons/meta.yaml index e07ffd0086e9d..fd0e442c7e4ad 100644 --- a/recipes/bioconductor-genomicdatacommons/meta.yaml +++ b/recipes/bioconductor-genomicdatacommons/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.2" %} +{% set version = "1.26.0" %} {% set name = "GenomicDataCommons" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ddc3c5db11c0776b0323b935b59b220 + md5: 6c945795f62ce3e0b470b07b892d3357 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicdatacommons", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-dplyr - r-httr @@ -32,10 +33,11 @@ requirements: - r-readr - r-rlang - r-tibble + - r-tidyr - r-xml2 run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-dplyr - r-httr @@ -45,6 +47,7 @@ requirements: - r-readr - r-rlang - r-tibble + - r-tidyr - r-xml2 test: commands: diff --git a/recipes/bioconductor-genomicdistributions/meta.yaml b/recipes/bioconductor-genomicdistributions/meta.yaml index d1f2fedfc6aa1..fb182b1896bd6 100644 --- a/recipes/bioconductor-genomicdistributions/meta.yaml +++ b/recipes/bioconductor-genomicdistributions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GenomicDistributions" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 851fd18793882aecf6c63c84f9005ce9 + md5: 0b8c2d9df85f9884bb40e3fcd015c824 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicdistributions", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-broom - r-data.table @@ -34,10 +35,10 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-broom - r-data.table diff --git a/recipes/bioconductor-genomicdistributionsdata/meta.yaml b/recipes/bioconductor-genomicdistributionsdata/meta.yaml index beca31a1d93ac..2cb349acc7580 100644 --- a/recipes/bioconductor-genomicdistributionsdata/meta.yaml +++ b/recipes/bioconductor-genomicdistributionsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GenomicDistributionsData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55e98f9b1fe5ee9ab222a5aa3866943a + md5: 84067e85ccbf3605bc1f5a1b7d8508ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicdistributionsdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-data.table run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-data.table - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomicdistributionsdata/post-link.sh b/recipes/bioconductor-genomicdistributionsdata/post-link.sh index cfc600cc2e0c5..08f6cdb719a09 100644 --- a/recipes/bioconductor-genomicdistributionsdata/post-link.sh +++ b/recipes/bioconductor-genomicdistributionsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genomicdistributionsdata-1.8.0" +installBiocDataPackage.sh "genomicdistributionsdata-1.10.0" diff --git a/recipes/bioconductor-genomicfeatures/meta.yaml b/recipes/bioconductor-genomicfeatures/meta.yaml index e1a4b4a46bd5c..705fb92048fa5 100644 --- a/recipes/bioconductor-genomicfeatures/meta.yaml +++ b/recipes/bioconductor-genomicfeatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.1" %} +{% set version = "1.54.1" %} {% set name = "GenomicFeatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc478bb79f2628bc4c58de1ff8d33668 + md5: 863085394fd911039eca1603e6393c1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicfeatures", max_pin="x.x") }}' noarch: generic # Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - r-rcurl - 'r-rsqlite >=2.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - r-rcurl diff --git a/recipes/bioconductor-genomicfiles/meta.yaml b/recipes/bioconductor-genomicfiles/meta.yaml index 36115b932696e..bb74043dc99a0 100644 --- a/recipes/bioconductor-genomicfiles/meta.yaml +++ b/recipes/bioconductor-genomicfiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "GenomicFiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5de71058341eb16a65d666bbd2618e5a + md5: 7a58dc35c19ed34afe95d505d15db3f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicfiles", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-genomicinstability/meta.yaml b/recipes/bioconductor-genomicinstability/meta.yaml index a0061cbd2d814..01dd64732ea05 100644 --- a/recipes/bioconductor-genomicinstability/meta.yaml +++ b/recipes/bioconductor-genomicinstability/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "genomicInstability" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f8709d46b6e2870ab2771f7099dc895 + md5: 0d7c244a904ea9286d4e965cddeaf2d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicinstability", max_pin="x.x") }}' noarch: generic # Suggests: SingleCellExperiment, ExperimentHub, pROC requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-mixtools run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-mixtools diff --git a/recipes/bioconductor-genomicinteractionnodes/meta.yaml b/recipes/bioconductor-genomicinteractionnodes/meta.yaml index a00e6f85b7526..322240c8d1118 100644 --- a/recipes/bioconductor-genomicinteractionnodes/meta.yaml +++ b/recipes/bioconductor-genomicinteractionnodes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "GenomicInteractionNodes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da185a0ec49bd142ea1fb4c365599d45 + md5: bacb75bdd25ea06d5102c1ef2648c588 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicinteractionnodes", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-genomicinteractions/meta.yaml b/recipes/bioconductor-genomicinteractions/meta.yaml index 923de96395878..64e03a3fa483f 100644 --- a/recipes/bioconductor-genomicinteractions/meta.yaml +++ b/recipes/bioconductor-genomicinteractions/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GenomicInteractions" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b50a2df0c508f4d8f54a739de6b9cfbe + md5: f4bccdd21d639ba8b9907ced202c0082 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicinteractions", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -39,16 +40,16 @@ requirements: - r-igraph - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-genomicozone/meta.yaml b/recipes/bioconductor-genomicozone/meta.yaml index 307bc8ba7dd6a..6c9364066561c 100644 --- a/recipes/bioconductor-genomicozone/meta.yaml +++ b/recipes/bioconductor-genomicozone/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "GenomicOZone" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ba77a29cf4e56d2fa6dcf8d38fc6982 + md5: c975a4b1c29d471efe90a5bba68247bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicozone", max_pin="x.x") }}' noarch: generic # Suggests: readxl, GEOquery, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ckmeans.1d.dp >=4.3.0' - r-ggplot2 @@ -35,12 +36,12 @@ requirements: - r-plyr - r-rdpack run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ckmeans.1d.dp >=4.3.0' - r-ggplot2 diff --git a/recipes/bioconductor-genomicplot/build.sh b/recipes/bioconductor-genomicplot/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genomicplot/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomicplot/meta.yaml b/recipes/bioconductor-genomicplot/meta.yaml new file mode 100644 index 0000000000000..de408ccbe32ff --- /dev/null +++ b/recipes/bioconductor-genomicplot/meta.yaml @@ -0,0 +1,87 @@ +{% set version = "1.0.0" %} +{% set name = "GenomicPlot" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ff0cee9d866f4cea69ee355bdac1f574 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicplot", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, AnnotationHub, AnnotationDbi, R.utils, Biobase, BSgenome.Hsapiens.UCSC.hg19, BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), BiocStyle, testthat +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rcas >=1.28.0,<1.29.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-circlize + - 'r-cowplot >=1.1.1' + - r-dplyr + - 'r-ggplot2 >=3.3.5' + - r-ggplotify + - r-ggpubr + - 'r-ggsci >=2.9' + - 'r-ggsignif >=0.6.3' + - 'r-scales >=1.2.0' + - r-tidyr + - r-venndiagram + - r-viridis + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rcas >=1.28.0,<1.29.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-circlize + - 'r-cowplot >=1.1.1' + - r-dplyr + - 'r-ggplot2 >=3.3.5' + - r-ggplotify + - r-ggpubr + - 'r-ggsci >=2.9' + - 'r-ggsignif >=0.6.3' + - 'r-scales >=1.2.0' + - r-tidyr + - r-venndiagram + - r-viridis +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Plot profiles of next generation sequencing data in genomic features' + description: 'Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. ''GenomicPlot'' facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + diff --git a/recipes/bioconductor-genomicranges/meta.yaml b/recipes/bioconductor-genomicranges/meta.yaml index ab068d4503ce5..895ba1c23b7d2 100644 --- a/recipes/bioconductor-genomicranges/meta.yaml +++ b/recipes/bioconductor-genomicranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.1" %} {% set name = "GenomicRanges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84ff182b349311589f7eece03f22a593 + md5: 19fe37133cae70c1c3a1a164e6c8eaed build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicranges", max_pin="x.x") }}' # Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-genomicscores/meta.yaml b/recipes/bioconductor-genomicscores/meta.yaml index e509330b4c55f..905f77be5004e 100644 --- a/recipes/bioconductor-genomicscores/meta.yaml +++ b/recipes/bioconductor-genomicscores/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.1" %} {% set name = "GenomicScores" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f26842350f8a2fc457e2f434dd415d0 + md5: 3f3be6b84303478d0d061081b2dcf261 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicscores", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-httr - r-xml run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-httr diff --git a/recipes/bioconductor-genomicstate/meta.yaml b/recipes/bioconductor-genomicstate/meta.yaml index 284f1eec4a561..641f4618a5d8d 100644 --- a/recipes/bioconductor-genomicstate/meta.yaml +++ b/recipes/bioconductor-genomicstate/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.15" %} {% set name = "GenomicState" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,37 +13,38 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 59c2d85a72f62cb12bad697fcbce5edc build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicstate", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, testthat (>= 2.1.0), glue, derfinderPlot, AnnotationHubData, RefManageR, GenomicRanges, covr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-genomicsupersignature/meta.yaml b/recipes/bioconductor-genomicsupersignature/meta.yaml index 8e732bb78eb01..231b42a102ceb 100644 --- a/recipes/bioconductor-genomicsupersignature/meta.yaml +++ b/recipes/bioconductor-genomicsupersignature/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GenomicSuperSignature" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f66e1c6addf266e6aa5523260c415e1f + md5: ecb55ebec91620ff435715563d8ba304 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomicsupersignature", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-flextable @@ -34,11 +35,11 @@ requirements: - r-irlba - r-plotly run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-flextable diff --git a/recipes/bioconductor-genomictuples/meta.yaml b/recipes/bioconductor-genomictuples/meta.yaml index 6de63c4f52739..f664c665aa978 100644 --- a/recipes/bioconductor-genomictuples/meta.yaml +++ b/recipes/bioconductor-genomictuples/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GenomicTuples" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07e23d625f7467ef01b7eadaa4d6b19a + md5: 69e0c80982690604f35d9878f6640f37 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genomictuples", max_pin="x.x") }}' # Suggests: testthat, knitr, BiocStyle, rmarkdown, covr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - 'r-rcpp >=0.11.2' - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - 'r-rcpp >=0.11.2' diff --git a/recipes/bioconductor-genproseq/meta.yaml b/recipes/bioconductor-genproseq/meta.yaml index b25797f9b5a78..0145607611a75 100644 --- a/recipes/bioconductor-genproseq/meta.yaml +++ b/recipes/bioconductor-genproseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.2" %} +{% set version = "1.6.0" %} {% set name = "GenProSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8dd618e58f4e340ab6af9604c2378b7 + md5: 15e772912f2019256df52d192edd5402 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genproseq", max_pin="x.x") }}' noarch: generic # Suggests: ggseqlogo, VAExprs, stringdist, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-deeppincs >=1.8.0,<1.9.0' - - 'bioconductor-ttgsea >=1.8.0,<1.9.0' + - 'bioconductor-deeppincs >=1.10.0,<1.11.0' + - 'bioconductor-ttgsea >=1.10.0,<1.11.0' - r-base - r-catencoders - r-keras @@ -31,8 +32,8 @@ requirements: - r-tensorflow - r-word2vec run: - - 'bioconductor-deeppincs >=1.8.0,<1.9.0' - - 'bioconductor-ttgsea >=1.8.0,<1.9.0' + - 'bioconductor-deeppincs >=1.10.0,<1.11.0' + - 'bioconductor-ttgsea >=1.10.0,<1.11.0' - r-base - r-catencoders - r-keras diff --git a/recipes/bioconductor-genvisr/meta.yaml b/recipes/bioconductor-genvisr/meta.yaml index a380858ba5d5c..1358bedd1c531 100644 --- a/recipes/bioconductor-genvisr/meta.yaml +++ b/recipes/bioconductor-genvisr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.31.1" %} +{% set version = "1.34.0" %} {% set name = "GenVisR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b2548a895a14be3c9cabc9a5ddde0e33 + md5: f05fdc7c5736ba49ccf4eebcc1bc28ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-genvisr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-dbi @@ -44,17 +45,17 @@ requirements: - r-scales - r-viridis run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-dbi diff --git a/recipes/bioconductor-geodiff/meta.yaml b/recipes/bioconductor-geodiff/meta.yaml index 00b6d228b2275..71a1b028708ae 100644 --- a/recipes/bioconductor-geodiff/meta.yaml +++ b/recipes/bioconductor-geodiff/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GeoDiff" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bfc04b2a9de212b7848725ccddd33b8a + md5: f719fddf3486b6aad1f36ca439b55114 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geodiff", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, dplyr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' - - 'bioconductor-nanostringnctools >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' + - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' - r-base - r-lme4 - r-matrix @@ -36,9 +37,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' - - 'bioconductor-nanostringnctools >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' + - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' - r-base - r-lme4 - r-matrix diff --git a/recipes/bioconductor-geoexplorer/meta.yaml b/recipes/bioconductor-geoexplorer/meta.yaml index 3bd3a3a3701cc..5002ad1d02b93 100644 --- a/recipes/bioconductor-geoexplorer/meta.yaml +++ b/recipes/bioconductor-geoexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GEOexplorer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,64 +11,87 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e158f37de271fa9305fca41cf23b887a + md5: 213a1b499ce1d0640b267c8fb41e3204 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geoexplorer", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, knitr, usethis, testthat (>= 3.0.0) +# Suggests: rmarkdown, usethis, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base + - r-car - r-dt + - r-enrichr - r-factoextra - r-ggplot2 - r-heatmaply - r-htmltools - - r-maptools + - r-httr + - r-knitr + - r-markdown - r-pheatmap - r-plotly + - r-r.utils + - r-readxl - r-scales - r-shiny - - r-shinybs - r-shinybusy + - r-shinycssloaders - r-shinyheatmaply - r-stringr - r-umap + - r-xfun + - r-xml + - r-xml2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base + - r-car - r-dt + - r-enrichr - r-factoextra - r-ggplot2 - r-heatmaply - r-htmltools - - r-maptools + - r-httr + - r-knitr + - r-markdown - r-pheatmap - r-plotly + - r-r.utils + - r-readxl - r-scales - r-shiny - - r-shinybs - r-shinybusy + - r-shinycssloaders - r-shinyheatmaply - r-stringr - r-umap + - r-xfun + - r-xml + - r-xml2 test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation' - description: 'GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of gene expression analysis on microarray gene expression datasets held on the GEO database. The outputs are interactive graphs that enable users to explore the results of the analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).' + summary: 'GEOexplorer: a webserver for gene expression analysis and visualisation' + description: 'GEOexplorer is a webserver and R/Bioconductor package and web application that enables users to perform gene expression analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-geofastq/meta.yaml b/recipes/bioconductor-geofastq/meta.yaml index f15f6a8c9aab1..df5a172e6e81f 100644 --- a/recipes/bioconductor-geofastq/meta.yaml +++ b/recipes/bioconductor-geofastq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GEOfastq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5c8bc6ae8926e6a803a5b1df7b3aa49 + md5: 339bd0c2f6a3f505457fc436997965a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geofastq", max_pin="x.x") }}' noarch: generic # Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-geometadb/meta.yaml b/recipes/bioconductor-geometadb/meta.yaml index 7128400abbc16..dc42ecd5d1cfd 100644 --- a/recipes/bioconductor-geometadb/meta.yaml +++ b/recipes/bioconductor-geometadb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "GEOmetadb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c6a5daf43e682620906dc428a4cb6cc + md5: 78e0bce3aa72836e1b126536221059c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geometadb", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, dplyr, tm, wordcloud +# Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud requirements: host: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-rsqlite run: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-rsqlite test: diff --git a/recipes/bioconductor-geomxtools/meta.yaml b/recipes/bioconductor-geomxtools/meta.yaml index 754dd51f882eb..f8e4400a66844 100644 --- a/recipes/bioconductor-geomxtools/meta.yaml +++ b/recipes/bioconductor-geomxtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.0" %} +{% set version = "3.5.0" %} {% set name = "GeomxTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1977ed1034bb7ae33b6ac8ff3d18d896 + md5: 7ac9d92476a27e642927f906be2756db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geomxtools", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-nanostringnctools >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -39,10 +40,10 @@ requirements: - r-seuratobject - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-nanostringnctools >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-geoquery/meta.yaml b/recipes/bioconductor-geoquery/meta.yaml index 9282be967f594..d4246ec8b5641 100644 --- a/recipes/bioconductor-geoquery/meta.yaml +++ b/recipes/bioconductor-geoquery/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.68.0" %} +{% set version = "2.70.0" %} {% set name = "GEOquery" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 006c81971e10ad7dd94c875daa8a75af + md5: 5e8f233065ccb97c7cbb231479c936a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geoquery", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-curl - r-data.table @@ -33,8 +34,8 @@ requirements: - r-tidyr - r-xml2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-curl - r-data.table @@ -61,4 +62,3 @@ extra: name: bioconductor-geoquery path: recipes/bioconductor-geoquery version: 2.48.0 - diff --git a/recipes/bioconductor-geosubmission/meta.yaml b/recipes/bioconductor-geosubmission/meta.yaml index b008d3688fa72..171c6416978eb 100644 --- a/recipes/bioconductor-geosubmission/meta.yaml +++ b/recipes/bioconductor-geosubmission/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "GEOsubmission" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 975c8bb07e646358a15315cdaf9665de + md5: 835a74433a1f0235676bf2d1012096af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geosubmission", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-geotcgadata/meta.yaml b/recipes/bioconductor-geotcgadata/meta.yaml index 0571cea50acf6..4cba7f0dfdbe6 100644 --- a/recipes/bioconductor-geotcgadata/meta.yaml +++ b/recipes/bioconductor-geotcgadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "GeoTcgaData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 463ef0f64e092337495a3f6da55b224a + md5: 653a353d37b0bcfbd892dfe12d420100 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geotcgadata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq, testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery, BiocGenerics requirements: host: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topconfects >=1.16.0,<1.17.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topconfects >=1.18.0,<1.19.0' - r-base - r-data.table - r-plyr run: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topconfects >=1.16.0,<1.17.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topconfects >=1.18.0,<1.19.0' - r-base - r-data.table - r-plyr diff --git a/recipes/bioconductor-gep2pep/meta.yaml b/recipes/bioconductor-gep2pep/meta.yaml index d975a9a963484..8250b9d598084 100644 --- a/recipes/bioconductor-gep2pep/meta.yaml +++ b/recipes/bioconductor-gep2pep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "gep2pep" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 98994b580cde9a2d9431af735cf8c60c + md5: 0a8f1b44003eba297c44f8115f870df0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gep2pep", max_pin="x.x") }}' noarch: generic # Suggests: WriteXLS, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-digest - r-foreach @@ -31,9 +32,9 @@ requirements: - 'r-repo >=2.1.1' - r-xml run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-digest - r-foreach diff --git a/recipes/bioconductor-gesper/meta.yaml b/recipes/bioconductor-gesper/meta.yaml index 5604170a7054e..083aafb62aa77 100644 --- a/recipes/bioconductor-gesper/meta.yaml +++ b/recipes/bioconductor-gesper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.31.0" %} +{% set version = "1.34.0" %} {% set name = "gespeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71dc46d44b385b5443c76ae92caa659e + md5: b29c5440e5f853e993e3ca2df2eae3e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gesper", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' - r-base - r-doparallel - r-dplyr @@ -33,9 +34,9 @@ requirements: - r-matrix - r-reshape2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-getdee2/meta.yaml b/recipes/bioconductor-getdee2/meta.yaml index cae189ec65783..1ff51ddaf967c 100644 --- a/recipes/bioconductor-getdee2/meta.yaml +++ b/recipes/bioconductor-getdee2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "getDEE2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0afa472875b2b4ab0fa9805c79faa93e + md5: 5bae73105adbd3fba6517601379594c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-getdee2", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-htm2txt run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-htm2txt test: diff --git a/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml b/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml index c17135a0cf002..6cda616d59429 100644 --- a/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml +++ b/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "GeuvadisTranscriptExpr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a37aba63d441f86e2b9eb68f34b92f0 + md5: 806de22bef0659a3b6f9db122d87a1d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geuvadistranscriptexpr", max_pin="x.x") }}' noarch: generic # Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh b/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh index f79467042f5fd..4723d360c3b55 100644 --- a/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh +++ b/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "geuvadistranscriptexpr-1.28.0" +installBiocDataPackage.sh "geuvadistranscriptexpr-1.30.0" diff --git a/recipes/bioconductor-geva/meta.yaml b/recipes/bioconductor-geva/meta.yaml index ff15ffe94bb29..05f850b06b2ec 100644 --- a/recipes/bioconductor-geva/meta.yaml +++ b/recipes/bioconductor-geva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "geva" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa42438cd413c4834920527e263b2549 + md5: ac06c7a9df29f5eb16fe102c81369ccb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-geva", max_pin="x.x") }}' noarch: generic # Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) requirements: diff --git a/recipes/bioconductor-gewist/meta.yaml b/recipes/bioconductor-gewist/meta.yaml index ae8837dbd5e53..5e0d3c2bb02e2 100644 --- a/recipes/bioconductor-gewist/meta.yaml +++ b/recipes/bioconductor-gewist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "GEWIST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed8e6e450912a74621c1138d8e93d1b1 + md5: 3fe24d9c2f80cfc18dc41b37b118be6e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gewist", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-gg4way/build.sh b/recipes/bioconductor-gg4way/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gg4way/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gg4way/meta.yaml b/recipes/bioconductor-gg4way/meta.yaml new file mode 100644 index 0000000000000..835f32f2578c0 --- /dev/null +++ b/recipes/bioconductor-gg4way/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.0.0" %} +{% set name = "gg4way" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 500552b8ab9c3fc5cc58fcf56378a928 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gg4way", max_pin="x.x") }}' + noarch: generic +# Suggests: airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat +requirements: + host: + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-glue + - r-janitor + - r-magrittr + - r-purrr + - r-rlang + - r-scales + - r-stringr + - r-tibble + - r-tidyr + run: + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-glue + - r-janitor + - r-magrittr + - r-purrr + - r-rlang + - r-scales + - r-stringr + - r-tibble + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: '4way Plots of Differential Expression' + description: '4way plots enable a comparison of the logFC values from two contrasts of differential gene expression. The gg4way package creates 4way plots using the ggplot2 framework and supports popular Bioconductor objects. The package also provides information about the correlation between contrasts and significant genes of interest.' + license_file: LICENSE + diff --git a/recipes/bioconductor-ggbio/meta.yaml b/recipes/bioconductor-ggbio/meta.yaml index 006af33b86405..2ae0c837632c1 100644 --- a/recipes/bioconductor-ggbio/meta.yaml +++ b/recipes/bioconductor-ggbio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "ggbio" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7251a7fc9affae5f6ab3ea60c2446ecf + md5: de7ec73480f41c35fca2a8a758fbc7d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggbio", max_pin="x.x") }}' noarch: generic # Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggally - 'r-ggplot2 >=1.0.0' @@ -50,25 +51,25 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggally - 'r-ggplot2 >=1.0.0' diff --git a/recipes/bioconductor-ggcyto/meta.yaml b/recipes/bioconductor-ggcyto/meta.yaml index 910a8c1868c48..996e3aeda5742 100644 --- a/recipes/bioconductor-ggcyto/meta.yaml +++ b/recipes/bioconductor-ggcyto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ggcyto" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e01a55fb67a3cb3881d74e693049486b + md5: f50828f54e40b73d30aa3ac0ef06de21 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggcyto", max_pin="x.x") }}' noarch: generic # Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - r-base - r-data.table - - 'r-ggplot2 >=3.3.0' + - 'r-ggplot2 >=3.4.2' - r-gridextra - r-hexbin - r-plyr @@ -34,12 +35,12 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - r-base - r-data.table - - 'r-ggplot2 >=3.3.0' + - 'r-ggplot2 >=3.4.2' - r-gridextra - r-hexbin - r-plyr diff --git a/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml b/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml index 2ba9f67beb951..4bb5bc685c883 100644 --- a/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml +++ b/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.1" %} {% set name = "GGHumanMethCancerPanelv1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,25 +13,26 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e8f4a37182b175fb33dd54f8093e6f52 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gghumanmethcancerpanelv1.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ggkegg/build.sh b/recipes/bioconductor-ggkegg/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ggkegg/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ggkegg/meta.yaml b/recipes/bioconductor-ggkegg/meta.yaml new file mode 100644 index 0000000000000..613b9acdc3d6a --- /dev/null +++ b/recipes/bioconductor-ggkegg/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.2" %} +{% set name = "ggkegg" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 747219ce420df145e10ee4b9243b17dc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggkegg", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - r-base + - r-cairo + - r-data.table + - r-dplyr + - r-getoptlong + - r-ggplot2 + - r-ggraph + - r-igraph + - r-magick + - r-patchwork + - r-shadowtext + - r-stringr + - r-tibble + - r-tidygraph + - r-xml + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - r-base + - r-cairo + - r-data.table + - r-dplyr + - r-getoptlong + - r-ggplot2 + - r-ggraph + - r-igraph + - r-magick + - r-patchwork + - r-shadowtext + - r-stringr + - r-tibble + - r-tidygraph + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'KEGG pathway visualization by ggplot2' + description: 'This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.' + license_file: LICENSE + diff --git a/recipes/bioconductor-ggmanh/meta.yaml b/recipes/bioconductor-ggmanh/meta.yaml index 392707f7f661c..ab0bfd97963ec 100644 --- a/recipes/bioconductor-ggmanh/meta.yaml +++ b/recipes/bioconductor-ggmanh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ggmanh" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d083b7129acff669ad41db946445336b + md5: dbbd8130e9ef70cb69c7e305af0c37d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggmanh", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), markdown, GenomicRanges requirements: host: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-ggplot2 - r-ggrepel @@ -30,8 +31,8 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-ggmsa/meta.yaml b/recipes/bioconductor-ggmsa/meta.yaml index b45906c0af140..1ca7bf62799d6 100644 --- a/recipes/bioconductor-ggmsa/meta.yaml +++ b/recipes/bioconductor-ggmsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ggmsa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 36c37e2d2e1f35d872621c6ff05af71a + md5: 1faea3aedc093bb7e151208c9a11b60c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggmsa", max_pin="x.x") }}' noarch: generic # Suggests: ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-r4rna >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-r4rna >=1.30.0,<1.31.0' - r-aplot - r-base - r-dplyr @@ -36,9 +37,9 @@ requirements: - r-statebins - r-tidyr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-r4rna >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-r4rna >=1.30.0,<1.31.0' - r-aplot - r-base - r-dplyr diff --git a/recipes/bioconductor-ggpa/meta.yaml b/recipes/bioconductor-ggpa/meta.yaml index 5d4544485bfb5..5d4865bce21db 100644 --- a/recipes/bioconductor-ggpa/meta.yaml +++ b/recipes/bioconductor-ggpa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "GGPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7d4034056bfd00a317aa0c6030422c9 + md5: 5c50ef4040a18ac94848d7c42484d28d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggpa", max_pin="x.x") }}' # Suggests: BiocStyle # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-ggsc/build.sh b/recipes/bioconductor-ggsc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ggsc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ggsc/meta.yaml b/recipes/bioconductor-ggsc/meta.yaml new file mode 100644 index 0000000000000..1441cbbb7e759 --- /dev/null +++ b/recipes/bioconductor-ggsc/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.2" %} +{% set name = "ggsc" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4c0a1656e9943cadf436244c65b18242 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggsc", max_pin="x.x") }}' +# Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cli + - r-dplyr + - r-ggplot2 + - r-rcpp + - r-rcpparmadillo + - r-rcppparallel + - r-rlang + - r-scattermore + - r-seurat + - r-tibble + - r-tidydr + - r-tidyr + - r-yulab.utils + - libblas + - liblapack + run: + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cli + - r-dplyr + - r-ggplot2 + - r-rcpp + - r-rcpparmadillo + - r-rcppparallel + - r-rlang + - r-scattermore + - r-seurat + - r-tibble + - r-tidydr + - r-tidyr + - r-yulab.utils + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Visualizing Single Cell Data' + description: 'Useful functions to visualize single cell and spatial data. It supports both ''SingleCellExperiment'' and ''Seurat'' objects. It also supports visualizing the data using grammar of graphics implemented in ''ggplot2''.' + diff --git a/recipes/bioconductor-ggspavis/meta.yaml b/recipes/bioconductor-ggspavis/meta.yaml index a28c488446c59..eabd7d3e68766 100644 --- a/recipes/bioconductor-ggspavis/meta.yaml +++ b/recipes/bioconductor-ggspavis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ggspavis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 94461bb1f26364b8f20a37ab49e8a4db + md5: c79337783dc059e449506a61c5579337 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggspavis", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggside run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggside diff --git a/recipes/bioconductor-ggtree/meta.yaml b/recipes/bioconductor-ggtree/meta.yaml index 498ac6b1d2938..2a7d2de5144dc 100644 --- a/recipes/bioconductor-ggtree/meta.yaml +++ b/recipes/bioconductor-ggtree/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "ggtree" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: efdbe433dc0a88c5582b0f69a0577865 + md5: 7e1894ce01245d811286b0ce1fbe8266 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggtree", max_pin="x.x") }}' noarch: generic # Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue requirements: host: - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-aplot - r-base @@ -34,10 +35,10 @@ requirements: - r-rlang - r-scales - r-tidyr - - 'r-tidytree >=0.3.9' + - 'r-tidytree >=0.4.5' - r-yulab.utils run: - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-aplot - r-base @@ -50,7 +51,7 @@ requirements: - r-rlang - r-scales - r-tidyr - - 'r-tidytree >=0.3.9' + - 'r-tidytree >=0.4.5' - r-yulab.utils test: commands: diff --git a/recipes/bioconductor-ggtreedendro/meta.yaml b/recipes/bioconductor-ggtreedendro/meta.yaml index 7291d3ea96fcc..262bc36ce9821 100644 --- a/recipes/bioconductor-ggtreedendro/meta.yaml +++ b/recipes/bioconductor-ggtreedendro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ggtreeDendro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 426abd017dfad28e2752ee6943d1f345 + md5: e5839d466e08665eb2475a99fb74e833 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggtreedendro", max_pin="x.x") }}' noarch: generic # Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-ggplot2 - r-tidytree run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-ggplot2 - r-tidytree diff --git a/recipes/bioconductor-ggtreeextra/meta.yaml b/recipes/bioconductor-ggtreeextra/meta.yaml index e16219e3ef5e3..43bbe1f1f6038 100644 --- a/recipes/bioconductor-ggtreeextra/meta.yaml +++ b/recipes/bioconductor-ggtreeextra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ggtreeExtra" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c39f713cf930c99e6f7106cd96159a8 + md5: 0bfd8a30c6fbd323763722927d30296a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggtreeextra", max_pin="x.x") }}' noarch: generic # Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-cli - r-ggnewscale @@ -30,7 +31,7 @@ requirements: - r-rlang - 'r-tidytree >=0.3.9' run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-base - r-cli - r-ggnewscale diff --git a/recipes/bioconductor-gigsea/meta.yaml b/recipes/bioconductor-gigsea/meta.yaml index f2495f207ccb8..0e0d6eec70f7b 100644 --- a/recipes/bioconductor-gigsea/meta.yaml +++ b/recipes/bioconductor-gigsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "GIGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e98747c8ff218c3ef2d5590f055c1084 + md5: 1325b20f84be334e607b7ebec7db0d07 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gigsea", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-gigseadata/meta.yaml b/recipes/bioconductor-gigseadata/meta.yaml index caf5e26c0c2d1..6430624693d11 100644 --- a/recipes/bioconductor-gigseadata/meta.yaml +++ b/recipes/bioconductor-gigseadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "GIGSEAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad905645333890eafd314cdac44f793a + md5: 470cdb6073d9af3d23056b55e6b8c98d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gigseadata", max_pin="x.x") }}' noarch: generic # Suggests: GIGSEA, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gigseadata/post-link.sh b/recipes/bioconductor-gigseadata/post-link.sh index 19ba27f282877..ee46d067c6e87 100644 --- a/recipes/bioconductor-gigseadata/post-link.sh +++ b/recipes/bioconductor-gigseadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gigseadata-1.18.0" +installBiocDataPackage.sh "gigseadata-1.20.0" diff --git a/recipes/bioconductor-girafe/meta.yaml b/recipes/bioconductor-girafe/meta.yaml index ca748fc02114f..8b2eb662a4fcf 100644 --- a/recipes/bioconductor-girafe/meta.yaml +++ b/recipes/bioconductor-girafe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "girafe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4d95b1c6c1147fd8833e62fbab42973b + md5: 4cf228e6d7f73cf97c923f1c349fb6c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-girafe", max_pin="x.x") }}' # Suggests: MASS, org.Mm.eg.db, RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-intervals >=0.13.1' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeintervals >=1.56.0,<1.57.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-intervals >=0.13.1' build: diff --git a/recipes/bioconductor-gispa/meta.yaml b/recipes/bioconductor-gispa/meta.yaml index 78995642ea117..7e2d4a3f793cc 100644 --- a/recipes/bioconductor-gispa/meta.yaml +++ b/recipes/bioconductor-gispa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "GISPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e309fc9a17caf08ad92b993a0cdd90ad + md5: 012a529b5359b149705fa54cb75c1818 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gispa", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-changepoint - r-data.table @@ -33,9 +34,9 @@ requirements: - r-plyr - r-scatterplot3d run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-changepoint - r-data.table diff --git a/recipes/bioconductor-glad/build.sh b/recipes/bioconductor-glad/build.sh index 78ffa6cbcade8..c74d5641a31dc 100644 --- a/recipes/bioconductor-glad/build.sh +++ b/recipes/bioconductor-glad/build.sh @@ -8,5 +8,5 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -touch GLAD -$R CMD INSTALL --build . +sed -i.bak 's/^ac_unique_file="GLAD"/ac_unique_file="NAMESPACE"/' configure +$R CMD INSTALL --build --configure-vars='GSL_LIBS="-L$PREFIX/lib -lgsl -lgslcblas -lm"' . \ No newline at end of file diff --git a/recipes/bioconductor-glad/meta.yaml b/recipes/bioconductor-glad/meta.yaml index 28765c4e9b1b2..98a43342fbfd0 100644 --- a/recipes/bioconductor-glad/meta.yaml +++ b/recipes/bioconductor-glad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.64.0" %} +{% set version = "2.66.0" %} {% set name = "GLAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0dc76c1fc2b069084b16a9150611ba6 + md5: f222e07624fb8b1c4780a4960b0f2008 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-glad", max_pin="x.x") }}' # SystemRequirements: gsl. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. requirements: host: diff --git a/recipes/bioconductor-gladiatox/meta.yaml b/recipes/bioconductor-gladiatox/meta.yaml index 5290df2495cf9..75bf22493ac9e 100644 --- a/recipes/bioconductor-gladiatox/meta.yaml +++ b/recipes/bioconductor-gladiatox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GladiaTOX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b642344445e36310ab07ddd46285a9a + md5: a8affcce15bf1f5e9d03220e0de3fbe9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gladiatox", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle requirements: @@ -31,7 +32,7 @@ requirements: - r-rcolorbrewer - r-rcurl - r-rjsonio - - r-rmysql + - r-rmariadb - r-rsqlite - r-stringr - r-tidyr @@ -48,7 +49,7 @@ requirements: - r-rcolorbrewer - r-rcurl - r-rjsonio - - r-rmysql + - r-rmariadb - r-rsqlite - r-stringr - r-tidyr diff --git a/recipes/bioconductor-glimma/meta.yaml b/recipes/bioconductor-glimma/meta.yaml index 7d696aad81cf4..32dc9bba1cbf7 100644 --- a/recipes/bioconductor-glimma/meta.yaml +++ b/recipes/bioconductor-glimma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "Glimma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f127e3ae006335a13734d71ef7aa2640 + md5: bea9aeee00dca519586661d33ba8dc74 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-glimma", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-htmlwidgets - r-jsonlite run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-htmlwidgets - r-jsonlite @@ -44,8 +45,8 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Interactive HTML graphics' - description: 'This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.' + summary: 'Interactive visualizations for gene expression analysis' + description: 'This package produces interactive visualizations for RNA-seq data analysis, utilizing output from limma, edgeR, or DESeq2. It produces interactive htmlwidgets versions of popular RNA-seq analysis plots to enhance the exploration of analysis results by overlaying interactive features. The plots can be viewed in a web browser or embedded in notebook documents.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: diff --git a/recipes/bioconductor-glmgampoi/meta.yaml b/recipes/bioconductor-glmgampoi/meta.yaml index d38b42353b0f4..68d5da5ce2f73 100644 --- a/recipes/bioconductor-glmgampoi/meta.yaml +++ b/recipes/bioconductor-glmgampoi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "glmGamPoi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 299c9cff01d7696e4e6cb23db4c12920 + md5: ff74c3d78a7edc7d0a5f4521f7c5b9b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-glmgampoi", max_pin="x.x") }}' # Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, Matrix, dplyr # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrixstats - r-rcpp @@ -38,14 +39,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrixstats - r-rcpp diff --git a/recipes/bioconductor-glmsparsenet/meta.yaml b/recipes/bioconductor-glmsparsenet/meta.yaml index 039338c617606..b0bfedfe3022a 100644 --- a/recipes/bioconductor-glmsparsenet/meta.yaml +++ b/recipes/bioconductor-glmsparsenet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "glmSparseNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19e521eeaadf8bbfeda74bdb69d0297c + md5: b029a96bf3a653a8a3c24d764c841512 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-glmsparsenet", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC, VennDiagram, BiocStyle, curatedTCGAData, TCGAutils requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-digest - r-dplyr @@ -40,9 +41,9 @@ requirements: - r-stringr - r-survminer run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-digest - r-dplyr diff --git a/recipes/bioconductor-globalancova/meta.yaml b/recipes/bioconductor-globalancova/meta.yaml index 60d2696f5ca30..84aa7d322bd84 100644 --- a/recipes/bioconductor-globalancova/meta.yaml +++ b/recipes/bioconductor-globalancova/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.18.0" %} +{% set version = "4.20.0" %} {% set name = "GlobalAncova" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6236d46ff193ab24e7ab0d85272b0ca3 + md5: 4fcc19ebc2bba1f610912cde1745b549 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-globalancova", max_pin="x.x") }}' # Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-corpcor - r-dendextend @@ -32,11 +33,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-corpcor - r-dendextend diff --git a/recipes/bioconductor-globalseq/meta.yaml b/recipes/bioconductor-globalseq/meta.yaml index f6cc742c6512c..0d5af193580c1 100644 --- a/recipes/bioconductor-globalseq/meta.yaml +++ b/recipes/bioconductor-globalseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "globalSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1df637d4f75b814a55fc9025ea33769 + md5: 1b427214cf1345b8d75ba69dc02adb77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-globalseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, SummarizedExperiment, S4Vectors requirements: diff --git a/recipes/bioconductor-globaltest/meta.yaml b/recipes/bioconductor-globaltest/meta.yaml index 7b419c131f313..7cd5098ec0714 100644 --- a/recipes/bioconductor-globaltest/meta.yaml +++ b/recipes/bioconductor-globaltest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "5.54.0" %} +{% set version = "5.56.0" %} {% set name = "globaltest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0dee254d67879077ccb02fbe682eaed6 + md5: ca389a7105fc08bc6172ce755d842a31 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-globaltest", max_pin="x.x") }}' noarch: generic # Suggests: vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival test: diff --git a/recipes/bioconductor-gloscope/build.sh b/recipes/bioconductor-gloscope/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gloscope/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gloscope/meta.yaml b/recipes/bioconductor-gloscope/meta.yaml new file mode 100644 index 0000000000000..c2c78a32218ab --- /dev/null +++ b/recipes/bioconductor-gloscope/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.0.0" %} +{% set name = "GloScope" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 00ab18ecdd0a5768690b841f2f2448e5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gloscope", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + - r-fnn + - r-ggplot2 + - r-mass + - r-mclust + - r-mvnfast + - r-rann + - r-rlang + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + - r-fnn + - r-ggplot2 + - r-mass + - r-mclust + - r-mvnfast + - r-rann + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Population-level Representation on scRNA-Seq data' + description: 'This package aims at representing and summarizing the entire single-cell profile of a sample. It allows researchers to perform important bioinformatic analyses at the sample-level such as visualization and quality control. The main functions Estimate sample distribution and calculate statistical divergence among samples, and visualize the distance matrix through MDS plots.' + diff --git a/recipes/bioconductor-gmapr/build.sh b/recipes/bioconductor-gmapr/build.sh index aa6ce291ac3aa..3c9546c924fe5 100644 --- a/recipes/bioconductor-gmapr/build.sh +++ b/recipes/bioconductor-gmapr/build.sh @@ -10,4 +10,4 @@ CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars # Remove object files (if present) that should not be in the source tarball rm -f src/samtools/*.[oa] -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gmapr/meta.yaml b/recipes/bioconductor-gmapr/meta.yaml index 862fc6f100cdd..45159a2ac666f 100644 --- a/recipes/bioconductor-gmapr/meta.yaml +++ b/recipes/bioconductor-gmapr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "gmapR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,47 +11,48 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbe4da38f2fda8cbcef73cae97c1ee28 + md5: 3398b4dd3f0c05c2a748f9ecb0a28c41 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gmapr", max_pin="x.x") }}' # Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-gmicr/meta.yaml b/recipes/bioconductor-gmicr/meta.yaml index d7eb8e039cc91..9e030aeb49653 100644 --- a/recipes/bioconductor-gmicr/meta.yaml +++ b/recipes/bioconductor-gmicr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "GmicR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e089a259f66dcf368cf5bb49c102e1ea + md5: 13466f8e105c84116d73b39d38eed3cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gmicr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-ape - r-base - r-bnlearn @@ -40,12 +41,12 @@ requirements: - r-shiny - r-wgcna run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-ape - r-base - r-bnlearn diff --git a/recipes/bioconductor-gmoviz/meta.yaml b/recipes/bioconductor-gmoviz/meta.yaml index 22c92bf2ca7e9..1a7e6dd17007e 100644 --- a/recipes/bioconductor-gmoviz/meta.yaml +++ b/recipes/bioconductor-gmoviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "gmoviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c48c8c41b980373fa3c764e4834ff8e3 + md5: 19164c63f0edf9ae927bef7bae0b1a12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gmoviz", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-colorspace - r-gridbase - r-pracma run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-colorspace diff --git a/recipes/bioconductor-gmrp/meta.yaml b/recipes/bioconductor-gmrp/meta.yaml index d320ffafc1366..b548aa45a5dea 100644 --- a/recipes/bioconductor-gmrp/meta.yaml +++ b/recipes/bioconductor-gmrp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "GMRP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ee7fe352b10cf36aef04482614d7ac0 + md5: d33e226ce1134e0f16d4d531fadc7339 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gmrp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-diagram - r-plotrix run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-diagram - r-plotrix diff --git a/recipes/bioconductor-gnet2/meta.yaml b/recipes/bioconductor-gnet2/meta.yaml index 5c0d53071785b..c4a8c0c2f55e4 100644 --- a/recipes/bioconductor-gnet2/meta.yaml +++ b/recipes/bioconductor-gnet2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GNET2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3764cd241d02bfc2308facf2cfdb800d + md5: 06382e36858e9d55d44aabba748d49b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gnet2", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-diagrammer - r-dplyr @@ -33,7 +34,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-diagrammer - r-dplyr diff --git a/recipes/bioconductor-gnosis/build.sh b/recipes/bioconductor-gnosis/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gnosis/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gnosis/meta.yaml b/recipes/bioconductor-gnosis/meta.yaml new file mode 100644 index 0000000000000..ed68757eb4d4d --- /dev/null +++ b/recipes/bioconductor-gnosis/meta.yaml @@ -0,0 +1,91 @@ +{% set version = "1.0.0" %} +{% set name = "GNOSIS" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e3cbf07a76da1ae0aa6e669bad2cb778 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gnosis", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - r-base + - r-car + - r-comparegroups + - r-dashboardthemes + - r-desctools + - r-dt + - r-fabricatr + - r-fontawesome + - r-magrittr + - r-operator.tools + - r-partykit + - r-rcolorbrewer + - r-reshape2 + - r-rpart + - r-rstatix + - r-shiny + - r-shinycssloaders + - r-shinydashboard + - r-shinydashboardplus + - r-shinyjs + - r-shinylogs + - r-shinymeta + - r-shinywidgets + - r-survival + - r-survminer + - r-tidyverse + run: + - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - r-base + - r-car + - r-comparegroups + - r-dashboardthemes + - r-desctools + - r-dt + - r-fabricatr + - r-fontawesome + - r-magrittr + - r-operator.tools + - r-partykit + - r-rcolorbrewer + - r-reshape2 + - r-rpart + - r-rstatix + - r-shiny + - r-shinycssloaders + - r-shinydashboard + - r-shinydashboardplus + - r-shinyjs + - r-shinylogs + - r-shinymeta + - r-shinywidgets + - r-survival + - r-survminer + - r-tidyverse +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Genomics explorer using statistical and survival analysis in R' + description: 'GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.' + license_file: LICENSE + diff --git a/recipes/bioconductor-go.db/meta.yaml b/recipes/bioconductor-go.db/meta.yaml index 3742220d4eb29..9311de2ff1dc9 100644 --- a/recipes/bioconductor-go.db/meta.yaml +++ b/recipes/bioconductor-go.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "GO.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f278f3cb015e04ead1cc3d982a3fd1b3 + md5: b23522167263afc45a9b115d01632cb1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-go.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-go.db/post-link.sh b/recipes/bioconductor-go.db/post-link.sh index 1a7bbea2aba0f..f1547533d3cd4 100644 --- a/recipes/bioconductor-go.db/post-link.sh +++ b/recipes/bioconductor-go.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "go.db-3.17.0" +installBiocDataPackage.sh "go.db-3.18.0" diff --git a/recipes/bioconductor-goexpress/meta.yaml b/recipes/bioconductor-goexpress/meta.yaml index 6bb8170489ffb..2ad3dd05dc553 100644 --- a/recipes/bioconductor-goexpress/meta.yaml +++ b/recipes/bioconductor-goexpress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GOexpress" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ecb2bcff2560c6f61a1da2407697903 + md5: b313b2555495c3d3fc5674120b7bb01b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-goexpress", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - 'r-ggplot2 >=0.9.0' - 'r-gplots >=2.13.0' @@ -31,8 +32,8 @@ requirements: - 'r-rcurl >=1.95' - 'r-stringr >=0.6.2' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - 'r-ggplot2 >=0.9.0' - 'r-gplots >=2.13.0' diff --git a/recipes/bioconductor-gofuncr/meta.yaml b/recipes/bioconductor-gofuncr/meta.yaml index 324860ad1e003..71d2d0bf7bc4f 100644 --- a/recipes/bioconductor-gofuncr/meta.yaml +++ b/recipes/bioconductor-gofuncr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GOfuncR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a81fecf10720e4ce20c7c4648b7fe1d + md5: d84c71ebda463871117ea00394d551ce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gofuncr", max_pin="x.x") }}' # Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-gtools >=3.5.0' - 'r-mapplots >=1.5' @@ -31,9 +32,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-gtools >=3.5.0' - 'r-mapplots >=1.5' diff --git a/recipes/bioconductor-golubesets/meta.yaml b/recipes/bioconductor-golubesets/meta.yaml index 181cf4e04483c..07b2c538aa5a1 100644 --- a/recipes/bioconductor-golubesets/meta.yaml +++ b/recipes/bioconductor-golubesets/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "golubEsets" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec7f4855c5a77d3ea3503a1102910a0c + md5: 49e3527c00f06c189a048a6b871f3d54 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-golubesets", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-golubesets/post-link.sh b/recipes/bioconductor-golubesets/post-link.sh index 9a15a0dca0cff..2a6d36332ced8 100644 --- a/recipes/bioconductor-golubesets/post-link.sh +++ b/recipes/bioconductor-golubesets/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "golubesets-1.42.0" +installBiocDataPackage.sh "golubesets-1.44.0" diff --git a/recipes/bioconductor-gopro/meta.yaml b/recipes/bioconductor-gopro/meta.yaml index 469642baa8eaf..28fc93fb2f3c8 100644 --- a/recipes/bioconductor-gopro/meta.yaml +++ b/recipes/bioconductor-gopro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GOpro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0112bd7b59baf1aae2c8bf7f3496600 + md5: c92dbcab08a7cdac3ee8ee6c28c6dc78 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gopro", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-dendextend @@ -35,12 +36,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bh - r-dendextend diff --git a/recipes/bioconductor-goprofiles/meta.yaml b/recipes/bioconductor-goprofiles/meta.yaml index 0d594871e1c39..f8cc90bc58c9f 100644 --- a/recipes/bioconductor-goprofiles/meta.yaml +++ b/recipes/bioconductor-goprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "goProfiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4da528658f42681fb65e8bc785b39804 + md5: ff2a664ff7284cf03e9caf932ad86d63 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-goprofiles", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-compquadform - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-compquadform - r-stringr diff --git a/recipes/bioconductor-gosemsim/meta.yaml b/recipes/bioconductor-gosemsim/meta.yaml index 028e3acfdbd90..186111722022f 100644 --- a/recipes/bioconductor-gosemsim/meta.yaml +++ b/recipes/bioconductor-gosemsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "GOSemSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d6dc404ac64c03d0d12f932b2133411 + md5: ea9c9c6e25cc507a2b5cff51f268d848 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat, ROCR + run_exports: '{{ pin_subpackage("bioconductor-gosemsim", max_pin="x.x") }}' +# Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat, tidyr, tidyselect, ROCR requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-rcpp + - r-rlang - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-rcpp + - r-rlang build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-goseq/meta.yaml b/recipes/bioconductor-goseq/meta.yaml index 3ff69348277b8..ee94c1535f052 100644 --- a/recipes/bioconductor-goseq/meta.yaml +++ b/recipes/bioconductor-goseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "goseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4607e3167133fc26bacc97e215fe0138 + md5: 4c39d7fbb51594a70dd3e54b1bc10375 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-goseq", max_pin="x.x") }}' noarch: generic # Suggests: edgeR, org.Hs.eg.db, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genelendatabase >=1.36.0,<1.37.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-biasedurn - r-mgcv run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genelendatabase >=1.36.0,<1.37.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-biasedurn - r-mgcv diff --git a/recipes/bioconductor-gosim/meta.yaml b/recipes/bioconductor-gosim/meta.yaml index a9cfe88fee26d..885c23bd98f98 100644 --- a/recipes/bioconductor-gosim/meta.yaml +++ b/recipes/bioconductor-gosim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "GOSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02736c160f8b114ae80c27bd92d14dfc + md5: 2fb07a8f5ac4b386b5063f52486bb82b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gosim", max_pin="x.x") }}' requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-cluster - r-corpcor @@ -35,13 +36,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-cluster - r-corpcor diff --git a/recipes/bioconductor-gosorensen/meta.yaml b/recipes/bioconductor-gosorensen/meta.yaml index f882b2d957f27..a6ccadcbdd826 100644 --- a/recipes/bioconductor-gosorensen/meta.yaml +++ b/recipes/bioconductor-gosorensen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "goSorensen" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3711f68b84fabd2730039daa4f81b38 + md5: 8fa5cc982341291dd857ab340abe4c73 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gosorensen", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goprofiles >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goprofiles >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base + - r-stringr run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goprofiles >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goprofiles >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base + - r-stringr test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,6 +42,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)' - description: 'This package implements inferential methods to compare gene lists (in this first release, to prove equivalence) in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.' + description: 'This package implements inferential methods to compare gene lists in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-gostag/meta.yaml b/recipes/bioconductor-gostag/meta.yaml index f6e7a62697ff4..4ea3c9b583493 100644 --- a/recipes/bioconductor-gostag/meta.yaml +++ b/recipes/bioconductor-gostag/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "goSTAG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7bc12d210ddda0a4b5f5edf28616fab7 + md5: 8d3245abbcc5813366a9393dc7bf79c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gostag", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-memoise run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - r-memoise test: diff --git a/recipes/bioconductor-gostats/meta.yaml b/recipes/bioconductor-gostats/meta.yaml index 5ad536fd0eae2..d2f24d9217bbd 100644 --- a/recipes/bioconductor-gostats/meta.yaml +++ b/recipes/bioconductor-gostats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.66.0" %} +{% set version = "2.68.0" %} {% set name = "GOstats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f2a76112093c47135db323a273405e2 + md5: 4489bff9142d2a3357ac2de0efc1b1b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gostats", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-gosummaries/meta.yaml b/recipes/bioconductor-gosummaries/meta.yaml index f5121955778cb..6c26068237b8d 100644 --- a/recipes/bioconductor-gosummaries/meta.yaml +++ b/recipes/bioconductor-gosummaries/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.37.0" %} {% set name = "GOsummaries" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9b6d1a50cb877d24e9264a02023a79e + md5: e31e67ed4c66122dcf79a694096ef539 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gosummaries", max_pin="x.x") }}' # Suggests: vegan requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-gprofiler @@ -31,7 +32,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-gprofiler diff --git a/recipes/bioconductor-gothic/meta.yaml b/recipes/bioconductor-gothic/meta.yaml index 6779ef8846164..7651748e307e3 100644 --- a/recipes/bioconductor-gothic/meta.yaml +++ b/recipes/bioconductor-gothic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "GOTHiC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f99fd13cc2e02957464e7b60647aeef + md5: 4674978396dedfc730c8ad85662dac8c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gothic", max_pin="x.x") }}' noarch: generic # Suggests: HiCDataLymphoblast requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-biocmanager - r-data.table - r-ggplot2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-biocmanager - r-data.table diff --git a/recipes/bioconductor-gotools/meta.yaml b/recipes/bioconductor-gotools/meta.yaml index 73f28508453af..0da93c1095d5d 100644 --- a/recipes/bioconductor-gotools/meta.yaml +++ b/recipes/bioconductor-gotools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "goTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68377c0224a6e3f7bac808ec7c4ae70c + md5: a91344726dcce37779380a18f6e9bc1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gotools", max_pin="x.x") }}' noarch: generic # Suggests: hgu133a.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-gp53cdf/meta.yaml b/recipes/bioconductor-gp53cdf/meta.yaml index 14b16bade6051..8bdbd9cb32bf1 100644 --- a/recipes/bioconductor-gp53cdf/meta.yaml +++ b/recipes/bioconductor-gp53cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "gp53cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2887dd15d3fa29b5c13b068c8d641f61 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gp53cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gpa/meta.yaml b/recipes/bioconductor-gpa/meta.yaml index 5d901016355f6..c5e078dff7b47 100644 --- a/recipes/bioconductor-gpa/meta.yaml +++ b/recipes/bioconductor-gpa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "GPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94cd599b75ea787687e4c66fbf54eb85 + md5: 2c1f0f3436c036a3e098d7780deb7282 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gpa", max_pin="x.x") }}' # Suggests: gpaExample # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-gpaexample/meta.yaml b/recipes/bioconductor-gpaexample/meta.yaml index b47ae952323c4..66694127c605d 100644 --- a/recipes/bioconductor-gpaexample/meta.yaml +++ b/recipes/bioconductor-gpaexample/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "gpaExample" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5cd543667831a4996249fcc3dee8224 + md5: e989af58ed5bbc10573f7438b3ee7836 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gpaexample", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gpaexample/post-link.sh b/recipes/bioconductor-gpaexample/post-link.sh index efcb7585c143c..b48e9f2168532 100644 --- a/recipes/bioconductor-gpaexample/post-link.sh +++ b/recipes/bioconductor-gpaexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gpaexample-1.12.0" +installBiocDataPackage.sh "gpaexample-1.14.0" diff --git a/recipes/bioconductor-gpls/meta.yaml b/recipes/bioconductor-gpls/meta.yaml index e2e521ed427a1..a685bbc90fd0d 100644 --- a/recipes/bioconductor-gpls/meta.yaml +++ b/recipes/bioconductor-gpls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "gpls" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c6d090f604af7c8c7b9f8478b7a7334f + md5: db6bc720156a5f7571a34e64b1189d3b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gpls", max_pin="x.x") }}' noarch: generic # Suggests: MASS requirements: diff --git a/recipes/bioconductor-gpumagic/meta.yaml b/recipes/bioconductor-gpumagic/meta.yaml index 378952cb58bfc..4aaa1e52b559b 100644 --- a/recipes/bioconductor-gpumagic/meta.yaml +++ b/recipes/bioconductor-gpumagic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "gpuMagic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9b10f314b0124f19525cc73763e9b15 + md5: b720e953b36ccc2db0c6b359f84b5c94 build: skip: True # [osx] - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gpumagic", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: 1. C++11, 2. a graphic driver or a CPU SDK. 3. ICD loader For Windows user, an ICD loader is required at C:/windows/system32/OpenCL.dll (Usually it is installed by the graphic driver). For Linux user (Except mac): ocl-icd-opencl-dev package is required. For Mac user, no action is needed for the system has installed the dependency. 4. GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - ocl-icd # [linux] + - khronos-opencl-icd-loader # [osx] + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-deriv - r-desctools @@ -32,9 +35,8 @@ requirements: - r-stringr - libblas - liblapack - - ocl-icd run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-deriv - r-desctools @@ -42,7 +44,6 @@ requirements: - r-pryr - r-rcpp - r-stringr - - ocl-icd build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-granie/meta.yaml b/recipes/bioconductor-granie/meta.yaml index caaac3289b655..b29c58c558196 100644 --- a/recipes/bioconductor-granie/meta.yaml +++ b/recipes/bioconductor-granie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.1" %} {% set name = "GRaNIE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14f7e1ef111e181c602e29d04b07a36a + md5: d9db703063398ccd263ce6b54def9266 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-granie", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, TFBSTools, motifmatchr, rbioapi +# Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, TFBSTools, motifmatchr, rbioapi, LDlinkR requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-checkmate - r-circlize @@ -60,18 +61,18 @@ requirements: - r-tidyselect - r-viridis run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-checkmate - r-circlize diff --git a/recipes/bioconductor-granulator/meta.yaml b/recipes/bioconductor-granulator/meta.yaml index a25a11f292d22..1a7ce94a61265 100644 --- a/recipes/bioconductor-granulator/meta.yaml +++ b/recipes/bioconductor-granulator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "granulator" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3dd49f32f5e06d8e71d2f9cf0061943b + md5: 05c4025460a33eb195280f676bd5695f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-granulator", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-graper/meta.yaml b/recipes/bioconductor-graper/meta.yaml index 36f59de7bbf4d..5f18d9093b48a 100644 --- a/recipes/bioconductor-graper/meta.yaml +++ b/recipes/bioconductor-graper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "graper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dfb81199dbe0b868891b0404ee6be865 + md5: e969608b591224df6c92d73194adea89 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graper", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: diff --git a/recipes/bioconductor-graph/meta.yaml b/recipes/bioconductor-graph/meta.yaml index cdff1216b3f78..79a97be096508 100644 --- a/recipes/bioconductor-graph/meta.yaml +++ b/recipes/bioconductor-graph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "graph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,7 +11,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cb2a06b2f76d5d7e1829110a2cac0790 + md5: 735b96df0f7c955806148170220b75b2 patches: - patch build: @@ -19,15 +19,16 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graph", max_pin="x.x") }}' # Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-graphalignment/meta.yaml b/recipes/bioconductor-graphalignment/meta.yaml index c8feeee759960..29442eaaf9529 100644 --- a/recipes/bioconductor-graphalignment/meta.yaml +++ b/recipes/bioconductor-graphalignment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "GraphAlignment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e833670324045ba6e5faf80b0dbddaa6 + md5: 0bc71a4722d0771d97671e81103bc8bb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graphalignment", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-graphat/meta.yaml b/recipes/bioconductor-graphat/meta.yaml index 85bd95713a136..39efd6cd695cd 100644 --- a/recipes/bioconductor-graphat/meta.yaml +++ b/recipes/bioconductor-graphat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "GraphAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3024a1e165c2da03487c727786f4c69d + md5: 075a7ac1af3518ac6ef4b9087107b482 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graphat", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-mcmcpack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-mcmcpack test: diff --git a/recipes/bioconductor-graphite/meta.yaml b/recipes/bioconductor-graphite/meta.yaml index 08b2ce2c7d527..cbbc5f5590f62 100644 --- a/recipes/bioconductor-graphite/meta.yaml +++ b/recipes/bioconductor-graphite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "graphite" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee3a1dfe540fddb10caaf9dc89cb9244 + md5: 532e304cdb96a828c4b764bfd36cce85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graphite", max_pin="x.x") }}' noarch: generic -# Suggests: checkmate, a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) +# Suggests: checkmate, a4Preproc, ALL, BiocStyle, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-httr - r-purrr - r-rappdirs - r-rlang run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-httr - r-purrr diff --git a/recipes/bioconductor-graphpac/meta.yaml b/recipes/bioconductor-graphpac/meta.yaml index 10cffce0ab041..c773413a30f97 100644 --- a/recipes/bioconductor-graphpac/meta.yaml +++ b/recipes/bioconductor-graphpac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "GraphPAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2ef8baf70be32173344ee1de04df841 + md5: 68794a35ae528c5cde68e7915611ace8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-graphpac", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-ipac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' - r-base - r-igraph - r-rmallow - r-tsp run: - - 'bioconductor-ipac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' - r-base - r-igraph - r-rmallow diff --git a/recipes/bioconductor-grasp2db/meta.yaml b/recipes/bioconductor-grasp2db/meta.yaml index 432e8571038f2..d1c3907d36ee0 100644 --- a/recipes/bioconductor-grasp2db/meta.yaml +++ b/recipes/bioconductor-grasp2db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "grasp2db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3fc90fc7c99e7da51dcbb687fd2d5515 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-grasp2db", max_pin="x.x") }}' noarch: generic # Suggests: gwascat, knitr requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-dbplyr - r-digest - r-dplyr - r-rsqlite run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-dbplyr - r-digest - r-dplyr - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-grenits/meta.yaml b/recipes/bioconductor-grenits/meta.yaml index 3cc7ca338509b..3625cf4b661d6 100644 --- a/recipes/bioconductor-grenits/meta.yaml +++ b/recipes/bioconductor-grenits/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.1" %} +{% set version = "1.54.0" %} {% set name = "GRENITS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: add877533a70243aba3429d02a1b9bd1 + md5: fd00e191f8c57c6ef54146263d21a089 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-grenits", max_pin="x.x") }}' # Suggests: network requirements: host: diff --git a/recipes/bioconductor-greylistchip/meta.yaml b/recipes/bioconductor-greylistchip/meta.yaml index 73198ac32ab4d..69807bd80c9c9 100644 --- a/recipes/bioconductor-greylistchip/meta.yaml +++ b/recipes/bioconductor-greylistchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "GreyListChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ed3e5d046abc71c57b41dcd6d67ef41 + md5: 42fa9dbbc56cc2c4fdf511ce67ee234e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-greylistchip", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-grmetrics/meta.yaml b/recipes/bioconductor-grmetrics/meta.yaml index 48850d9efee42..138a1f01df8f1 100644 --- a/recipes/bioconductor-grmetrics/meta.yaml +++ b/recipes/bioconductor-grmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "GRmetrics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 26897f28f8310a63c26bfee3ef9aa5f1 + md5: 16b27cb79eafe9dbdbb84f0626c5f8da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-grmetrics", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, tinytex requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-drc - r-ggplot2 - r-plotly run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-drc - r-ggplot2 diff --git a/recipes/bioconductor-grndata/meta.yaml b/recipes/bioconductor-grndata/meta.yaml index 4835bd51bcf00..19ec93513a47e 100644 --- a/recipes/bioconductor-grndata/meta.yaml +++ b/recipes/bioconductor-grndata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "grndata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e105a77f883593cbe67ddbdbe5ad91e3 + md5: 0ebac67277a5ca915f9a971d3659af5e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-grndata", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-grndata/post-link.sh b/recipes/bioconductor-grndata/post-link.sh index 5abbe76404e07..cc47b0a1e8a7f 100644 --- a/recipes/bioconductor-grndata/post-link.sh +++ b/recipes/bioconductor-grndata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "grndata-1.32.0" +installBiocDataPackage.sh "grndata-1.34.0" diff --git a/recipes/bioconductor-grohmm/meta.yaml b/recipes/bioconductor-grohmm/meta.yaml index e0cf197abaf2b..0861380ba58c9 100644 --- a/recipes/bioconductor-grohmm/meta.yaml +++ b/recipes/bioconductor-grohmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "groHMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b485a920aa3764cdae9b4d49acbbe67 + md5: 0b1077948ddc9895c57188ca2560bc10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-grohmm", max_pin="x.x") }}' # Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass build: diff --git a/recipes/bioconductor-gsalightning/meta.yaml b/recipes/bioconductor-gsalightning/meta.yaml index bc51010324050..f343d529a8d02 100644 --- a/recipes/bioconductor-gsalightning/meta.yaml +++ b/recipes/bioconductor-gsalightning/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "GSALightning" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 99107f0b7eb3b834af9628c73cdd2232 + md5: c6828603275d57045e613f1e7c0f143d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsalightning", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-gsar/meta.yaml b/recipes/bioconductor-gsar/meta.yaml index a49a1d187b976..294a6678158ba 100644 --- a/recipes/bioconductor-gsar/meta.yaml +++ b/recipes/bioconductor-gsar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GSAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 992d2824583ed572a43b035014d13681 + md5: 9828682d8721bde17ea31c9ed807174d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsar", max_pin="x.x") }}' noarch: generic # Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle requirements: diff --git a/recipes/bioconductor-gsbenchmark/meta.yaml b/recipes/bioconductor-gsbenchmark/meta.yaml index 0c3705cce95ea..562dacde1d6fc 100644 --- a/recipes/bioconductor-gsbenchmark/meta.yaml +++ b/recipes/bioconductor-gsbenchmark/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GSBenchMark" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67ad80e0d9aca2b2403031b8f5d79f57 + md5: bedfa52de1b414ae5fe9d5fc376380ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsbenchmark", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gsbenchmark/post-link.sh b/recipes/bioconductor-gsbenchmark/post-link.sh index 639c923dcdb2d..7e75d49468c5e 100644 --- a/recipes/bioconductor-gsbenchmark/post-link.sh +++ b/recipes/bioconductor-gsbenchmark/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gsbenchmark-1.20.0" +installBiocDataPackage.sh "gsbenchmark-1.22.0" diff --git a/recipes/bioconductor-gsca/meta.yaml b/recipes/bioconductor-gsca/meta.yaml index 111c55efa76c6..a02a1031371d3 100644 --- a/recipes/bioconductor-gsca/meta.yaml +++ b/recipes/bioconductor-gsca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "GSCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84486e7f5a9c1efb94dd0e8fd46347c1 + md5: 6cf569e7be20a330c190c8c3af6f0654 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsca", max_pin="x.x") }}' noarch: generic # Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-gplots @@ -30,7 +31,7 @@ requirements: - r-shiny - r-sp run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-gse103322/meta.yaml b/recipes/bioconductor-gse103322/meta.yaml index 9d5041b4df503..78cde2aa8566a 100644 --- a/recipes/bioconductor-gse103322/meta.yaml +++ b/recipes/bioconductor-gse103322/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GSE103322" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f0ae42096e6851fc40f3c45831d38c7 + md5: 3816b430b716edaaa0ef22dba38cf58e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gse103322", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, SummarizedExperiment, SingleCellExperiment requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gse103322/post-link.sh b/recipes/bioconductor-gse103322/post-link.sh index 400e8f8c47a7d..719c9773297fe 100644 --- a/recipes/bioconductor-gse103322/post-link.sh +++ b/recipes/bioconductor-gse103322/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse103322-1.6.0" +installBiocDataPackage.sh "gse103322-1.8.0" diff --git a/recipes/bioconductor-gse13015/meta.yaml b/recipes/bioconductor-gse13015/meta.yaml index ad1dd80f10e5c..f6b004027246e 100644 --- a/recipes/bioconductor-gse13015/meta.yaml +++ b/recipes/bioconductor-gse13015/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GSE13015" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 749148d0e8ddb719e43d6513e340e8b6 + md5: 99fae6872abf6820842a1340f7fd6b4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gse13015", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gse13015/post-link.sh b/recipes/bioconductor-gse13015/post-link.sh index dcba32af32068..03e9a7afbddbe 100644 --- a/recipes/bioconductor-gse13015/post-link.sh +++ b/recipes/bioconductor-gse13015/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse13015-1.8.0" +installBiocDataPackage.sh "gse13015-1.10.0" diff --git a/recipes/bioconductor-gse159526/meta.yaml b/recipes/bioconductor-gse159526/meta.yaml index 41485e8f1644d..abca80d825751 100644 --- a/recipes/bioconductor-gse159526/meta.yaml +++ b/recipes/bioconductor-gse159526/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GSE159526" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 930aac8c4e8b481b62e489d6e5d94487 + md5: d89442c94cb87f0760a9f0f85426a8fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gse159526", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown, testthat, minfi, tibble, sessioninfo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gse159526/post-link.sh b/recipes/bioconductor-gse159526/post-link.sh index 7caa9a6ed0578..70558b3f8c891 100644 --- a/recipes/bioconductor-gse159526/post-link.sh +++ b/recipes/bioconductor-gse159526/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse159526-1.6.0" +installBiocDataPackage.sh "gse159526-1.8.0" diff --git a/recipes/bioconductor-gse62944/meta.yaml b/recipes/bioconductor-gse62944/meta.yaml index 4bd7db2ce4430..925d457637f38 100644 --- a/recipes/bioconductor-gse62944/meta.yaml +++ b/recipes/bioconductor-gse62944/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "GSE62944" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8759202f2247d2a60d0bb17acfffad6a + md5: 5b6c58aaee948c9cd0e0d52b5adcf264 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gse62944", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, DESeq2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gse62944/post-link.sh b/recipes/bioconductor-gse62944/post-link.sh index 49a2bf82549c1..35edd4d1cec52 100644 --- a/recipes/bioconductor-gse62944/post-link.sh +++ b/recipes/bioconductor-gse62944/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse62944-1.28.1" +installBiocDataPackage.sh "gse62944-1.30.0" diff --git a/recipes/bioconductor-gseabase/meta.yaml b/recipes/bioconductor-gseabase/meta.yaml index f7a33aceccb03..87db5ecfad250 100644 --- a/recipes/bioconductor-gseabase/meta.yaml +++ b/recipes/bioconductor-gseabase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "GSEABase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac49fd7057e13a7485d3fcd18036e2f8 + md5: a9d4d48654c9a05cdec2f09f8f805c4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gseabase", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr, RUnit requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-xml run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-xml test: diff --git a/recipes/bioconductor-gseabenchmarker/meta.yaml b/recipes/bioconductor-gseabenchmarker/meta.yaml index 2c863dcc8f95f..d3a50bed81819 100644 --- a/recipes/bioconductor-gseabenchmarker/meta.yaml +++ b/recipes/bioconductor-gseabenchmarker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "GSEABenchmarkeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34229c527aba8c7025fa9d310f3f2d16 + md5: 9f297d155b3c254f091eb70a180ea9fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gseabenchmarker", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichmentbrowser >=2.30.0,<2.31.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.20.0,<1.21.0' - - 'bioconductor-keggdzpathwaysgeo >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.22.0,<1.23.0' + - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-enrichmentbrowser >=2.30.0,<2.31.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.20.0,<1.21.0' - - 'bioconductor-keggdzpathwaysgeo >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.22.0,<1.23.0' + - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-gsealm/meta.yaml b/recipes/bioconductor-gsealm/meta.yaml index e0da1b02b43b4..502e5017b9cf4 100644 --- a/recipes/bioconductor-gsealm/meta.yaml +++ b/recipes/bioconductor-gsealm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "GSEAlm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2df157d143a03b871109690f6b4769c7 + md5: b88623d080b75bb6775026e9e6c4dd9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsealm", max_pin="x.x") }}' noarch: generic # Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-gseamining/meta.yaml b/recipes/bioconductor-gseamining/meta.yaml index 2ade682c1a61e..bff37cad1e697 100644 --- a/recipes/bioconductor-gseamining/meta.yaml +++ b/recipes/bioconductor-gseamining/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GSEAmining" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,14 +11,15 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 473b3365763356450a2e7820736ca4dd + md5: 703f12fed97e95761b2cd41894da0645 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gseamining", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat +# Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm requirements: host: - r-base diff --git a/recipes/bioconductor-gsean/meta.yaml b/recipes/bioconductor-gsean/meta.yaml index 699c899ca2f21..56e88aeaa6ee8 100644 --- a/recipes/bioconductor-gsean/meta.yaml +++ b/recipes/bioconductor-gsean/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.2" %} +{% set version = "1.22.0" %} {% set name = "gsean" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 86ad318c3f149e10fc6561c415b1ca96 + md5: 501dfe30896b53197345abe9d1600247 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsean", max_pin="x.x") }}' # Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown requirements: host: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-ppinfer >=1.26.0,<1.27.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-ppinfer >=1.28.0,<1.29.0' - r-base - libblas - liblapack run: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-ppinfer >=1.26.0,<1.27.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-ppinfer >=1.28.0,<1.29.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-gsgalgor/meta.yaml b/recipes/bioconductor-gsgalgor/meta.yaml index 13bc612d97a4a..cf311c036c026 100644 --- a/recipes/bioconductor-gsgalgor/meta.yaml +++ b/recipes/bioconductor-gsgalgor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GSgalgoR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f05f9acb6cf8bdc69944006f950d689 + md5: 09d5b90490f44ee7384c71762228244d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsgalgor", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat requirements: diff --git a/recipes/bioconductor-gsreg/meta.yaml b/recipes/bioconductor-gsreg/meta.yaml index 44f757afe803f..42f7a252d92c8 100644 --- a/recipes/bioconductor-gsreg/meta.yaml +++ b/recipes/bioconductor-gsreg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "GSReg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c4d1a7a4a517c6c05a30694549f144f + md5: 631e2589b571bfcdf38b5673ba0693d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsreg", max_pin="x.x") }}' # Suggests: GenomicRanges, GSBenchMark requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-gsri/meta.yaml b/recipes/bioconductor-gsri/meta.yaml index 1d0bb1fb961a6..80acc691c0711 100644 --- a/recipes/bioconductor-gsri/meta.yaml +++ b/recipes/bioconductor-gsri/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.48.0" %} +{% set version = "2.50.0" %} {% set name = "GSRI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be540e94ade102397a842e6857d772d4 + md5: 686ab91e4ee0adeb4828a5b2ac2f6943 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsri", max_pin="x.x") }}' noarch: generic # Suggests: limma, hgu95av2.db requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-les >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-les >=1.52.0,<1.53.0' - r-base - r-fdrtool run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-les >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-les >=1.52.0,<1.53.0' - r-base - r-fdrtool test: diff --git a/recipes/bioconductor-gsva/meta.yaml b/recipes/bioconductor-gsva/meta.yaml index 4d6b781e794e2..b921c6e030815 100644 --- a/recipes/bioconductor-gsva/meta.yaml +++ b/recipes/bioconductor-gsva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.2" %} +{% set version = "1.50.0" %} {% set name = "GSVA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4732baaf15d6d75e98374e143039d541 + md5: e21af1ab9dabfa5801fb978b50f992e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsva", max_pin="x.x") }}' # Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-matrix >=1.5-0' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-matrix >=1.5-0' build: @@ -60,7 +61,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'Gene Set Variation Analysis for microarray and RNA-seq data' + summary: 'Gene Set Variation Analysis for Microarray and RNA-Seq Data' description: 'Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: diff --git a/recipes/bioconductor-gsvadata/meta.yaml b/recipes/bioconductor-gsvadata/meta.yaml index 7c0fcff56d32d..b4a138b0bd959 100644 --- a/recipes/bioconductor-gsvadata/meta.yaml +++ b/recipes/bioconductor-gsvadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "GSVAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 745225b064d2d82499906b03543ee0ac + md5: 3c2d6a66967ab8c3c2545fc3323282b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gsvadata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - 'bioconductor-hgu95a.db >=3.13.0,<3.14.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - 'bioconductor-hgu95a.db >=3.13.0,<3.14.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gsvadata/post-link.sh b/recipes/bioconductor-gsvadata/post-link.sh index 7f3de7e3f402e..47efe8a70a147 100644 --- a/recipes/bioconductor-gsvadata/post-link.sh +++ b/recipes/bioconductor-gsvadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gsvadata-1.36.0" +installBiocDataPackage.sh "gsvadata-1.38.0" diff --git a/recipes/bioconductor-gtrellis/meta.yaml b/recipes/bioconductor-gtrellis/meta.yaml index 6eb24455fff17..161c476c7d085 100644 --- a/recipes/bioconductor-gtrellis/meta.yaml +++ b/recipes/bioconductor-gtrellis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "gtrellis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b3e1e7fce6888cb1ead8c1ad4f637708 + md5: 795b74d96310e3cd9a5771bd8695cf64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gtrellis", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.8' - r-getoptlong run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.4.8' - r-getoptlong diff --git a/recipes/bioconductor-guideseq/meta.yaml b/recipes/bioconductor-guideseq/meta.yaml index 0ada362630533..b3a7b618ced7e 100644 --- a/recipes/bioconductor-guideseq/meta.yaml +++ b/recipes/bioconductor-guideseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "GUIDEseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9005588165cf4614cf71fefb7fa0e42d + md5: fe01afa9546bc7bdc1fbeea8c8bda8db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-guideseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-crisprseek >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-crisprseek >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -49,20 +50,20 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-crisprseek >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-crisprseek >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-guitar/meta.yaml b/recipes/bioconductor-guitar/meta.yaml index 282ac72e4515c..5ead73d849ee9 100644 --- a/recipes/bioconductor-guitar/meta.yaml +++ b/recipes/bioconductor-guitar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "Guitar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2c085559ba2fd466f795f3ae5877db7 + md5: e62e4238e3e3b939a2195eb384079bb3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-guitar", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-ggplot2 - r-knitr - r-magrittr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-gviz/meta.yaml b/recipes/bioconductor-gviz/meta.yaml index 49cf722385529..e0c413f6a6708 100644 --- a/recipes/bioconductor-gviz/meta.yaml +++ b/recipes/bioconductor-gviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.1" %} {% set name = "Gviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea2e7a3016f67158d00b4d116482da04 + md5: 2e1eba2ac7cb0d1178f17bba471b0a62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gviz", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-digest >=0.6.8' - r-lattice @@ -45,23 +46,23 @@ requirements: - 'r-matrixstats >=0.8.14' - r-rcolorbrewer run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-digest >=0.6.8' - r-lattice diff --git a/recipes/bioconductor-gwas.bayes/meta.yaml b/recipes/bioconductor-gwas.bayes/meta.yaml index c0cf1fbc23391..e00fe8aad9e30 100644 --- a/recipes/bioconductor-gwas.bayes/meta.yaml +++ b/recipes/bioconductor-gwas.bayes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GWAS.BAYES" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e8733509e3803574f9b92e9902010d8 + md5: cf62f1d1c5f69ef4051bf659da548b1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwas.bayes", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-caret >=6.0-86' - 'r-ga >=3.2' @@ -29,7 +30,7 @@ requirements: - 'r-matrix >=1.2-18' - 'r-memoise >=1.1.0' run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-caret >=6.0-86' - 'r-ga >=3.2' diff --git a/recipes/bioconductor-gwascat/meta.yaml b/recipes/bioconductor-gwascat/meta.yaml index 8458e47b680fb..fd05265aa675a 100644 --- a/recipes/bioconductor-gwascat/meta.yaml +++ b/recipes/bioconductor-gwascat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "gwascat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47e8a78f635d5137f6ce804a50edfb9f + md5: a7cbd1d5ac4b3d4fbb8d1fbd77269e44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwascat", max_pin="x.x") }}' noarch: generic # Suggests: DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-readr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-readr test: diff --git a/recipes/bioconductor-gwascatdata/meta.yaml b/recipes/bioconductor-gwascatdata/meta.yaml index 44fc9e5897fe5..993381303c0d2 100644 --- a/recipes/bioconductor-gwascatdata/meta.yaml +++ b/recipes/bioconductor-gwascatdata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.6" %} {% set name = "gwascatData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fa09db539ac0a16ba136e810a5b9970a build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwascatdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat, AnnotationHub, rmarkdown, knitr requirements: @@ -27,7 +28,7 @@ requirements: - r-base - r-data.table - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gwasdata/meta.yaml b/recipes/bioconductor-gwasdata/meta.yaml index f81ccc89c6f9b..f30c72237cf4e 100644 --- a/recipes/bioconductor-gwasdata/meta.yaml +++ b/recipes/bioconductor-gwasdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.1" %} +{% set version = "1.40.0" %} {% set name = "GWASdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f613097e6cc22f457d1de41f8e677aa6 + md5: 57fec70f980b9e476f0c59d397797815 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwasdata", max_pin="x.x") }}' noarch: generic # Suggests: ncdf4 requirements: host: - - 'bioconductor-gwastools >=1.46.0,<1.47.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-gwastools >=1.46.0,<1.47.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-gwasdata/post-link.sh b/recipes/bioconductor-gwasdata/post-link.sh index 691a1bc8e0e26..11e8192ddace6 100644 --- a/recipes/bioconductor-gwasdata/post-link.sh +++ b/recipes/bioconductor-gwasdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gwasdata-1.38.1" +installBiocDataPackage.sh "gwasdata-1.40.0" diff --git a/recipes/bioconductor-gwastools/meta.yaml b/recipes/bioconductor-gwastools/meta.yaml index 5e09816c4bd28..1607a30635493 100644 --- a/recipes/bioconductor-gwastools/meta.yaml +++ b/recipes/bioconductor-gwastools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "GWASTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71908b60ba4de5563bc3729ee64193cb + md5: af968b8e8a3e4a1981cae02cb2a781ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwastools", max_pin="x.x") }}' noarch: generic -# Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel +# Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base - r-data.table - r-dbi @@ -35,10 +36,10 @@ requirements: - r-sandwich - r-survival run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base - r-data.table - r-dbi diff --git a/recipes/bioconductor-gwasurvivr/meta.yaml b/recipes/bioconductor-gwasurvivr/meta.yaml index 87a442730f93c..c62748b8cba02 100644 --- a/recipes/bioconductor-gwasurvivr/meta.yaml +++ b/recipes/bioconductor-gwasurvivr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "gwasurvivr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 53493a3fa552b7a0d357cfb2a459a6aa + md5: 699843eb7ff1528732a6a2e093600aef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwasurvivr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-survival run: - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-survival diff --git a/recipes/bioconductor-gwena/meta.yaml b/recipes/bioconductor-gwena/meta.yaml index c0772b6ce57ac..9ded48032ed13 100644 --- a/recipes/bioconductor-gwena/meta.yaml +++ b/recipes/bioconductor-gwena/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GWENA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7db0c32d0fd31879561c5325e0f5b571 + md5: 8f1bd435deae9546d0ec3f8605a0b682 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gwena", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors (>= 0.22.1), BiocStyle (>= 2.15.8) requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-cluster >=2.1.0' - 'r-dplyr >=0.8.3' @@ -40,7 +41,7 @@ requirements: - 'r-tidyr >=1.0.0' - 'r-wgcna >=1.67' run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-cluster >=2.1.0' - 'r-dplyr >=0.8.3' diff --git a/recipes/bioconductor-h10kcod.db/meta.yaml b/recipes/bioconductor-h10kcod.db/meta.yaml index 4ca070938e6ba..c4c1dfaeef710 100644 --- a/recipes/bioconductor-h10kcod.db/meta.yaml +++ b/recipes/bioconductor-h10kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "h10kcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a555739cea229f286953c3297c145e9c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-h10kcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-h20kcod.db/meta.yaml b/recipes/bioconductor-h20kcod.db/meta.yaml index 36fa342084d4d..8427bc3859258 100644 --- a/recipes/bioconductor-h20kcod.db/meta.yaml +++ b/recipes/bioconductor-h20kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "h20kcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3647facb272f58424f4c94ef92e8ee45 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-h20kcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-h5vc/meta.yaml b/recipes/bioconductor-h5vc/meta.yaml index b0e9d79f7de3e..d5c396bb578ac 100644 --- a/recipes/bioconductor-h5vc/meta.yaml +++ b/recipes/bioconductor-h5vc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "h5vc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8322cd34695b64b550a28eac35740c63 + md5: 2d827ac4606ef723005e479de8540b7a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-h5vc", max_pin="x.x") }}' # Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-h5vcdata >=2.20.0,<2.21.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-h5vcdata >=2.22.0,<2.23.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-abind - r-base - r-batchjobs @@ -40,16 +41,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-h5vcdata >=2.20.0,<2.21.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-h5vcdata >=2.22.0,<2.23.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-abind - r-base - r-batchjobs diff --git a/recipes/bioconductor-h5vcdata/meta.yaml b/recipes/bioconductor-h5vcdata/meta.yaml index 3b31e5f911d04..7edd272d4b3ef 100644 --- a/recipes/bioconductor-h5vcdata/meta.yaml +++ b/recipes/bioconductor-h5vcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "h5vcData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e233ff9873648c459591fda6942a8790 + md5: c251316e2d6dc6cb90e8faad0015103b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-h5vcdata", max_pin="x.x") }}' noarch: generic # Suggests: h5vc requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-h5vcdata/post-link.sh b/recipes/bioconductor-h5vcdata/post-link.sh index f44cf91b76794..1962bfe15c1eb 100644 --- a/recipes/bioconductor-h5vcdata/post-link.sh +++ b/recipes/bioconductor-h5vcdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "h5vcdata-2.20.0" +installBiocDataPackage.sh "h5vcdata-2.22.0" diff --git a/recipes/bioconductor-hapfabia/meta.yaml b/recipes/bioconductor-hapfabia/meta.yaml index f317c897e36cc..ff56c6ea7dada 100644 --- a/recipes/bioconductor-hapfabia/meta.yaml +++ b/recipes/bioconductor-hapfabia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapFabia" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43b510f5d1b6e18ad523e0429a84618b + md5: a14370aec9e86245541aea68b90c3812 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapfabia", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fabia >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fabia >=2.48.0,<2.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fabia >=2.46.0,<2.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fabia >=2.48.0,<2.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hapmap100khind/meta.yaml b/recipes/bioconductor-hapmap100khind/meta.yaml index bc6cd30450d6f..3b61d5d83e55f 100644 --- a/recipes/bioconductor-hapmap100khind/meta.yaml +++ b/recipes/bioconductor-hapmap100khind/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmap100khind" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ec3213b4ced09f678386a981176e3410 + md5: 0168028295626d811e305d4008ce9996 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmap100khind", max_pin="x.x") }}' noarch: generic # Suggests: oligo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap100khind/post-link.sh b/recipes/bioconductor-hapmap100khind/post-link.sh index 0a039b707cc55..d9f5a26dbbc86 100644 --- a/recipes/bioconductor-hapmap100khind/post-link.sh +++ b/recipes/bioconductor-hapmap100khind/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap100khind-1.42.0" +installBiocDataPackage.sh "hapmap100khind-1.44.0" diff --git a/recipes/bioconductor-hapmap100kxba/meta.yaml b/recipes/bioconductor-hapmap100kxba/meta.yaml index 0191502c36e6b..50530871601de 100644 --- a/recipes/bioconductor-hapmap100kxba/meta.yaml +++ b/recipes/bioconductor-hapmap100kxba/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmap100kxba" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46a995b0ad38d46aebdf89c52678c587 + md5: b4a619fb108a36920109307fbf63985b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmap100kxba", max_pin="x.x") }}' noarch: generic # Suggests: oligo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap100kxba/post-link.sh b/recipes/bioconductor-hapmap100kxba/post-link.sh index 6f5564a5a776c..e71f400872e77 100644 --- a/recipes/bioconductor-hapmap100kxba/post-link.sh +++ b/recipes/bioconductor-hapmap100kxba/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap100kxba-1.42.0" +installBiocDataPackage.sh "hapmap100kxba-1.44.0" diff --git a/recipes/bioconductor-hapmap370k/meta.yaml b/recipes/bioconductor-hapmap370k/meta.yaml index cb3865a809e87..4711fa3319d8d 100644 --- a/recipes/bioconductor-hapmap370k/meta.yaml +++ b/recipes/bioconductor-hapmap370k/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "hapmap370k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 569556341a45da799372aaf1012be72e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmap370k", max_pin="x.x") }}' noarch: generic # Suggests: crlmm requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap500knsp/meta.yaml b/recipes/bioconductor-hapmap500knsp/meta.yaml index 63f11361b25e2..379eb3e96b54a 100644 --- a/recipes/bioconductor-hapmap500knsp/meta.yaml +++ b/recipes/bioconductor-hapmap500knsp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmap500knsp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c54725a8ec3607d9db051ef7dfb8b16f + md5: 15b799bba4a395ccf715acfc7bbdae04 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmap500knsp", max_pin="x.x") }}' noarch: generic # Suggests: oligo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap500knsp/post-link.sh b/recipes/bioconductor-hapmap500knsp/post-link.sh index f7cfbfd4b45a1..1d91347c61c09 100644 --- a/recipes/bioconductor-hapmap500knsp/post-link.sh +++ b/recipes/bioconductor-hapmap500knsp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap500knsp-1.42.0" +installBiocDataPackage.sh "hapmap500knsp-1.44.0" diff --git a/recipes/bioconductor-hapmap500ksty/meta.yaml b/recipes/bioconductor-hapmap500ksty/meta.yaml index c9e4a88c27127..d4b94cf67c00c 100644 --- a/recipes/bioconductor-hapmap500ksty/meta.yaml +++ b/recipes/bioconductor-hapmap500ksty/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmap500ksty" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b283985ebfd5c8eace1e5f436fb1d07c + md5: 7a1d4983ac3e411dadedc130d85c2557 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmap500ksty", max_pin="x.x") }}' noarch: generic # Suggests: oligo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmap500ksty/post-link.sh b/recipes/bioconductor-hapmap500ksty/post-link.sh index ce7389adcc9e4..fe55de17a68f4 100644 --- a/recipes/bioconductor-hapmap500ksty/post-link.sh +++ b/recipes/bioconductor-hapmap500ksty/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap500ksty-1.42.0" +installBiocDataPackage.sh "hapmap500ksty-1.44.0" diff --git a/recipes/bioconductor-hapmapsnp5/meta.yaml b/recipes/bioconductor-hapmapsnp5/meta.yaml index a9c280b8ca83e..d3d9f4de67114 100644 --- a/recipes/bioconductor-hapmapsnp5/meta.yaml +++ b/recipes/bioconductor-hapmapsnp5/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmapsnp5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ccc4fe2a3fcb840365fb2b3bdec3cfd8 + md5: 2f14e60f39cf94c43f2dd0e5aa5a48e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmapsnp5", max_pin="x.x") }}' noarch: generic # Suggests: oligo requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmapsnp5/post-link.sh b/recipes/bioconductor-hapmapsnp5/post-link.sh index b4eb52c418b84..de833d94f68c6 100644 --- a/recipes/bioconductor-hapmapsnp5/post-link.sh +++ b/recipes/bioconductor-hapmapsnp5/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmapsnp5-1.42.0" +installBiocDataPackage.sh "hapmapsnp5-1.44.0" diff --git a/recipes/bioconductor-hapmapsnp6/meta.yaml b/recipes/bioconductor-hapmapsnp6/meta.yaml index 499bcbdbecc09..17aec4ff0bb9d 100644 --- a/recipes/bioconductor-hapmapsnp6/meta.yaml +++ b/recipes/bioconductor-hapmapsnp6/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hapmapsnp6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a6ca8fb7d228e64ba1567d4cb7bcd81e + md5: 2635c012a513343484177db2070209e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hapmapsnp6", max_pin="x.x") }}' noarch: generic # Suggests: oligo, oligoClasses requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hapmapsnp6/post-link.sh b/recipes/bioconductor-hapmapsnp6/post-link.sh index eb074feda8ad7..44c99a5802936 100644 --- a/recipes/bioconductor-hapmapsnp6/post-link.sh +++ b/recipes/bioconductor-hapmapsnp6/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmapsnp6-1.42.0" +installBiocDataPackage.sh "hapmapsnp6-1.44.0" diff --git a/recipes/bioconductor-harbchip/meta.yaml b/recipes/bioconductor-harbchip/meta.yaml index 7ef59a1f169ca..ee6acbfff7d6f 100644 --- a/recipes/bioconductor-harbchip/meta.yaml +++ b/recipes/bioconductor-harbchip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "harbChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5713ddec61a7771a7c8be36ced779ef1 + md5: f5948fc0f4c1ced0a43e85c1885f5d9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harbchip", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-harbchip/post-link.sh b/recipes/bioconductor-harbchip/post-link.sh index 0300d3a1f20b5..d2133dee6fc33 100644 --- a/recipes/bioconductor-harbchip/post-link.sh +++ b/recipes/bioconductor-harbchip/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "harbchip-1.38.0" +installBiocDataPackage.sh "harbchip-1.40.0" diff --git a/recipes/bioconductor-harman/meta.yaml b/recipes/bioconductor-harman/meta.yaml index 64348ff3cf2d6..aa06daaaff680 100644 --- a/recipes/bioconductor-harman/meta.yaml +++ b/recipes/bioconductor-harman/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Harman" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c60199c4fb9c66f65597ea11d926f410 + md5: aaec4256c0cb2949d553ff81d94e48d2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harman", max_pin="x.x") }}' # Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva requirements: host: diff --git a/recipes/bioconductor-harmandata/meta.yaml b/recipes/bioconductor-harmandata/meta.yaml index ab52d0029ec7c..f0076f4ffdd6a 100644 --- a/recipes/bioconductor-harmandata/meta.yaml +++ b/recipes/bioconductor-harmandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "HarmanData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43bca3e57aee5603fda4b7be1cb9c738 + md5: 7df1447aff75abdf025678b51a0ee8fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harmandata", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3) requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-harmandata/post-link.sh b/recipes/bioconductor-harmandata/post-link.sh index f61d2ad4aff59..bfce705eabe09 100644 --- a/recipes/bioconductor-harmandata/post-link.sh +++ b/recipes/bioconductor-harmandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "harmandata-1.28.0" +installBiocDataPackage.sh "harmandata-1.30.0" diff --git a/recipes/bioconductor-harmonizedtcgadata/meta.yaml b/recipes/bioconductor-harmonizedtcgadata/meta.yaml index 38b5ec17a9e77..c421c5e1b4ec4 100644 --- a/recipes/bioconductor-harmonizedtcgadata/meta.yaml +++ b/recipes/bioconductor-harmonizedtcgadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "HarmonizedTCGAData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c615eb02dbda3204fb5f3d9308a0115c + md5: f6e8f685a67152c6f382089c0e6aae01 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harmonizedtcgadata", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-harmonizedtcgadata/post-link.sh b/recipes/bioconductor-harmonizedtcgadata/post-link.sh index a524f01cbd414..dbe5eabb855e7 100644 --- a/recipes/bioconductor-harmonizedtcgadata/post-link.sh +++ b/recipes/bioconductor-harmonizedtcgadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "harmonizedtcgadata-1.22.0" +installBiocDataPackage.sh "harmonizedtcgadata-1.24.0" diff --git a/recipes/bioconductor-harmonizr/build.sh b/recipes/bioconductor-harmonizr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-harmonizr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-harmonizr/meta.yaml b/recipes/bioconductor-harmonizr/meta.yaml new file mode 100644 index 0000000000000..ee8a16ab953cf --- /dev/null +++ b/recipes/bioconductor-harmonizr/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "HarmonizR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6e81c009fe8678273d8091378ae2f8e3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harmonizr", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - r-base + - 'r-doparallel >=1.0.16' + - 'r-foreach >=1.5.1' + - 'r-janitor >=2.1.0' + - 'r-plyr >=1.8.6' + - 'r-seriation >=1.3.5' + run: + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - r-base + - 'r-doparallel >=1.0.16' + - 'r-foreach >=1.5.1' + - 'r-janitor >=2.1.0' + - 'r-plyr >=1.8.6' + - 'r-seriation >=1.3.5' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Handles missing values and makes more data available' + description: 'An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-harshlight/meta.yaml b/recipes/bioconductor-harshlight/meta.yaml index 023d6e9ae198e..2a5a3f49a1f5e 100644 --- a/recipes/bioconductor-harshlight/meta.yaml +++ b/recipes/bioconductor-harshlight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "Harshlight" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e7e404fef55917ab6b589f77430a8ec + md5: 36adabb3111ae035069431431dd9434a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-harshlight", max_pin="x.x") }}' requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-altcdfenvs >=2.62.0,<2.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-altcdfenvs >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-altcdfenvs >=2.62.0,<2.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-altcdfenvs >=2.64.0,<2.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hca/meta.yaml b/recipes/bioconductor-hca/meta.yaml index ed97a3695a444..0d284f48c3444 100644 --- a/recipes/bioconductor-hca/meta.yaml +++ b/recipes/bioconductor-hca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "hca" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0bad76d71df17bd87e1f256b1ece6bfc + md5: 8a1c812efb51ab7e30a7d419bdf918a3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hca", max_pin="x.x") }}' noarch: generic # Suggests: LoomExperiment, SummarizedExperiment, SingleCellExperiment, S4Vectors, methods, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-digest - r-dplyr @@ -34,7 +35,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-digest - r-dplyr diff --git a/recipes/bioconductor-hcadata/meta.yaml b/recipes/bioconductor-hcadata/meta.yaml index 510ec4f2806c0..de0348abe7497 100644 --- a/recipes/bioconductor-hcadata/meta.yaml +++ b/recipes/bioconductor-hcadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "HCAData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8a2e18f3a29f80ba013759f6c87619e + md5: 4f16bf5904ca21c0fb0bd6515d7ab4d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hcadata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), BiocSingular, scater, scuttle, Rtsne, igraph, iSEE, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hcadata/post-link.sh b/recipes/bioconductor-hcadata/post-link.sh index a7d7e277e5273..66d5690d2efbb 100644 --- a/recipes/bioconductor-hcadata/post-link.sh +++ b/recipes/bioconductor-hcadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hcadata-1.16.0" +installBiocDataPackage.sh "hcadata-1.18.0" diff --git a/recipes/bioconductor-hcatonsildata/meta.yaml b/recipes/bioconductor-hcatonsildata/meta.yaml new file mode 100644 index 0000000000000..c329508ef650e --- /dev/null +++ b/recipes/bioconductor-hcatonsildata/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "HCATonsilData" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dda9d216f608690d05bd5ffbcb73bb05 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hcatonsildata", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac, zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle +requirements: + host: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-base64enc + - r-htmltools + - r-rmarkdown + run: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-base64enc + - r-htmltools + - r-rmarkdown + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Provide programmatic access to the tonsil cell atlas datasets' + description: 'This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary.' + license_file: LICENSE + diff --git a/recipes/bioconductor-hcatonsildata/post-link.sh b/recipes/bioconductor-hcatonsildata/post-link.sh new file mode 100644 index 0000000000000..55f8721ee344a --- /dev/null +++ b/recipes/bioconductor-hcatonsildata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "hcatonsildata-1.0.0" diff --git a/recipes/bioconductor-hcatonsildata/pre-unlink.sh b/recipes/bioconductor-hcatonsildata/pre-unlink.sh new file mode 100644 index 0000000000000..7b67c6f0a09f6 --- /dev/null +++ b/recipes/bioconductor-hcatonsildata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HCATonsilData diff --git a/recipes/bioconductor-hcg110.db/meta.yaml b/recipes/bioconductor-hcg110.db/meta.yaml index 11261857c2e11..c77a258d0c61b 100644 --- a/recipes/bioconductor-hcg110.db/meta.yaml +++ b/recipes/bioconductor-hcg110.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hcg110.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4c536c3539a61d7f1f67dac149f10b11 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hcg110.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hcg110cdf/meta.yaml b/recipes/bioconductor-hcg110cdf/meta.yaml index 7e24db7b745c9..6460e345d15fd 100644 --- a/recipes/bioconductor-hcg110cdf/meta.yaml +++ b/recipes/bioconductor-hcg110cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hcg110cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b53167876217ddb301204719da23eafc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hcg110cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hcg110probe/meta.yaml b/recipes/bioconductor-hcg110probe/meta.yaml index 28ac1ca33e9d9..43ac0da0bf42d 100644 --- a/recipes/bioconductor-hcg110probe/meta.yaml +++ b/recipes/bioconductor-hcg110probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hcg110probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 51af8d6a7090ea7c5fe630dcea68bfb3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hcg110probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hd2013sgi/meta.yaml b/recipes/bioconductor-hd2013sgi/meta.yaml index c9386c47fc272..bfee69a492903 100644 --- a/recipes/bioconductor-hd2013sgi/meta.yaml +++ b/recipes/bioconductor-hd2013sgi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "HD2013SGI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4cc03451c32df17e2a946ab45d32659e + md5: f8c7020a4fbfcb5c4026cea93e5a5bc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hd2013sgi", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle # SystemRequirements: GNU make requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' - r-base - r-gplots - r-lsd - r-rcolorbrewer - r-vcd run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' - r-base - r-gplots - r-lsd - r-rcolorbrewer - r-vcd - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hd2013sgi/post-link.sh b/recipes/bioconductor-hd2013sgi/post-link.sh index ec3b2ce7c28e1..498c6fc12a428 100644 --- a/recipes/bioconductor-hd2013sgi/post-link.sh +++ b/recipes/bioconductor-hd2013sgi/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hd2013sgi-1.40.0" +installBiocDataPackage.sh "hd2013sgi-1.42.0" diff --git a/recipes/bioconductor-hdcytodata/meta.yaml b/recipes/bioconductor-hdcytodata/meta.yaml index b4b799a8de2e3..45497fcf65184 100644 --- a/recipes/bioconductor-hdcytodata/meta.yaml +++ b/recipes/bioconductor-hdcytodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "HDCytoData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ab01564970b77ca4d62db12c07a1ed4 + md5: 8f962c6124539fea7a4a02a30e776de8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hdcytodata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hdcytodata/post-link.sh b/recipes/bioconductor-hdcytodata/post-link.sh index 8b22d0b2aedcd..d0ac96449fd70 100644 --- a/recipes/bioconductor-hdcytodata/post-link.sh +++ b/recipes/bioconductor-hdcytodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hdcytodata-1.20.0" +installBiocDataPackage.sh "hdcytodata-1.22.0" diff --git a/recipes/bioconductor-hdf5array/meta.yaml b/recipes/bioconductor-hdf5array/meta.yaml index 9a96452b591ca..6f725cd98876b 100644 --- a/recipes/bioconductor-hdf5array/meta.yaml +++ b/recipes/bioconductor-hdf5array/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "HDF5Array" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13cc3879d4e7ef05ed4ffaa9c0e80429 + md5: c59fcd283e0f9877f68457524b9d86bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hdf5array", max_pin="x.x") }}' # Suggests: BiocParallel, GenomicRanges, SummarizedExperiment (>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix build: diff --git a/recipes/bioconductor-hdo.db/meta.yaml b/recipes/bioconductor-hdo.db/meta.yaml index 28a3ad127fb79..451b87e2c1add 100644 --- a/recipes/bioconductor-hdo.db/meta.yaml +++ b/recipes/bioconductor-hdo.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "HDO.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 007a50523f1de27048dfc97f4d458f59 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hdo.db", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hdtd/meta.yaml b/recipes/bioconductor-hdtd/meta.yaml index d01a3252b7342..f9eedc12bc226 100644 --- a/recipes/bioconductor-hdtd/meta.yaml +++ b/recipes/bioconductor-hdtd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "HDTD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c3037443550f72d6e196587d5b8af94 + md5: c990bac6152195272ae3aa3557f8b82b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hdtd", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: diff --git a/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml b/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml index 56d07db97bf39..e9081da4b5fd8 100644 --- a/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml +++ b/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "healthyControlsPresenceChecker" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cc422930fe0cf3237bc707d107517381 + md5: 50ba7cea9e361d43c78d64ce1c89ba1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-healthycontrolspresencechecker", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-geneexpressionfromgeo - r-magrittr - r-xml2 run: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' - r-base - r-geneexpressionfromgeo - r-magrittr - r-xml2 - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh b/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh index 9d5fddf3a957a..a259bb6b38c3a 100644 --- a/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh +++ b/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "healthycontrolspresencechecker-1.4.0" +installBiocDataPackage.sh "healthycontrolspresencechecker-1.6.0" diff --git a/recipes/bioconductor-healthyflowdata/meta.yaml b/recipes/bioconductor-healthyflowdata/meta.yaml index fac084e69c483..8797dd046a6e7 100644 --- a/recipes/bioconductor-healthyflowdata/meta.yaml +++ b/recipes/bioconductor-healthyflowdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "healthyFlowData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 478453f16b73527c4f1a9c5697d0b576 + md5: ed0a9c99295e278a8445368a2cb226df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-healthyflowdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-healthyflowdata/post-link.sh b/recipes/bioconductor-healthyflowdata/post-link.sh index a0537a8057659..0e206a9e263b2 100644 --- a/recipes/bioconductor-healthyflowdata/post-link.sh +++ b/recipes/bioconductor-healthyflowdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "healthyflowdata-1.38.0" +installBiocDataPackage.sh "healthyflowdata-1.40.0" diff --git a/recipes/bioconductor-heatmaps/meta.yaml b/recipes/bioconductor-heatmaps/meta.yaml index 95d30caecdb5e..5e3b7691db75b 100644 --- a/recipes/bioconductor-heatmaps/meta.yaml +++ b/recipes/bioconductor-heatmaps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "heatmaps" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d94b93fd4532100c3d31e9cb7985c6c5 + md5: 68b0a507dd5b2bcdfef2106195429dc2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-heatmaps", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth - r-matrix - r-plotrix - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth - r-matrix diff --git a/recipes/bioconductor-heatplus/meta.yaml b/recipes/bioconductor-heatplus/meta.yaml index d2c6de8674d1f..2e65c161b133c 100644 --- a/recipes/bioconductor-heatplus/meta.yaml +++ b/recipes/bioconductor-heatplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.0" %} {% set name = "Heatplus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ffa5d82b6d75383ab65c286ff8b9d707 + md5: 459fb0dbd1242699e9f394f156a7e0c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-heatplus", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, hgu95av2.db, limma requirements: diff --git a/recipes/bioconductor-heebodata/meta.yaml b/recipes/bioconductor-heebodata/meta.yaml index ad3e7a9b3d12a..b2bccf7c7e017 100644 --- a/recipes/bioconductor-heebodata/meta.yaml +++ b/recipes/bioconductor-heebodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "HEEBOdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf931bc3409e110143d9090c8cb37c9a + md5: 885df0689d6663e079e952ea297ee777 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-heebodata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-heebodata/post-link.sh b/recipes/bioconductor-heebodata/post-link.sh index 9fe644ff2fb14..af9b31ef9b0a2 100644 --- a/recipes/bioconductor-heebodata/post-link.sh +++ b/recipes/bioconductor-heebodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "heebodata-1.38.0" +installBiocDataPackage.sh "heebodata-1.40.0" diff --git a/recipes/bioconductor-helloranges/meta.yaml b/recipes/bioconductor-helloranges/meta.yaml index 3d920b2f06697..5e449934f1360 100644 --- a/recipes/bioconductor-helloranges/meta.yaml +++ b/recipes/bioconductor-helloranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "HelloRanges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,47 +11,48 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ab315f2b6ce576e79f3c00634c2ad24 + md5: a83b42b9a323f3f3e356bfa8bbc0fd85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-helloranges", max_pin="x.x") }}' noarch: generic -# Suggests: HelloRangesData, BiocStyle +# Suggests: HelloRangesData, BiocStyle, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-docopt run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-docopt test: diff --git a/recipes/bioconductor-hellorangesdata/meta.yaml b/recipes/bioconductor-hellorangesdata/meta.yaml index 5abcb2471cc13..4b189bec162c2 100644 --- a/recipes/bioconductor-hellorangesdata/meta.yaml +++ b/recipes/bioconductor-hellorangesdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "HelloRangesData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34dbe70ca5ea008e5a17803388bed705 + md5: 6ae6ac65f3af7f41136eb6fb3558eb2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hellorangesdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hellorangesdata/post-link.sh b/recipes/bioconductor-hellorangesdata/post-link.sh index 242daf849104e..3a9fee9bcee90 100644 --- a/recipes/bioconductor-hellorangesdata/post-link.sh +++ b/recipes/bioconductor-hellorangesdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hellorangesdata-1.26.0" +installBiocDataPackage.sh "hellorangesdata-1.28.0" diff --git a/recipes/bioconductor-help/meta.yaml b/recipes/bioconductor-help/meta.yaml index 819de68209db2..02757fe4dc641 100644 --- a/recipes/bioconductor-help/meta.yaml +++ b/recipes/bioconductor-help/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "HELP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e664628988f8c6e0b63403618256654 + md5: d7a1038ee6eb5ec01393b39e30e028fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-help", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-hem/meta.yaml b/recipes/bioconductor-hem/meta.yaml index 9e13985e30272..d6fe622e155cb 100644 --- a/recipes/bioconductor-hem/meta.yaml +++ b/recipes/bioconductor-hem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "HEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5099d4d170fe1738efbb549fabbf70a1 + md5: 3ad1825d95504eaf9e2bcad8438816f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hem", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hermes/meta.yaml b/recipes/bioconductor-hermes/meta.yaml index cb190ad49ec97..628da60c967f4 100644 --- a/recipes/bioconductor-hermes/meta.yaml +++ b/recipes/bioconductor-hermes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "hermes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7a2aabc5a9a77c759a57a56683e6e351 + md5: af1e1dd4bab597cfb7b0bd12a1e9e7dd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hermes", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr, withr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - 'r-checkmate >=2.1' @@ -52,18 +53,18 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - 'r-checkmate >=2.1' diff --git a/recipes/bioconductor-heron/build.sh b/recipes/bioconductor-heron/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-heron/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-heron/meta.yaml b/recipes/bioconductor-heron/meta.yaml new file mode 100644 index 0000000000000..abc4916803605 --- /dev/null +++ b/recipes/bioconductor-heron/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.0.0" %} +{% set name = "HERON" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9c146a8d99bada338098732e1de5a5e2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-heron", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cluster + - r-data.table + - r-harmonicmeanp + - r-matrix + - r-matrixstats + - r-metap + - r-spdep + run: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cluster + - r-data.table + - r-harmonicmeanp + - r-matrix + - r-matrixstats + - r-metap + - r-spdep +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Hierarchical Epitope pROtein biNding' + description: 'HERON is a software package for analyzing peptide binding array data. In addition to identifying significant binding probes, HERON also provides functions for finding epitopes (string of consecutive peptides within a protein). HERON also calculates significance on the probe, epitope, and protein level by employing meta p-value methods. HERON is designed for obtaining calls on the sample level and calculates fractions of hits for different conditions.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-herper/meta.yaml b/recipes/bioconductor-herper/meta.yaml index a315614ff78d6..1ec27237788bd 100644 --- a/recipes/bioconductor-herper/meta.yaml +++ b/recipes/bioconductor-herper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Herper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a83b6c90414e5508e93fea96042b9b2 + md5: dad437a472cae186246d3cf0f6b44964 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-herper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown, seqCNA requirements: diff --git a/recipes/bioconductor-hgc/meta.yaml b/recipes/bioconductor-hgc/meta.yaml index 51b48cf81af8b..415c8beba464a 100644 --- a/recipes/bioconductor-hgc/meta.yaml +++ b/recipes/bioconductor-hgc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "HGC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cac848972223a04ae6d10ba3599b4bcf + md5: 7a8ac62af3106b62952c79c162937a3c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgc", max_pin="x.x") }}' # Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) # SystemRequirements: C++11 requirements: diff --git a/recipes/bioconductor-hgfocus.db/meta.yaml b/recipes/bioconductor-hgfocus.db/meta.yaml index af9be261c0a2e..7aed356288bfa 100644 --- a/recipes/bioconductor-hgfocus.db/meta.yaml +++ b/recipes/bioconductor-hgfocus.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgfocus.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a6bee48c0aa947d3c7d25ef2c5a4d485 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgfocus.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgfocuscdf/meta.yaml b/recipes/bioconductor-hgfocuscdf/meta.yaml index 38c059916b7e8..eff511fe7d21c 100644 --- a/recipes/bioconductor-hgfocuscdf/meta.yaml +++ b/recipes/bioconductor-hgfocuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgfocuscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9883e53bfd9ddb9ad5f3a9c2e47bbd2c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgfocuscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgfocusprobe/meta.yaml b/recipes/bioconductor-hgfocusprobe/meta.yaml index b8d1a35b27883..778b13ab99e1f 100644 --- a/recipes/bioconductor-hgfocusprobe/meta.yaml +++ b/recipes/bioconductor-hgfocusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgfocusprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a399ed276b89e3d80946b6cbbf167b4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgfocusprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a.db/meta.yaml b/recipes/bioconductor-hgu133a.db/meta.yaml index 4ead650e6e28e..7f4d6907ae274 100644 --- a/recipes/bioconductor-hgu133a.db/meta.yaml +++ b/recipes/bioconductor-hgu133a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu133a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 97675c27b13624bdfd760460dbca6bf0 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2.db/meta.yaml b/recipes/bioconductor-hgu133a2.db/meta.yaml index 5451366bc530a..4d8b4ac0c42dd 100644 --- a/recipes/bioconductor-hgu133a2.db/meta.yaml +++ b/recipes/bioconductor-hgu133a2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu133a2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e3bf9c5c9941f5f378cbc3dbeb9919ee build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133a2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2cdf/meta.yaml b/recipes/bioconductor-hgu133a2cdf/meta.yaml index 2c72bc37d575d..f9a09d9b3bf33 100644 --- a/recipes/bioconductor-hgu133a2cdf/meta.yaml +++ b/recipes/bioconductor-hgu133a2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133a2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 566bc70f0bb94a376bf88f191a2f067e build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133a2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2frmavecs/meta.yaml b/recipes/bioconductor-hgu133a2frmavecs/meta.yaml index af2cc6fcc3608..94e507f7794fa 100644 --- a/recipes/bioconductor-hgu133a2frmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133a2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.2.0" %} {% set name = "hgu133a2frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4bf8cf5cbaf288ce0a9618d764c87044 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133a2frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133a2probe/meta.yaml b/recipes/bioconductor-hgu133a2probe/meta.yaml index d6bb19c287baf..6ee5643b2e00d 100644 --- a/recipes/bioconductor-hgu133a2probe/meta.yaml +++ b/recipes/bioconductor-hgu133a2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133a2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 736b43cfc37a297ccc0d30cb75fcc95a build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133a2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133abarcodevecs/meta.yaml b/recipes/bioconductor-hgu133abarcodevecs/meta.yaml index 47b87218b5752..c86306fc1565e 100644 --- a/recipes/bioconductor-hgu133abarcodevecs/meta.yaml +++ b/recipes/bioconductor-hgu133abarcodevecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "hgu133abarcodevecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: af366465c10e3dbc799cdedab97d179d + md5: 4a6ec67e649f7ca004242fd860f79521 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133abarcodevecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133abarcodevecs/post-link.sh b/recipes/bioconductor-hgu133abarcodevecs/post-link.sh index b1a041adb2aa2..fba77b0ea4940 100644 --- a/recipes/bioconductor-hgu133abarcodevecs/post-link.sh +++ b/recipes/bioconductor-hgu133abarcodevecs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu133abarcodevecs-1.38.0" +installBiocDataPackage.sh "hgu133abarcodevecs-1.40.0" diff --git a/recipes/bioconductor-hgu133acdf/meta.yaml b/recipes/bioconductor-hgu133acdf/meta.yaml index badb6b318aba0..d4d21cf580157 100644 --- a/recipes/bioconductor-hgu133acdf/meta.yaml +++ b/recipes/bioconductor-hgu133acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d3e0e22b2d3943d26c94e7c01b91035c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133afrmavecs/meta.yaml b/recipes/bioconductor-hgu133afrmavecs/meta.yaml index 55c69a277dee1..97d6ef809ddbb 100644 --- a/recipes/bioconductor-hgu133afrmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133afrmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "hgu133afrmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 85034ab02491f5b3699d210cef50812d build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133afrmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133aprobe/meta.yaml b/recipes/bioconductor-hgu133aprobe/meta.yaml index 333427025e466..289e639bf7daa 100644 --- a/recipes/bioconductor-hgu133aprobe/meta.yaml +++ b/recipes/bioconductor-hgu133aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 76cd9c54b0a8a0240dbb0fc758959d62 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133atagcdf/meta.yaml b/recipes/bioconductor-hgu133atagcdf/meta.yaml index 7e52e847c7760..96ad110b6ed05 100644 --- a/recipes/bioconductor-hgu133atagcdf/meta.yaml +++ b/recipes/bioconductor-hgu133atagcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133atagcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 01f8809e0deb5b83f3f0decec881a1d8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133atagcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133atagprobe/meta.yaml b/recipes/bioconductor-hgu133atagprobe/meta.yaml index cac2c3028f5e8..26c2b3d196144 100644 --- a/recipes/bioconductor-hgu133atagprobe/meta.yaml +++ b/recipes/bioconductor-hgu133atagprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133atagprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 97aeaf9ac9450369cf030581b8ec5a53 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133atagprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133b.db/meta.yaml b/recipes/bioconductor-hgu133b.db/meta.yaml index ffedbcc4e1d0b..1667653d2b6b0 100644 --- a/recipes/bioconductor-hgu133b.db/meta.yaml +++ b/recipes/bioconductor-hgu133b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu133b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ff7930c99300c1022fde06ebe5c4a8cc build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133bcdf/meta.yaml b/recipes/bioconductor-hgu133bcdf/meta.yaml index 5fe9e5a76a972..0d9eb06173948 100644 --- a/recipes/bioconductor-hgu133bcdf/meta.yaml +++ b/recipes/bioconductor-hgu133bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 649aaa5e6275be6ee4d24d80ca390ea5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133bprobe/meta.yaml b/recipes/bioconductor-hgu133bprobe/meta.yaml index 92c0cd13bbe02..ea232fc9d19a3 100644 --- a/recipes/bioconductor-hgu133bprobe/meta.yaml +++ b/recipes/bioconductor-hgu133bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 203750510e51450e1267e08c241151c4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2.db/meta.yaml b/recipes/bioconductor-hgu133plus2.db/meta.yaml index 08cb39b045275..cf1fe96b56771 100644 --- a/recipes/bioconductor-hgu133plus2.db/meta.yaml +++ b/recipes/bioconductor-hgu133plus2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu133plus2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 459fcf4880a9eaa25b373c5635fede3d build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml b/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml index 22db1c1b61c76..cb5e8dfdb2d01 100644 --- a/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml +++ b/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "hgu133plus2barcodevecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a30a110289e8dff08599c97adb71adb0 + md5: 624bad8617d806474bc9406dc3c22384 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2barcodevecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh b/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh index b08192bf7142d..f44c331060ecf 100644 --- a/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh +++ b/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu133plus2barcodevecs-1.38.0" +installBiocDataPackage.sh "hgu133plus2barcodevecs-1.40.0" diff --git a/recipes/bioconductor-hgu133plus2cdf/meta.yaml b/recipes/bioconductor-hgu133plus2cdf/meta.yaml index 98627976fb3e1..9e57c07dda204 100644 --- a/recipes/bioconductor-hgu133plus2cdf/meta.yaml +++ b/recipes/bioconductor-hgu133plus2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133plus2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 284fef2f0b777d7b53451538ddd53de3 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2cellscore/meta.yaml b/recipes/bioconductor-hgu133plus2cellscore/meta.yaml index b37309c611db0..8d4b60ba2ced3 100644 --- a/recipes/bioconductor-hgu133plus2cellscore/meta.yaml +++ b/recipes/bioconductor-hgu133plus2cellscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "hgu133plus2CellScore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 348bb596918ca6f6a51d72d20003545c + md5: 486b7084ad0056c1031545af9c6dd515 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2cellscore", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2cellscore/post-link.sh b/recipes/bioconductor-hgu133plus2cellscore/post-link.sh index f327ced153ca1..5db37f89ca4fd 100644 --- a/recipes/bioconductor-hgu133plus2cellscore/post-link.sh +++ b/recipes/bioconductor-hgu133plus2cellscore/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu133plus2cellscore-1.20.0" +installBiocDataPackage.sh "hgu133plus2cellscore-1.22.0" diff --git a/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml b/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml index c749cf9021e82..a4180048a8637 100644 --- a/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "hgu133plus2frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a4781cbcccc1ee17dfd16259f1c7bebc build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu133plus2probe/meta.yaml b/recipes/bioconductor-hgu133plus2probe/meta.yaml index 57d9103819acc..15f9e2c0e4cd0 100644 --- a/recipes/bioconductor-hgu133plus2probe/meta.yaml +++ b/recipes/bioconductor-hgu133plus2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu133plus2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7a244787a0269bc72732ac3d830f34dd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu219.db/meta.yaml b/recipes/bioconductor-hgu219.db/meta.yaml index 394a442bf04bf..6207dd4fbfcc9 100644 --- a/recipes/bioconductor-hgu219.db/meta.yaml +++ b/recipes/bioconductor-hgu219.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgu219.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a4a0fd2ac170a75d8b17618615fcd7a0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu219.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu219cdf/meta.yaml b/recipes/bioconductor-hgu219cdf/meta.yaml index 63ab00e91e157..b692201bd81cd 100644 --- a/recipes/bioconductor-hgu219cdf/meta.yaml +++ b/recipes/bioconductor-hgu219cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu219cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 157a4280a9de960902260ab18f678949 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu219cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu219probe/meta.yaml b/recipes/bioconductor-hgu219probe/meta.yaml index 1e63c73163662..ce6e47caba3dd 100644 --- a/recipes/bioconductor-hgu219probe/meta.yaml +++ b/recipes/bioconductor-hgu219probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu219probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c5bb2f7b2e0f8fa89e6a30befaee6497 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu219probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu2beta7/meta.yaml b/recipes/bioconductor-hgu2beta7/meta.yaml index 1f6449fe5fdfd..e96e80fe95558 100644 --- a/recipes/bioconductor-hgu2beta7/meta.yaml +++ b/recipes/bioconductor-hgu2beta7/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "hgu2beta7" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2f1a9cc48f2608678e7349d6671a4949 + md5: 0643f49d27bf1dd6b73fb9192b23ebaa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu2beta7", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu2beta7/post-link.sh b/recipes/bioconductor-hgu2beta7/post-link.sh index 3d43283a70466..344f6120b8df6 100644 --- a/recipes/bioconductor-hgu2beta7/post-link.sh +++ b/recipes/bioconductor-hgu2beta7/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu2beta7-1.40.0" +installBiocDataPackage.sh "hgu2beta7-1.42.0" diff --git a/recipes/bioconductor-hgu95a.db/meta.yaml b/recipes/bioconductor-hgu95a.db/meta.yaml index c753b74895da7..304c7640fc879 100644 --- a/recipes/bioconductor-hgu95a.db/meta.yaml +++ b/recipes/bioconductor-hgu95a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b228ec0eded3ba9bccf033c2fff8f7b8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95acdf/meta.yaml b/recipes/bioconductor-hgu95acdf/meta.yaml index 5d2431beba4fa..1b49083b8669c 100644 --- a/recipes/bioconductor-hgu95acdf/meta.yaml +++ b/recipes/bioconductor-hgu95acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: afc999d77b1532154d45911ad15a5897 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95aprobe/meta.yaml b/recipes/bioconductor-hgu95aprobe/meta.yaml index 2ccd8e5b546e5..0d469c84c6f9b 100644 --- a/recipes/bioconductor-hgu95aprobe/meta.yaml +++ b/recipes/bioconductor-hgu95aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 67d94ecdc1889acc19dafd19d26700a2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2.db/meta.yaml b/recipes/bioconductor-hgu95av2.db/meta.yaml index 010ebe9638fc3..3ff766aa5fb19 100644 --- a/recipes/bioconductor-hgu95av2.db/meta.yaml +++ b/recipes/bioconductor-hgu95av2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95av2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0ada3f3c2507992b94d2daa7de8b7fbf build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95av2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2/meta.yaml b/recipes/bioconductor-hgu95av2/meta.yaml index ef089c5177fb9..78e1d0a7807fd 100644 --- a/recipes/bioconductor-hgu95av2/meta.yaml +++ b/recipes/bioconductor-hgu95av2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.2.0" %} {% set name = "hgu95av2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b92585c0f43e91bd1abd234b9465a6a7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95av2", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2cdf/meta.yaml b/recipes/bioconductor-hgu95av2cdf/meta.yaml index 928d636c24950..11a1128c63fc1 100644 --- a/recipes/bioconductor-hgu95av2cdf/meta.yaml +++ b/recipes/bioconductor-hgu95av2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95av2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 026bae2f76433593f75ca6c79bc9a9d0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95av2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95av2probe/meta.yaml b/recipes/bioconductor-hgu95av2probe/meta.yaml index 760925c3269eb..8eb701c5659f3 100644 --- a/recipes/bioconductor-hgu95av2probe/meta.yaml +++ b/recipes/bioconductor-hgu95av2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95av2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d3efb56f7e7a264b633fac787a5a2b95 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95av2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95b.db/meta.yaml b/recipes/bioconductor-hgu95b.db/meta.yaml index 84238ff673fde..ac0f7ed32a448 100644 --- a/recipes/bioconductor-hgu95b.db/meta.yaml +++ b/recipes/bioconductor-hgu95b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 12334c263cfd9f7dc835762b4661edc1 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95bcdf/meta.yaml b/recipes/bioconductor-hgu95bcdf/meta.yaml index 0789a97b2b662..32b337096ddfa 100644 --- a/recipes/bioconductor-hgu95bcdf/meta.yaml +++ b/recipes/bioconductor-hgu95bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e6e56b7a107bb2df25b3c25a8191385d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95bprobe/meta.yaml b/recipes/bioconductor-hgu95bprobe/meta.yaml index 75853474446ae..c651f98a9e74e 100644 --- a/recipes/bioconductor-hgu95bprobe/meta.yaml +++ b/recipes/bioconductor-hgu95bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 60dcb57fd402dc24d53ef9390c893cfc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95c.db/meta.yaml b/recipes/bioconductor-hgu95c.db/meta.yaml index 2bf3c22c651f2..5a2400c03379f 100644 --- a/recipes/bioconductor-hgu95c.db/meta.yaml +++ b/recipes/bioconductor-hgu95c.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95c.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 680cdfc3e63853ace2ec47caa00ded36 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95c.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95ccdf/meta.yaml b/recipes/bioconductor-hgu95ccdf/meta.yaml index 22675144bbd32..1ea680ebb03a3 100644 --- a/recipes/bioconductor-hgu95ccdf/meta.yaml +++ b/recipes/bioconductor-hgu95ccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95ccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 976151eac05c320aec7a24397a6b5806 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95ccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95cprobe/meta.yaml b/recipes/bioconductor-hgu95cprobe/meta.yaml index 6d216269dc104..a111dd5f829b2 100644 --- a/recipes/bioconductor-hgu95cprobe/meta.yaml +++ b/recipes/bioconductor-hgu95cprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95cprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3fe935a52c70105dc7a214174c946455 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95cprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95d.db/meta.yaml b/recipes/bioconductor-hgu95d.db/meta.yaml index afceca15d1376..50de9e491ea14 100644 --- a/recipes/bioconductor-hgu95d.db/meta.yaml +++ b/recipes/bioconductor-hgu95d.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95d.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 90ecf383640f6ab7314fa1babcdd5a0b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95d.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95dcdf/meta.yaml b/recipes/bioconductor-hgu95dcdf/meta.yaml index 090b3ad17eb89..483baf4b30cfe 100644 --- a/recipes/bioconductor-hgu95dcdf/meta.yaml +++ b/recipes/bioconductor-hgu95dcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95dcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 36e11ff001b1bec3f34ba7c93132ad6f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95dcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95dprobe/meta.yaml b/recipes/bioconductor-hgu95dprobe/meta.yaml index 1846e53e2baa7..030c64728d67d 100644 --- a/recipes/bioconductor-hgu95dprobe/meta.yaml +++ b/recipes/bioconductor-hgu95dprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95dprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 165ce5029f49fc515b9ee0e6a6a29cb5 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95dprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95e.db/meta.yaml b/recipes/bioconductor-hgu95e.db/meta.yaml index 10cbaa486cf3e..2a6007514b8b7 100644 --- a/recipes/bioconductor-hgu95e.db/meta.yaml +++ b/recipes/bioconductor-hgu95e.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hgu95e.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 116bd146279d19d50a7233bc61c22104 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95e.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95ecdf/meta.yaml b/recipes/bioconductor-hgu95ecdf/meta.yaml index 7ec42cf88cbf1..909814914ac7e 100644 --- a/recipes/bioconductor-hgu95ecdf/meta.yaml +++ b/recipes/bioconductor-hgu95ecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95ecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fa27cfff62a38fc51640d797bd628105 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95ecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgu95eprobe/meta.yaml b/recipes/bioconductor-hgu95eprobe/meta.yaml index 12a28fd1e1e2c..e25fb81f9803c 100644 --- a/recipes/bioconductor-hgu95eprobe/meta.yaml +++ b/recipes/bioconductor-hgu95eprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hgu95eprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9e5407ab80c5bbb4065484be0b9c6191 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgu95eprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hguatlas13k.db/meta.yaml b/recipes/bioconductor-hguatlas13k.db/meta.yaml index 82cf7b2b762cb..631974fa66149 100644 --- a/recipes/bioconductor-hguatlas13k.db/meta.yaml +++ b/recipes/bioconductor-hguatlas13k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hguatlas13k.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ab9ffe1a1de44c0f938129f193e7fb63 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hguatlas13k.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgubeta7.db/meta.yaml b/recipes/bioconductor-hgubeta7.db/meta.yaml index 15941b6ed04f7..f952f59819473 100644 --- a/recipes/bioconductor-hgubeta7.db/meta.yaml +++ b/recipes/bioconductor-hgubeta7.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgubeta7.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1b8b065f95d2089985f59f22dcabc824 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgubeta7.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgudkfz31.db/meta.yaml b/recipes/bioconductor-hgudkfz31.db/meta.yaml index 15bad4e0ba983..797b9e34dc787 100644 --- a/recipes/bioconductor-hgudkfz31.db/meta.yaml +++ b/recipes/bioconductor-hgudkfz31.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hguDKFZ31.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fa3ba493cebdac4253dea8fe5d58452b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgudkfz31.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4100a.db/meta.yaml b/recipes/bioconductor-hgug4100a.db/meta.yaml index 6e31ffc0fe574..25b4d28578ec5 100644 --- a/recipes/bioconductor-hgug4100a.db/meta.yaml +++ b/recipes/bioconductor-hgug4100a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4100a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b7856928278a77d71f963410ea4f2376 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4100a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4101a.db/meta.yaml b/recipes/bioconductor-hgug4101a.db/meta.yaml index e95648d842503..bbddbf83684d0 100644 --- a/recipes/bioconductor-hgug4101a.db/meta.yaml +++ b/recipes/bioconductor-hgug4101a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4101a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e4731217efbffd05d3ee7eec68ce0aa0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4101a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4110b.db/meta.yaml b/recipes/bioconductor-hgug4110b.db/meta.yaml index a05d1cd3cc88c..288b0336f7a3f 100644 --- a/recipes/bioconductor-hgug4110b.db/meta.yaml +++ b/recipes/bioconductor-hgug4110b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4110b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a9edcdbc121f22d4dec335a64598ff0e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4110b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4111a.db/meta.yaml b/recipes/bioconductor-hgug4111a.db/meta.yaml index a693fd1e3985a..23c816d0468e7 100644 --- a/recipes/bioconductor-hgug4111a.db/meta.yaml +++ b/recipes/bioconductor-hgug4111a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4111a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a5f2c3b463915fa1ab0ca21e6b0f5840 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4111a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4112a.db/meta.yaml b/recipes/bioconductor-hgug4112a.db/meta.yaml index 6c34b11fe0f15..1d650ea7689f3 100644 --- a/recipes/bioconductor-hgug4112a.db/meta.yaml +++ b/recipes/bioconductor-hgug4112a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hgug4112a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 67ecf8c887e2ebe1941cc51d0f5fb468 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4112a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hgug4845a.db/meta.yaml b/recipes/bioconductor-hgug4845a.db/meta.yaml index 5417eb330561c..56bdebf753da7 100644 --- a/recipes/bioconductor-hgug4845a.db/meta.yaml +++ b/recipes/bioconductor-hgug4845a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.3" %} {% set name = "hgug4845a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 46133d7bcb6d8c24c026304e8ddd150d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hgug4845a.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hguqiagenv3.db/meta.yaml b/recipes/bioconductor-hguqiagenv3.db/meta.yaml index 01608bf04fb8f..a89094655e843 100644 --- a/recipes/bioconductor-hguqiagenv3.db/meta.yaml +++ b/recipes/bioconductor-hguqiagenv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "hguqiagenv3.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 91ebb82e773ff799befdb8921b38e90e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hguqiagenv3.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hi16cod.db/meta.yaml b/recipes/bioconductor-hi16cod.db/meta.yaml index f332984279757..6f2d6f8fea470 100644 --- a/recipes/bioconductor-hi16cod.db/meta.yaml +++ b/recipes/bioconductor-hi16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "hi16cod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: abdc77937e8d37fa5468691376ceb6a5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hi16cod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hiannotator/meta.yaml b/recipes/bioconductor-hiannotator/meta.yaml index 9cdebfe36ac76..2e398493417b3 100644 --- a/recipes/bioconductor-hiannotator/meta.yaml +++ b/recipes/bioconductor-hiannotator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "hiAnnotator" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea7eef5accdcba1b8f0d29b7120bef7e + md5: 67e0fbd27bb6f634ccb9912642a2aeb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hiannotator", max_pin="x.x") }}' noarch: generic # Suggests: knitr, doParallel, testthat, BiocGenerics, markdown requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-foreach @@ -31,9 +32,9 @@ requirements: - r-iterators - r-scales run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-dplyr - r-foreach diff --git a/recipes/bioconductor-hibag/meta.yaml b/recipes/bioconductor-hibag/meta.yaml index 179a6f0eff2a6..1c32235779499 100644 --- a/recipes/bioconductor-hibag/meta.yaml +++ b/recipes/bioconductor-hibag/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "HIBAG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,13 +11,14 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1cef1399370a7c97f74d0c913a1dc390 + md5: 80772de8231b22269fb6ee5401af8292 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ -# Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, markdown, rmarkdown + run_exports: '{{ pin_subpackage("bioconductor-hibag", max_pin="x.x") }}' +# Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, markdown, rmarkdown, Rsamtools # SystemRequirements: C++11, GNU make requirements: host: diff --git a/recipes/bioconductor-hibed/meta.yaml b/recipes/bioconductor-hibed/meta.yaml new file mode 100644 index 0000000000000..428afabbff047 --- /dev/null +++ b/recipes/bioconductor-hibed/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "HiBED" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 282aec6967013cdaa790ff191e4139b4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hibed", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-flowsorted.blood.epic >=2.6.0,<2.7.0' + - 'bioconductor-flowsorted.dlpfc.450k >=1.38.0,<1.39.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - r-tibble + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-flowsorted.blood.epic >=2.6.0,<2.7.0' + - 'bioconductor-flowsorted.dlpfc.450k >=1.38.0,<1.39.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - r-tibble + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: HiBED + description: 'Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-hibed/post-link.sh b/recipes/bioconductor-hibed/post-link.sh new file mode 100644 index 0000000000000..f600caeca45ee --- /dev/null +++ b/recipes/bioconductor-hibed/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "hibed-1.0.0" diff --git a/recipes/bioconductor-hibed/pre-unlink.sh b/recipes/bioconductor-hibed/pre-unlink.sh new file mode 100644 index 0000000000000..6d37acd5139b7 --- /dev/null +++ b/recipes/bioconductor-hibed/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HiBED diff --git a/recipes/bioconductor-hicbricks/meta.yaml b/recipes/bioconductor-hicbricks/meta.yaml index 62562b1137691..929d6db889cb6 100644 --- a/recipes/bioconductor-hicbricks/meta.yaml +++ b/recipes/bioconductor-hicbricks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "HiCBricks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96079aa0b99e8e59f4131ca070d4b978 + md5: 1c92df374e0660e328cbf53f181afd61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicbricks", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-data.table @@ -43,12 +44,12 @@ requirements: - r-tibble - r-viridis run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-hiccompare/meta.yaml b/recipes/bioconductor-hiccompare/meta.yaml index 03eff48770c1c..2ad1ed7f62ae8 100644 --- a/recipes/bioconductor-hiccompare/meta.yaml +++ b/recipes/bioconductor-hiccompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "HiCcompare" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67b8090713c4a7bb88e2cb00a8de8088 + md5: 081a94597115ed9f99e23930935648dd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hiccompare", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, multiHiCcompare requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -37,12 +38,12 @@ requirements: - r-mgcv - r-pheatmap run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-hicdatahumanimr90/meta.yaml b/recipes/bioconductor-hicdatahumanimr90/meta.yaml index 8867f1b1be109..f9a4a366087d4 100644 --- a/recipes/bioconductor-hicdatahumanimr90/meta.yaml +++ b/recipes/bioconductor-hicdatahumanimr90/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "HiCDataHumanIMR90" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b6b0a8e4ccf7bd132a94748c2678be4 + md5: 02854f68384130b0bcd3d0f84d94b856 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicdatahumanimr90", max_pin="x.x") }}' noarch: generic # Suggests: HiTC requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hicdatahumanimr90/post-link.sh b/recipes/bioconductor-hicdatahumanimr90/post-link.sh index 2cd37706644ae..5079a3784185d 100644 --- a/recipes/bioconductor-hicdatahumanimr90/post-link.sh +++ b/recipes/bioconductor-hicdatahumanimr90/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hicdatahumanimr90-1.20.0" +installBiocDataPackage.sh "hicdatahumanimr90-1.22.0" diff --git a/recipes/bioconductor-hicdatalymphoblast/meta.yaml b/recipes/bioconductor-hicdatalymphoblast/meta.yaml index afbbac6b1b5bb..36a2e897eb980 100644 --- a/recipes/bioconductor-hicdatalymphoblast/meta.yaml +++ b/recipes/bioconductor-hicdatalymphoblast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "HiCDataLymphoblast" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f43877109c87896da3954f156798d19f + md5: 4e51d696b30a37414375e6987c7ab59c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicdatalymphoblast", max_pin="x.x") }}' noarch: generic # Suggests: ShortRead requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hicdatalymphoblast/post-link.sh b/recipes/bioconductor-hicdatalymphoblast/post-link.sh index 8012f2140899e..acbb04bef68ba 100644 --- a/recipes/bioconductor-hicdatalymphoblast/post-link.sh +++ b/recipes/bioconductor-hicdatalymphoblast/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hicdatalymphoblast-1.36.0" +installBiocDataPackage.sh "hicdatalymphoblast-1.38.0" diff --git a/recipes/bioconductor-hicdcplus/meta.yaml b/recipes/bioconductor-hicdcplus/meta.yaml index a0cc479209923..e014d6b12ff12 100644 --- a/recipes/bioconductor-hicdcplus/meta.yaml +++ b/recipes/bioconductor-hicdcplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "HiCDCPlus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14987ba2a7f97050a3ec2cc233edc3fd + md5: d129ae6d6c11f6f92e52399c46754b1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicdcplus", max_pin="x.x") }}' # Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs # SystemRequirements: JRE 8+ requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bbmle - r-data.table @@ -44,15 +45,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bbmle - r-data.table diff --git a/recipes/bioconductor-hicdoc/meta.yaml b/recipes/bioconductor-hicdoc/meta.yaml index f6b88458d963c..4fc805acafb41 100644 --- a/recipes/bioconductor-hicdoc/meta.yaml +++ b/recipes/bioconductor-hicdoc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "HiCDOC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d250c9afdc0cba742586f5202a6f54c1 + md5: 334df180a7e5e2851bbf6724e8537ffd build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager + run_exports: '{{ pin_subpackage("bioconductor-hicdoc", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-multihiccompare >=1.18.0,<1.19.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-multihiccompare >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base + - r-cowplot - r-data.table - - r-ggextra - r-ggplot2 - - r-ggpubr - r-gridextra - r-gtools - r-pbapply @@ -43,21 +42,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-multihiccompare >=1.18.0,<1.19.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-multihiccompare >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base + - r-cowplot - r-data.table - - r-ggextra - r-ggplot2 - - r-ggpubr - r-gridextra - r-gtools - r-pbapply @@ -71,8 +68,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 3)' + license: 'file LICENSE' summary: 'A/B compartment detection and differential analysis' description: 'HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + license_file: LICENSE diff --git a/recipes/bioconductor-hicexperiment/meta.yaml b/recipes/bioconductor-hicexperiment/meta.yaml index 564b6ffd902fe..e0267b602fd7d 100644 --- a/recipes/bioconductor-hicexperiment/meta.yaml +++ b/recipes/bioconductor-hicexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "HiCExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9208ad11b1c8c4b78cfd51e1f02c0c6e + md5: 98efc0440886cc84faef975a12f290a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicexperiment", max_pin="x.x") }}' noarch: generic # Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-matrix - r-strawr - r-vroom run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-matrix diff --git a/recipes/bioconductor-hicontacts/meta.yaml b/recipes/bioconductor-hicontacts/meta.yaml index 561198fdc347d..29ba194cc6150 100644 --- a/recipes/bioconductor-hicontacts/meta.yaml +++ b/recipes/bioconductor-hicontacts/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "HiContacts" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 023fb0be166964d39ef76d52646605b9 + md5: f7f7341e5b4cbfcd13b04fadd9c472c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicontacts", max_pin="x.x") }}' noarch: generic # Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -43,16 +44,16 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-hicontactsdata/meta.yaml b/recipes/bioconductor-hicontactsdata/meta.yaml index 0cc453c74a918..02887a5d7f1f6 100644 --- a/recipes/bioconductor-hicontactsdata/meta.yaml +++ b/recipes/bioconductor-hicontactsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "HiContactsData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d406482f89b932de475c12470bc8ef2 + md5: bcd518f48342168f7a814a442cf9564c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicontactsdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat, methods, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hicontactsdata/post-link.sh b/recipes/bioconductor-hicontactsdata/post-link.sh index 5d68ca935f0be..7b88fae0e188f 100644 --- a/recipes/bioconductor-hicontactsdata/post-link.sh +++ b/recipes/bioconductor-hicontactsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hicontactsdata-1.2.0" +installBiocDataPackage.sh "hicontactsdata-1.4.0" diff --git a/recipes/bioconductor-hicool/meta.yaml b/recipes/bioconductor-hicool/meta.yaml index 317fa4a355f3a..e83c1ddf394de 100644 --- a/recipes/bioconductor-hicool/meta.yaml +++ b/recipes/bioconductor-hicool/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "HiCool" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 85a6824de7561e4879ae698959606ae3 + md5: 04aa2ef16336d5c43fc0a02291ba7887 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicool", max_pin="x.x") }}' noarch: generic # Suggests: HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-plotly @@ -38,13 +39,13 @@ requirements: - r-stringr - r-vroom run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hicexperiment >=1.0.0,<1.1.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-plotly diff --git a/recipes/bioconductor-hicvenndiagram/build.sh b/recipes/bioconductor-hicvenndiagram/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hicvenndiagram/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hicvenndiagram/meta.yaml b/recipes/bioconductor-hicvenndiagram/meta.yaml new file mode 100644 index 0000000000000..1af9811467c2e --- /dev/null +++ b/recipes/bioconductor-hicvenndiagram/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.0" %} +{% set name = "hicVennDiagram" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 11577b64cc67b69e4b9d712a76cd3310 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicvenndiagram", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, GenomicRanges, ChIPpeakAnno, grid +requirements: + host: + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-complexupset + - r-eulerr + - r-ggplot2 + - r-htmlwidgets + - r-reshape2 + - r-svglite + run: + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-complexupset + - r-eulerr + - r-ggplot2 + - r-htmlwidgets + - r-reshape2 + - r-svglite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Venn Diagram for genomic interaction data' + description: 'A package to generate high-resolution Venn and Upset plots for genomic interaction data from HiC, ChIA-PET, HiChIP, PLAC-Seq, Hi-TrAC, HiCAR and etc. The package generates plots specifically crafted to eliminate the deceptive visual representation caused by the counts method.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-hiergwas/meta.yaml b/recipes/bioconductor-hiergwas/meta.yaml index b41f1c2b2abd5..917a0f7876b4a 100644 --- a/recipes/bioconductor-hiergwas/meta.yaml +++ b/recipes/bioconductor-hiergwas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "hierGWAS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45c3d0bd8020ffaecf28ef7286a7a576 + md5: 9f15cfa27c8d57b818fc7913d8a9093b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hiergwas", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit, MASS requirements: diff --git a/recipes/bioconductor-hierinf/meta.yaml b/recipes/bioconductor-hierinf/meta.yaml index d65f0760094db..b55d1417ca221 100644 --- a/recipes/bioconductor-hierinf/meta.yaml +++ b/recipes/bioconductor-hierinf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "hierinf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8798721587604faf688e4c1b508d672f + md5: 44446a50b3747865eadceabe415ce6f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hierinf", max_pin="x.x") }}' noarch: generic # Suggests: knitr, MASS, testthat requirements: diff --git a/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml b/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml index 3567a002b6c79..936d3d703dbea 100644 --- a/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml +++ b/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "HighlyReplicatedRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5773c61f0e87d562b2c18aec8992689 + md5: a397cddffb2dfea70943930b992ea7c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-highlyreplicatedrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh b/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh index f6a1f5964f310..fdd22acfec305 100644 --- a/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh +++ b/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "highlyreplicatedrnaseq-1.12.0" +installBiocDataPackage.sh "highlyreplicatedrnaseq-1.14.0" diff --git a/recipes/bioconductor-hiiragi2013/meta.yaml b/recipes/bioconductor-hiiragi2013/meta.yaml index c674fc61ef82e..1db7f4d8b615d 100644 --- a/recipes/bioconductor-hiiragi2013/meta.yaml +++ b/recipes/bioconductor-hiiragi2013/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Hiiragi2013" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5e1b258226d9b83620113705d7328537 + md5: dde13f333fe218976f71b626ed5eefa4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hiiragi2013", max_pin="x.x") }}' noarch: generic # Suggests: ArrayExpress, BiocStyle requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - 'bioconductor-mouse4302.db >=3.13.0,<3.14.0' - r-base - r-boot @@ -39,11 +40,11 @@ requirements: - r-rcolorbrewer - r-xtable run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' - 'bioconductor-mouse4302.db >=3.13.0,<3.14.0' - r-base - r-boot @@ -57,7 +58,7 @@ requirements: - r-rcolorbrewer - r-xtable - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hiiragi2013/post-link.sh b/recipes/bioconductor-hiiragi2013/post-link.sh index 54941404046eb..6c78d22253936 100644 --- a/recipes/bioconductor-hiiragi2013/post-link.sh +++ b/recipes/bioconductor-hiiragi2013/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hiiragi2013-1.36.0" +installBiocDataPackage.sh "hiiragi2013-1.38.0" diff --git a/recipes/bioconductor-hilbertcurve/meta.yaml b/recipes/bioconductor-hilbertcurve/meta.yaml index a798fd8a3c838..f707d6bb5a83d 100644 --- a/recipes/bioconductor-hilbertcurve/meta.yaml +++ b/recipes/bioconductor-hilbertcurve/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "HilbertCurve" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ef390a5043853c3354d9e42c80b07c6 + md5: 97eed8a87d8bb062c5d0b900823f6bcc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hilbertcurve", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.3.3' - r-png - r-polylabelr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-circlize >=0.3.3' - r-png diff --git a/recipes/bioconductor-hilbertvis/meta.yaml b/recipes/bioconductor-hilbertvis/meta.yaml index 451f5b82abc9f..5429956b9e0ec 100644 --- a/recipes/bioconductor-hilbertvis/meta.yaml +++ b/recipes/bioconductor-hilbertvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "HilbertVis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: beb6450c2b3c3d94e39eb524d45afe67 + md5: b30abc9c50034b41daf1399031d657e3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hilbertvis", max_pin="x.x") }}' # Suggests: IRanges, EBImage requirements: host: diff --git a/recipes/bioconductor-hilbertvisgui/meta.yaml b/recipes/bioconductor-hilbertvisgui/meta.yaml index 48b6967bdc1f3..4f51df3df8f16 100644 --- a/recipes/bioconductor-hilbertvisgui/meta.yaml +++ b/recipes/bioconductor-hilbertvisgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "HilbertVisGUI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 136f8bed06155ff4bb34296d1badeeaf + md5: e9e6a2cce82ff0dfcf0828ae7d123537 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hilbertvisgui", max_pin="x.x") }}' # Suggests: lattice, IRanges # SystemRequirements: gtkmm-2.4, GNU make requirements: host: - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' - r-base - libblas - liblapack run: - - 'bioconductor-hilbertvis >=1.58.0,<1.59.0' + - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-hilda/meta.yaml b/recipes/bioconductor-hilda/meta.yaml index c033529d0324a..903151efa8394 100644 --- a/recipes/bioconductor-hilda/meta.yaml +++ b/recipes/bioconductor-hilda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "HiLDA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 049c4b0dd5f94cdfe518adce6ea1a06b + md5: e1961cfe72082b160cafb7bed5376673 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hilda", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle # SystemRequirements: JAGS 4.0.0 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-abind - r-base - r-cowplot @@ -41,14 +42,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-abind - r-base - r-cowplot diff --git a/recipes/bioconductor-hipathia/meta.yaml b/recipes/bioconductor-hipathia/meta.yaml index 2b581de926e97..60ebebd0e0391 100644 --- a/recipes/bioconductor-hipathia/meta.yaml +++ b/recipes/bioconductor-hipathia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.0.2" %} +{% set version = "3.2.0" %} {% set name = "hipathia" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c860da6e2d2c33a8d0d95fb98937e84f + md5: 819d2eecca55d3d4708934bbe69e82a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hipathia", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-coin - r-dplyr @@ -41,13 +42,13 @@ requirements: - r-tibble - r-visnetwork run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-coin - r-dplyr diff --git a/recipes/bioconductor-hippo/meta.yaml b/recipes/bioconductor-hippo/meta.yaml index 80bf3cdc252fc..6daf28263c519 100644 --- a/recipes/bioconductor-hippo/meta.yaml +++ b/recipes/bioconductor-hippo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "HIPPO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9bdc02f89b2c3955b27e6b1f88c56009 + md5: 6c249e5f8b3f2a0622642c945e8d0566 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hippo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-dplyr - r-ggplot2 @@ -35,7 +36,7 @@ requirements: - r-rtsne - r-umap run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-hireadsprocessor/meta.yaml b/recipes/bioconductor-hireadsprocessor/meta.yaml index a8a127edfc54f..fa5d6a94b7947 100644 --- a/recipes/bioconductor-hireadsprocessor/meta.yaml +++ b/recipes/bioconductor-hireadsprocessor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "hiReadsProcessor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5784280fe7e882437b725ade4fa5be3b + md5: 8a194956515b40e5dc75f90cafdea5c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hireadsprocessor", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, markdown # SystemRequirements: BLAT, UCSC hg18 in 2bit format for BLAT requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiannotator >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiannotator >=1.36.0,<1.37.0' - r-base - r-dplyr - r-readxl - r-soniclength run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiannotator >=1.34.0,<1.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiannotator >=1.36.0,<1.37.0' - r-base - r-dplyr - r-readxl diff --git a/recipes/bioconductor-hireewas/meta.yaml b/recipes/bioconductor-hireewas/meta.yaml index 87c98011e2791..88bfdf68e2cc3 100644 --- a/recipes/bioconductor-hireewas/meta.yaml +++ b/recipes/bioconductor-hireewas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "HIREewas" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68ec415918f2959671fd619fb8fbcf90 + md5: fd57bb11c16b2d194d7950ce0d918899 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hireewas", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, BiocGenerics requirements: host: diff --git a/recipes/bioconductor-hitc/meta.yaml b/recipes/bioconductor-hitc/meta.yaml index 98920c992a893..6d1346745d845 100644 --- a/recipes/bioconductor-hitc/meta.yaml +++ b/recipes/bioconductor-hitc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "HiTC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5dceec926506e3c6a416c44671e5cb5f + md5: e530516c0386e2e9bb6ff9afbed5893f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hitc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, HiCDataHumanIMR90 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-matrix - r-rcolorbrewer run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-matrix - r-rcolorbrewer diff --git a/recipes/bioconductor-hivcdnavantwout03/meta.yaml b/recipes/bioconductor-hivcdnavantwout03/meta.yaml index 6602f1bbdecd6..9f5b6824060b5 100644 --- a/recipes/bioconductor-hivcdnavantwout03/meta.yaml +++ b/recipes/bioconductor-hivcdnavantwout03/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "HIVcDNAvantWout03" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 349ef6469ce73790078ba4b5d5206856 + md5: 4936f53bb66cdf1983a8bcbcd667a188 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hivcdnavantwout03", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hivcdnavantwout03/post-link.sh b/recipes/bioconductor-hivcdnavantwout03/post-link.sh index 4e772af309820..0eb40797b7714 100644 --- a/recipes/bioconductor-hivcdnavantwout03/post-link.sh +++ b/recipes/bioconductor-hivcdnavantwout03/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hivcdnavantwout03-1.40.0" +installBiocDataPackage.sh "hivcdnavantwout03-1.42.0" diff --git a/recipes/bioconductor-hivprtplus2cdf/meta.yaml b/recipes/bioconductor-hivprtplus2cdf/meta.yaml index b28324248c239..31d0377db8de7 100644 --- a/recipes/bioconductor-hivprtplus2cdf/meta.yaml +++ b/recipes/bioconductor-hivprtplus2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hivprtplus2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 143d9c2f5f328786bae7bb8dc4daf261 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hivprtplus2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hmdbquery/meta.yaml b/recipes/bioconductor-hmdbquery/meta.yaml index 47353fc6f4f3d..a34079bd13563 100644 --- a/recipes/bioconductor-hmdbquery/meta.yaml +++ b/recipes/bioconductor-hmdbquery/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "hmdbQuery" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07cb71866c0245628fece30b4d78c20c + md5: 32b8de26d3b369730bdd7c734da1be06 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hmdbquery", max_pin="x.x") }}' noarch: generic # Suggests: knitr, annotate, gwascat, testthat, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-xml run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-xml test: diff --git a/recipes/bioconductor-hmmcopy/meta.yaml b/recipes/bioconductor-hmmcopy/meta.yaml index ed6c77c7597a7..a89ef06cc7afb 100644 --- a/recipes/bioconductor-hmmcopy/meta.yaml +++ b/recipes/bioconductor-hmmcopy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "HMMcopy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a987a0438c7464de68cbebfae70d0c21 + md5: 4785371e1642cd191330693396010a6e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hmmcopy", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-hmp16sdata/meta.yaml b/recipes/bioconductor-hmp16sdata/meta.yaml index 71a98fda6e53f..36851b9076422 100644 --- a/recipes/bioconductor-hmp16sdata/meta.yaml +++ b/recipes/bioconductor-hmp16sdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "HMP16SData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a62c1eec817f876e015ee98ab937dfc6 + md5: a137f917000e15acffca9bb0baac8fbb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hmp16sdata", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, cowplot, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-dplyr @@ -35,10 +36,10 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-dplyr @@ -49,7 +50,7 @@ requirements: - r-stringr - r-tibble - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hmp16sdata/post-link.sh b/recipes/bioconductor-hmp16sdata/post-link.sh index 53146c48205ef..43a01f6fffd29 100644 --- a/recipes/bioconductor-hmp16sdata/post-link.sh +++ b/recipes/bioconductor-hmp16sdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hmp16sdata-1.20.0" +installBiocDataPackage.sh "hmp16sdata-1.22.0" diff --git a/recipes/bioconductor-hmp2data/meta.yaml b/recipes/bioconductor-hmp2data/meta.yaml index 6cb82db03492c..0f1a1a16733fa 100644 --- a/recipes/bioconductor-hmp2data/meta.yaml +++ b/recipes/bioconductor-hmp2data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "HMP2Data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff1bf8c6b78ebe9c09578c775c35a54a + md5: f334416386d2c1af677494e1fd5743d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hmp2data", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-data.table @@ -36,12 +37,12 @@ requirements: - r-magrittr - r-readr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-data.table @@ -51,7 +52,7 @@ requirements: - r-magrittr - r-readr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hmp2data/post-link.sh b/recipes/bioconductor-hmp2data/post-link.sh index 4529a31a1c7c9..22fac5c1ff254 100644 --- a/recipes/bioconductor-hmp2data/post-link.sh +++ b/recipes/bioconductor-hmp2data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hmp2data-1.14.0" +installBiocDataPackage.sh "hmp2data-1.16.0" diff --git a/recipes/bioconductor-homo.sapiens/meta.yaml b/recipes/bioconductor-homo.sapiens/meta.yaml index e9410c2285835..4f0fdece86a13 100644 --- a/recipes/bioconductor-homo.sapiens/meta.yaml +++ b/recipes/bioconductor-homo.sapiens/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1" %} {% set name = "Homo.sapiens" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 653b60cfcdaefd171729115cd629b585 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-homo.sapiens", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hoodscanr/build.sh b/recipes/bioconductor-hoodscanr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hoodscanr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hoodscanr/meta.yaml b/recipes/bioconductor-hoodscanr/meta.yaml new file mode 100644 index 0000000000000..61cbf0679547a --- /dev/null +++ b/recipes/bioconductor-hoodscanr/meta.yaml @@ -0,0 +1,64 @@ +{% set version = "1.0.0" %} +{% set name = "hoodscanR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c5ac598990d1f80bfa526c576abc8d84 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hoodscanr", max_pin="x.x") }}' +# Suggests: testthat (>= 3.0.0), BiocStyle +requirements: + host: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-circlize + - r-ggplot2 + - r-knitr + - r-rann + - 'r-rcpp >=1.0.9' + - r-rlang + - r-rmarkdown + - r-scico + - libblas + - liblapack + run: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-circlize + - r-ggplot2 + - r-knitr + - r-rann + - 'r-rcpp >=1.0.9' + - r-rlang + - r-rmarkdown + - r-scico + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Spatial cellular neighbourhood scanning in R' + description: 'hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.' + license_file: LICENSE + diff --git a/recipes/bioconductor-hopach/meta.yaml b/recipes/bioconductor-hopach/meta.yaml index da2f11af0c567..e515605dc2dc5 100644 --- a/recipes/bioconductor-hopach/meta.yaml +++ b/recipes/bioconductor-hopach/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.60.0" %} +{% set version = "2.62.0" %} {% set name = "hopach" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 467cdea6eebc9401118e603250a9bd49 + md5: 0310e9a4e3a34dfe2bb4edf0dbb38b16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hopach", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-cluster - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-cluster build: diff --git a/recipes/bioconductor-hpaanalyze/meta.yaml b/recipes/bioconductor-hpaanalyze/meta.yaml index 29f4ddb00001f..73545f1379178 100644 --- a/recipes/bioconductor-hpaanalyze/meta.yaml +++ b/recipes/bioconductor-hpaanalyze/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "HPAanalyze" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ebdbe83c9d26b640324bb4274e06c457 + md5: 0916d6c86a23a3c136b3d0f1de2a25f4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hpaanalyze", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown, devtools, BiocStyle requirements: diff --git a/recipes/bioconductor-hpannot/meta.yaml b/recipes/bioconductor-hpannot/meta.yaml index 44551ef27ed75..0f3297ff458a5 100644 --- a/recipes/bioconductor-hpannot/meta.yaml +++ b/recipes/bioconductor-hpannot/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "hpAnnot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fbc94a00b0f33b41bc5ff53fbe060663 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hpannot", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hpar/meta.yaml b/recipes/bioconductor-hpar/meta.yaml index e03e05050d958..a49dd41f591c0 100644 --- a/recipes/bioconductor-hpar/meta.yaml +++ b/recipes/bioconductor-hpar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "hpar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f2a2355b84c7204ab11bec266f8b63c0 + md5: f970b068a2112cd8bf1a8dfb7d29d86a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hpar", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle, testthat, rmarkdown, dplyr, DT requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base test: commands: diff --git a/recipes/bioconductor-hpip/meta.yaml b/recipes/bioconductor-hpip/meta.yaml index 4149d4c6262cf..a97924166d6b7 100644 --- a/recipes/bioconductor-hpip/meta.yaml +++ b/recipes/bioconductor-hpip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "HPiP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90bdbe4811dfb9bad8305ce85a67810f + md5: cbf5bf4735e100b22b184490854f8427 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hpip", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr requirements: diff --git a/recipes/bioconductor-hpo.db/meta.yaml b/recipes/bioconductor-hpo.db/meta.yaml new file mode 100644 index 0000000000000..64e2223e94fa9 --- /dev/null +++ b/recipes/bioconductor-hpo.db/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.99.2" %} +{% set name = "HPO.db" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 977cfb31ff344c58fd2dd0a2c6b765ab +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hpo.db", max_pin="x.x") }}' + noarch: generic +# Suggests: rmarkdown, knitr, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + - r-dbi + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + - r-dbi + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A set of annotation maps describing the entire Human Phenotype Ontology' + description: 'Human Phenotype Ontology (HPO) was developed to create a consistent description of gene products with disease perspectives, and is essential for supporting functional genomics in disease context. Accurate disease descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.We have developed the [DOSE](https://bioconductor.org/packages/DOSE/) package for semantic similarity analysis and disease enrichment analysis, and `DOSE` import an Bioconductor package ''DO.db'' to get the relationship(such as parent and child) between MPO terms. But `DO.db` hasn''t been updated for years, and a lot of semantic information is [missing](https://github.com/YuLab-SMU/DOSE/issues/57). So we developed the new package `HPO.db` for Human Human Phenotype Ontology annotation.' + diff --git a/recipes/bioconductor-hpo.db/post-link.sh b/recipes/bioconductor-hpo.db/post-link.sh new file mode 100644 index 0000000000000..4ac86e1be7109 --- /dev/null +++ b/recipes/bioconductor-hpo.db/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "hpo.db-0.99.2" diff --git a/recipes/bioconductor-hpo.db/pre-unlink.sh b/recipes/bioconductor-hpo.db/pre-unlink.sh new file mode 100644 index 0000000000000..9a0102a6c36f3 --- /dev/null +++ b/recipes/bioconductor-hpo.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HPO.db diff --git a/recipes/bioconductor-hs25kresogen.db/meta.yaml b/recipes/bioconductor-hs25kresogen.db/meta.yaml index 8483c7419e451..6c8d7424a4441 100644 --- a/recipes/bioconductor-hs25kresogen.db/meta.yaml +++ b/recipes/bioconductor-hs25kresogen.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.5.0" %} {% set name = "hs25kresogen.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a3800d072ce0e5f6f5d8299538b99cca build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hs25kresogen.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hs6ug171.db/meta.yaml b/recipes/bioconductor-hs6ug171.db/meta.yaml index 1e054aa31431c..17b3f570c6ea2 100644 --- a/recipes/bioconductor-hs6ug171.db/meta.yaml +++ b/recipes/bioconductor-hs6ug171.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Hs6UG171.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7aaf8a2441941f70247275c93735ed3b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hs6ug171.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml b/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml index 557b34846786b..d5d0b53d117d3 100644 --- a/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml +++ b/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "HsAgilentDesign026652.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dcd2c748bf9d7c002611cd5cf2ff38c0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hsagilentdesign026652.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hsmmsinglecell/meta.yaml b/recipes/bioconductor-hsmmsinglecell/meta.yaml index 90bf4930e5134..642e145c87cf4 100644 --- a/recipes/bioconductor-hsmmsinglecell/meta.yaml +++ b/recipes/bioconductor-hsmmsinglecell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "HSMMSingleCell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 52c7427453286b6ba0f069bdf32457ac + md5: dae440cd20110d25cd699a9a792ac4b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hsmmsinglecell", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hsmmsinglecell/post-link.sh b/recipes/bioconductor-hsmmsinglecell/post-link.sh index 2641c42f34ab9..eac2f6e837b9c 100644 --- a/recipes/bioconductor-hsmmsinglecell/post-link.sh +++ b/recipes/bioconductor-hsmmsinglecell/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hsmmsinglecell-1.20.0" +installBiocDataPackage.sh "hsmmsinglecell-1.22.0" diff --git a/recipes/bioconductor-hspec/meta.yaml b/recipes/bioconductor-hspec/meta.yaml index 02477afe83c34..cdb859d14a07b 100644 --- a/recipes/bioconductor-hspec/meta.yaml +++ b/recipes/bioconductor-hspec/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "Hspec" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0ade3e3147c8f0086e9be2312cccdfeb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hspec", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hspeccdf/meta.yaml b/recipes/bioconductor-hspeccdf/meta.yaml index 9b21052295be1..9d7ecbfd4107f 100644 --- a/recipes/bioconductor-hspeccdf/meta.yaml +++ b/recipes/bioconductor-hspeccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.1" %} {% set name = "hspeccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 89f81adf91094710558ce6aec79fc7fd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hspeccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hta20probeset.db/meta.yaml b/recipes/bioconductor-hta20probeset.db/meta.yaml index 6f17e022b4c21..8954764a4ca49 100644 --- a/recipes/bioconductor-hta20probeset.db/meta.yaml +++ b/recipes/bioconductor-hta20probeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hta20probeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8cc15bb71f3c2776015e55a2d7df2c2f build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hta20probeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml b/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml index 53b86adaec017..e8c9ccf5eb116 100644 --- a/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hta20transcriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9debbc190cc5f9f0ad97fbc452fe7025 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hta20transcriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133a.db/meta.yaml b/recipes/bioconductor-hthgu133a.db/meta.yaml index 441fc2ed9e54c..726b1974b31d6 100644 --- a/recipes/bioconductor-hthgu133a.db/meta.yaml +++ b/recipes/bioconductor-hthgu133a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hthgu133a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 769ed088760102b61edfb73454d4c642 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133acdf/meta.yaml b/recipes/bioconductor-hthgu133acdf/meta.yaml index b389ed5eb5dc1..beceffbf2be85 100644 --- a/recipes/bioconductor-hthgu133acdf/meta.yaml +++ b/recipes/bioconductor-hthgu133acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b92e543867f1f0c08bfa9299e123d608 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133afrmavecs/meta.yaml b/recipes/bioconductor-hthgu133afrmavecs/meta.yaml index e0c87d4d7752c..c0d9ce5809f99 100644 --- a/recipes/bioconductor-hthgu133afrmavecs/meta.yaml +++ b/recipes/bioconductor-hthgu133afrmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.0" %} {% set name = "hthgu133afrmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: be3f3d67a94dca3b080c184fba5ff6d8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133afrmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133aprobe/meta.yaml b/recipes/bioconductor-hthgu133aprobe/meta.yaml index e5e532ddf982f..e97081613b6ed 100644 --- a/recipes/bioconductor-hthgu133aprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cdc17ea670719f055ee75bea1415c754 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133b.db/meta.yaml b/recipes/bioconductor-hthgu133b.db/meta.yaml index c3e967bc610b3..3f1e467464b75 100644 --- a/recipes/bioconductor-hthgu133b.db/meta.yaml +++ b/recipes/bioconductor-hthgu133b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hthgu133b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8501401a7385e28173ea7b60aa3bf3d2 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133bcdf/meta.yaml b/recipes/bioconductor-hthgu133bcdf/meta.yaml index df1055745d8cc..de3ebaee98b4e 100644 --- a/recipes/bioconductor-hthgu133bcdf/meta.yaml +++ b/recipes/bioconductor-hthgu133bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 935ae53fb168d9c7890d71020ef4c366 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133bprobe/meta.yaml b/recipes/bioconductor-hthgu133bprobe/meta.yaml index 10ebfd0f24b6d..4cb19a19a6c5e 100644 --- a/recipes/bioconductor-hthgu133bprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8a2e306638a81fdec3b10a014c04c6b9 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133plusa.db/meta.yaml b/recipes/bioconductor-hthgu133plusa.db/meta.yaml index cd705a0211333..b6fdded12559a 100644 --- a/recipes/bioconductor-hthgu133plusa.db/meta.yaml +++ b/recipes/bioconductor-hthgu133plusa.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hthgu133plusa.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 477cb32e1d8eb6da894486ad810b4232 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133plusa.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133plusb.db/meta.yaml b/recipes/bioconductor-hthgu133plusb.db/meta.yaml index bbbc178516b64..091a03b1a4e40 100644 --- a/recipes/bioconductor-hthgu133plusb.db/meta.yaml +++ b/recipes/bioconductor-hthgu133plusb.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hthgu133plusb.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f3214792ba174598b0559937f46de937 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133plusb.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133pluspm.db/meta.yaml b/recipes/bioconductor-hthgu133pluspm.db/meta.yaml index 9d1d8b6afe384..b7b803fc73c0b 100644 --- a/recipes/bioconductor-hthgu133pluspm.db/meta.yaml +++ b/recipes/bioconductor-hthgu133pluspm.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hthgu133pluspm.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b0b3cb0174608d5705ae6c80dac02e3c build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133pluspm.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml b/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml index 11cf38a94bffc..a4bcc1b6c3e99 100644 --- a/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml +++ b/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133pluspmcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 56d15101d59decac7811caa15b349a9c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133pluspmcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml b/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml index aa659bd92d900..4906c52b78aba 100644 --- a/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hthgu133pluspmprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 74713e822a689007892d0eb92dbd456b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hthgu133pluspmprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430a.db/meta.yaml b/recipes/bioconductor-htmg430a.db/meta.yaml index 992f7a3ddbcfd..e8fbd4bfd804b 100644 --- a/recipes/bioconductor-htmg430a.db/meta.yaml +++ b/recipes/bioconductor-htmg430a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "htmg430a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 171e457946a6b485b2ebd928b233abb3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430acdf/meta.yaml b/recipes/bioconductor-htmg430acdf/meta.yaml index cfe9d18a3c394..4e08e47255617 100644 --- a/recipes/bioconductor-htmg430acdf/meta.yaml +++ b/recipes/bioconductor-htmg430acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aef7a3c3af7d2624ee6fc6f2d22472e2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430aprobe/meta.yaml b/recipes/bioconductor-htmg430aprobe/meta.yaml index 6cbe7e27d40fd..6c1055bf656d9 100644 --- a/recipes/bioconductor-htmg430aprobe/meta.yaml +++ b/recipes/bioconductor-htmg430aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e50cc49b8887b6ef8ee1152ec12d5010 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430b.db/meta.yaml b/recipes/bioconductor-htmg430b.db/meta.yaml index f6e1f271c9b60..24cdd2d9eedb8 100644 --- a/recipes/bioconductor-htmg430b.db/meta.yaml +++ b/recipes/bioconductor-htmg430b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "htmg430b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 70849a636e972a9be604a3320d3bd814 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430bcdf/meta.yaml b/recipes/bioconductor-htmg430bcdf/meta.yaml index d32357e1f15e4..b404825d00bc8 100644 --- a/recipes/bioconductor-htmg430bcdf/meta.yaml +++ b/recipes/bioconductor-htmg430bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 53cc1408504a5f07b5655aa46b969157 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430bprobe/meta.yaml b/recipes/bioconductor-htmg430bprobe/meta.yaml index d40dc72edf64d..bcfd9933555af 100644 --- a/recipes/bioconductor-htmg430bprobe/meta.yaml +++ b/recipes/bioconductor-htmg430bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f0e3eb56925d786762dee0c2dc82b530 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430pm.db/meta.yaml b/recipes/bioconductor-htmg430pm.db/meta.yaml index bd147bd809bba..b5ad88deeedc5 100644 --- a/recipes/bioconductor-htmg430pm.db/meta.yaml +++ b/recipes/bioconductor-htmg430pm.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "htmg430pm.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f89738ce2e33d1c626aa2d15cd28a49b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430pm.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430pmcdf/meta.yaml b/recipes/bioconductor-htmg430pmcdf/meta.yaml index 6598a4053c830..02705c76b099c 100644 --- a/recipes/bioconductor-htmg430pmcdf/meta.yaml +++ b/recipes/bioconductor-htmg430pmcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430pmcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 016a54b47adbbed7db989787646a0084 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430pmcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htmg430pmprobe/meta.yaml b/recipes/bioconductor-htmg430pmprobe/meta.yaml index 7963d5f2b45b5..cd3aa90766fbd 100644 --- a/recipes/bioconductor-htmg430pmprobe/meta.yaml +++ b/recipes/bioconductor-htmg430pmprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htmg430pmprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f0e053fcc0ca4b5f8c539fc0a3fcb076 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htmg430pmprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htqpcr/meta.yaml b/recipes/bioconductor-htqpcr/meta.yaml index 0b89fd93b0257..4edbbedacde98 100644 --- a/recipes/bioconductor-htqpcr/meta.yaml +++ b/recipes/bioconductor-htqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "HTqPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b6c73d30c4d92cb932c68e530ac22d4 + md5: 2deab9ff0c0269549b377a0867482f60 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htqpcr", max_pin="x.x") }}' noarch: generic # Suggests: statmod requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-rcolorbrewer run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-gplots - r-rcolorbrewer diff --git a/recipes/bioconductor-htrat230pm.db/meta.yaml b/recipes/bioconductor-htrat230pm.db/meta.yaml index ce30dfb169040..949dfe5fa1ff5 100644 --- a/recipes/bioconductor-htrat230pm.db/meta.yaml +++ b/recipes/bioconductor-htrat230pm.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "htrat230pm.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 46ed50806c568bf269fe4c51d3df3955 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htrat230pm.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htrat230pmcdf/meta.yaml b/recipes/bioconductor-htrat230pmcdf/meta.yaml index 045ccb437f648..fc6ec741ec909 100644 --- a/recipes/bioconductor-htrat230pmcdf/meta.yaml +++ b/recipes/bioconductor-htrat230pmcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htrat230pmcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c6683d16e8aacccd326f7a7eebb79b98 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htrat230pmcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htrat230pmprobe/meta.yaml b/recipes/bioconductor-htrat230pmprobe/meta.yaml index 720e243a1d53e..b1e1040532964 100644 --- a/recipes/bioconductor-htrat230pmprobe/meta.yaml +++ b/recipes/bioconductor-htrat230pmprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htrat230pmprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e4deeca2dc406367ac4a347e370267cf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htrat230pmprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htratfocus.db/meta.yaml b/recipes/bioconductor-htratfocus.db/meta.yaml index dc4fbc3c4b3f7..a270b55119363 100644 --- a/recipes/bioconductor-htratfocus.db/meta.yaml +++ b/recipes/bioconductor-htratfocus.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "htratfocus.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 88be90edb1acb31faedde0b66b27a150 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htratfocus.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htratfocuscdf/meta.yaml b/recipes/bioconductor-htratfocuscdf/meta.yaml index 4d6249beb0e25..e0495aa07b0d0 100644 --- a/recipes/bioconductor-htratfocuscdf/meta.yaml +++ b/recipes/bioconductor-htratfocuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htratfocuscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 04b4952f7d8b607a7eb0f779c08c57dc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htratfocuscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htratfocusprobe/meta.yaml b/recipes/bioconductor-htratfocusprobe/meta.yaml index 89cf2296d49f0..e79a05ee51073 100644 --- a/recipes/bioconductor-htratfocusprobe/meta.yaml +++ b/recipes/bioconductor-htratfocusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "htratfocusprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 26a0963d8aff314a4a1f2c47e9147a8a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htratfocusprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-htseqgenie/meta.yaml b/recipes/bioconductor-htseqgenie/meta.yaml index 41cdbbce8ef23..088cb8b6a16d9 100644 --- a/recipes/bioconductor-htseqgenie/meta.yaml +++ b/recipes/bioconductor-htseqgenie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.30.0" %} +{% set version = "4.32.0" %} {% set name = "HTSeqGenie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,54 +11,55 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ace11ef8422722f14ec1c7fcf7b6164 + md5: 000b728da136ce28e0204ed5b8752792 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htseqgenie", max_pin="x.x") }}' noarch: generic -# Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, LungCancerLines, org.Hs.eg.db +# Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, LungCancerLines, org.Hs.eg.db, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gmapr >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-varianttools >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gmapr >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-varianttools >=1.44.0,<1.45.0' - r-base - 'r-cairo >=1.5.5' - 'r-hwriter >=1.3.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gmapr >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-varianttools >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gmapr >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-varianttools >=1.44.0,<1.45.0' - r-base - 'r-cairo >=1.5.5' - 'r-hwriter >=1.3.0' diff --git a/recipes/bioconductor-htsfilter/meta.yaml b/recipes/bioconductor-htsfilter/meta.yaml index 5a140bf362057..84f5596a79d3c 100644 --- a/recipes/bioconductor-htsfilter/meta.yaml +++ b/recipes/bioconductor-htsfilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "HTSFilter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e65f6c1f3249d76932b78a1910d0b687 + md5: 6eb5ebe090ac02b5a0099f63f3e6ccc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-htsfilter", max_pin="x.x") }}' noarch: generic # Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base test: commands: diff --git a/recipes/bioconductor-hu35ksuba.db/meta.yaml b/recipes/bioconductor-hu35ksuba.db/meta.yaml index 2cb97faadc36e..aa6d56d193767 100644 --- a/recipes/bioconductor-hu35ksuba.db/meta.yaml +++ b/recipes/bioconductor-hu35ksuba.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hu35ksuba.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4c2306a80f26bacb6172e84c896ef911 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksuba.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubacdf/meta.yaml b/recipes/bioconductor-hu35ksubacdf/meta.yaml index b3c4ade0e8d97..6e0051e83251d 100644 --- a/recipes/bioconductor-hu35ksubacdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c8b82c4755eb62818ca0dbf22de5d25e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubaprobe/meta.yaml b/recipes/bioconductor-hu35ksubaprobe/meta.yaml index 5f0068482c219..27ff012919986 100644 --- a/recipes/bioconductor-hu35ksubaprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubaprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubaprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 49bd19ec3b6404211f2e410e473fa644 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubaprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubb.db/meta.yaml b/recipes/bioconductor-hu35ksubb.db/meta.yaml index 906cc80272b08..26b4effc29790 100644 --- a/recipes/bioconductor-hu35ksubb.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubb.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hu35ksubb.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b82ece4860eddff8010faecaae802312 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubb.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubbcdf/meta.yaml b/recipes/bioconductor-hu35ksubbcdf/meta.yaml index 89c4be6fce455..058b2d719b0ab 100644 --- a/recipes/bioconductor-hu35ksubbcdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d873b6c521e926b331f799baf10a4e13 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubbprobe/meta.yaml b/recipes/bioconductor-hu35ksubbprobe/meta.yaml index 94b5b39aa7c4a..f268e43a45ffd 100644 --- a/recipes/bioconductor-hu35ksubbprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubbprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubbprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a63051d0faf38a56f17d5865cbed9b1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubbprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubc.db/meta.yaml b/recipes/bioconductor-hu35ksubc.db/meta.yaml index e4b8f21730a8c..12eff013b1335 100644 --- a/recipes/bioconductor-hu35ksubc.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubc.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hu35ksubc.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 57e60b8d025e0e8cf7ac2b355111cf2d build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubc.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubccdf/meta.yaml b/recipes/bioconductor-hu35ksubccdf/meta.yaml index a46bf48696983..e74f1c9802053 100644 --- a/recipes/bioconductor-hu35ksubccdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: de96e69680c5f8747c99d170272d7c3c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubcprobe/meta.yaml b/recipes/bioconductor-hu35ksubcprobe/meta.yaml index 4c768cd883634..e34a24730e4a9 100644 --- a/recipes/bioconductor-hu35ksubcprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubcprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubcprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b10453ea061b09172192bd21baa9083d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubcprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubd.db/meta.yaml b/recipes/bioconductor-hu35ksubd.db/meta.yaml index 8321b024f45f6..1e4d5c25aa532 100644 --- a/recipes/bioconductor-hu35ksubd.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubd.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hu35ksubd.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5ce6b6ede0f9733fd4dc527a28114327 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubd.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubdcdf/meta.yaml b/recipes/bioconductor-hu35ksubdcdf/meta.yaml index 9190d08512c9c..bc47065d4bc5e 100644 --- a/recipes/bioconductor-hu35ksubdcdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubdcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6f6423426969f306fb0d5171e75b5380 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubdcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu35ksubdprobe/meta.yaml b/recipes/bioconductor-hu35ksubdprobe/meta.yaml index 8f374a04f9e97..aecbeb343c4d5 100644 --- a/recipes/bioconductor-hu35ksubdprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubdprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubdprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 430a9b8ccd646d8cb06e6c1d750eec23 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu35ksubdprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800.db/meta.yaml b/recipes/bioconductor-hu6800.db/meta.yaml index f9ea39f7a4194..b0075ffaca4fd 100644 --- a/recipes/bioconductor-hu6800.db/meta.yaml +++ b/recipes/bioconductor-hu6800.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "hu6800.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aa1cb6c107dee6d2ed1929b48aa831e9 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800cdf/meta.yaml b/recipes/bioconductor-hu6800cdf/meta.yaml index a3d7f7eb47cc0..e614aa6fa22fa 100644 --- a/recipes/bioconductor-hu6800cdf/meta.yaml +++ b/recipes/bioconductor-hu6800cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fa2b2ab8f3aba517c63ad2e65873d2f0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800probe/meta.yaml b/recipes/bioconductor-hu6800probe/meta.yaml index 314442af32bc1..f27bcb41f1371 100644 --- a/recipes/bioconductor-hu6800probe/meta.yaml +++ b/recipes/bioconductor-hu6800probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7a2383bd870cbc0628c210174e911250 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subacdf/meta.yaml b/recipes/bioconductor-hu6800subacdf/meta.yaml index 269fa0149a80e..14d7f881b2a7e 100644 --- a/recipes/bioconductor-hu6800subacdf/meta.yaml +++ b/recipes/bioconductor-hu6800subacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9e8ec301e066e400564976cd9750297e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800subacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subbcdf/meta.yaml b/recipes/bioconductor-hu6800subbcdf/meta.yaml index 38d19b590969e..2d20ea344463a 100644 --- a/recipes/bioconductor-hu6800subbcdf/meta.yaml +++ b/recipes/bioconductor-hu6800subbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 529aad5e4e73594c8cb66274d7e4adc5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800subbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subccdf/meta.yaml b/recipes/bioconductor-hu6800subccdf/meta.yaml index f6e7904c7ab0c..85db4b5ce728c 100644 --- a/recipes/bioconductor-hu6800subccdf/meta.yaml +++ b/recipes/bioconductor-hu6800subccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 020fe3a6bdf44efbde15432b968433e8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800subccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hu6800subdcdf/meta.yaml b/recipes/bioconductor-hu6800subdcdf/meta.yaml index 8633581ede40a..f3b36b1e7d49c 100644 --- a/recipes/bioconductor-hu6800subdcdf/meta.yaml +++ b/recipes/bioconductor-hu6800subdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hu6800subdcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7966c21babb23e18cca4faafc8720f0a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hu6800subdcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hubpub/meta.yaml b/recipes/bioconductor-hubpub/meta.yaml index 3249609e8a7d1..ce98d178e7182 100644 --- a/recipes/bioconductor-hubpub/meta.yaml +++ b/recipes/bioconductor-hubpub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "HubPub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51721091a3789f40a9c60732c92da643 + md5: 9595496f838fced99c75d9604456df25 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hubpub", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHubData, ExperimentHubData, testthat, knitr, rmarkdown, BiocStyle, requirements: host: - - 'bioconductor-biocthis >=1.10.0,<1.11.0' + - 'bioconductor-biocthis >=1.12.0,<1.13.0' - r-available - r-aws.s3 - r-base @@ -30,7 +31,7 @@ requirements: - r-fs - r-usethis run: - - 'bioconductor-biocthis >=1.10.0,<1.11.0' + - 'bioconductor-biocthis >=1.12.0,<1.13.0' - r-available - r-aws.s3 - r-base diff --git a/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml b/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml index f5e632bc3dcf2..f52623a6d6adc 100644 --- a/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml +++ b/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "huex.1.0.st.v2frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 982935d07b526ff555790e309fe4147e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huex.1.0.st.v2frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huex10stprobeset.db/meta.yaml b/recipes/bioconductor-huex10stprobeset.db/meta.yaml index 5e94fe7224db8..e46db4b591594 100644 --- a/recipes/bioconductor-huex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-huex10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "huex10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fda9fc7340aeda2564a76756d2b8d4d3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huex10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml index b955652056f57..466ce65126903 100644 --- a/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "huex10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0789a1e8ee4474bd64c2772eab0db247 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huex10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huexexonprobesetlocation/meta.yaml b/recipes/bioconductor-huexexonprobesetlocation/meta.yaml index 4e27b068904df..5d2372d38e4b0 100644 --- a/recipes/bioconductor-huexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.0" %} {% set name = "HuExExonProbesetLocation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 11bf1b88d9e90711b4064497f611da4f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huexexonprobesetlocation", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml b/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml index 184e2dcafb9b8..eda440ed446a7 100644 --- a/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.2" %} {% set name = "HuExExonProbesetLocationHg18" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bb00b7f5e4db2b04dca5951aa6bd073e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huexexonprobesetlocationhg18", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml b/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml index 05c44b77e47ed..e74f60f8e47af 100644 --- a/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.0.3" %} {% set name = "HuExExonProbesetLocationHg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1a3843c95c82dc71a043d902961ba33a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huexexonprobesetlocationhg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml index 2cda95075af1c..f4e9cd4365fe4 100644 --- a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml +++ b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "hugene.1.0.st.v1frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 711a69e6fa6dd3737a90615222416dfc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene.1.0.st.v1frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10stprobeset.db/meta.yaml b/recipes/bioconductor-hugene10stprobeset.db/meta.yaml index d8d7c54e93ff4..f70af17a40af8 100644 --- a/recipes/bioconductor-hugene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a4a87d64564cbec1e4bb1f9e5a67add build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml index 9474e61d516a9..b7a09239b1a3a 100644 --- a/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a32fb5729d37e96f157b0a1085dff43e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10stv1cdf/meta.yaml b/recipes/bioconductor-hugene10stv1cdf/meta.yaml index c54c5659638c1..bb829c36e72d1 100644 --- a/recipes/bioconductor-hugene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-hugene10stv1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hugene10stv1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f1fb1c7076ac40b9e709f18e645d6181 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene10stv1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene10stv1probe/meta.yaml b/recipes/bioconductor-hugene10stv1probe/meta.yaml index 288a450e096b6..8f44196d5f02b 100644 --- a/recipes/bioconductor-hugene10stv1probe/meta.yaml +++ b/recipes/bioconductor-hugene10stv1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "hugene10stv1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6ed3c17dd026acf008658a5994044c62 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene10stv1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene11stprobeset.db/meta.yaml b/recipes/bioconductor-hugene11stprobeset.db/meta.yaml index f619a84eceed7..a66804c1c2f9b 100644 --- a/recipes/bioconductor-hugene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene11stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene11stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4d22ec32dedd6c8603d5f545faeb4ba4 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene11stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml index 7d8d4ebef3d56..ea292b35aa0c2 100644 --- a/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene11sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7fed70c4bd904655459a41b5667f7c23 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene11sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene20stprobeset.db/meta.yaml b/recipes/bioconductor-hugene20stprobeset.db/meta.yaml index 48ebdce03070f..8a24073d3fade 100644 --- a/recipes/bioconductor-hugene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene20stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene20stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bf7909fc41a80da59099327a6d9abb57 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene20stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml index 1208738d62693..761de8398ee20 100644 --- a/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene20sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0b929a3a959662e8a7265f58b81b4e35 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene20sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene21stprobeset.db/meta.yaml b/recipes/bioconductor-hugene21stprobeset.db/meta.yaml index 66c1e3cd428e0..e76e57e758538 100644 --- a/recipes/bioconductor-hugene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene21stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene21stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2b816dca48d0b2e1a946469b8d85d257 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene21stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml index d8dee7131293e..e6f8ab5591590 100644 --- a/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "hugene21sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ca90de6093bbad760abfcf0cfeada830 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hugene21sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human.db0/meta.yaml b/recipes/bioconductor-human.db0/meta.yaml index 8421a6640099b..4e65c14b082c3 100644 --- a/recipes/bioconductor-human.db0/meta.yaml +++ b/recipes/bioconductor-human.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "human.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4597ee42fd14b0e83754027205d4ca17 + md5: e3b04d46f0618785b37fb84bb899295e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human.db0/post-link.sh b/recipes/bioconductor-human.db0/post-link.sh index abdd185f80b1c..ec096e9328845 100644 --- a/recipes/bioconductor-human.db0/post-link.sh +++ b/recipes/bioconductor-human.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "human.db0-3.17.0" +installBiocDataPackage.sh "human.db0-3.18.0" diff --git a/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml b/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml index d0f2dfd66c790..d5179e02efca6 100644 --- a/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml +++ b/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.4" %} {% set name = "human1mduov3bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0ff9f1e8bcc6348d6777bbb982ae0325 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human1mduov3bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human1mv1ccrlmm/meta.yaml b/recipes/bioconductor-human1mv1ccrlmm/meta.yaml index 6db7fa7d0e95b..31b085def1cd8 100644 --- a/recipes/bioconductor-human1mv1ccrlmm/meta.yaml +++ b/recipes/bioconductor-human1mv1ccrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human1mv1cCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b9f638c7b0ede50cb070f1bae85eb4dc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human1mv1ccrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml b/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml index 40c13ad7bd002..6d828cffe3c89 100644 --- a/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml +++ b/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human370quadv3cCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 33c3ccc3793ed95647418b746a5177f9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human370quadv3ccrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human370v1ccrlmm/meta.yaml b/recipes/bioconductor-human370v1ccrlmm/meta.yaml index ad69b1464d1fd..36f4345a136f5 100644 --- a/recipes/bioconductor-human370v1ccrlmm/meta.yaml +++ b/recipes/bioconductor-human370v1ccrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "human370v1cCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9ec4192f533faee2b14484de02548075 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human370v1ccrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human550v3bcrlmm/meta.yaml b/recipes/bioconductor-human550v3bcrlmm/meta.yaml index 7b775b368e034..7c0d212370923 100644 --- a/recipes/bioconductor-human550v3bcrlmm/meta.yaml +++ b/recipes/bioconductor-human550v3bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.4" %} {% set name = "human550v3bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 20e6b008fab5e1084354c87ad50d18a8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human550v3bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml b/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml index 800f56624e589..9c38228c1a8c5 100644 --- a/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human610quadv1bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 609cf09410774e084ee6a3286652bb1a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human610quadv1bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human650v3acrlmm/meta.yaml b/recipes/bioconductor-human650v3acrlmm/meta.yaml index 80118154e125f..9808f0f0abf83 100644 --- a/recipes/bioconductor-human650v3acrlmm/meta.yaml +++ b/recipes/bioconductor-human650v3acrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human650v3aCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4b0de367ccc0f7499dcffe21ef1893c2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human650v3acrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-human660quadv1acrlmm/meta.yaml b/recipes/bioconductor-human660quadv1acrlmm/meta.yaml index 6bfc093423ad5..fd3e90ca86186 100644 --- a/recipes/bioconductor-human660quadv1acrlmm/meta.yaml +++ b/recipes/bioconductor-human660quadv1acrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "human660quadv1aCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5fd2d94a462e150c888f13c5c0975c36 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-human660quadv1acrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanaffydata/meta.yaml b/recipes/bioconductor-humanaffydata/meta.yaml index b54ab8e296b47..c746ebbe83689 100644 --- a/recipes/bioconductor-humanaffydata/meta.yaml +++ b/recipes/bioconductor-humanaffydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "HumanAffyData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bbb55417c9bdc12d387677c47cb8fc19 + md5: 11341e772169b7141b9bd22161e14417 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanaffydata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanaffydata/post-link.sh b/recipes/bioconductor-humanaffydata/post-link.sh index dc899f9b002ee..596705396fd7e 100644 --- a/recipes/bioconductor-humanaffydata/post-link.sh +++ b/recipes/bioconductor-humanaffydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "humanaffydata-1.26.0" +installBiocDataPackage.sh "humanaffydata-1.28.0" diff --git a/recipes/bioconductor-humanchrloc/meta.yaml b/recipes/bioconductor-humanchrloc/meta.yaml index 2c1bf4c51a2c8..e535202d4443c 100644 --- a/recipes/bioconductor-humanchrloc/meta.yaml +++ b/recipes/bioconductor-humanchrloc/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.1.6" %} {% set name = "humanCHRLOC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 113450c0822000c9b4e8a0141cf4b819 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanchrloc", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml index 21f2a40ff19ac..00664a6615e8e 100644 --- a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml +++ b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "humancytosnp12v2p1hCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: edf80245ddb28afb9fbaa6668187bf3a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humancytosnp12v2p1hcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml index 3ed5297328e11..7b086ab8634cb 100644 --- a/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.3" %} {% set name = "humanomni1quadv1bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e81b2603f37d4cda3f28cd69a7296a23 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanomni1quadv1bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml index b57f45359f1d6..ea1f4ab912275 100644 --- a/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "humanomni25quadv1bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2ee1fa7bf712d7f81a167079c975d49f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanomni25quadv1bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml index a6a531e67d6c3..f90cbd61ccc35 100644 --- a/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "humanomni5quadv1bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3ac4d6867c3d5590a6308d6edff0912b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanomni5quadv1bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml b/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml index f7f3a1ad3d2a4..b15927786e117 100644 --- a/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.1" %} {% set name = "humanomniexpress12v1bCrlmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: abdb730fc230db669e588e024ee7624b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanomniexpress12v1bcrlmm", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanstemcell/meta.yaml b/recipes/bioconductor-humanstemcell/meta.yaml index 8fe0e1e4e82e5..c0d2b5a0d197e 100644 --- a/recipes/bioconductor-humanstemcell/meta.yaml +++ b/recipes/bioconductor-humanstemcell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.40.0" %} +{% set version = "0.42.0" %} {% set name = "humanStemCell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8388d74f0e892de07e04e2e200041e6d + md5: be6367d8fa19187d644247ed8795eb0e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humanstemcell", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-humanstemcell/post-link.sh b/recipes/bioconductor-humanstemcell/post-link.sh index 84918843e521c..959dc8dc69bda 100644 --- a/recipes/bioconductor-humanstemcell/post-link.sh +++ b/recipes/bioconductor-humanstemcell/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "humanstemcell-0.40.0" +installBiocDataPackage.sh "humanstemcell-0.42.0" diff --git a/recipes/bioconductor-humantranscriptomecompendium/meta.yaml b/recipes/bioconductor-humantranscriptomecompendium/meta.yaml index 00cb3e294ac9c..104d5c4efe8ea 100644 --- a/recipes/bioconductor-humantranscriptomecompendium/meta.yaml +++ b/recipes/bioconductor-humantranscriptomecompendium/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.17.0" %} {% set name = "HumanTranscriptomeCompendium" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98846960141df3feafef02d8aff9590b + md5: 00689fd704a35eea4e0ba38516603b49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-humantranscriptomecompendium", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, beeswarm, tximportData, DT, tximport, dplyr, magrittr, BiocFileCache, testthat, rhdf5client, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-ssrch >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-ssrch >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-shiny run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-ssrch >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-ssrch >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-shiny test: diff --git a/recipes/bioconductor-hummingbird/meta.yaml b/recipes/bioconductor-hummingbird/meta.yaml index 4fb842a74040f..506999c697083 100644 --- a/recipes/bioconductor-hummingbird/meta.yaml +++ b/recipes/bioconductor-hummingbird/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "hummingbird" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 715ef224bb7c7b1b85e2ee22c2b5f52a + md5: 3f2788dadae0f811072b04866fc9e5ed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hummingbird", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-huo22.db/meta.yaml b/recipes/bioconductor-huo22.db/meta.yaml index ec7936b6b3d7c..b0ae8869cbd58 100644 --- a/recipes/bioconductor-huo22.db/meta.yaml +++ b/recipes/bioconductor-huo22.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "HuO22.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ddabf6c01f94c1dfd6ab35b40852828a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-huo22.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hwgcod.db/meta.yaml b/recipes/bioconductor-hwgcod.db/meta.yaml index 6eb2d50cbb487..dfb997797f058 100644 --- a/recipes/bioconductor-hwgcod.db/meta.yaml +++ b/recipes/bioconductor-hwgcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "hwgcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a46bf1a242853bbab26351a11b18030a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hwgcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-hybridmtest/meta.yaml b/recipes/bioconductor-hybridmtest/meta.yaml index 28eb5b06abebc..009114237f60b 100644 --- a/recipes/bioconductor-hybridmtest/meta.yaml +++ b/recipes/bioconductor-hybridmtest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "HybridMTest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd6c87352381d3c242791b824acc784e + md5: a2b1764b0e458f82e6055a3ebdf90933 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hybridmtest", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fdrtool - r-mass - r-survival run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fdrtool - r-mass diff --git a/recipes/bioconductor-hyper/build.sh b/recipes/bioconductor-hyper/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hyper/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hyper/meta.yaml b/recipes/bioconductor-hyper/meta.yaml new file mode 100644 index 0000000000000..99a5d17a40f21 --- /dev/null +++ b/recipes/bioconductor-hyper/meta.yaml @@ -0,0 +1,79 @@ +{% set version = "2.0.0" %} +{% set name = "hypeR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d2de417437ab81645e7d4702021f349f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hyper", max_pin="x.x") }}' + noarch: generic +# Suggests: tidyverse, devtools, testthat, knitr +requirements: + host: + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - r-base + - r-dplyr + - r-ggforce + - r-ggplot2 + - r-htmltools + - r-httr + - r-igraph + - r-kableextra + - r-magrittr + - r-msigdbr + - r-openxlsx + - r-purrr + - r-r6 + - r-reactable + - r-reshape2 + - r-rlang + - r-rmarkdown + - r-scales + - r-shiny + - r-stringr + - r-visnetwork + run: + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - r-base + - r-dplyr + - r-ggforce + - r-ggplot2 + - r-htmltools + - r-httr + - r-igraph + - r-kableextra + - r-magrittr + - r-msigdbr + - r-openxlsx + - r-purrr + - r-r6 + - r-reactable + - r-reshape2 + - r-rlang + - r-rmarkdown + - r-scales + - r-shiny + - r-stringr + - r-visnetwork +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'An R Package For Geneset Enrichment Workflows' + description: 'An R Package for Geneset Enrichment Workflows.' + license_file: LICENSE + diff --git a/recipes/bioconductor-hyperdraw/meta.yaml b/recipes/bioconductor-hyperdraw/meta.yaml index 21883a6196bb8..10d2f229c833c 100644 --- a/recipes/bioconductor-hyperdraw/meta.yaml +++ b/recipes/bioconductor-hyperdraw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "hyperdraw" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c3cf1dd57ee69e05f8da913acb35477f + md5: 2b1ec2cf9ea920a241f821baa08bb393 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hyperdraw", max_pin="x.x") }}' noarch: generic # SystemRequirements: graphviz requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - graphviz run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-hypergraph >=1.72.0,<1.73.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-hypergraph >=1.74.0,<1.75.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - graphviz test: diff --git a/recipes/bioconductor-hypergraph/meta.yaml b/recipes/bioconductor-hypergraph/meta.yaml index e51ca8cc87f7d..b46a9d8bbdee9 100644 --- a/recipes/bioconductor-hypergraph/meta.yaml +++ b/recipes/bioconductor-hypergraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "hypergraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8bf5823131a132c2be422e4caab4808d + md5: e97653a8503ba0bcb6da1dbdf1a3552b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hypergraph", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-iaseq/meta.yaml b/recipes/bioconductor-iaseq/meta.yaml index 7772ed35787bd..45a697e239e4e 100644 --- a/recipes/bioconductor-iaseq/meta.yaml +++ b/recipes/bioconductor-iaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "iASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 74ee0ce567f55f4ff926ec7b03e6d594 + md5: 3086632b16254c5b1f22c4f376bd43a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iaseq", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-iasva/meta.yaml b/recipes/bioconductor-iasva/meta.yaml index ed0ae3531538c..500fa9d1f76ca 100644 --- a/recipes/bioconductor-iasva/meta.yaml +++ b/recipes/bioconductor-iasva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "iasva" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 792ad17be82086c6159523192f4c53c6 + md5: a52a31d7564e175a288943ae77b22a93 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iasva", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot, DescTools, RColorBrewer requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-irlba run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-irlba diff --git a/recipes/bioconductor-ibbig/meta.yaml b/recipes/bioconductor-ibbig/meta.yaml index 0bd364e0773a1..3ed3cdcd3bd2e 100644 --- a/recipes/bioconductor-ibbig/meta.yaml +++ b/recipes/bioconductor-ibbig/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "iBBiG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acb9cdbf601cecd9d30682529bb0db9e + md5: 6114f0b7d488fd60923a6607bf2d59f2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ibbig", max_pin="x.x") }}' # Suggests: methods requirements: host: diff --git a/recipes/bioconductor-ibh/meta.yaml b/recipes/bioconductor-ibh/meta.yaml index d11cb9df8d7cd..9af60c615d1d4 100644 --- a/recipes/bioconductor-ibh/meta.yaml +++ b/recipes/bioconductor-ibh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "ibh" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fbf555dde7ce9991ec258efe6c02c0a1 + md5: 3c87bb1083990548eb09c4e43459ba1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ibh", max_pin="x.x") }}' noarch: generic # Suggests: yeastCC, stats requirements: host: - - 'bioconductor-simpintlists >=1.36.0,<1.37.0' + - 'bioconductor-simpintlists >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-simpintlists >=1.36.0,<1.37.0' + - 'bioconductor-simpintlists >=1.38.0,<1.39.0' - r-base test: commands: diff --git a/recipes/bioconductor-ibmq/meta.yaml b/recipes/bioconductor-ibmq/meta.yaml index e32affd825da3..4633abf58f473 100644 --- a/recipes/bioconductor-ibmq/meta.yaml +++ b/recipes/bioconductor-ibmq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "iBMQ" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8840fcc3cdb49e919fe22cda90a58f3 + md5: 9737c0aee38670491b2f29f73dcb743c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ibmq", max_pin="x.x") }}' # SystemRequirements: GSL and OpenMP requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - 'r-ggplot2 >=0.9.2' - libblas - liblapack - gsl run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - 'r-ggplot2 >=0.9.2' - gsl diff --git a/recipes/bioconductor-icare/meta.yaml b/recipes/bioconductor-icare/meta.yaml index ca7712cc724fd..aded7a26c7465 100644 --- a/recipes/bioconductor-icare/meta.yaml +++ b/recipes/bioconductor-icare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "iCARE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d89ab78df6a178cd7ddeffbba91211a + md5: 9230befcb5d16fdc72a6f87b50397789 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icare", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: diff --git a/recipes/bioconductor-icens/meta.yaml b/recipes/bioconductor-icens/meta.yaml index 36bc7e42950fe..ee1fb6954e914 100644 --- a/recipes/bioconductor-icens/meta.yaml +++ b/recipes/bioconductor-icens/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "Icens" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 916d3bb72a63cbebfe3890bc15003075 + md5: 07481f23c5b4fdfe9ff465e5a57e33c2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icens", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-icetea/meta.yaml b/recipes/bioconductor-icetea/meta.yaml index 0ca22f27c1f24..916fb97d57978 100644 --- a/recipes/bioconductor-icetea/meta.yaml +++ b/recipes/bioconductor-icetea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "icetea" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,55 +11,56 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fba08db47284c487627226270b90e5bd + md5: 2e7e3e32b56771089cefcc4295456e49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icetea", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.12.0,<3.13.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.12.0,<3.13.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-icheck/meta.yaml b/recipes/bioconductor-icheck/meta.yaml index 6a71607982e40..51520bfa018ee 100644 --- a/recipes/bioconductor-icheck/meta.yaml +++ b/recipes/bioconductor-icheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "iCheck" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b3e3bfe2b8158dd1cc31da69c188f57 + md5: 4404db494985157058a6af6d8c29b0c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icheck", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geneselectmmd >=2.44.0,<2.45.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geneselectmmd >=2.46.0,<2.47.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-gplots - r-lmtest @@ -34,12 +35,12 @@ requirements: - r-rgl - r-scatterplot3d run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geneselectmmd >=2.44.0,<2.45.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geneselectmmd >=2.46.0,<2.47.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-gplots - r-lmtest diff --git a/recipes/bioconductor-ichip/meta.yaml b/recipes/bioconductor-ichip/meta.yaml index 3a6c2a4d17a41..6a06380a203bd 100644 --- a/recipes/bioconductor-ichip/meta.yaml +++ b/recipes/bioconductor-ichip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "iChip" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 656d9d28237e68c9e522a9605fee4716 + md5: d50d8db2c1de02e8a1df4de992aa64f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ichip", max_pin="x.x") }}' requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-iclusterplus/build.sh b/recipes/bioconductor-iclusterplus/build.sh index 26b985e8ff4dc..0f7012ed24200 100644 --- a/recipes/bioconductor-iclusterplus/build.sh +++ b/recipes/bioconductor-iclusterplus/build.sh @@ -9,4 +9,4 @@ CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars autoreconf -fi -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iclusterplus/meta.yaml b/recipes/bioconductor-iclusterplus/meta.yaml index 92bc2e5c98015..73b999c654735 100644 --- a/recipes/bioconductor-iclusterplus/meta.yaml +++ b/recipes/bioconductor-iclusterplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "iClusterPlus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,7 +11,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 951e6b1ec59b05d436130fc3b9b7c6f9 + md5: 133b682823ec6ab41f6f6579413d461d patches: - 0001-Detect-compiler-with-gfortran-suffix.patch build: @@ -19,6 +19,7 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iclusterplus", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: @@ -42,4 +43,3 @@ about: summary: 'Integrative clustering of multi-type genomic data' description: 'Integrative clustering of multiple genomic data using a joint latent variable model.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - diff --git a/recipes/bioconductor-icnv/meta.yaml b/recipes/bioconductor-icnv/meta.yaml index 51defd03f7da6..b1c5eb62c6e2d 100644 --- a/recipes/bioconductor-icnv/meta.yaml +++ b/recipes/bioconductor-icnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "iCNV" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1064b8c5da8ebf9cd18a1fd0cebb6caf + md5: ff1415b4764c18a3609c4eb3b6d65a30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icnv", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, WES.1KG.WUGSC requirements: host: - - 'bioconductor-codex >=1.32.0,<1.33.0' + - 'bioconductor-codex >=1.34.0,<1.35.0' - r-base - r-data.table - r-dplyr @@ -31,7 +32,7 @@ requirements: - r-tidyr - r-truncnorm run: - - 'bioconductor-codex >=1.32.0,<1.33.0' + - 'bioconductor-codex >=1.34.0,<1.35.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-icobra/meta.yaml b/recipes/bioconductor-icobra/meta.yaml index 72fc1539129e6..0a0ef086aa674 100644 --- a/recipes/bioconductor-icobra/meta.yaml +++ b/recipes/bioconductor-icobra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "iCOBRA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 778bba4697e06cbecbb9f0e8e920c4b0 + md5: dc297e102e2b6ee717a494f652a6d6bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-icobra", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dplyr - r-dt @@ -35,7 +36,7 @@ requirements: - r-shinydashboard - r-upsetr run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-ideal/build_failure.linux-64.yaml b/recipes/bioconductor-ideal/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..19d2276079b9f --- /dev/null +++ b/recipes/bioconductor-ideal/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 67de6b5cdabab9789f4141c7b4df882eca324c62877eb622c009398c5cadd390 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-plotly + - r-shinyace + - r-shinybs + - r-upsetr + - bioconductor-limma >=3.58.0,<3.59.0 + - r-rintrojs + - r-base64enc + - bioconductor-iranges >=2.36.0,<2.37.0 + - bioconductor-goseq >=1.54.0,<1.55.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-gplots + - r-rentrez + - bioconductor-topgo >=2.54.0,<2.55.0 + - r-base 4.3.* + - r-shinydashboard + - bioconductor-deseq2 >=1.42.0,<1.43.0 + - bioconductor-go.db >=3.18.0,<3.19.0 + - bioconductor-genomicranges >=1.54.0,<1.55.0 + - r-heatmaply + - r-knitr + - r-shiny >=0.12.0 + - bioconductor-gostats >=2.68.0,<2.69.0 + - r-dplyr + - bioconductor-pcaexplorer >=2.28.0,<2.29.0 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-dt + - r-ggplot2 >=2.0.0 + - r-ggrepel + - bioconductor-annotationdbi >=1.64.0,<1.65.0 + - bioconductor-ihw >=1.30.0,<1.31.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-stringr + - r-pheatmap + - r-rlang + - r-rmarkdown + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-ihw[version='>=1.30.0,<1.31.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ideal/meta.yaml b/recipes/bioconductor-ideal/meta.yaml index 13555fc84538f..3cbe305f544a5 100644 --- a/recipes/bioconductor-ideal/meta.yaml +++ b/recipes/bioconductor-ideal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "ideal" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 24f07cba791fbdfe1bdf0539b78de343 + md5: d4714305a9be71a4b4c71da0fb624148 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ideal", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-ihw >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcaexplorer >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-ihw >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcaexplorer >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-base64enc - r-dplyr @@ -57,20 +58,20 @@ requirements: - r-stringr - r-upsetr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-ihw >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcaexplorer >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-ihw >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcaexplorer >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-base64enc - r-dplyr diff --git a/recipes/bioconductor-ideoviz/meta.yaml b/recipes/bioconductor-ideoviz/meta.yaml index 0495cf2897371..3e85ceeaf3c0f 100644 --- a/recipes/bioconductor-ideoviz/meta.yaml +++ b/recipes/bioconductor-ideoviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.37.0" %} {% set name = "IdeoViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a1eaca9a4537ad7486a764085dde3b6 + md5: 187ebcc3f7a11124ebbe137722672ffc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ideoviz", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-idiogram/meta.yaml b/recipes/bioconductor-idiogram/meta.yaml index a94f98655c26c..6fa4e077bdb2d 100644 --- a/recipes/bioconductor-idiogram/meta.yaml +++ b/recipes/bioconductor-idiogram/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "idiogram" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7ce45f1fab62bc32ee380625a7a756f8 + md5: 2ee94ac9719c77f8a2f6b691662a7909 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-idiogram", max_pin="x.x") }}' noarch: generic # Suggests: hu6800.db, hgu95av2.db, golubEsets requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-plotrix run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-plotrix test: diff --git a/recipes/bioconductor-idpr/meta.yaml b/recipes/bioconductor-idpr/meta.yaml index 5392789f5d86e..3450da1b12fbd 100644 --- a/recipes/bioconductor-idpr/meta.yaml +++ b/recipes/bioconductor-idpr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "idpr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b3a120730d6d86dc3a8c8de14a3e5e67 + md5: 16fb786981b0e04b0d094c4867303555 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-idpr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, msa, ape, testthat, seqinr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-dplyr >=0.8.5' - 'r-ggplot2 >=3.3.0' @@ -30,7 +31,7 @@ requirements: - 'r-plyr >=1.8.6' - 'r-rlang >=0.4.6' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-dplyr >=0.8.5' - 'r-ggplot2 >=3.3.0' diff --git a/recipes/bioconductor-idr2d/meta.yaml b/recipes/bioconductor-idr2d/meta.yaml index cd5ce13ee1773..f2c297502502b 100644 --- a/recipes/bioconductor-idr2d/meta.yaml +++ b/recipes/bioconductor-idr2d/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "idr2d" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b990982c2b666e7dca09c02ab628b038 + md5: 6662b2b18dc8c6029ad40099c5fcd6a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-idr2d", max_pin="x.x") }}' noarch: generic # Suggests: DT (>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) # SystemRequirements: Python (>= 3.5.0), hic-straw requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-dplyr >=0.7.6' - 'r-futile.logger >=1.4.3' @@ -35,9 +36,9 @@ requirements: - 'r-scales >=1.0.0' - 'r-stringr >=1.3.1' run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - 'r-dplyr >=0.7.6' - 'r-futile.logger >=1.4.3' diff --git a/recipes/bioconductor-ifaa/meta.yaml b/recipes/bioconductor-ifaa/meta.yaml index 2a4a8b2311405..59789aaa6e7d1 100644 --- a/recipes/bioconductor-ifaa/meta.yaml +++ b/recipes/bioconductor-ifaa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "IFAA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2fed85b602afd876a82a6f150f7edcc6 + md5: 393ac86513ddc9adf474c654b5127394 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ifaa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-desctools - 'r-doparallel >=1.0.11' @@ -36,8 +37,8 @@ requirements: - r-parallelly - r-stringr run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-desctools - 'r-doparallel >=1.0.11' diff --git a/recipes/bioconductor-igc/meta.yaml b/recipes/bioconductor-igc/meta.yaml index 3f15202e91f05..f9eeb7f8b07b8 100644 --- a/recipes/bioconductor-igc/meta.yaml +++ b/recipes/bioconductor-igc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "iGC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1b2d13eef5b7eb28baba5a0d230f216 + md5: 14007fadd58eaea3e345ba53a279f783 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-igc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-iggeneusage/meta.yaml b/recipes/bioconductor-iggeneusage/meta.yaml index 09daed914d666..23adf82cfe2f0 100644 --- a/recipes/bioconductor-iggeneusage/meta.yaml +++ b/recipes/bioconductor-iggeneusage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "IgGeneUsage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d8a81fe690de659ee3671911b6079a9 + md5: 231f1af3465f435ca3bb099a93e51e5b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iggeneusage", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel # SystemRequirements: GNU make requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bh >=1.66.0' - 'r-rcpp >=0.12.0' @@ -31,10 +32,11 @@ requirements: - 'r-rstan >=2.18.1' - 'r-rstantools >=2.2.0' - 'r-stanheaders >=2.18.0' + - r-tidyr - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bh >=1.66.0' - 'r-rcpp >=0.12.0' @@ -44,6 +46,7 @@ requirements: - 'r-rstan >=2.18.1' - 'r-rstantools >=2.2.0' - 'r-stanheaders >=2.18.0' + - r-tidyr build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-igvr/meta.yaml b/recipes/bioconductor-igvr/meta.yaml index 3e29ec06ef9a8..cb1fe14f9bcc1 100644 --- a/recipes/bioconductor-igvr/meta.yaml +++ b/recipes/bioconductor-igvr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "igvR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4462dcfae2acb5eac59801713beae32b + md5: 318b9d244079439576763028e1731a18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-igvr", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-browserviz >=2.22.0,<2.23.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-browserviz >=2.24.0,<2.25.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-httpuv - r-httr - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-browserviz >=2.22.0,<2.23.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-browserviz >=2.24.0,<2.25.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-httpuv - r-httr diff --git a/recipes/bioconductor-chipxpress/build_failure.linux-64.yaml b/recipes/bioconductor-ihw/build_failure.linux-64.yaml similarity index 82% rename from recipes/bioconductor-chipxpress/build_failure.linux-64.yaml rename to recipes/bioconductor-ihw/build_failure.linux-64.yaml index 553b01a33d979..49c95de2d51b7 100644 --- a/recipes/bioconductor-chipxpress/build_failure.linux-64.yaml +++ b/recipes/bioconductor-ihw/build_failure.linux-64.yaml @@ -1,33 +1,35 @@ -recipe_sha: a49a4fee0ecc177366a04192b85dfff0fac7cc562b60204a83649bffef6c0934 # The commit at which this recipe failed to build. +recipe_sha: df348495dada1a372be82599b073dacb131efa9c20367ac100389a77a59630c4 # The commit at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- + conda-forge/linux-64 [2K[1A[2K[0G[] 4.9s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s conda-forge/linux-64 100%[2K[1A[2K[0Gconda-forge/linux-64 [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 992.2kB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m [?25l[2K[0G[] 0.0s [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.3MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s [?25hMamba failed to solve: - - bioconductor-biobase >=2.60.0,<2.61.0 - - r-bigmemory - - bioconductor-frma >=1.52.0,<1.53.0 + - bioconductor-lpsymphony >=1.30.0,<1.31.0 - r-base 4.3.* - - bioconductor-chipxpressdata >=1.38.0,<1.39.0 - - bioconductor-affy >=1.78.0,<1.79.0 - - bioconductor-geoquery >=2.68.0,<2.69.0 - - r-biganalytics + - r-slam + - r-fdrtool + - bioconductor-biocgenerics >=0.48.0,<0.49.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - nothing provides requested bioconductor-chipxpressdata >=1.38.0,<1.39.0 + - - nothing provides requested bioconductor-lpsymphony >=1.30.0,<1.31.0 - Leaving build/test directories: @@ -50,23 +52,21 @@ log: |- File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve raise RuntimeError("Solver could not find solution." error_string) RuntimeError: Solver could not find solution.Mamba failed to solve: - - bioconductor-biobase >=2.60.0,<2.61.0 - - r-bigmemory - - bioconductor-frma >=1.52.0,<1.53.0 + - bioconductor-lpsymphony >=1.30.0,<1.31.0 - r-base 4.3.* - - bioconductor-chipxpressdata >=1.38.0,<1.39.0 - - bioconductor-affy >=1.78.0,<1.79.0 - - bioconductor-geoquery >=2.68.0,<2.69.0 - - r-biganalytics + - r-slam + - r-fdrtool + - bioconductor-biocgenerics >=0.48.0,<0.49.0 with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - nothing provides requested bioconductor-chipxpressdata >=1.38.0,<1.39.0 + - - nothing provides requested bioconductor-lpsymphony >=1.30.0,<1.31.0 - During handling of the above exception, another exception occurred: @@ -100,5 +100,5 @@ log: |- actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-chipxpressdata[version='>=1.38.0,<1.39.0']")} + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-lpsymphony[version='>=1.30.0,<1.31.0']")} # Last 100 lines of the build log. diff --git a/recipes/bioconductor-ihw/meta.yaml b/recipes/bioconductor-ihw/meta.yaml index 18b067cac3df1..74e07fd5f88d8 100644 --- a/recipes/bioconductor-ihw/meta.yaml +++ b/recipes/bioconductor-ihw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "IHW" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03d60f5df56eb3abb74d8b8c8f7788a2 + md5: aa53165d5f689e8bfdebb02838ae9dab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ihw", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-lpsymphony >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-lpsymphony >=1.30.0,<1.31.0' - r-base - r-fdrtool - r-slam run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-lpsymphony >=1.28.0,<1.29.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-lpsymphony >=1.30.0,<1.31.0' - r-base - r-fdrtool - r-slam diff --git a/recipes/bioconductor-ihwpaper/build_failure.linux-64.yaml b/recipes/bioconductor-ihwpaper/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0d1d099182dc8 --- /dev/null +++ b/recipes/bioconductor-ihwpaper/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 366efc448b56ba6b7e86a876417279bedf04156e08c60e0c035fe672c82e0ddc # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - r-ggplot2 + - libgcc-ng >=12 + - r-rcpp + - libstdcxx-ng >=12 + - bioconductor-biobase >=2.62.0,<2.63.0 + - r-fdrtool + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - liblapack 3.9.* *netlib + - libblas 3.9.* *netlib + - bioconductor-deseq2 >=1.42.0,<1.43.0 + - r-dplyr + - r-base 4.3.* + - bioconductor-genefilter >=1.84.0,<1.85.0 + - bioconductor-ihw >=1.30.0,<1.31.0 + - bioconductor-qvalue >=2.34.0,<2.35.0 + - r-cowplot + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-ggplot2 + - libgcc-ng >=12 + - r-rcpp + - libstdcxx-ng >=12 + - bioconductor-biobase >=2.62.0,<2.63.0 + - r-fdrtool + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-ihw[version='>=1.30.0,<1.31.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ihwpaper/build_failure.osx-64.yaml b/recipes/bioconductor-ihwpaper/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e81f7f57656d0 --- /dev/null +++ b/recipes/bioconductor-ihwpaper/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 366efc448b56ba6b7e86a876417279bedf04156e08c60e0c035fe672c82e0ddc # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + - r-dplyr + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - libcxx >=14 + - bioconductor-qvalue >=2.34.0,<2.35.0 + - bioconductor-biobase >=2.62.0,<2.63.0 + - bioconductor-genefilter >=1.84.0,<1.85.0 + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-cowplot + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 + - + + Leaving build/test directories: + Work: + /opt/mambaforge/envs/bioconda/conda-bld/work + Test: + /opt/mambaforge/envs/bioconda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + Build: + source activate /opt/mambaforge/envs/bioconda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-ggplot2 + - bioconductor-ihw >=1.30.0,<1.31.0 + - liblapack 3.9.* *netlib + - bioconductor-deseq2 >=1.42.0,<1.43.0 + - libblas 3.9.* *netlib + - r-fdrtool + - r-rcpp + - r-base 4.3.* + - r-dplyr + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - libcxx >=14 + - bioconductor-qvalue >=2.34.0,<2.35.0 + - bioconductor-biobase >=2.62.0,<2.63.0 + - bioconductor-genefilter >=1.84.0,<1.85.0 + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - r-cowplot + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-ihw[version='>=1.30.0,<1.31.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ihwpaper/meta.yaml b/recipes/bioconductor-ihwpaper/meta.yaml index c2f712f88e0a3..4251fc13e6670 100644 --- a/recipes/bioconductor-ihwpaper/meta.yaml +++ b/recipes/bioconductor-ihwpaper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "IHWpaper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 282cb3abcd7ee2a5d1c34c468ce806c2 + md5: 21e65d900bf8e6015fd006fbf01237d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ihwpaper", max_pin="x.x") }}' # Suggests: testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-ihw >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-ihw >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -37,14 +38,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-ihw >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-ihw >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -52,7 +53,7 @@ requirements: - r-ggplot2 - r-rcpp - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-ihwpaper/post-link.sh b/recipes/bioconductor-ihwpaper/post-link.sh index 8a0180657a601..cceb85018f40b 100644 --- a/recipes/bioconductor-ihwpaper/post-link.sh +++ b/recipes/bioconductor-ihwpaper/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ihwpaper-1.28.0" +installBiocDataPackage.sh "ihwpaper-1.30.0" diff --git a/recipes/bioconductor-illumina450probevariants.db/meta.yaml b/recipes/bioconductor-illumina450probevariants.db/meta.yaml index 3106b6aca5224..1458b848396e0 100644 --- a/recipes/bioconductor-illumina450probevariants.db/meta.yaml +++ b/recipes/bioconductor-illumina450probevariants.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Illumina450ProbeVariants.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 362d8731f6c9067d58742be0d772a7ac + md5: ca34eec73a57e5f226b70a20ef706ee3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illumina450probevariants.db", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illumina450probevariants.db/post-link.sh b/recipes/bioconductor-illumina450probevariants.db/post-link.sh index 46896196e904f..1d85e7fc79149 100644 --- a/recipes/bioconductor-illumina450probevariants.db/post-link.sh +++ b/recipes/bioconductor-illumina450probevariants.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "illumina450probevariants.db-1.36.0" +installBiocDataPackage.sh "illumina450probevariants.db-1.38.0" diff --git a/recipes/bioconductor-illuminadatatestfiles/meta.yaml b/recipes/bioconductor-illuminadatatestfiles/meta.yaml index b4c3b0c264549..b9af46bf149a1 100644 --- a/recipes/bioconductor-illuminadatatestfiles/meta.yaml +++ b/recipes/bioconductor-illuminadatatestfiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "IlluminaDataTestFiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e11e060ddd803add7efac25b34ab2ff5 + md5: 3afa4b143fbb1dd18b3a7acd8f2984b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminadatatestfiles", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminadatatestfiles/post-link.sh b/recipes/bioconductor-illuminadatatestfiles/post-link.sh index cc992fa91951b..a8b688442f90a 100644 --- a/recipes/bioconductor-illuminadatatestfiles/post-link.sh +++ b/recipes/bioconductor-illuminadatatestfiles/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "illuminadatatestfiles-1.38.0" +installBiocDataPackage.sh "illuminadatatestfiles-1.40.0" diff --git a/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml index 7ae72f80d8e3d..ae8bb8780986d 100644 --- a/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.4.8" %} {% set name = "IlluminaHumanMethylation27k.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 70586bda9db01d598723bb439c315367 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation27k.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml index 13588a0775555..7a1f7e62ecb9c 100644 --- a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylation27kanno.ilmn12.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 765851336506120467c2e3cc6beef7ed build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml index 2c8526441bde7..f08b35ab5f4d1 100644 --- a/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.4.0" %} {% set name = "IlluminaHumanMethylation27kmanifest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c4cdda637dccf85f193342c7262b02a6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation27kmanifest", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml index fb4c92a4c07bd..263014c5c77c9 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.1" %} {% set name = "IlluminaHumanMethylation450kanno.ilmn12.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: aeafc54d887b128ed265fa704a3efa42 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml index 86f91eb9c31f9..9c9f591b02e13 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.4.0" %} {% set name = "IlluminaHumanMethylation450kmanifest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 664d1f5a3892974334faa26757269509 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation450kmanifest", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml index e4b5db62fa0c1..19a1c6a35f21c 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.0.6" %} {% set name = "IlluminaHumanMethylation450kprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 84c31861fcbaddbf2a9c500b8d8d767d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation450kprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml index c49025c692ee2..54f90a3b90e8d 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b2.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6a8e2398a0f930aa7828a1412fb21e88 build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml index db9900e6987cf..5f0e19275d213 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b3.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2dac8e889486386eaea1bb7ce1beea2e build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml index 0b249a0348a72..70a78787f09b0 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2d0c05917bcbf9ba1e354380d4e17a77 build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml index 4bd377524a966..2f570b1de65ff 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.3.0" %} {% set name = "IlluminaHumanMethylationEPICmanifest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c6b0268de177badfe0b8184002da7e16 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicmanifest", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv1.db/meta.yaml b/recipes/bioconductor-illuminahumanv1.db/meta.yaml index 8d558abb79012..cc147efd5d97d 100644 --- a/recipes/bioconductor-illuminahumanv1.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2c362256b7be2861b8bf6e0d1fe46786 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv1.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv2.db/meta.yaml b/recipes/bioconductor-illuminahumanv2.db/meta.yaml index 9161dd42903b4..e86b530f95ba8 100644 --- a/recipes/bioconductor-illuminahumanv2.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 006de5f671a9a68fb27a6b6bce39c555 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv2.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml b/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml index 2894b87d91690..b94e962adf513 100644 --- a/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.8.0" %} {% set name = "illuminaHumanv2BeadID.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b5a2b2deaa9a9b245a141043e7bc5270 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv2beadid.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv3.db/meta.yaml b/recipes/bioconductor-illuminahumanv3.db/meta.yaml index b0ca58eadc49d..004dc46800cdb 100644 --- a/recipes/bioconductor-illuminahumanv3.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv3.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7d9e7534f0b60f0e3e7473e545ef373d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv3.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanv4.db/meta.yaml b/recipes/bioconductor-illuminahumanv4.db/meta.yaml index 0c26073b8d705..e40ca66f6cf27 100644 --- a/recipes/bioconductor-illuminahumanv4.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv4.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv4.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 42d554559ac0106dc71317ffaf466421 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv4.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml b/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml index e5dd2c30187ae..dcb880875fc8c 100644 --- a/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanWGDASLv3.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 32e8e24555c16f6d0148438d4a841ab8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanwgdaslv3.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml b/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml index 5f61508cc064d..da9c7a5e9aa5d 100644 --- a/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanWGDASLv4.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4cc1f192de838f2b6c1b148706d354ca build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminahumanwgdaslv4.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminaio/meta.yaml b/recipes/bioconductor-illuminaio/meta.yaml index 1f45cdc02f008..54acd4f3c77da 100644 --- a/recipes/bioconductor-illuminaio/meta.yaml +++ b/recipes/bioconductor-illuminaio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.42.0" %} +{% set version = "0.44.0" %} {% set name = "illuminaio" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b049b6f3cf366b151994de20502d7df4 + md5: 5bf0b60249c92ef8408564391a69a97d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminaio", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle requirements: host: diff --git a/recipes/bioconductor-illuminamousev1.db/meta.yaml b/recipes/bioconductor-illuminamousev1.db/meta.yaml index 9a4c1ebb7aab7..f0095683a0190 100644 --- a/recipes/bioconductor-illuminamousev1.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 13818c3b9acabe75550492bbe638fc05 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminamousev1.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminamousev1p1.db/meta.yaml b/recipes/bioconductor-illuminamousev1p1.db/meta.yaml index 4403ddfb1b720..e2dbd5a55ed59 100644 --- a/recipes/bioconductor-illuminamousev1p1.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev1p1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev1p1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f6a4af01480a6f8d1d2d9b9b64a2b073 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminamousev1p1.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminamousev2.db/meta.yaml b/recipes/bioconductor-illuminamousev2.db/meta.yaml index 4c6f1570a86b9..405b1d50f2aa1 100644 --- a/recipes/bioconductor-illuminamousev2.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fba228a71f264f976d8cdb035861974d build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminamousev2.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-illuminaratv1.db/meta.yaml b/recipes/bioconductor-illuminaratv1.db/meta.yaml index 0337c5cbcc114..68fc32da96338 100644 --- a/recipes/bioconductor-illuminaratv1.db/meta.yaml +++ b/recipes/bioconductor-illuminaratv1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.26.0" %} {% set name = "illuminaRatv1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5de2324d7b96c0cdb3301ef269341aa8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-illuminaratv1.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-imas/meta.yaml b/recipes/bioconductor-imas/meta.yaml index f68bfd0d5c84f..9000f1e30f504 100644 --- a/recipes/bioconductor-imas/meta.yaml +++ b/recipes/bioconductor-imas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "IMAS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc40485d764674bc1b01b1b5dccc80fc + md5: c86deaedf1d19981dbfcea7a3b53d331 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-imas", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-ivas >=2.20.0,<2.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-ivas >=2.22.0,<2.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach @@ -43,17 +44,17 @@ requirements: - r-matrix - r-survival run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-ivas >=2.20.0,<2.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-ivas >=2.22.0,<2.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-imcdatasets/meta.yaml b/recipes/bioconductor-imcdatasets/meta.yaml index 2208795414271..50be0d4514827 100644 --- a/recipes/bioconductor-imcdatasets/meta.yaml +++ b/recipes/bioconductor-imcdatasets/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "imcdatasets" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1e0e9d5ecc4a826887de1abc773d86b3 + md5: 6e687f10502d7d9d369c384e99977953 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-imcdatasets", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat requirements: host: - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-imcdatasets/post-link.sh b/recipes/bioconductor-imcdatasets/post-link.sh index f353b2a1ae091..12db5126d417b 100644 --- a/recipes/bioconductor-imcdatasets/post-link.sh +++ b/recipes/bioconductor-imcdatasets/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "imcdatasets-1.8.0" +installBiocDataPackage.sh "imcdatasets-1.10.0" diff --git a/recipes/bioconductor-imcrtools/meta.yaml b/recipes/bioconductor-imcrtools/meta.yaml index b56409bd2fdbe..50de270226360 100644 --- a/recipes/bioconductor-imcrtools/meta.yaml +++ b/recipes/bioconductor-imcrtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.3" %} +{% set version = "1.8.0" %} {% set name = "imcRtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94eb20c85197b1461d9d5ab126b31c9d + md5: 483b782cf0adc433cf956e4ca52c393c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-imcrtools", max_pin="x.x") }}' noarch: generic # Suggests: CATALYST, grid, BiocStyle, knitr, rmarkdown, markdown, testthat requirements: host: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-concaveman @@ -52,16 +53,16 @@ requirements: - r-viridis - r-vroom run: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-concaveman diff --git a/recipes/bioconductor-imman/meta.yaml b/recipes/bioconductor-imman/meta.yaml index a70a804e1068e..4a0b5412457fe 100644 --- a/recipes/bioconductor-imman/meta.yaml +++ b/recipes/bioconductor-imman/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "IMMAN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3588d8794020fb9d369910d822b5b1e4 + md5: 6e3ac40584a93ea233ba0b082a4d79aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-imman", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-igraph - r-seqinr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-igraph - r-seqinr diff --git a/recipes/bioconductor-immunespacer/meta.yaml b/recipes/bioconductor-immunespacer/meta.yaml index e195e9f0a49c0..20db0e898252b 100644 --- a/recipes/bioconductor-immunespacer/meta.yaml +++ b/recipes/bioconductor-immunespacer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ImmuneSpaceR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7365d830f8a7ec436b6737932cb6c1b + md5: 3d19d0b03625db9bd86ce96b98dbe438 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-immunespacer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, covr, withr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-curl - r-data.table @@ -41,10 +42,10 @@ requirements: - r-rmarkdown - r-scales run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-immunoclust/meta.yaml b/recipes/bioconductor-immunoclust/meta.yaml index de5de744faf41..32861095ef561 100644 --- a/recipes/bioconductor-immunoclust/meta.yaml +++ b/recipes/bioconductor-immunoclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "immunoClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5d377e5265f45ceb2a4da80d355fc47 + md5: b83f47eaa19d45984b19f4071b455873 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-immunoclust", max_pin="x.x") }}' # Suggests: BiocStyle, utils, testthat +# SystemRequirements: gsl requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-lattice - libblas - liblapack + - gsl run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-lattice + - gsl build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-immunotation/meta.yaml b/recipes/bioconductor-immunotation/meta.yaml index 232bdbeb588c2..eb969b28a159d 100644 --- a/recipes/bioconductor-immunotation/meta.yaml +++ b/recipes/bioconductor-immunotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "immunotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4dff1d35e677b860b005364788695243 + md5: b05bb33e3987de27d181d8e44e468f62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-immunotation", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT requirements: diff --git a/recipes/bioconductor-impcdata/meta.yaml b/recipes/bioconductor-impcdata/meta.yaml index f99c7b47fac93..6d8b9e6c09f7b 100644 --- a/recipes/bioconductor-impcdata/meta.yaml +++ b/recipes/bioconductor-impcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "IMPCdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3db8a9ef20ab4890eb5dede2f53fc44 + md5: c4a243d4a15f680abfb5d61a951c620d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-impcdata", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-impute/meta.yaml b/recipes/bioconductor-impute/meta.yaml index ffa18e5707df0..0f5d1d5aed6cc 100644 --- a/recipes/bioconductor-impute/meta.yaml +++ b/recipes/bioconductor-impute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.1" %} +{% set version = "1.76.0" %} {% set name = "impute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cf3ffdc0f5d6caac43d3e3e7d73a8096 + md5: 8e974dcc31c3507ebcc8984b2d7943f9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-impute", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-indac.db/meta.yaml b/recipes/bioconductor-indac.db/meta.yaml index be1f05bca5b39..280f0ef419b4f 100644 --- a/recipes/bioconductor-indac.db/meta.yaml +++ b/recipes/bioconductor-indac.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "indac.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cba72edcf7278033151e0eac077d8ff8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-indac.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-indeed/meta.yaml b/recipes/bioconductor-indeed/meta.yaml index e8089c504c58d..1e3e32686ddea 100644 --- a/recipes/bioconductor-indeed/meta.yaml +++ b/recipes/bioconductor-indeed/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "INDEED" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7441181a9c207fbd3288dd9b8ee500b7 + md5: 457badfae1608eb2c198b89526abe740 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-indeed", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) requirements: diff --git a/recipes/bioconductor-inetgrate/build.sh b/recipes/bioconductor-inetgrate/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-inetgrate/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-inetgrate/meta.yaml b/recipes/bioconductor-inetgrate/meta.yaml new file mode 100644 index 0000000000000..2e2f82d637edc --- /dev/null +++ b/recipes/bioconductor-inetgrate/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "iNETgrate" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fb3e503060d4294162e8690a6bb41059 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-inetgrate", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks (>= 2.29.4) +requirements: + host: + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-pigengene >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-caret + - r-glmnet + - r-gplots + - r-igraph + - r-matrixstats + - r-rfast + - r-survival + - r-tidyr + - r-tidyselect + - r-wgcna + run: + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-pigengene >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-caret + - r-glmnet + - r-gplots + - r-igraph + - r-matrixstats + - r-rfast + - r-survival + - r-tidyr + - r-tidyselect + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Integrates DNA methylation data with gene expression in a single gene network' + description: 'The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-infercnv/meta.yaml b/recipes/bioconductor-infercnv/meta.yaml index 015d148d0fac9..846a226731767 100644 --- a/recipes/bioconductor-infercnv/meta.yaml +++ b/recipes/bioconductor-infercnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.1" %} {% set name = "infercnv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e09bfc20a01a9aebdf76bd5bb15eb0e + md5: d5bce5518c27e86b3fb26b6fedad5d7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-infercnv", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat # SystemRequirements: JAGS 4.x.y requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-argparse - r-base @@ -56,10 +57,10 @@ requirements: - r-tidyr - 'jags 4.*.*' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-argparse - r-base diff --git a/recipes/bioconductor-infinityflow/meta.yaml b/recipes/bioconductor-infinityflow/meta.yaml index d4b597682299b..f1047378cf0e6 100644 --- a/recipes/bioconductor-infinityflow/meta.yaml +++ b/recipes/bioconductor-infinityflow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "infinityFlow" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54c32c8b8be6ae8dd92483ea3fe25f2b + md5: e65e5163632d9351a8a1f1bb30d74d8f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-infinityflow", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-generics - r-gtools @@ -33,8 +34,8 @@ requirements: - r-uwot - r-xgboost run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-generics - r-gtools diff --git a/recipes/bioconductor-inpas/meta.yaml b/recipes/bioconductor-inpas/meta.yaml index 0c6fd56ba7c4d..9d51c47ac6612 100644 --- a/recipes/bioconductor-inpas/meta.yaml +++ b/recipes/bioconductor-inpas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "InPAS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d43e5034da4ada85c372c1f7f415a95a + md5: d11dbf3351e3fec486c3da1a61bf6050 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-inpas", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics,BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cleanupdtseq >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cleanupdtseq >=1.40.0,<1.41.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-batchtools - r-depmixs4 @@ -48,19 +49,19 @@ requirements: - r-reshape2 - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cleanupdtseq >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cleanupdtseq >=1.40.0,<1.41.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-batchtools - r-depmixs4 diff --git a/recipes/bioconductor-inpower/meta.yaml b/recipes/bioconductor-inpower/meta.yaml index 991b764e5def3..352b849653f39 100644 --- a/recipes/bioconductor-inpower/meta.yaml +++ b/recipes/bioconductor-inpower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "INPower" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af7a75d26eefaadd42eb6b31e5d4aae0 + md5: 3b769c08ded506c713da036c30fe4da9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-inpower", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-inspect/build_failure.linux-64.yaml b/recipes/bioconductor-inspect/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..95ece71c08362 --- /dev/null +++ b/recipes/bioconductor-inspect/build_failure.linux-64.yaml @@ -0,0 +1,33 @@ +recipe_sha: b6bbddaaff8dbbb23dad96d68412111023807b708179b0d3fa28588e58a8759a # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + Error: object ‘read.xls’ is not exported by 'namespace:gdata' +category: |- + compiler error +log: |- + 14:32:11 BIOCONDA INFO (OUT) ERROR: lazy loading failed for package ‘INSPEcT’ + 14:32:11 BIOCONDA INFO (OUT) During startup - Warning message: + 14:32:11 BIOCONDA INFO (OUT) Setting LC_TIME failed, using "C" + 14:32:11 BIOCONDA INFO (OUT) Error: object ‘read.xls’ is not exported by 'namespace:gdata' + 14:32:11 BIOCONDA INFO (OUT) Execution halted + 14:32:11 BIOCONDA INFO (OUT) * removing ‘/opt/conda/conda-bld/bioconductor-inspect_1702304851717/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/INSPEcT’ + 14:32:12 BIOCONDA INFO (OUT) Traceback (most recent call last): + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in + 14:32:12 BIOCONDA INFO (OUT) sys.exit(main()) + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 14:32:12 BIOCONDA INFO (OUT) call_conda_build(action, config) + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 14:32:12 BIOCONDA INFO (OUT) result = api.build( + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 14:32:12 BIOCONDA INFO (OUT) return build_tree( + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + 14:32:12 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + 14:32:12 BIOCONDA INFO (OUT) utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + 14:32:12 BIOCONDA INFO (OUT) return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + 14:32:12 BIOCONDA INFO (OUT) raise subprocess.CalledProcessError(proc.returncode, _args) + 14:32:12 BIOCONDA INFO (OUT) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-inspect_1702304851717/work/conda_build.sh']' returned non-zero exit status 1. + 14:32:21 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmp24i5m63r/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-inspect:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:2.11.0 /bin/bash /opt/build_script.bash + diff --git a/recipes/bioconductor-inspect/meta.yaml b/recipes/bioconductor-inspect/meta.yaml index c1d37877c12d5..8036e06f7ea1b 100644 --- a/recipes/bioconductor-inspect/meta.yaml +++ b/recipes/bioconductor-inspect/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.31.0" %} {% set name = "INSPEcT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 731b56f9ee71c545653a62ba8bada39c + md5: e48ba19e529a7072f52817ecd08d2b9c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-inspect", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plgem >=1.72.0,<1.73.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plgem >=1.74.0,<1.75.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-desolve @@ -44,20 +45,20 @@ requirements: - r-rootsolve - r-shiny run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plgem >=1.72.0,<1.73.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plgem >=1.74.0,<1.75.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-desolve diff --git a/recipes/bioconductor-intact/meta.yaml b/recipes/bioconductor-intact/meta.yaml index 60af61e8dc338..a273c8c9b8cd1 100644 --- a/recipes/bioconductor-intact/meta.yaml +++ b/recipes/bioconductor-intact/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "INTACT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ceaf5b083b46ba3d8dd3948502fef80 + md5: d8646f4acb0cbb31ccf53a672818be40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intact", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-intad/meta.yaml b/recipes/bioconductor-intad/meta.yaml index d8c2c7e930a40..754ba4a2adcb7 100644 --- a/recipes/bioconductor-intad/meta.yaml +++ b/recipes/bioconductor-intad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "InTAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21d458b9b5a25c878f821311e1fd1cdf + md5: 2502f954bc06e364560216eb972c18f7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intad", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggpubr - r-mclust run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggpubr diff --git a/recipes/bioconductor-intansv/meta.yaml b/recipes/bioconductor-intansv/meta.yaml index e37045506cf7c..7b67061f38d88 100644 --- a/recipes/bioconductor-intansv/meta.yaml +++ b/recipes/bioconductor-intansv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "intansv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5af1bb5f5651006c1f7eaa0e439d4bcf + md5: d23f9f69f23ab113ea9ac7100cafb3f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intansv", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-plyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-plyr test: diff --git a/recipes/bioconductor-interaccircos/meta.yaml b/recipes/bioconductor-interaccircos/meta.yaml index 0889e8f21d8f0..df5cf27ff94e8 100644 --- a/recipes/bioconductor-interaccircos/meta.yaml +++ b/recipes/bioconductor-interaccircos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "interacCircos" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec5b4dc1bd80300f335376278c1b37fc + md5: d97429da8da823bf80547b4ac8ca2505 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interaccircos", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-interactionset/meta.yaml b/recipes/bioconductor-interactionset/meta.yaml index 4177427dc658b..246555c250fde 100644 --- a/recipes/bioconductor-interactionset/meta.yaml +++ b/recipes/bioconductor-interactionset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "InteractionSet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a37d06db719d31ff11c614171d612d0 + md5: 273175864f47083ba4b983c72ba0c1dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interactionset", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-interactivecomplexheatmap/meta.yaml b/recipes/bioconductor-interactivecomplexheatmap/meta.yaml index 8453899d820fb..1fc9f6c2b98ff 100644 --- a/recipes/bioconductor-interactivecomplexheatmap/meta.yaml +++ b/recipes/bioconductor-interactivecomplexheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "InteractiveComplexHeatmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0c5ce2f87cb18bd8dd6523db4abc358 + md5: 87fef3e4c9035cbfab5dc4a2242223dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interactivecomplexheatmap", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges, data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap, cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3, GOexpress, SingleCellExperiment, scater, gplots, pheatmap, airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve (>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clisymbols - r-digest @@ -36,9 +37,9 @@ requirements: - r-shiny - r-svglite run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clisymbols - r-digest diff --git a/recipes/bioconductor-interactivedisplay/build_failure.linux-64.yaml b/recipes/bioconductor-interactivedisplay/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9eba9918043d4 --- /dev/null +++ b/recipes/bioconductor-interactivedisplay/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9c517fc772ed28be827019592f5023b076b81fbe7358c247a963d5f1d48acc90 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + sysroot_linux-64: 2.12-he073ed8_16 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h0c5db8f_5 conda-forge + toml: 0.10.2-pyhd8ed1ab_0 conda-forge + tomlkit: 0.12.3-pyha770c72_0 conda-forge + tzdata: 2023c-h71feb2d_0 conda-forge + wheel: 0.42.0-pyhd8ed1ab_0 conda-forge + xmltodict: 0.13.0-pyhd8ed1ab_0 conda-forge + xorg-kbproto: 1.0.7-h7f98852_1002 conda-forge + xorg-libice: 1.1.1-hd590300_0 conda-forge + xorg-libsm: 1.2.4-h7391055_0 conda-forge + xorg-libx11: 1.8.7-h8ee46fc_0 conda-forge + xorg-libxau: 1.0.11-hd590300_0 conda-forge + xorg-libxdmcp: 1.1.3-h7f98852_0 conda-forge + xorg-libxext: 1.3.4-h0b41bf4_2 conda-forge + xorg-libxrender: 0.9.11-hd590300_0 conda-forge + xorg-libxt: 1.3.0-hd590300_1 conda-forge + xorg-renderproto: 0.11.1-h7f98852_1002 conda-forge + xorg-xextproto: 7.3.0-h0b41bf4_1003 conda-forge + xorg-xproto: 7.0.31-h7f98852_1007 conda-forge + xz: 5.2.6-h166bdaf_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.2.3-pyhd8ed1ab_0 conda-forge + zlib: 1.2.13-hd590300_5 conda-forge + zstd: 1.5.5-hfc55251_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... + To install TinyTeX with tinytex::install_tinytex() the system must have a functional Perl + installation with a File::Find module. Most end-user systems will already satisfy this + requirement; however, some minimal contexts (e.g., containers) may not. Perl is available + via Conda Forge as the package perl. See https://github.com/rstudio/tinytex/issues/419 + + + done + [34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.0MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.5MB/s 0.0s + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.0MB/s 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.5MB/s 0.0s + [?25h + ## Package Plan ## + + environment location: /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_build_env + + + Source cache directory is: /opt/conda/conda-bld/src_cache + INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: interactiveDisplay_1.40.0_4adec73e76.tar.gz + INFO:conda_build.source:Downloading source to cache: interactiveDisplay_1.40.0_4adec73e76.tar.gz + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/interactiveDisplay_1.40.0.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/interactiveDisplay_1.40.0.tar.gz + Success + INFO:conda_build.source:Success + Extracting download + source tree in: /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/work + export PREFIX=/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/work + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library + * installing *source* package interactiveDisplay ... + ** using staged installation + ** R + ** data + ** inst + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + Installing package into $PREFIX/lib/R/library/00LOCK-work/00new + (as lib is unspecified) + Error in contrib.url(repos, type) : + trying to use CRAN without setting a mirror + Error: unable to load R code in package interactiveDisplay + Execution halted + ERROR: lazy loading failed for package interactiveDisplay + * removing /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/interactiveDisplay + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-interactivedisplay/meta.yaml b/recipes/bioconductor-interactivedisplay/meta.yaml index bf5cbb9038509..d76299068acbc 100644 --- a/recipes/bioconductor-interactivedisplay/meta.yaml +++ b/recipes/bioconductor-interactivedisplay/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "interactiveDisplay" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32075538ec509a9743bb5e6baf5b0655 + md5: 4adec73e763df3dc2e697e41bff3ead8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interactivedisplay", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-interactivedisplaybase >=1.38.0,<1.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-gridsvg @@ -33,12 +34,11 @@ requirements: - r-reshape2 - r-shiny - r-xml - - r-biocmanager run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-interactivedisplaybase >=1.38.0,<1.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-gridsvg @@ -47,10 +47,8 @@ requirements: - r-reshape2 - r-shiny - r-xml - - r-biocmanager test: commands: - - ls $PREFIX/bin - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' diff --git a/recipes/bioconductor-interactivedisplaybase/meta.yaml b/recipes/bioconductor-interactivedisplaybase/meta.yaml index 7e4aac617b04d..6457aaceb53ef 100644 --- a/recipes/bioconductor-interactivedisplaybase/meta.yaml +++ b/recipes/bioconductor-interactivedisplaybase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "interactiveDisplayBase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b348c5193f2b96439ef86cb82c03247f + md5: 9ae8be7104ab2debe258b504bcd24e38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interactivedisplaybase", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dt - r-shiny run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dt - r-shiny diff --git a/recipes/bioconductor-intercellar/meta.yaml b/recipes/bioconductor-intercellar/meta.yaml index 950572f1a13c1..81dde8f9efb34 100644 --- a/recipes/bioconductor-intercellar/meta.yaml +++ b/recipes/bioconductor-intercellar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "InterCellar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aebf615461677efa93c2c73cbcdfa318 + md5: a331a8a5f0161dd1e5afa2430660b785 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intercellar", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - r-base - r-circlize - r-colorspace @@ -58,8 +59,8 @@ requirements: - r-visnetwork - r-wordcloud2 run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - r-base - r-circlize - r-colorspace diff --git a/recipes/bioconductor-interest/meta.yaml b/recipes/bioconductor-interest/meta.yaml index 66e3569a8415b..80b57c6986664 100644 --- a/recipes/bioconductor-interest/meta.yaml +++ b/recipes/bioconductor-interest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "IntEREst" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,51 +11,52 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a96a9adbc5e4a9299cdbeed5f7061ced + md5: b9b473ea53b89a32487163ef6a664905 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interest", max_pin="x.x") }}' noarch: generic # Suggests: clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dbi - r-rmysql - r-seqinr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dbi - r-rmysql diff --git a/recipes/bioconductor-interminer/meta.yaml b/recipes/bioconductor-interminer/meta.yaml index 2269b69153c9a..bd1ae0276f056 100644 --- a/recipes/bioconductor-interminer/meta.yaml +++ b/recipes/bioconductor-interminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "InterMineR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09d5528d9f3bdfcfddfa5a54ebf99f98 + md5: a401e91084a8393592ceb3305b6cbfa2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-interminer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, Gviz, knitr, rmarkdown, GO.db, org.Hs.eg.db requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-httr - r-igraph @@ -35,11 +36,11 @@ requirements: - r-xml - r-xml2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-httr - r-igraph diff --git a/recipes/bioconductor-intomics/meta.yaml b/recipes/bioconductor-intomics/meta.yaml index 599f5b5e98d63..7eb05b0cf719f 100644 --- a/recipes/bioconductor-intomics/meta.yaml +++ b/recipes/bioconductor-intomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "IntOMICS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eec7530ce0fd9941c0cfe06c864e7511 + md5: 61628ea37535123f71455b77b194b08c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intomics", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, curatedTCGAData, TCGAutils, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bestnormalize - r-bnlearn @@ -36,7 +37,7 @@ requirements: - r-rcolorbrewer - r-rlang run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bestnormalize - r-bnlearn diff --git a/recipes/bioconductor-intramirexplorer/meta.yaml b/recipes/bioconductor-intramirexplorer/meta.yaml index dc6432a215aac..8e70e8e286ee9 100644 --- a/recipes/bioconductor-intramirexplorer/meta.yaml +++ b/recipes/bioconductor-intramirexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "IntramiRExploreR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f037f313236ed7acb47a038d70b7593 + md5: e319d73695e5e1f12d9fc79896c49674 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-intramirexplorer", max_pin="x.x") }}' noarch: generic # Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat requirements: host: - - 'bioconductor-fgnet >=3.34.0,<3.35.0' + - 'bioconductor-fgnet >=3.36.0,<3.37.0' - r-base - 'r-igraph >=1.0.1' - 'r-knitr >=1.12.3' run: - - 'bioconductor-fgnet >=3.34.0,<3.35.0' + - 'bioconductor-fgnet >=3.36.0,<3.37.0' - r-base - 'r-igraph >=1.0.1' - 'r-knitr >=1.12.3' diff --git a/recipes/bioconductor-ioniser/meta.yaml b/recipes/bioconductor-ioniser/meta.yaml index 400b9e5ff444b..d6dce6d5af852 100644 --- a/recipes/bioconductor-ioniser/meta.yaml +++ b/recipes/bioconductor-ioniser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "IONiseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1247c90a347c1886045bdca153fe5196 + md5: 10a3ed3f75ba8be8989b90d197096b40 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ioniser", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-bit64 - r-dplyr @@ -36,12 +37,12 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-bit64 - r-dplyr diff --git a/recipes/bioconductor-ipac/meta.yaml b/recipes/bioconductor-ipac/meta.yaml index 51dc95556d71c..c8ac07446c2ae 100644 --- a/recipes/bioconductor-ipac/meta.yaml +++ b/recipes/bioconductor-ipac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "iPAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f48c2f8e363a774893839a48379a8d87 + md5: 2ea1fca8a80c62d82be0ef8d6313e52b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ipac", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-gdata - r-scatterplot3d run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-gdata - r-scatterplot3d diff --git a/recipes/bioconductor-ipath/meta.yaml b/recipes/bioconductor-ipath/meta.yaml index 6f73e3afe26e8..c942c0964afed 100644 --- a/recipes/bioconductor-ipath/meta.yaml +++ b/recipes/bioconductor-ipath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "iPath" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 186f06f5b67f1987457d4b8a8b999d9b + md5: 71bdeccc2d0192cd080c4c190831d792 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ipath", max_pin="x.x") }}' # Suggests: rmarkdown, BiocStyle, knitr # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ggplot2 - r-ggpubr @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ggplot2 - r-ggpubr diff --git a/recipes/bioconductor-ipddb/meta.yaml b/recipes/bioconductor-ipddb/meta.yaml index 90e5b808a3a52..685bfe5c5e978 100644 --- a/recipes/bioconductor-ipddb/meta.yaml +++ b/recipes/bioconductor-ipddb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ipdDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0afd5495c9ebce5bb6ad475f9d44236e + md5: 0346f5dcca05a1bfb117214c54f36524 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ipddb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-assertthat - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-assertthat - r-base - r-dbi diff --git a/recipes/bioconductor-ipo/meta.yaml b/recipes/bioconductor-ipo/meta.yaml index b488d197c0948..85a6e762813ff 100644 --- a/recipes/bioconductor-ipo/meta.yaml +++ b/recipes/bioconductor-ipo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "IPO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d99c69c85047b339955ff0a6bc2365d0 + md5: a1275d6f177754744bcceb9a8aed44a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ipo", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-rsm run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-rsm test: diff --git a/recipes/bioconductor-iranges/meta.yaml b/recipes/bioconductor-iranges/meta.yaml index 04fb73abd9293..9f429ff8f8074 100644 --- a/recipes/bioconductor-iranges/meta.yaml +++ b/recipes/bioconductor-iranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.1" %} +{% set version = "2.36.0" %} {% set name = "IRanges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9b9645aee1db4455dea509cedd7e157 + md5: 87618d2e5ee94d7ab81d2e1c4d847120 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iranges", max_pin="x.x") }}' # Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-isanalytics/meta.yaml b/recipes/bioconductor-isanalytics/meta.yaml index ae6d0b78dc25b..bb03455bd7935 100644 --- a/recipes/bioconductor-isanalytics/meta.yaml +++ b/recipes/bioconductor-isanalytics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "ISAnalytics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ceb361c936fc5adc1ae9eb2b5122839c + md5: d1962980b18dd3ff8fdcc1bb0c855eaf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isanalytics", max_pin="x.x") }}' noarch: generic # Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, vegan, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, data.table, Rcapture requirements: diff --git a/recipes/bioconductor-isee/meta.yaml b/recipes/bioconductor-isee/meta.yaml index 09bb9622763bd..1cb011c60e377 100644 --- a/recipes/bioconductor-isee/meta.yaml +++ b/recipes/bioconductor-isee/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "iSEE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a933b7c4b34541ff8e3f477b24c354c2 + md5: e6d2be3afb9bc484d594cbd21887ec53 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isee", max_pin="x.x") }}' noarch: generic # Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-colourpicker @@ -43,11 +44,11 @@ requirements: - r-vipor - r-viridislite run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-colourpicker diff --git a/recipes/bioconductor-iseede/build.sh b/recipes/bioconductor-iseede/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iseede/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iseede/meta.yaml b/recipes/bioconductor-iseede/meta.yaml new file mode 100644 index 0000000000000..68f2097a44e14 --- /dev/null +++ b/recipes/bioconductor-iseede/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.0" %} +{% set name = "iSEEde" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4d6215b9243635ed9dd3b6fcf5cbf166 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseede", max_pin="x.x") }}' + noarch: generic +# Suggests: airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-shiny + run: + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'iSEE extension for panels related to differential expression analysis' + description: 'This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.' + diff --git a/recipes/bioconductor-iseehex/meta.yaml b/recipes/bioconductor-iseehex/meta.yaml index 721af6f3acd45..45547ab3c80ac 100644 --- a/recipes/bioconductor-iseehex/meta.yaml +++ b/recipes/bioconductor-iseehex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "iSEEhex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 49e7fb29541fb2ac12ad0ac21926d277 + md5: 9bc98dc14114c756f97c130adf061a4b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseehex", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), scRNAseq, scater requirements: host: - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-hexbin - r-shiny run: - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-hexbin diff --git a/recipes/bioconductor-iseehub/meta.yaml b/recipes/bioconductor-iseehub/meta.yaml index 3cc96f0d3f3f5..0a193959471a0 100644 --- a/recipes/bioconductor-iseehub/meta.yaml +++ b/recipes/bioconductor-iseehub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.1" %} +{% set version = "1.4.0" %} {% set name = "iSEEhub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98bd83d25a30d3029b20350423b76e6e + md5: 6ebb32da66242f608b83522fca1d9a62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseehub", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), nullrangesData requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-dt @@ -35,12 +36,12 @@ requirements: - r-shinydashboard - r-shinyjs run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-dt diff --git a/recipes/bioconductor-iseeindex/build.sh b/recipes/bioconductor-iseeindex/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iseeindex/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iseeindex/meta.yaml b/recipes/bioconductor-iseeindex/meta.yaml new file mode 100644 index 0000000000000..e795471cb94d1 --- /dev/null +++ b/recipes/bioconductor-iseeindex/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.0.0" %} +{% set name = "iSEEindex" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 98a9141431a3206fd242b5b0b4056c41 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseeindex", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), yaml +requirements: + host: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dt + - r-paws.storage + - r-rintrojs + - r-shiny + - r-shinydashboard + - r-shinyjs + - r-stringr + - r-urltools + run: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dt + - r-paws.storage + - r-rintrojs + - r-shiny + - r-shinydashboard + - r-shinyjs + - r-stringr + - r-urltools +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'iSEE extension for a landing page to a custom collection of data sets' + description: 'This package provides an interface to any collection of data sets within a single iSEE web-application. The main functionality of this package is to define a custom landing page allowing app maintainers to list a custom collection of data sets that users can selected from and directly load objects into an iSEE web-application.' + diff --git a/recipes/bioconductor-iseepathways/build.sh b/recipes/bioconductor-iseepathways/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iseepathways/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iseepathways/meta.yaml b/recipes/bioconductor-iseepathways/meta.yaml new file mode 100644 index 0000000000000..b1ecb82d75020 --- /dev/null +++ b/recipes/bioconductor-iseepathways/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.0" %} +{% set name = "iSEEpathways" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 52b84dcbd5e5ab0a6bbdc27120d7e86a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseepathways", max_pin="x.x") }}' + noarch: generic +# Suggests: airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-shiny + - r-shinywidgets + run: + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-shiny + - r-shinywidgets +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'iSEE extension for panels related to pathway analysis' + description: 'This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.' + diff --git a/recipes/bioconductor-iseeu/meta.yaml b/recipes/bioconductor-iseeu/meta.yaml index 5ad45b2cbf5f2..b0845ec64ecd3 100644 --- a/recipes/bioconductor-iseeu/meta.yaml +++ b/recipes/bioconductor-iseeu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "iSEEu" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 320331a5b0bf6929e03ba9003d0d8aad + md5: d9349d85759c37c8a971b4ffcebcecea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseeu", max_pin="x.x") }}' noarch: generic # Suggests: scRNAseq, scater, scran, airway, edgeR, AnnotationDbi, org.Hs.eg.db, GO.db, KEGGREST, knitr, igraph, rmarkdown, BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0), covr requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-iseehex >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-iseehex >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colourpicker - r-dt @@ -34,12 +35,12 @@ requirements: - r-shiny - r-shinyace run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-isee >=2.12.0,<2.13.0' - - 'bioconductor-iseehex >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-isee >=2.14.0,<2.15.0' + - 'bioconductor-iseehex >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colourpicker - r-dt diff --git a/recipes/bioconductor-iseq/meta.yaml b/recipes/bioconductor-iseq/meta.yaml index c55d6f5819474..326c46a55f5f7 100644 --- a/recipes/bioconductor-iseq/meta.yaml +++ b/recipes/bioconductor-iseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "iSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f68d848b58ee7cc917534a00c27d69c + md5: 1798c4c248175516afc66ee7f45d5051 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseq", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-islet/meta.yaml b/recipes/bioconductor-islet/meta.yaml index 19564678e2d71..78b454e10d2aa 100644 --- a/recipes/bioconductor-islet/meta.yaml +++ b/recipes/bioconductor-islet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ISLET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a76f8e90e5662a93b09be8f1f06b863 + md5: 5cf5ae7df60062c1822ca64c3989a4e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-islet", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit +# Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-abind - r-base + - r-lme4 - r-matrix + - r-nnls + - r-purrr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-abind - r-base + - r-lme4 - r-matrix + - r-nnls + - r-purrr test: commands: - '$R -e "library(''{{ name }}'')"' @@ -39,6 +48,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Individual-Specific ceLl typE referencing Tool' - description: 'ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis. It can also conduct test to identify cell-type-specific differential expression (csDE) genes.' + description: 'ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis and conduct test to identify cell-type-specific differential expression (csDE) genes. It also improves estimated cell type mixture proportions by integrating personalized reference panels.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' diff --git a/recipes/bioconductor-isobar/meta.yaml b/recipes/bioconductor-isobar/meta.yaml index dd3209fcd717f..b900b92c86f60 100644 --- a/recipes/bioconductor-isobar/meta.yaml +++ b/recipes/bioconductor-isobar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "isobar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1795587748211afa4d437207a552d936 + md5: bf7b66ee10cfc2f8b24f22642bbc395a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isobar", max_pin="x.x") }}' noarch: generic # Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-distr - r-ggplot2 - r-plyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-distr - r-ggplot2 diff --git a/recipes/bioconductor-isobayes/build.sh b/recipes/bioconductor-isobayes/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-isobayes/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isobayes/meta.yaml b/recipes/bioconductor-isobayes/meta.yaml new file mode 100644 index 0000000000000..39f49ed83d0d2 --- /dev/null +++ b/recipes/bioconductor-isobayes/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.0.1" %} +{% set name = "IsoBayes" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d9e1de9f5a1f8279117fde4cc997725d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isobayes", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, testthat, BiocStyle +# SystemRequirements: C++17 +requirements: + host: + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-data.table + - r-doparallel + - r-dorng + - r-foreach + - r-ggplot2 + - r-glue + - r-hdinterval + - r-iterators + - r-rcpp + - r-rcpparmadillo + - libblas + - liblapack + run: + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-data.table + - r-doparallel + - r-dorng + - r-foreach + - r-ggplot2 + - r-glue + - r-hdinterval + - r-iterators + - r-rcpp + - r-rcpparmadillo + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'IsoBayes: Single Isoform protein inference Method via Bayesian Analyses' + description: 'IsoBayes is a Bayesian method to perform inference on single protein isoforms. Our approach infers the presence/absence of protein isoforms, and also estimates their abundance; additionally, it provides a measure of the uncertainty of these estimates, via: i) the posterior probability that a protein isoform is present in the sample; ii) a posterior credible interval of its abundance. IsoBayes inputs liquid cromatography mass spectrometry (MS) data, and can work with both PSM counts, and intensities. When available, trascript isoform abundances (i.e., TPMs) are also incorporated: TPMs are used to formulate an informative prior for the respective protein isoform relative abundance. We further identify isoforms where the relative abundance of proteins and transcripts significantly differ. We use a two-layer latent variable approach to model two sources of uncertainty typical of MS data: i) peptides may be erroneously detected (even when absent); ii) many peptides are compatible with multiple protein isoforms. In the first layer, we sample the presence/absence of each peptide based on its estimated probability of being mistakenly detected, also known as PEP (i.e., posterior error probability). In the second layer, for peptides that were estimated as being present, we allocate their abundance across the protein isoforms they map to. These two steps allow us to recover the presence and abundance of each protein isoform.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-isocorrector/meta.yaml b/recipes/bioconductor-isocorrector/meta.yaml index 9bf3067bb9cbd..f21aefe95aded 100644 --- a/recipes/bioconductor-isocorrector/meta.yaml +++ b/recipes/bioconductor-isocorrector/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "IsoCorrectoR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90680864d0b6b71e3da4ae275894e35f + md5: ba3b19c2ad9ed8f9b7f6929c49828bb5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isocorrector", max_pin="x.x") }}' noarch: generic # Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle requirements: diff --git a/recipes/bioconductor-isocorrectorgui/meta.yaml b/recipes/bioconductor-isocorrectorgui/meta.yaml index cbf371b5fd158..93ca3c9414cfc 100644 --- a/recipes/bioconductor-isocorrectorgui/meta.yaml +++ b/recipes/bioconductor-isocorrectorgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "IsoCorrectoRGUI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e197b90dc85263bbc0ef320e2a3b08c + md5: 2f46ff7c7647616cced839067b9e1b39 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isocorrectorgui", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-isocorrector >=1.18.0,<1.19.0' + - 'bioconductor-isocorrector >=1.20.0,<1.21.0' - r-base - r-readxl - r-tcltk2 run: - - 'bioconductor-isocorrector >=1.18.0,<1.19.0' + - 'bioconductor-isocorrector >=1.20.0,<1.21.0' - r-base - r-readxl - r-tcltk2 diff --git a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml index 73d0d270ba44e..83124db0611eb 100644 --- a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml +++ b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.1" %} +{% set version = "2.2.0" %} {% set name = "IsoformSwitchAnalyzeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 764485e548e3d6cea542d472e5da6b32 + md5: 6aad6b0133da9e103b4385ff31b7028c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isoformswitchanalyzer", max_pin="x.x") }}' # Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pfamanalyzer >=1.0.0,<1.1.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-saturn >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-tximeta >=1.18.0,<1.19.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pfamanalyzer >=1.2.0,<1.3.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-saturn >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-tximeta >=1.20.0,<1.21.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - r-dplyr @@ -59,26 +60,26 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pfamanalyzer >=1.0.0,<1.1.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-saturn >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-tximeta >=1.18.0,<1.19.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pfamanalyzer >=1.2.0,<1.3.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-saturn >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-tximeta >=1.20.0,<1.21.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dbi - r-dplyr diff --git a/recipes/bioconductor-isolde/meta.yaml b/recipes/bioconductor-isolde/meta.yaml index 64ca75be07f2e..4999dfce68598 100644 --- a/recipes/bioconductor-isolde/meta.yaml +++ b/recipes/bioconductor-isolde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ISoLDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,13 +11,14 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc7e409a60d1773ea7b12e413f20ef82 + md5: 448414b250ff7c903395638de3688411 build: - skip: true # [osx] - number: 0 + skip: True # [osx] + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isolde", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-isomirs/meta.yaml b/recipes/bioconductor-isomirs/meta.yaml index 1dea0e508a153..f101815c26500 100644 --- a/recipes/bioconductor-isomirs/meta.yaml +++ b/recipes/bioconductor-isomirs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "isomiRs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b48363905238cb50facd569971942f72 + md5: 95b301f966153c00b98359bb6a0986cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-isomirs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-degreport >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-degreport >=1.38.0,<1.39.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertive.sets - r-base - r-broom @@ -50,16 +51,16 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-degreport >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-degreport >=1.38.0,<1.39.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertive.sets - r-base - r-broom diff --git a/recipes/bioconductor-italics/meta.yaml b/recipes/bioconductor-italics/meta.yaml index c549517d8af3a..a6482e448f84b 100644 --- a/recipes/bioconductor-italics/meta.yaml +++ b/recipes/bioconductor-italics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.60.0" %} +{% set version = "2.62.0" %} {% set name = "ITALICS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 144200839aef6c79c6f6d7ea1a90d0d0 + md5: 05a5c23fcec3a45b6ff9b36b66b89752 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-italics", max_pin="x.x") }}' noarch: generic # Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-italicsdata >=2.38.0,<2.39.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-italicsdata >=2.40.0,<2.41.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - 'bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0' - r-base - r-dbi run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-italicsdata >=2.38.0,<2.39.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-italicsdata >=2.40.0,<2.41.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - 'bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0' - r-base - r-dbi diff --git a/recipes/bioconductor-italicsdata/meta.yaml b/recipes/bioconductor-italicsdata/meta.yaml index 4c530d3cbb61a..9a246291d9dd4 100644 --- a/recipes/bioconductor-italicsdata/meta.yaml +++ b/recipes/bioconductor-italicsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "ITALICSData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 390829582a6ace43fc47218d8f11e3c0 + md5: e154526c43e11840acfd4c92ff1cee8f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-italicsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-italicsdata/post-link.sh b/recipes/bioconductor-italicsdata/post-link.sh index 3492e076baef6..606e7a5f75eef 100644 --- a/recipes/bioconductor-italicsdata/post-link.sh +++ b/recipes/bioconductor-italicsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "italicsdata-2.38.0" +installBiocDataPackage.sh "italicsdata-2.40.0" diff --git a/recipes/bioconductor-iterativebma/meta.yaml b/recipes/bioconductor-iterativebma/meta.yaml index 34e78b6da95c9..60232f6f7d1a5 100644 --- a/recipes/bioconductor-iterativebma/meta.yaml +++ b/recipes/bioconductor-iterativebma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "iterativeBMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e4143bab9e90dfd557a054ce813f67b + md5: be5e8911f1a2493bdf001fbe0a7cecfa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iterativebma", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-bma - r-leaps run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-bma - r-leaps diff --git a/recipes/bioconductor-iterativebmasurv/meta.yaml b/recipes/bioconductor-iterativebmasurv/meta.yaml index 3692bf30ef168..3d92067ce1446 100644 --- a/recipes/bioconductor-iterativebmasurv/meta.yaml +++ b/recipes/bioconductor-iterativebmasurv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "iterativeBMAsurv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7cc92900486c78f40ed28fbc4f5058e + md5: d2ced120a3665f0ebb69a462a072ad63 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iterativebmasurv", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-iterclust/meta.yaml b/recipes/bioconductor-iterclust/meta.yaml index f4fdf6993584d..e6ec04af4f7eb 100644 --- a/recipes/bioconductor-iterclust/meta.yaml +++ b/recipes/bioconductor-iterclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "iterClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5cad04ff9c73325942d2e3409f70149 + md5: af72d13d4200d5883ae63a99f0a49a69 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iterclust", max_pin="x.x") }}' noarch: generic # Suggests: tsne, bcellViper requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster test: diff --git a/recipes/bioconductor-ivas/meta.yaml b/recipes/bioconductor-ivas/meta.yaml index 366afca6ebbe3..2759fdf777900 100644 --- a/recipes/bioconductor-ivas/meta.yaml +++ b/recipes/bioconductor-ivas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "IVAS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0cf4fb64fd7d23e080c55936659e5259 + md5: bf3c824233bc6ad5feffc4463554f57f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ivas", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach @@ -38,15 +39,15 @@ requirements: - r-lme4 - r-matrix run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-ivygapse/meta.yaml b/recipes/bioconductor-ivygapse/meta.yaml index bbdb49d43cfe0..cd26902f032a0 100644 --- a/recipes/bioconductor-ivygapse/meta.yaml +++ b/recipes/bioconductor-ivygapse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "ivygapSE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21c568e4f1ff5b0da5e6bac07de65eb4 + md5: d58fa85c46a9447719fa06aa57cc217d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ivygapse", max_pin="x.x") }}' noarch: generic # Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat, rmarkdown, BiocStyle, magick, statmod, codetools requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-hwriter @@ -32,8 +33,8 @@ requirements: - r-survminer - r-upsetr run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-hwriter diff --git a/recipes/bioconductor-iwtomics/meta.yaml b/recipes/bioconductor-iwtomics/meta.yaml index 7a8494052df91..4149664fdced6 100644 --- a/recipes/bioconductor-iwtomics/meta.yaml +++ b/recipes/bioconductor-iwtomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "IWTomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6226d4962dd65dd0089c609e940bedf7 + md5: f571644700ff672c2ac90aa49b611158 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iwtomics", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda - r-gtable - r-kernsmooth run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda - r-gtable diff --git a/recipes/bioconductor-iyer517/meta.yaml b/recipes/bioconductor-iyer517/meta.yaml index 1c593ed51557a..0f3cf9d1d1a9d 100644 --- a/recipes/bioconductor-iyer517/meta.yaml +++ b/recipes/bioconductor-iyer517/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "Iyer517" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 962d1b3895541924544fd080008a5bc9 + md5: 81226f1ad5acd16cff4c7371f37d1881 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iyer517", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-iyer517/post-link.sh b/recipes/bioconductor-iyer517/post-link.sh index 9103dc3771e2b..6eb9d2b69a88b 100644 --- a/recipes/bioconductor-iyer517/post-link.sh +++ b/recipes/bioconductor-iyer517/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "iyer517-1.42.0" +installBiocDataPackage.sh "iyer517-1.44.0" diff --git a/recipes/bioconductor-jaspar2014/meta.yaml b/recipes/bioconductor-jaspar2014/meta.yaml index 4fba103ceb0d6..a7de5670f7d7f 100644 --- a/recipes/bioconductor-jaspar2014/meta.yaml +++ b/recipes/bioconductor-jaspar2014/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "JASPAR2014" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63249cf2e663d3823da3359b8e584ede + md5: 6ef536411db46944f6d5b9a23ee13be6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2014", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2014/post-link.sh b/recipes/bioconductor-jaspar2014/post-link.sh index fa7b37c9d1561..0e2548b04d68b 100644 --- a/recipes/bioconductor-jaspar2014/post-link.sh +++ b/recipes/bioconductor-jaspar2014/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "jaspar2014-1.36.0" +installBiocDataPackage.sh "jaspar2014-1.38.0" diff --git a/recipes/bioconductor-jaspar2016/meta.yaml b/recipes/bioconductor-jaspar2016/meta.yaml index a4fb2145e9b1a..9085e136ba423 100644 --- a/recipes/bioconductor-jaspar2016/meta.yaml +++ b/recipes/bioconductor-jaspar2016/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "JASPAR2016" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9022c6f9720312b9da10800535edec62 + md5: 2976e4678291944f664396385049180b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2016", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2016/post-link.sh b/recipes/bioconductor-jaspar2016/post-link.sh index 628e268562d10..692043bcfa04f 100644 --- a/recipes/bioconductor-jaspar2016/post-link.sh +++ b/recipes/bioconductor-jaspar2016/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "jaspar2016-1.28.0" +installBiocDataPackage.sh "jaspar2016-1.30.0" diff --git a/recipes/bioconductor-jaspar2018/meta.yaml b/recipes/bioconductor-jaspar2018/meta.yaml index 4e513a835be7d..d6ddb786027d8 100644 --- a/recipes/bioconductor-jaspar2018/meta.yaml +++ b/recipes/bioconductor-jaspar2018/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.1" %} {% set name = "JASPAR2018" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d91fce6ea0dc9fa6a3be6ebc05c1af5d build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2018", max_pin="x.x") }}' noarch: generic # Suggests: TFBSTools (>= 1.15.6) requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2020/meta.yaml b/recipes/bioconductor-jaspar2020/meta.yaml index a7be771640b73..4fb9b4b049b1e 100644 --- a/recipes/bioconductor-jaspar2020/meta.yaml +++ b/recipes/bioconductor-jaspar2020/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.10" %} {% set name = "JASPAR2020" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bfcaf41ebf0935b8d146afd37719de2d build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2020", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, TFBSTools (>= 1.23.1) requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2022/build_failure.linux-64.yaml b/recipes/bioconductor-jaspar2022/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..12aa18bc75ecd --- /dev/null +++ b/recipes/bioconductor-jaspar2022/build_failure.linux-64.yaml @@ -0,0 +1,43 @@ +recipe_sha: 686f49bcd245205318d59d6a520044055090f8bfdb5ed23f0ddd8ceb5b88b41e # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + ValueError: unsupported format character 'T' (0x54) at index 5523 +category: |- + compiler error +log: |- + 09:04:38 BIOCONDA INFO (OUT) ERROR: loading failed + 09:04:38 BIOCONDA INFO (OUT) * removing ‘/opt/conda/conda-bld/bioconductor-jaspar2022_1702026057787/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/R/library/JASPAR2022’ + 09:04:38 BIOCONDA INFO (OUT) + 09:04:38 BIOCONDA INFO (OUT) return code: 1 + 09:04:38 BIOCONDA INFO (OUT) + 09:04:38 BIOCONDA INFO (OUT) kwargs: + 09:04:38 BIOCONDA INFO (OUT) {} + 09:04:38 BIOCONDA INFO (OUT) + 09:04:38 BIOCONDA INFO (OUT) : + 09:04:38 BIOCONDA INFO (OUT) + 09:04:38 BIOCONDA INFO (OUT) During handling of the above exception, another exception occurred: + 09:04:38 BIOCONDA INFO (OUT) + 09:04:38 BIOCONDA INFO (OUT) Traceback (most recent call last): + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in + 09:04:38 BIOCONDA INFO (OUT) sys.exit(main()) + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 09:04:38 BIOCONDA INFO (OUT) call_conda_build(action, config) + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 09:04:38 BIOCONDA INFO (OUT) result = api.build( + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 09:04:38 BIOCONDA INFO (OUT) return build_tree( + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree + 09:04:38 BIOCONDA INFO (OUT) test(pkg, config=metadata.config.copy(), stats=stats) + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test + 09:04:38 BIOCONDA INFO (OUT) environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1068, in create_env + 09:04:38 BIOCONDA INFO (OUT) "too short in" in str(exc) + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda/__init__.py", line 104, in __str__ + 09:04:38 BIOCONDA INFO (OUT) return "\n".join(str(e) for e in self.errors) + "\n" + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda/__init__.py", line 104, in + 09:04:38 BIOCONDA INFO (OUT) return "\n".join(str(e) for e in self.errors) + "\n" + 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda/__init__.py", line 58, in __str__ + 09:04:38 BIOCONDA INFO (OUT) return str(self.message % self._kwargs) + 09:04:38 BIOCONDA INFO (OUT) ValueError: unsupported format character 'T' (0x54) at index 5523 + 09:04:47 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmptio6n346/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-jaspar2022:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:2.11.0 /bin/bash /opt/build_script.bash + diff --git a/recipes/bioconductor-jaspar2022/meta.yaml b/recipes/bioconductor-jaspar2022/meta.yaml index a3cb58956eea5..f9be32b043fea 100644 --- a/recipes/bioconductor-jaspar2022/meta.yaml +++ b/recipes/bioconductor-jaspar2022/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.7" %} {% set name = "JASPAR2022" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 282af23228198a377fa9bd76c94dd5eb build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2022", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, TFBSTools (>= 1.31.2) requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-jaspar2024/meta.yaml b/recipes/bioconductor-jaspar2024/meta.yaml new file mode 100644 index 0000000000000..76fe59cb071b2 --- /dev/null +++ b/recipes/bioconductor-jaspar2024/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "0.99.6" %} +{% set name = "JASPAR2024" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9c8144547873a36473a5f9cad793f578 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jaspar2024", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, RSQLite +requirements: + host: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + run: + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: GPL-2 + summary: 'Data package for JASPAR database (version 2024)' + description: 'JASPAR (https://testjaspar.uio.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20 percent increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF-binding sites in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + diff --git a/recipes/bioconductor-jaspar2024/post-link.sh b/recipes/bioconductor-jaspar2024/post-link.sh new file mode 100644 index 0000000000000..699e53fdaf711 --- /dev/null +++ b/recipes/bioconductor-jaspar2024/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "jaspar2024-0.99.6" diff --git a/recipes/bioconductor-jaspar2024/pre-unlink.sh b/recipes/bioconductor-jaspar2024/pre-unlink.sh new file mode 100644 index 0000000000000..fb38fe4c01a48 --- /dev/null +++ b/recipes/bioconductor-jaspar2024/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ JASPAR2024 diff --git a/recipes/bioconductor-jazaerimetadata.db/meta.yaml b/recipes/bioconductor-jazaerimetadata.db/meta.yaml index ba4e64d4fc9d4..102a58956d8c4 100644 --- a/recipes/bioconductor-jazaerimetadata.db/meta.yaml +++ b/recipes/bioconductor-jazaerimetadata.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "JazaeriMetaData.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3a154a74ac2acebe3471b039c9d9a4dc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-jazaerimetadata.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-karyoploter/meta.yaml b/recipes/bioconductor-karyoploter/meta.yaml index 87701bc6b9367..f19c5440e562c 100644 --- a/recipes/bioconductor-karyoploter/meta.yaml +++ b/recipes/bioconductor-karyoploter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "karyoploteR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a91ddbf95305d1b2d7537e0648b69597 + md5: b9fcbfd3b5d7f3349cce595751b31a41 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-karyoploter", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-bezier - r-digest - r-memoise run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-bezier - r-digest diff --git a/recipes/bioconductor-katdetectr/meta.yaml b/recipes/bioconductor-katdetectr/meta.yaml index cebbe6099fde9..3ee2e89e53520 100644 --- a/recipes/bioconductor-katdetectr/meta.yaml +++ b/recipes/bioconductor-katdetectr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "katdetectr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aef9b68945ff582541a046cc4ca01557 + md5: 7ae9895a26f752a9e8502913ef8ce410 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-katdetectr", max_pin="x.x") }}' noarch: generic # Suggests: scales (>= 1.2.0), knitr (>= 1.37), rmarkdown (>= 2.13), testthat (>= 3.0.0), BiocStyle (>= 2.26.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-maftools >=2.16.0,<2.17.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-changepoint >=2.2.3' - 'r-changepoint.np >=1.0.3' @@ -45,18 +46,18 @@ requirements: - 'r-tibble >=3.1.6' - 'r-tidyr >=1.2.0' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-maftools >=2.16.0,<2.17.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-changepoint >=2.2.3' - 'r-changepoint.np >=1.0.3' diff --git a/recipes/bioconductor-kboost/meta.yaml b/recipes/bioconductor-kboost/meta.yaml index 01b41adc99a96..8c45d97eb7d3f 100644 --- a/recipes/bioconductor-kboost/meta.yaml +++ b/recipes/bioconductor-kboost/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "KBoost" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1931b8d58cb833db15f7a321acbf5608 + md5: 853c93af3367a8af56b60aea8495f44b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kboost", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-kcsmart/meta.yaml b/recipes/bioconductor-kcsmart/meta.yaml index 94f10d9fc9b55..e23a15eee3b25 100644 --- a/recipes/bioconductor-kcsmart/meta.yaml +++ b/recipes/bioconductor-kcsmart/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.58.0" %} +{% set version = "2.60.0" %} {% set name = "KCsmart" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fa9942f40a2363507b71aefaea90658 + md5: e50f547d912df8deb29537d5e27fc5d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kcsmart", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - r-kernsmooth run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - r-kernsmooth test: diff --git a/recipes/bioconductor-kebabs/meta.yaml b/recipes/bioconductor-kebabs/meta.yaml index ee341cf72deee..d3fae5cd61e11 100644 --- a/recipes/bioconductor-kebabs/meta.yaml +++ b/recipes/bioconductor-kebabs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "kebabs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f175288f436debe8eb7617836263df01 + md5: d6c4a16d9fd157b1e68acc8d4816017e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kebabs", max_pin="x.x") }}' # Suggests: SparseM, Biobase, BiocGenerics, knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-apcluster - r-base - r-e1071 @@ -34,10 +35,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-apcluster - r-base - r-e1071 diff --git a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml index 863b25df9b046..184fb7d2a89ea 100644 --- a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml +++ b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "KEGGandMetacoreDzPathwaysGEO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a4483556f83ea2f860efe15052eebe9 + md5: 3a5180de47f1c28949b77db9f79b44ed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-keggandmetacoredzpathwaysgeo", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh index b922daf4b0474..30e63a47b1f7d 100644 --- a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh +++ b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "keggandmetacoredzpathwaysgeo-1.20.0" +installBiocDataPackage.sh "keggandmetacoredzpathwaysgeo-1.22.0" diff --git a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml index 17e283c691bfa..1cbbda4787238 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml +++ b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "KEGGdzPathwaysGEO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfdb271eede41d51e01844f8c7b06b70 + md5: 2f30f9ac05c04214d25a9d49fb4ce8bd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-keggdzpathwaysgeo", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh index ea3d52b80514f..872a58fcfdea7 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh +++ b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "keggdzpathwaysgeo-1.38.0" +installBiocDataPackage.sh "keggdzpathwaysgeo-1.40.0" diff --git a/recipes/bioconductor-kegggraph/meta.yaml b/recipes/bioconductor-kegggraph/meta.yaml index de4bc9cdf6fd2..d5e9a057135c4 100644 --- a/recipes/bioconductor-kegggraph/meta.yaml +++ b/recipes/bioconductor-kegggraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "KEGGgraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5aaf23d2bbd58de35e6d03aa1d61de6b + md5: 9a4fb63b5bab3eeb0af51af22fa2dc16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kegggraph", max_pin="x.x") }}' noarch: generic # Suggests: RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-rcurl - 'r-xml >=2.3-0' run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-rcurl - 'r-xml >=2.3-0' diff --git a/recipes/bioconductor-kegglincs/meta.yaml b/recipes/bioconductor-kegglincs/meta.yaml index 3afae5ed786f9..f94dbdc65d52e 100644 --- a/recipes/bioconductor-kegglincs/meta.yaml +++ b/recipes/bioconductor-kegglincs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "KEGGlincs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f4e8a9944dc0cf5c69cf22425054b71 + md5: 9ef4b8d4652560f3e9fddb3209adb0dd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kegglincs", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager (>= 1.20.3), knitr, graph # SystemRequirements: Cytoscape (>= 3.3.0), Java (>= 8) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-kodata >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-kodata >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-gtools - r-httr @@ -37,12 +38,12 @@ requirements: - r-xml - 'cytoscape >=3.3.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-kodata >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-kodata >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-gtools - r-httr diff --git a/recipes/bioconductor-keggorthology/meta.yaml b/recipes/bioconductor-keggorthology/meta.yaml index dc3a795c2a023..9d57eb0840070 100644 --- a/recipes/bioconductor-keggorthology/meta.yaml +++ b/recipes/bioconductor-keggorthology/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.52.0" %} +{% set version = "2.54.0" %} {% set name = "keggorthology" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bc7b0a7f975976918bc42630a5063139 + md5: 56d510a339dd4fb984bad81624d83142 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-keggorthology", max_pin="x.x") }}' noarch: generic # Suggests: RBGL,ALL requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - 'bioconductor-hgu95av2.db >=3.13.0,<3.14.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - 'bioconductor-hgu95av2.db >=3.13.0,<3.14.0' - r-base - r-dbi diff --git a/recipes/bioconductor-keggrest/meta.yaml b/recipes/bioconductor-keggrest/meta.yaml index 440747d88b20b..3da5fe6a36e58 100644 --- a/recipes/bioconductor-keggrest/meta.yaml +++ b/recipes/bioconductor-keggrest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "KEGGREST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 884dbd36ae576a2c3c62ceec855cf077 + md5: 805cb8808b0ffa6f57999b880337b504 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-keggrest", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, markdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-httr - r-png run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-httr - r-png diff --git a/recipes/bioconductor-kidpack/meta.yaml b/recipes/bioconductor-kidpack/meta.yaml index 613abaca81982..c56508e1335ec 100644 --- a/recipes/bioconductor-kidpack/meta.yaml +++ b/recipes/bioconductor-kidpack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "kidpack" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4b8ee4f61037cd1b55cee61efe7101e9 + md5: 26f5ad5fba1c63156e282d8eac7ac385 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kidpack", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-kidpack/post-link.sh b/recipes/bioconductor-kidpack/post-link.sh index 55b9d6d1a1d2d..ac98a263cffef 100644 --- a/recipes/bioconductor-kidpack/post-link.sh +++ b/recipes/bioconductor-kidpack/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "kidpack-1.42.0" +installBiocDataPackage.sh "kidpack-1.44.0" diff --git a/recipes/bioconductor-kinswingr/meta.yaml b/recipes/bioconductor-kinswingr/meta.yaml index ad5f4f07ab129..8f1012a7708bc 100644 --- a/recipes/bioconductor-kinswingr/meta.yaml +++ b/recipes/bioconductor-kinswingr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "KinSwingR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7872f2ffd62b269f62e8a9dd5b64adba + md5: fae1cbd6c179b4fdd5ac12a32ce50eb7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kinswingr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-data.table - r-sqldf run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-data.table - r-sqldf diff --git a/recipes/bioconductor-knowseq/meta.yaml b/recipes/bioconductor-knowseq/meta.yaml index df2607b654937..b000d31472de7 100644 --- a/recipes/bioconductor-knowseq/meta.yaml +++ b/recipes/bioconductor-knowseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "KnowSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73da4e117a703251b6ea5e3a5e74ff41 + md5: b57c9661e3de8e27e79e3809a609acda build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-knowseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-caret - r-e1071 @@ -43,10 +44,10 @@ requirements: - r-stringr - r-xml run: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-caret - r-e1071 diff --git a/recipes/bioconductor-kodata/meta.yaml b/recipes/bioconductor-kodata/meta.yaml index f398239257119..c6d97424dd478 100644 --- a/recipes/bioconductor-kodata/meta.yaml +++ b/recipes/bioconductor-kodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "KOdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11d0727f1c7e40be104b3d24168f2ae7 + md5: 40e099053eae889ad66256a94427ac54 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kodata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-kodata/post-link.sh b/recipes/bioconductor-kodata/post-link.sh index 1040e3628131f..d0c7715575049 100644 --- a/recipes/bioconductor-kodata/post-link.sh +++ b/recipes/bioconductor-kodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "kodata-1.26.0" +installBiocDataPackage.sh "kodata-1.28.0" diff --git a/recipes/bioconductor-lace/meta.yaml b/recipes/bioconductor-lace/meta.yaml index 6ba5c9df85469..40a6921d22e8c 100644 --- a/recipes/bioconductor-lace/meta.yaml +++ b/recipes/bioconductor-lace/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "LACE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b13337a86c2b8b322531939e79e94166 + md5: d11f64211d10d293c2931b49765b5d61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lace", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bsplus - r-callr @@ -60,8 +61,8 @@ requirements: - r-svglite - r-tidyr run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bsplus - r-callr diff --git a/recipes/bioconductor-lapmix/meta.yaml b/recipes/bioconductor-lapmix/meta.yaml index 4b5789801fb82..76e3e6dc36bb5 100644 --- a/recipes/bioconductor-lapmix/meta.yaml +++ b/recipes/bioconductor-lapmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "lapmix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 088e76c4d42b5f1c432cffebd1bb0188 + md5: 5d2611d1b39b06b05ed64ffab459a5a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lapmix", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-lapointe.db/meta.yaml b/recipes/bioconductor-lapointe.db/meta.yaml index e1e73ef07267e..2e19eca313c84 100644 --- a/recipes/bioconductor-lapointe.db/meta.yaml +++ b/recipes/bioconductor-lapointe.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "LAPOINTE.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 434b25ad7411201d8be6bb1a0463b387 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lapointe.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lbe/meta.yaml b/recipes/bioconductor-lbe/meta.yaml index d1dd76272ef40..5c71cafda8ca6 100644 --- a/recipes/bioconductor-lbe/meta.yaml +++ b/recipes/bioconductor-lbe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "LBE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0f317f8253df3b83ef48202063e0417f + md5: 36559f365f1dbd53056e6b43bc1e06e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lbe", max_pin="x.x") }}' noarch: generic # Suggests: qvalue requirements: diff --git a/recipes/bioconductor-ldblock/meta.yaml b/recipes/bioconductor-ldblock/meta.yaml index eea6863caf204..9863043358259 100644 --- a/recipes/bioconductor-ldblock/meta.yaml +++ b/recipes/bioconductor-ldblock/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "ldblock" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a63dbccca085d4b33bcf2b19215c22f + md5: 579c380a003913fde7767f15b47a6692 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ldblock", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats, VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75, Rsamtools, GenomicFiles (>= 1.13.6) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httr - r-matrix - r-rlang run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httr - r-matrix diff --git a/recipes/bioconductor-lea/meta.yaml b/recipes/bioconductor-lea/meta.yaml index aa0936c3594b2..51dd613a14f2e 100644 --- a/recipes/bioconductor-lea/meta.yaml +++ b/recipes/bioconductor-lea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.12.2" %} +{% set version = "3.14.0" %} {% set name = "LEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66645aa4efbb19674772b485df256216 + md5: e32cbc2a97921f9b911eef1a5d1ef3d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lea", max_pin="x.x") }}' # Suggests: knitr requirements: host: diff --git a/recipes/bioconductor-ledpred/meta.yaml b/recipes/bioconductor-ledpred/meta.yaml index ef41921f97eb4..add26d8b55ec8 100644 --- a/recipes/bioconductor-ledpred/meta.yaml +++ b/recipes/bioconductor-ledpred/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "LedPred" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a868e369e350943980eaa621d63503c + md5: 4a083c0408938618b62557ece5682e61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ledpred", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-leebamviews/meta.yaml b/recipes/bioconductor-leebamviews/meta.yaml index 09d78a9570174..23ddd91fec827 100644 --- a/recipes/bioconductor-leebamviews/meta.yaml +++ b/recipes/bioconductor-leebamviews/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "leeBamViews" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8364b9ac80fcc1cbdd4eca1501d6651b + md5: 58f7c7fdbb1f949f48924ac79d31b580 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-leebamviews", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, org.Sc.sgd.db, edgeR requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-leebamviews/post-link.sh b/recipes/bioconductor-leebamviews/post-link.sh index 0440089dce09f..f1275b766d7ad 100644 --- a/recipes/bioconductor-leebamviews/post-link.sh +++ b/recipes/bioconductor-leebamviews/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "leebamviews-1.36.0" +installBiocDataPackage.sh "leebamviews-1.38.0" diff --git a/recipes/bioconductor-lefser/meta.yaml b/recipes/bioconductor-lefser/meta.yaml index 875f2cf293425..e6ee9347ff280 100644 --- a/recipes/bioconductor-lefser/meta.yaml +++ b/recipes/bioconductor-lefser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.1" %} {% set name = "lefser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 02d16723642d25f2432b098f6fa4f04c + md5: c3b2deaf4b58de1bb930164df11a388f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lefser", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, testthat, pkgdown, covr, withr +# Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, testthat, pkgdown, covr, withr requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-coin - r-ggplot2 - r-mass run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-coin - r-ggplot2 diff --git a/recipes/bioconductor-lemur/build.sh b/recipes/bioconductor-lemur/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-lemur/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lemur/build_failure.osx-64.yaml b/recipes/bioconductor-lemur/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..9beef668bed41 --- /dev/null +++ b/recipes/bioconductor-lemur/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 9ec1f5c47eca7b1c8d8b7db53ce0866846a9c61f157f39bec7526f0c5cbe3856 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-base 4.3.* + - bioconductor-matrixgenerics >=1.14.0,<1.15.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed + - + + Leaving build/test directories: + Work: + /opt/mambaforge/envs/bioconda/conda-bld/work + Test: + /opt/mambaforge/envs/bioconda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + Build: + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + source activate /opt/mambaforge/envs/bioconda/conda-bld/_build_env + + + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-hdf5array >=1.30.0,<1.31.0 + - r-rcpparmadillo + - r-rcpp + - r-harmony + - r-matrixstats + - r-vctrs + - liblapack 3.9.* *netlib + - bioconductor-delayedmatrixstats >=1.24.0,<1.25.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - libblas 3.9.* *netlib + - bioconductor-biocneighbors >=1.20.0,<1.21.0 + - libcxx >=14 + - bioconductor-biocgenerics >=0.48.0,<0.49.0 + - r-irlba + - r-matrix + - r-rlang + - bioconductor-limma >=3.58.0,<3.59.0 + - bioconductor-glmgampoi >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-base 4.3.* + - bioconductor-matrixgenerics >=1.14.0,<1.15.0 + - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-base[version='>=4.3,<4.4.0a0']"), MatchSpec("bioconductor-summarizedexperiment==1.32.0=r43hdfd78af_0")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-lemur/meta.yaml b/recipes/bioconductor-lemur/meta.yaml new file mode 100644 index 0000000000000..71c676e618440 --- /dev/null +++ b/recipes/bioconductor-lemur/meta.yaml @@ -0,0 +1,78 @@ +{% set version = "1.0.4" %} +{% set name = "lemur" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 76ef0d01a8f6f23e0f125274af96522d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lemur", max_pin="x.x") }}' +# Suggests: testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-harmony + - r-irlba + - r-matrix + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + - r-rlang + - r-vctrs + - libblas + - liblapack + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-harmony + - r-irlba + - r-matrix + - r-matrixstats + - r-rcpp + - r-rcpparmadillo + - r-rlang + - r-vctrs + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Latent Embedding Multivariate Regression' + description: 'Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.' + license_file: LICENSE + diff --git a/recipes/bioconductor-les/meta.yaml b/recipes/bioconductor-les/meta.yaml index 6a17dc15d9a18..2c610c014b1e5 100644 --- a/recipes/bioconductor-les/meta.yaml +++ b/recipes/bioconductor-les/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "les" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5484dca35e8f46307aa2d8729a1ba1fa + md5: b0418480f87e364b451a3f940bcdcb8c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-les", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, limma requirements: diff --git a/recipes/bioconductor-leukemiaseset/meta.yaml b/recipes/bioconductor-leukemiaseset/meta.yaml index 5e567639f1d1d..d3bfaf2adc95a 100644 --- a/recipes/bioconductor-leukemiaseset/meta.yaml +++ b/recipes/bioconductor-leukemiaseset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "leukemiasEset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f2498f78d93dc35ed04c9e2e8abfad7 + md5: f9e8274856b0d78de6da7ec0bce171f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-leukemiaseset", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-leukemiaseset/post-link.sh b/recipes/bioconductor-leukemiaseset/post-link.sh index d2bae20eed808..f03618f99ae1e 100644 --- a/recipes/bioconductor-leukemiaseset/post-link.sh +++ b/recipes/bioconductor-leukemiaseset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "leukemiaseset-1.36.0" +installBiocDataPackage.sh "leukemiaseset-1.38.0" diff --git a/recipes/bioconductor-levi/meta.yaml b/recipes/bioconductor-levi/meta.yaml index a1f8a6f2379e3..863283e9eb2fd 100644 --- a/recipes/bioconductor-levi/meta.yaml +++ b/recipes/bioconductor-levi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "levi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dd7ccfc06d8acb7def3c3f53cfc7680b + md5: fff39f74d44cb186d14ebb591b3fa3a1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-levi", max_pin="x.x") }}' # Suggests: rmarkdown, BiocStyle requirements: host: diff --git a/recipes/bioconductor-lfa/meta.yaml b/recipes/bioconductor-lfa/meta.yaml index e3d2e660065c6..ef404bf4b9e2b 100644 --- a/recipes/bioconductor-lfa/meta.yaml +++ b/recipes/bioconductor-lfa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.11" %} +{% set version = "2.2.0" %} {% set name = "lfa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 58264321db9388649768e3fc74e9a4ab + md5: 83d3c5671422b432d992834ae675e020 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lfa", max_pin="x.x") }}' # Suggests: knitr, ggplot2, testthat, BEDMatrix, genio requirements: host: diff --git a/recipes/bioconductor-liebermanaidenhic2009/meta.yaml b/recipes/bioconductor-liebermanaidenhic2009/meta.yaml index 53f1731a0f859..d71d5f911cfaf 100644 --- a/recipes/bioconductor-liebermanaidenhic2009/meta.yaml +++ b/recipes/bioconductor-liebermanaidenhic2009/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "LiebermanAidenHiC2009" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43f7f158c73c12d62e6cf471cd690667 + md5: 34818101f902d251b339864716cd2d1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-liebermanaidenhic2009", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-liebermanaidenhic2009/post-link.sh b/recipes/bioconductor-liebermanaidenhic2009/post-link.sh index 44699d13bf699..e899cf7938d0f 100644 --- a/recipes/bioconductor-liebermanaidenhic2009/post-link.sh +++ b/recipes/bioconductor-liebermanaidenhic2009/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "liebermanaidenhic2009-0.38.0" +installBiocDataPackage.sh "liebermanaidenhic2009-0.40.0" diff --git a/recipes/bioconductor-limma/meta.yaml b/recipes/bioconductor-limma/meta.yaml index 6ac8b334140e0..0441416406623 100644 --- a/recipes/bioconductor-limma/meta.yaml +++ b/recipes/bioconductor-limma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.56.2" %} +{% set version = "3.58.1" %} {% set name = "limma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4b1df28cbb7c38b621db2ee3c42e6cc8 + md5: f52a816d0d34b01f721654f90a1fb5f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn + run_exports: '{{ pin_subpackage("bioconductor-limma", max_pin="x.x") }}' +# Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn requirements: host: - r-base + - r-statmod - libblas - liblapack run: - r-base + - r-statmod build: - {{ compiler('c') }} - make diff --git a/recipes/bioconductor-limmagui/meta.yaml b/recipes/bioconductor-limmagui/meta.yaml index 80cbd76d1e52e..f6bc9994f2951 100644 --- a/recipes/bioconductor-limmagui/meta.yaml +++ b/recipes/bioconductor-limmagui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "limmaGUI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfdbc7483e30730dd2fc9072e8f96bb7 + md5: b0c7c34dfac5955d26908f730a73b880 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-limmagui", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-r2html - r-tkrplot - r-xtable run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-r2html - r-tkrplot diff --git a/recipes/bioconductor-lineagepulse/meta.yaml b/recipes/bioconductor-lineagepulse/meta.yaml index ae7329e00d703..a99b5c3e27db3 100644 --- a/recipes/bioconductor-lineagepulse/meta.yaml +++ b/recipes/bioconductor-lineagepulse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.21.0" %} {% set name = "LineagePulse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b8c7c63f4301507c384fe65eee3990d + md5: c17825342234d6f0e327853b8fc52944 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lineagepulse", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-ggplot2 @@ -32,10 +33,10 @@ requirements: - r-matrix - r-rcolorbrewer run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-lineagespot/meta.yaml b/recipes/bioconductor-lineagespot/meta.yaml index 229810771245a..a0a3a46e80bc1 100644 --- a/recipes/bioconductor-lineagespot/meta.yaml +++ b/recipes/bioconductor-lineagespot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "lineagespot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b44c5d4601a486a1047c3c5bc1f0e274 + md5: 7a06bfea8fdf81ea88ebe7f4478607f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lineagespot", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-httr - r-stringr run: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-httr diff --git a/recipes/bioconductor-linkhd/meta.yaml b/recipes/bioconductor-linkhd/meta.yaml index ef08fe0904124..c4ba0e55eb6ef 100644 --- a/recipes/bioconductor-linkhd/meta.yaml +++ b/recipes/bioconductor-linkhd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "LinkHD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d22be0c6560788254aff6967d0b953c + md5: 64515bedacee602d8f8c92785e075039 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-linkhd", max_pin="x.x") }}' noarch: generic # Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - r-cluster - r-data.table @@ -34,7 +35,7 @@ requirements: - r-scales - r-vegan run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-linnorm/meta.yaml b/recipes/bioconductor-linnorm/meta.yaml index fb21be3973482..5c346153764e9 100644 --- a/recipes/bioconductor-linnorm/meta.yaml +++ b/recipes/bioconductor-linnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.1" %} +{% set version = "2.26.0" %} {% set name = "Linnorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aecbf8861def918c6f11fa1b10714a28 + md5: 8fc0ff0d6e9c2d274137b0e99ce0f4a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat + run_exports: '{{ pin_subpackage("bioconductor-linnorm", max_pin="x.x") }}' +# Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat, matrixStats requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-amap - r-apcluster - r-base @@ -42,7 +43,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-amap - r-apcluster - r-base diff --git a/recipes/bioconductor-lintind/meta.yaml b/recipes/bioconductor-lintind/meta.yaml index d401f17371fcc..954eb5cb07f07 100644 --- a/recipes/bioconductor-lintind/meta.yaml +++ b/recipes/bioconductor-lintind/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "LinTInd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 229a83bd7db103d7e92cbf8378c0dcb5 + md5: 3dd8f8601ee8df3a0a53a02dc0c4d272 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lintind", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-cowplot @@ -41,11 +42,11 @@ requirements: - r-stringdist - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-cowplot diff --git a/recipes/bioconductor-lionessr/meta.yaml b/recipes/bioconductor-lionessr/meta.yaml index 7c51b62f289ac..6af7c447fb9c4 100644 --- a/recipes/bioconductor-lionessr/meta.yaml +++ b/recipes/bioconductor-lionessr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "lionessR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3b3552c919620f8bf987753d882d5802 + md5: 4301a7fed98cbe717433fa80791ad9a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lionessr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, igraph, reshape2, limma, requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-lipidr/meta.yaml b/recipes/bioconductor-lipidr/meta.yaml index 757575e6e210e..046cb235bf30f 100644 --- a/recipes/bioconductor-lipidr/meta.yaml +++ b/recipes/bioconductor-lipidr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.1" %} +{% set version = "2.16.0" %} {% set name = "lipidr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f8d642d778bcb314c248231f46ddad43 + md5: 27b17acc2b4de0439304799e0a7cba2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lipidr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling, testthat requirements: host: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -36,11 +37,11 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-liquidassociation/meta.yaml b/recipes/bioconductor-liquidassociation/meta.yaml index 7a4f3a1785241..456d16ad1c383 100644 --- a/recipes/bioconductor-liquidassociation/meta.yaml +++ b/recipes/bioconductor-liquidassociation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "LiquidAssociation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea14603091d58ee44de956e48a0911bb + md5: b484ed119d8ef9ebb19bfd7497eb33af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-liquidassociation", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' - - 'bioconductor-yeastcc >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-yeastcc >=1.42.0,<1.43.0' - r-base - r-geepack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' - - 'bioconductor-yeastcc >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - 'bioconductor-yeastcc >=1.42.0,<1.43.0' - r-base - r-geepack test: diff --git a/recipes/bioconductor-lisaclust/meta.yaml b/recipes/bioconductor-lisaclust/meta.yaml index fe1b83d19530e..0658217e488ff 100644 --- a/recipes/bioconductor-lisaclust/meta.yaml +++ b/recipes/bioconductor-lisaclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.1" %} {% set name = "lisaClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91925b5c9bbe5d0f3afb6e81b1496003 + md5: fa6fe90f1866b21dce3d34bb8471c9e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lisaclust", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spicyr >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-spicyr >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-class - r-concaveman @@ -38,15 +39,16 @@ requirements: - r-purrr - r-spatstat.explore - r-spatstat.geom + - r-spatstat.random - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spicyr >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-spicyr >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-class - r-concaveman @@ -57,6 +59,7 @@ requirements: - r-purrr - r-spatstat.explore - r-spatstat.geom + - r-spatstat.random - r-tidyr test: commands: diff --git a/recipes/bioconductor-listeretalbsseq/meta.yaml b/recipes/bioconductor-listeretalbsseq/meta.yaml index 5a665140c3d5e..dee27377bbb58 100644 --- a/recipes/bioconductor-listeretalbsseq/meta.yaml +++ b/recipes/bioconductor-listeretalbsseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.1" %} +{% set version = "1.34.0" %} {% set name = "ListerEtAlBSseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b0138cce25976d0d9180442505679d2 + md5: 302e026ae021a5f26c149b5086569db1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-listeretalbsseq", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-methylpipe >=1.34.0,<1.35.0' + - 'bioconductor-methylpipe >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-methylpipe >=1.34.0,<1.35.0' + - 'bioconductor-methylpipe >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-listeretalbsseq/post-link.sh b/recipes/bioconductor-listeretalbsseq/post-link.sh index b6aae194fcd09..683046c9aced0 100644 --- a/recipes/bioconductor-listeretalbsseq/post-link.sh +++ b/recipes/bioconductor-listeretalbsseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "listeretalbsseq-1.32.1" +installBiocDataPackage.sh "listeretalbsseq-1.34.0" diff --git a/recipes/bioconductor-lmdme/meta.yaml b/recipes/bioconductor-lmdme/meta.yaml index 946b71daa6bf8..3a621770cd470 100644 --- a/recipes/bioconductor-lmdme/meta.yaml +++ b/recipes/bioconductor-lmdme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "lmdme" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 66a2da7ce067e15aab8fccdb7f124eed + md5: 9a1b98d738df482adb30496ac028b924 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lmdme", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-stemhypoxia >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-stemhypoxia >=1.38.0,<1.39.0' - r-base - r-pls run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-stemhypoxia >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-stemhypoxia >=1.38.0,<1.39.0' - r-base - r-pls test: diff --git a/recipes/bioconductor-lobstahs/meta.yaml b/recipes/bioconductor-lobstahs/meta.yaml index dada12f2bd5f3..eea31dbdaeae0 100644 --- a/recipes/bioconductor-lobstahs/meta.yaml +++ b/recipes/bioconductor-lobstahs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "LOBSTAHS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f66c6f04dd23801992184f8b1f6515ec + md5: 45092babf761359e504ae5ad71d21ab8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lobstahs", max_pin="x.x") }}' noarch: generic # Suggests: PtH2O2lipids, knitr, rmarkdown requirements: host: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base test: commands: diff --git a/recipes/bioconductor-loci2path/meta.yaml b/recipes/bioconductor-loci2path/meta.yaml index fc0b0ebc53368..a8e5177b97e07 100644 --- a/recipes/bioconductor-loci2path/meta.yaml +++ b/recipes/bioconductor-loci2path/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "loci2path" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b0dfe9a1ddd6aa3d993d369c452786ea + md5: 3527f58dccf385bbc6f71a4c659a37c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-loci2path", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-pheatmap - r-rcolorbrewer - r-wordcloud run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-pheatmap diff --git a/recipes/bioconductor-logicfs/meta.yaml b/recipes/bioconductor-logicfs/meta.yaml index d8e679ffb6237..6824cb2b44a4e 100644 --- a/recipes/bioconductor-logicfs/meta.yaml +++ b/recipes/bioconductor-logicfs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "logicFS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4840a9d851ffe6dbbb08fa539ddbb5b + md5: af46ee02e89efc5057af01be3f530a4f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-logicfs", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, siggenes requirements: diff --git a/recipes/bioconductor-lola/meta.yaml b/recipes/bioconductor-lola/meta.yaml index 88217cfeea8ac..58d33f706a825 100644 --- a/recipes/bioconductor-lola/meta.yaml +++ b/recipes/bioconductor-lola/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "LOLA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f85cca2393dba22ce00574478e065c11 + md5: e3ff8271b0433c6098fd7380af165742 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lola", max_pin="x.x") }}' noarch: generic # Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-reshape2 diff --git a/recipes/bioconductor-loomexperiment/meta.yaml b/recipes/bioconductor-loomexperiment/meta.yaml index 514eb89c78660..a46c9fe2eeebc 100644 --- a/recipes/bioconductor-loomexperiment/meta.yaml +++ b/recipes/bioconductor-loomexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "LoomExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48fb26e59c5d77ce931e53d1dd251334 + md5: f69aaf53b56cebfe748b8c0c029af481 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-loomexperiment", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, reticulate requirements: host: - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-stringr run: - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-stringr diff --git a/recipes/bioconductor-lowmacaannotation/meta.yaml b/recipes/bioconductor-lowmacaannotation/meta.yaml index e9be52191301f..5ad4a74a0e5db 100644 --- a/recipes/bioconductor-lowmacaannotation/meta.yaml +++ b/recipes/bioconductor-lowmacaannotation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "LowMACAAnnotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9e0d3fe7f30fe48aef9c4387eb5bacfa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lowmacaannotation", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lpe/meta.yaml b/recipes/bioconductor-lpe/meta.yaml index ff237d9fe0b82..d286d7876465c 100644 --- a/recipes/bioconductor-lpe/meta.yaml +++ b/recipes/bioconductor-lpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "LPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 583b56963ed12c046a559fe3db8e3a4c + md5: 9001fbe949f64e59e79de1f81bd4aa01 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lpe", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-lpeadj/meta.yaml b/recipes/bioconductor-lpeadj/meta.yaml index 5d8587e24b716..c56a4a44fc24f 100644 --- a/recipes/bioconductor-lpeadj/meta.yaml +++ b/recipes/bioconductor-lpeadj/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "LPEadj" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54870f0c718c22c66d51a3831463415b + md5: ebb9c5bc6d113688787fadb2739bc75a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lpeadj", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-lpe >=1.74.0,<1.75.0' + - 'bioconductor-lpe >=1.76.0,<1.77.0' - r-base run: - - 'bioconductor-lpe >=1.74.0,<1.75.0' + - 'bioconductor-lpe >=1.76.0,<1.77.0' - r-base test: commands: diff --git a/recipes/bioconductor-lpnet/meta.yaml b/recipes/bioconductor-lpnet/meta.yaml index ef802e2badfa7..b0d2a9dd75db3 100644 --- a/recipes/bioconductor-lpnet/meta.yaml +++ b/recipes/bioconductor-lpnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "lpNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bdabe53b6db49978cb400e44c75651f7 + md5: b2aa2f27ba2f75f595f718f9c9f6e737 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lpnet", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-lpsymphony/build.sh b/recipes/bioconductor-lpsymphony/build.sh index daad3abb543cb..b12d3b6a8730e 100644 --- a/recipes/bioconductor-lpsymphony/build.sh +++ b/recipes/bioconductor-lpsymphony/build.sh @@ -10,4 +10,4 @@ CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars sed -i.bak "s/-TP//" src/SYMPHONY/SYMPHONY/configure.ac sed -i.bak "s/-TP//" src/SYMPHONY/SYMPHONY/configure -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lpsymphony/build_failure.linux-64.yaml b/recipes/bioconductor-lpsymphony/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7895e96771c2c --- /dev/null +++ b/recipes/bioconductor-lpsymphony/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: fc3c0b78a302a196c67dd12bb2d7378a8e0cfce2422bd52ac55af76b95b1b9c6 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking if $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c supports -c -o file.o... yes + checking whether the $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c linker ($BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld) supports shared libraries... yes + cat: ld.so.conf.d/*.conf: No such file or directory + checking dynamic linker characteristics... GNU/Linux ld.so + checking how to hardcode library paths into programs... immediate + appending configuration tag "F77" to libtool + checking if libtool supports shared libraries... yes + checking whether to build shared libraries... no + checking whether to build static libraries... yes + checking for x86_64-conda-linux-gnu-gfortran option to produce PIC... -fPIC + checking if x86_64-conda-linux-gnu-gfortran PIC flag -fPIC works... yes + checking if x86_64-conda-linux-gnu-gfortran static flag -static works... no + checking if x86_64-conda-linux-gnu-gfortran supports -c -o file.o... yes + checking whether the x86_64-conda-linux-gnu-gfortran linker ($BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld) supports shared libraries... yes + cat: ld.so.conf.d/*.conf: No such file or directory + checking dynamic linker characteristics... GNU/Linux ld.so + checking how to hardcode library paths into programs... immediate + configure: Build is "x86_64-conda-linux-gnu". + checking if library version is set... no + checking whether source of project Blas is available and should be compiled... no, source file ./ThirdParty/Blas/daxpy.f not available + checking whether source of project Lapack is available and should be compiled... no, source file ./ThirdParty/Lapack/LAPACK/SRC/dlarf.f not available + checking whether source of project Glpk is available and should be compiled... no, source file ./ThirdParty/Glpk/glpk/src/glplpx01.c not available + checking whether source of project Sample is available and should be compiled... no + checking whether source of project miblib3 is available and should be compiled... no + checking whether source of project CoinUtils is available and should be compiled... yes, source in CoinUtils + checking whether source of project Osi is available and should be compiled... yes, source in Osi + checking whether source of project Clp is available and should be compiled... yes, source in Clp + checking whether source of project Cgl is available and should be compiled... yes, source in Cgl + checking whether source of project DyLP is available and should be compiled... no + checking whether source of project Vol is available and should be compiled... no + checking whether source of project SYMPHONY is available and should be compiled... yes, source in SYMPHONY + checking whether Clp is required... yes + checking which command should be used to link input files... ln -s + configure: creating ./config.status + config.status: creating Makefile + config.status: executing depfiles commands + configure: configuring in CoinUtils + configure: running /bin/sh './configure' --prefix=$SRC_DIR/src/SYMPHONY '--enable-static' '--disable-shared' '--with-pic' '--with-application=no' '--disable-dependency-tracking' '--disable-zlib' '--disable-bzlib' '--disable-cplex-libcheck' '--disable-glpk-libcheck' '--disable-osl-libcheck' '--disable-soplex-libcheck' '--disable-xpress-libcheck' 'CFLAGS=-w -g -O2' 'CXXFLAGS=-w -g -O2' 'CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include' 'CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp' 'CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib' 'build_alias=x86_64-conda-linux-gnu' 'host_alias=x86_64-conda-linux-gnu' --cache-file=/dev/null --srcdir=. + configure: loading site script $SRC_DIR/src/SYMPHONY/share/config.site + checking build system type... x86_64-conda-linux-gnu + checking for svnversion... no + checking whether we want to compile in debug mode... no + checking for x86_64-conda-linux-gnu-gcc... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + checking for C compiler default output file name... a.out + checking whether the C compiler works... yes + checking whether we are cross compiling... no + checking for suffix of executables... + checking for suffix of object files... o + checking whether we are using the GNU C compiler... yes + checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc accepts -g... yes + checking for $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc option to accept ANSI C... none needed + configure: C compiler options are: -w -g -O2 -DCOINUTILS_BUILD + checking for x86_64-conda-linux-gnu-g... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + checking whether we are using the GNU C compiler... yes + checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c accepts -g... yes + checking whether C compiler $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c works... yes + configure: C compiler options are: -w -g -O2 -DCOINUTILS_BUILD + configure: Trying to determine Fortran compiler name + checking for x86_64-conda-linux-gnu-gfortran... x86_64-conda-linux-gnu-gfortran + checking for x86_64-conda-linux-gnu-gfortran... (cached) x86_64-conda-linux-gnu-gfortran + checking whether we are using the GNU Fortran 77 compiler... yes + checking whether x86_64-conda-linux-gnu-gfortran accepts -g... yes + configure: Fortran compiler options are: -O3 -pipe + checking how to get verbose linking output from x86_64-conda-linux-gnu-gfortran... -v + checking for Fortran libraries of x86_64-conda-linux-gnu-gfortran... -L$PREFIX/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0 -L$PREFIX/bin/../lib/gcc -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../.. -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib -lgfortran -lm -lgcc_s -lquadmath + configure: Corrected Fortran libraries: -L$PREFIX/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0 -L$PREFIX/bin/../lib/gcc -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../.. -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib -lgfortran -lm -lquadmath + configure: error: linking to Fortran libraries from C fails + See config.log' for more details. + checking for dummy main to link with Fortran libraries... unknown + configure: error: /bin/sh './configure' failed for CoinUtils + ** libs + using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 12.3.0-3) 12.3.0 + make[1]: Entering directory '$SRC_DIR/src/SYMPHONY' + Making all in CoinUtils + make[2]: *** No rule to make target 'all'. Stop. + make[2]: Entering directory '$SRC_DIR/src/SYMPHONY/CoinUtils' + make[2]: Leaving directory '$SRC_DIR/src/SYMPHONY/CoinUtils' + make[1]: *** [Makefile:324: all-recursive] Error 1 + make[1]: Leaving directory '$SRC_DIR/src/SYMPHONY' + make: *** [Makevars:14: SYMPHONY.ts] Error 2 + ERROR: compilation failed for package lpsymphony + * removing /opt/conda/conda-bld/bioconductor-lpsymphony_1703079915102/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/R/library/lpsymphony + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-lpsymphony_1703079915102/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-lpsymphony/meta.yaml b/recipes/bioconductor-lpsymphony/meta.yaml index 59fe830c990dd..141bac727f2ab 100644 --- a/recipes/bioconductor-lpsymphony/meta.yaml +++ b/recipes/bioconductor-lpsymphony/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "lpsymphony" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a04276f8329ae09e82e3e16bc3a7b78e + md5: 106ec54272f27574ea1eea2d5721d7e4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lpsymphony", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-lrbasedbi/meta.yaml b/recipes/bioconductor-lrbasedbi/meta.yaml index 49e21f44674dc..ea0d85aceaab3 100644 --- a/recipes/bioconductor-lrbasedbi/meta.yaml +++ b/recipes/bioconductor-lrbasedbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "LRBaseDbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 557f533713533ea65e003805bed36368 + md5: 4ed780d2b26059691bd1a1e859ca5003 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lrbasedbi", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-dbi - r-rsqlite diff --git a/recipes/bioconductor-lrcell/meta.yaml b/recipes/bioconductor-lrcell/meta.yaml index 4478c83b35c15..e7c109ef9e482 100644 --- a/recipes/bioconductor-lrcell/meta.yaml +++ b/recipes/bioconductor-lrcell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "LRcell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38340be2b5eefde6251d6dc2fb14aff7 + md5: 845d68fab279d4a81933621a81085179 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lrcell", max_pin="x.x") }}' noarch: generic # Suggests: LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr - r-ggplot2 - r-ggrepel - r-magrittr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-lrcelltypemarkers/meta.yaml b/recipes/bioconductor-lrcelltypemarkers/meta.yaml index d4d5a86cb8c07..ab499894e1e20 100644 --- a/recipes/bioconductor-lrcelltypemarkers/meta.yaml +++ b/recipes/bioconductor-lrcelltypemarkers/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "LRcellTypeMarkers" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 342747afa842b8009a5e2a6183c1bd83 + md5: f5731667b56b631291d22a830d212f04 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lrcelltypemarkers", max_pin="x.x") }}' noarch: generic # Suggests: LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lrcelltypemarkers/post-link.sh b/recipes/bioconductor-lrcelltypemarkers/post-link.sh index a402099179b36..5ea30236a697f 100644 --- a/recipes/bioconductor-lrcelltypemarkers/post-link.sh +++ b/recipes/bioconductor-lrcelltypemarkers/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lrcelltypemarkers-1.8.0" +installBiocDataPackage.sh "lrcelltypemarkers-1.10.0" diff --git a/recipes/bioconductor-lumi/meta.yaml b/recipes/bioconductor-lumi/meta.yaml index 6ebb4746e410d..1511bffa3477a 100644 --- a/recipes/bioconductor-lumi/meta.yaml +++ b/recipes/bioconductor-lumi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.52.0" %} +{% set version = "2.54.0" %} {% set name = "lumi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e8abe917a62ecdf21d85b510773a0bed + md5: 59fdd5b0a2e145d7a8772635121bb2ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumi", max_pin="x.x") }}' noarch: generic # Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-kernsmooth @@ -38,14 +39,14 @@ requirements: - r-nleqslv - r-rsqlite run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dbi - r-kernsmooth diff --git a/recipes/bioconductor-lumibarnes/meta.yaml b/recipes/bioconductor-lumibarnes/meta.yaml index 7833a1d0b2a49..a83dcd4119b6d 100644 --- a/recipes/bioconductor-lumibarnes/meta.yaml +++ b/recipes/bioconductor-lumibarnes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "lumiBarnes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 971e2cf62606ab98813418f8032b20dc + md5: 2be75f5470fd60f9919045fc8147b613 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumibarnes", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumibarnes/post-link.sh b/recipes/bioconductor-lumibarnes/post-link.sh index 4ea7acd69238d..96d26854e3ad0 100644 --- a/recipes/bioconductor-lumibarnes/post-link.sh +++ b/recipes/bioconductor-lumibarnes/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lumibarnes-1.40.0" +installBiocDataPackage.sh "lumibarnes-1.42.0" diff --git a/recipes/bioconductor-lumihumanall.db/meta.yaml b/recipes/bioconductor-lumihumanall.db/meta.yaml index 22fcb67087468..e61a5dd476ab5 100644 --- a/recipes/bioconductor-lumihumanall.db/meta.yaml +++ b/recipes/bioconductor-lumihumanall.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.22.0" %} {% set name = "lumiHumanAll.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ce7e219b50833ceab203f0bbfb11d917 build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumihumanall.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumihumanidmapping/meta.yaml b/recipes/bioconductor-lumihumanidmapping/meta.yaml index ee31fe63c1247..6a28062e422f4 100644 --- a/recipes/bioconductor-lumihumanidmapping/meta.yaml +++ b/recipes/bioconductor-lumihumanidmapping/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.10.1" %} {% set name = "lumiHumanIDMapping" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,24 +13,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 007e5aa2f1596cc08d888ba6dce7148a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumihumanidmapping", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - r-dbi - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumimouseall.db/meta.yaml b/recipes/bioconductor-lumimouseall.db/meta.yaml index 1c8ed90955b5d..7046c1ded1218 100644 --- a/recipes/bioconductor-lumimouseall.db/meta.yaml +++ b/recipes/bioconductor-lumimouseall.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.22.0" %} {% set name = "lumiMouseAll.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6f12330377aaddc83bfa9c37477b999e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumimouseall.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumimouseidmapping/meta.yaml b/recipes/bioconductor-lumimouseidmapping/meta.yaml index 944b71d3a338c..4d70e4fb54cf8 100644 --- a/recipes/bioconductor-lumimouseidmapping/meta.yaml +++ b/recipes/bioconductor-lumimouseidmapping/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.10.0" %} {% set name = "lumiMouseIDMapping" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 305aba80ebf6ef4c26899302ea9e50e8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumimouseidmapping", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumiratall.db/meta.yaml b/recipes/bioconductor-lumiratall.db/meta.yaml index 4b230f3339cde..2bec6ec9618a5 100644 --- a/recipes/bioconductor-lumiratall.db/meta.yaml +++ b/recipes/bioconductor-lumiratall.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.22.0" %} {% set name = "lumiRatAll.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 65027624574d5e33f18b0a54a54f4be9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumiratall.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lumiratidmapping/meta.yaml b/recipes/bioconductor-lumiratidmapping/meta.yaml index 373ae2eee954b..fa2629353e6c9 100644 --- a/recipes/bioconductor-lumiratidmapping/meta.yaml +++ b/recipes/bioconductor-lumiratidmapping/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.10.0" %} {% set name = "lumiRatIDMapping" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1122fc25e3fff62678bed36f9d7b5709 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lumiratidmapping", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml index 5a52744c9da9d..5af4751df9291 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml +++ b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "LungCancerACvsSCCGEO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4313ab0bff32de6945d2b4e159979b4f + md5: f353aa0cc36dc25e67cdf1ba0738985e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lungcanceracvssccgeo", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh index 6145d97cbb5fb..b44b1fa903eb7 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh +++ b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lungcanceracvssccgeo-1.36.0" +installBiocDataPackage.sh "lungcanceracvssccgeo-1.38.0" diff --git a/recipes/bioconductor-lungcancerlines/meta.yaml b/recipes/bioconductor-lungcancerlines/meta.yaml index 085d28a4fdb82..a54b8590d329e 100644 --- a/recipes/bioconductor-lungcancerlines/meta.yaml +++ b/recipes/bioconductor-lungcancerlines/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "LungCancerLines" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be24350e8e8312e9421f0f4dd1ffbf85 + md5: 17b67ca0eac14ef832832b949972b277 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lungcancerlines", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lungcancerlines/post-link.sh b/recipes/bioconductor-lungcancerlines/post-link.sh index 0e6a6de527781..3191b811f3162 100644 --- a/recipes/bioconductor-lungcancerlines/post-link.sh +++ b/recipes/bioconductor-lungcancerlines/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lungcancerlines-0.38.0" +installBiocDataPackage.sh "lungcancerlines-0.40.0" diff --git a/recipes/bioconductor-lungexpression/meta.yaml b/recipes/bioconductor-lungexpression/meta.yaml index b89c507fd4577..13240159ee3d6 100644 --- a/recipes/bioconductor-lungexpression/meta.yaml +++ b/recipes/bioconductor-lungexpression/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "lungExpression" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56e3a841d35e5167328f7a3cc3f04349 + md5: 35eab717cb2e24c92faf417ad7fb9cb8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lungexpression", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lungexpression/post-link.sh b/recipes/bioconductor-lungexpression/post-link.sh index 68c94b5c0228b..a98eb220db162 100644 --- a/recipes/bioconductor-lungexpression/post-link.sh +++ b/recipes/bioconductor-lungexpression/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lungexpression-0.38.0" +installBiocDataPackage.sh "lungexpression-0.40.0" diff --git a/recipes/bioconductor-lydata/meta.yaml b/recipes/bioconductor-lydata/meta.yaml index ea78d701bde18..5bd099c210424 100644 --- a/recipes/bioconductor-lydata/meta.yaml +++ b/recipes/bioconductor-lydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "lydata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: caffcda965c0d055e69f6f0eb2fe9d67 + md5: 4541ec0aad2bbee135b19b0bed4ea0af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lydata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-lydata/post-link.sh b/recipes/bioconductor-lydata/post-link.sh index b3fde371b303b..1e814b39963f5 100644 --- a/recipes/bioconductor-lydata/post-link.sh +++ b/recipes/bioconductor-lydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lydata-1.26.0" +installBiocDataPackage.sh "lydata-1.28.0" diff --git a/recipes/bioconductor-lymphoseq/meta.yaml b/recipes/bioconductor-lymphoseq/meta.yaml index 5b8ca6d01685f..444c73883de46 100644 --- a/recipes/bioconductor-lymphoseq/meta.yaml +++ b/recipes/bioconductor-lymphoseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "LymphoSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88d2862cfcae6c156660190a4dcf631c + md5: c7a311767150648a29d45e5cd5ee5c30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lymphoseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, pheatmap, wordcloud, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - 'bioconductor-lymphoseqdb >=0.99.0,<0.100.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - r-circlize - r-data.table @@ -39,10 +40,10 @@ requirements: - r-upsetr - r-venndiagram run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - 'bioconductor-lymphoseqdb >=0.99.0,<0.100.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - r-circlize - r-data.table diff --git a/recipes/bioconductor-lymphoseqdb/meta.yaml b/recipes/bioconductor-lymphoseqdb/meta.yaml index e6bf9ca1dd2c0..9ae31ac173cd1 100644 --- a/recipes/bioconductor-lymphoseqdb/meta.yaml +++ b/recipes/bioconductor-lymphoseqdb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.2" %} {% set name = "LymphoSeqDB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 22fc0dc2439ef497982a5ffddda1e418 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lymphoseqdb", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-m10kcod.db/meta.yaml b/recipes/bioconductor-m10kcod.db/meta.yaml index cd3a43bcb94bf..82e91d08de883 100644 --- a/recipes/bioconductor-m10kcod.db/meta.yaml +++ b/recipes/bioconductor-m10kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "m10kcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 04811628e4b37cd6d24e0b2a17d79ab8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m10kcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-m20kcod.db/meta.yaml b/recipes/bioconductor-m20kcod.db/meta.yaml index 8e44660a56326..6f7477b00a514 100644 --- a/recipes/bioconductor-m20kcod.db/meta.yaml +++ b/recipes/bioconductor-m20kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "m20kcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f2f734fb41e1ae4e949abf09687733bf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m20kcod.db", max_pin="x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20231202 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-m3c/meta.yaml b/recipes/bioconductor-m3c/meta.yaml index 582342cbed4ad..d5ae69bc55ced 100644 --- a/recipes/bioconductor-m3c/meta.yaml +++ b/recipes/bioconductor-m3c/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "M3C" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a15f91d6f63abdcffa1131c797fd619c + md5: e04534528d39712026e9b1de15a12c3d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m3c", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-m3dexampledata/meta.yaml b/recipes/bioconductor-m3dexampledata/meta.yaml index 211786630fde3..f1420a70bec4e 100644 --- a/recipes/bioconductor-m3dexampledata/meta.yaml +++ b/recipes/bioconductor-m3dexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "M3DExampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1181ab509a8a85961ef586709f3eaba3 + md5: 6988767aab7572ae3e701fd6854c061f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m3dexampledata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-m3dexampledata/post-link.sh b/recipes/bioconductor-m3dexampledata/post-link.sh index 77c73e1387515..72da968afa952 100644 --- a/recipes/bioconductor-m3dexampledata/post-link.sh +++ b/recipes/bioconductor-m3dexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "m3dexampledata-1.26.0" +installBiocDataPackage.sh "m3dexampledata-1.28.0" diff --git a/recipes/bioconductor-m3drop/meta.yaml b/recipes/bioconductor-m3drop/meta.yaml index c72f822e24787..29a92577f3e60 100644 --- a/recipes/bioconductor-m3drop/meta.yaml +++ b/recipes/bioconductor-m3drop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "M3Drop" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d8dec066ec2a494fd8e2b9c2771ab37 + md5: ad347f93f1a297543e7ab0e74437dd4d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m3drop", max_pin="x.x") }}' noarch: generic # Suggests: ROCR, knitr, M3DExampleData, scater, SingleCellExperiment, monocle, Seurat, Biobase requirements: diff --git a/recipes/bioconductor-m6aboost/meta.yaml b/recipes/bioconductor-m6aboost/meta.yaml index d93a008c5c87b..929ee2436e646 100644 --- a/recipes/bioconductor-m6aboost/meta.yaml +++ b/recipes/bioconductor-m6aboost/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "m6Aboost" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e39557c678ff999ad58cdaa49b01746b + md5: 17bd39bcc17e45a0bb22be3e2e15c533 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-m6aboost", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-adabag - r-base - r-dplyr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-adabag - r-base - r-dplyr diff --git a/recipes/bioconductor-maaslin2/meta.yaml b/recipes/bioconductor-maaslin2/meta.yaml index 8842f8735025c..344540a1fbdb1 100644 --- a/recipes/bioconductor-maaslin2/meta.yaml +++ b/recipes/bioconductor-maaslin2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "Maaslin2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f70167c230537ebff1f132b2a2d46bf + md5: 0f92778b2d59935191e2ac58621da8f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maaslin2", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-biglm - r-car @@ -46,8 +47,8 @@ requirements: - r-tibble - r-vegan run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-biglm - r-car diff --git a/recipes/bioconductor-macarron/meta.yaml b/recipes/bioconductor-macarron/meta.yaml index 83b29fe0c4d5f..ff3a24d53a9d3 100644 --- a/recipes/bioconductor-macarron/meta.yaml +++ b/recipes/bioconductor-macarron/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "Macarron" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2f02b7a780b42d3e9a805aa266ef831 + md5: 525669e56fccd2be5524315ee6a0eafb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macarron", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown, markdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-maaslin2 >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dynamictreecut @@ -37,10 +38,10 @@ requirements: - r-wgcna - r-xml2 run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-maaslin2 >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dynamictreecut diff --git a/recipes/bioconductor-macat/meta.yaml b/recipes/bioconductor-macat/meta.yaml index 7be249417b94a..292acdbbc3be8 100644 --- a/recipes/bioconductor-macat/meta.yaml +++ b/recipes/bioconductor-macat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "macat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f26ab5982050f5b89a52fd0ef72ba31e + md5: cad43ea7bcc92da57a4e5918581d0143 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macat", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2.db, stjudem requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-macorrplot/meta.yaml b/recipes/bioconductor-macorrplot/meta.yaml index e08eeb78ddd2d..26005f13bc3d4 100644 --- a/recipes/bioconductor-macorrplot/meta.yaml +++ b/recipes/bioconductor-macorrplot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "maCorrPlot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad53b8a9ed8797daef76c81929eb25c8 + md5: 4d4be51b04e4ff3e09aff6643eeed215 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macorrplot", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-macrophage/meta.yaml b/recipes/bioconductor-macrophage/meta.yaml index 66381d83d9755..54570f039c559 100644 --- a/recipes/bioconductor-macrophage/meta.yaml +++ b/recipes/bioconductor-macrophage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "macrophage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 94a66e9f410a44d2aa240ebc4cf5c106 + md5: 5f83cf12d699a285cd228119b1d95cf0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macrophage", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-macrophage/post-link.sh b/recipes/bioconductor-macrophage/post-link.sh index e21678c7de8a2..07ecd9410ed61 100644 --- a/recipes/bioconductor-macrophage/post-link.sh +++ b/recipes/bioconductor-macrophage/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "macrophage-1.16.0" +installBiocDataPackage.sh "macrophage-1.18.0" diff --git a/recipes/bioconductor-macsdata/meta.yaml b/recipes/bioconductor-macsdata/meta.yaml index e698607b03c87..9b6e64baa9952 100644 --- a/recipes/bioconductor-macsdata/meta.yaml +++ b/recipes/bioconductor-macsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MACSdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5f6edbf074b1f0f5cb5d0d546cdbd0a + md5: 1d10f4fe6b20d5c09148b8011fb3183f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-macsdata/post-link.sh b/recipes/bioconductor-macsdata/post-link.sh index eb83aa26c36d6..5b08e731f2aa8 100644 --- a/recipes/bioconductor-macsdata/post-link.sh +++ b/recipes/bioconductor-macsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "macsdata-1.8.0" +installBiocDataPackage.sh "macsdata-1.10.0" diff --git a/recipes/bioconductor-macsquantifyr/meta.yaml b/recipes/bioconductor-macsquantifyr/meta.yaml index b7f36ac6f8545..d34ebb85df598 100644 --- a/recipes/bioconductor-macsquantifyr/meta.yaml +++ b/recipes/bioconductor-macsquantifyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MACSQuantifyR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a6252d72b886c783344a123b6b8b324a + md5: b0bc5dd3ddff22c28356a8af09704f82 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macsquantifyr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, R.utils, spelling requirements: diff --git a/recipes/bioconductor-macsr/meta.yaml b/recipes/bioconductor-macsr/meta.yaml index d550c04c1780c..69879b8a4a240 100644 --- a/recipes/bioconductor-macsr/meta.yaml +++ b/recipes/bioconductor-macsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MACSr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cee42ba19dbef311158effc2860c8ed6 + md5: bab4dacc8d41a2a47798bc740181f014 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-macsr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, MACSdata requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-reticulate run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-reticulate test: diff --git a/recipes/bioconductor-made4/meta.yaml b/recipes/bioconductor-made4/meta.yaml index 931cd5da58c55..924483d6772f8 100644 --- a/recipes/bioconductor-made4/meta.yaml +++ b/recipes/bioconductor-made4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "made4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a9e234449f176b7ca00e61605dae1c5 + md5: ae8a8a420c5f5ebd8a729767baf0a762 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-made4", max_pin="x.x") }}' noarch: generic # Suggests: affy, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ade4 - r-base - r-gplots - r-rcolorbrewer - r-scatterplot3d run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ade4 - r-base - r-gplots diff --git a/recipes/bioconductor-madseq/meta.yaml b/recipes/bioconductor-madseq/meta.yaml index 928d177cace5f..54bf4e92bbf41 100644 --- a/recipes/bioconductor-madseq/meta.yaml +++ b/recipes/bioconductor-madseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MADSEQ" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,50 +11,51 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2e25b4e8cf74ac0ef392ddb4d7214b1 + md5: c64d51251670d105945b18d12dcd5fec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-madseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-coda - 'r-rjags >=4.6' - r-vcfr - r-vgam run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-coda - 'r-rjags >=4.6' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml index be99ecb9bd161..2b6aa7f5d2729 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase1.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a20471906a41678ce710879e92d2a9dc build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase1.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml index 38d35b744a3c0..370e667cdc070 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase1.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ece6b758ca0e1a8a307b5cd5829671f4 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase1.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml index 825c493200e85..1db40c302708a 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase3.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ee57d9cb6a1748932407d20b9bffd8a2 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase3.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml index 4de3ba7d81011..e5eef7f32a86d 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase3.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ac3cbbf52eb2026f067a4f42c6654555 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase3.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml index b246266b6fe51..a96f0e68085a4 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 303332c918996d8cb3e7b7c74d694dd1 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml index dffd2da0880cd..8ee13e3ac78c2 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4d523554a2b0eb296bada9d33a78eefc build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml index 2f42f1af107df..acc4810915163 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.nonTCGA.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cf447f59cc8b1cd7ca395fd3fe6e4730 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.nontcga.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml index 1a7713ca04870..4e474b21e0b3f 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.nonTCGA.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: da3a699e9776b0b769b3bc1e9fb742f0 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.nontcga.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml index 357433b83fe2e..6a2aeb3790b7b 100644 --- a/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomAD.r2.1.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0e842b24476aeb834f57f9302a36ea18 build: - number: 7 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomad.r2.1.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml index c18f6c455ea03..e55b30222e669 100644 --- a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomAD.r2.1.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 12221c461930ae1ecfe925943a619d56 build: - number: 9 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomad.r2.1.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml index 306a937c8d05c..0a1f9568b4c16 100644 --- a/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomADex.r2.1.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a0ab5b74997669fabb8aecfd9ef7f767 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomadex.r2.1.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml index f01decacb0e1e..9c24dd865ddc8 100644 --- a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomADex.r2.1.hs37d5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6ca4d742571687a13906d99cea2dbf1f build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomadex.r2.1.hs37d5", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml index 2c94cbac23ecb..06fdf2b8407e8 100644 --- a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.TOPMed.freeze5.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7fdb58eb69187ade189689da58ca6266 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.topmed.freeze5.hg19", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml index b976d65bd270b..485f8cd9f87c6 100644 --- a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "MafDb.TOPMed.freeze5.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a3355623fde26b83dfd346a32829f073 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafdb.topmed.freeze5.hg38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafh5.gnomad.v3.1.1.grch38/meta.yaml b/recipes/bioconductor-mafh5.gnomad.v3.1.1.grch38/meta.yaml index 9a2a78841bcb4..a0ae0f400cc7a 100644 --- a/recipes/bioconductor-mafh5.gnomad.v3.1.1.grch38/meta.yaml +++ b/recipes/bioconductor-mafh5.gnomad.v3.1.1.grch38/meta.yaml @@ -41,7 +41,7 @@ requirements: - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mafh5.gnomad.v3.1.2.grch38/meta.yaml b/recipes/bioconductor-mafh5.gnomad.v3.1.2.grch38/meta.yaml index 22bb4faead093..906283e9f2b28 100644 --- a/recipes/bioconductor-mafh5.gnomad.v3.1.2.grch38/meta.yaml +++ b/recipes/bioconductor-mafh5.gnomad.v3.1.2.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.15.0" %} {% set name = "MafH5.gnomAD.v3.1.2.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,35 +13,36 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e9c85173866caf998cf1af7dd35aac0b build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mafh5.gnomad.v3.1.2.grch38", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maftools/meta.yaml b/recipes/bioconductor-maftools/meta.yaml index 86123ebc13b62..45bb795699803 100644 --- a/recipes/bioconductor-maftools/meta.yaml +++ b/recipes/bioconductor-maftools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "maftools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b54e39e3b9f5f9123ce2755efdd2cc92 + md5: 3dadc2b7f6f1693ae23a41b61f541db4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maftools", max_pin="x.x") }}' # Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, pheatmap, curl # SystemRequirements: GNU make requirements: host: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-rcolorbrewer @@ -31,9 +32,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-rcolorbrewer diff --git a/recipes/bioconductor-magar/meta.yaml b/recipes/bioconductor-magar/meta.yaml index 37aa9da557ce8..e87b79b60d97d 100644 --- a/recipes/bioconductor-magar/meta.yaml +++ b/recipes/bioconductor-magar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MAGAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17a56f640a48d9270666b77554644c7b + md5: 27ccb3bf6acaabe9b9d29b52f9d98213 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-magar", max_pin="x.x") }}' noarch: generic # Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager requirements: host: - - 'bioconductor-crlmm >=1.58.0,<1.59.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-rnbeads >=2.18.0,<2.19.0' - - 'bioconductor-rnbeads.hg19 >=1.32.0,<1.33.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-crlmm >=1.60.0,<1.61.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-rnbeads >=2.20.0,<2.21.0' + - 'bioconductor-rnbeads.hg19 >=1.34.0,<1.35.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-argparse - r-base - r-bigstatsr @@ -40,12 +41,12 @@ requirements: - r-rjson - r-upsetr run: - - 'bioconductor-crlmm >=1.58.0,<1.59.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-rnbeads >=2.18.0,<2.19.0' - - 'bioconductor-rnbeads.hg19 >=1.32.0,<1.33.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-crlmm >=1.60.0,<1.61.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-rnbeads >=2.20.0,<2.21.0' + - 'bioconductor-rnbeads.hg19 >=1.34.0,<1.35.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-argparse - r-base - r-bigstatsr diff --git a/recipes/bioconductor-mageckflute/meta.yaml b/recipes/bioconductor-mageckflute/meta.yaml index a7b7a298d0692..3a485e0d36c7c 100644 --- a/recipes/bioconductor-mageckflute/meta.yaml +++ b/recipes/bioconductor-mageckflute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "MAGeCKFlute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3471b341d90f59e6ef5c9ae15ed4e6d0 + md5: 09a3c95fe59a959ce069f5ad56e75276 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mageckflute", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, BiocStyle, dendextend, graphics, knitr, pheatmap, png, scales, sva, BiocManager requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-depmap >=1.14.0,<1.15.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-depmap >=1.16.0,<1.17.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-ggplot2 - r-ggrepel @@ -34,12 +35,12 @@ requirements: - r-msigdbr - r-reshape2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-depmap >=1.14.0,<1.15.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-depmap >=1.16.0,<1.17.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-magpie/meta.yaml b/recipes/bioconductor-magpie/meta.yaml index f600033cb56df..9b8edec7aca44 100644 --- a/recipes/bioconductor-magpie/meta.yaml +++ b/recipes/bioconductor-magpie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "magpie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 52ffa8a06a288f5a51ea9337aa99733e + md5: 019cf9b038353b96851fe65fa55f3d08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-magpie", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tress >=1.6.0,<1.7.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tress >=1.8.0,<1.9.0' - r-aod - r-base - r-matrix @@ -39,16 +40,16 @@ requirements: - r-rcolorbrewer - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tress >=1.6.0,<1.7.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tress >=1.8.0,<1.9.0' - r-aod - r-base - r-matrix diff --git a/recipes/bioconductor-magrene/meta.yaml b/recipes/bioconductor-magrene/meta.yaml index 062f1bacc7482..54cc0f1df97ec 100644 --- a/recipes/bioconductor-magrene/meta.yaml +++ b/recipes/bioconductor-magrene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "magrene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: df1a679707bfc6783f48a7489c8e0c8b + md5: 7d02392d3081830451c4fae90ed50177 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-magrene", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-mai/meta.yaml b/recipes/bioconductor-mai/meta.yaml index 4f88bbb8b24e2..e1039188b4612 100644 --- a/recipes/bioconductor-mai/meta.yaml +++ b/recipes/bioconductor-mai/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "MAI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 990f4687d2c061d10aea5f5d78795328 + md5: ac8dbd997d58657f8ed6b64f5cdee7a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mai", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-doparallel @@ -34,9 +35,9 @@ requirements: - r-missforest - r-tidyverse run: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-doparallel diff --git a/recipes/bioconductor-mait/meta.yaml b/recipes/bioconductor-mait/meta.yaml index 5351c8eb39d02..695444af43443 100644 --- a/recipes/bioconductor-mait/meta.yaml +++ b/recipes/bioconductor-mait/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MAIT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37e3772801390dcf734e87c62b98471b + md5: f32e9e8e908202848634b26a5ece4d8f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mait", max_pin="x.x") }}' # Suggests: faahKO requirements: host: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-agricolae - r-base - r-caret @@ -35,8 +36,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-agricolae - r-base - r-caret diff --git a/recipes/bioconductor-maizecdf/meta.yaml b/recipes/bioconductor-maizecdf/meta.yaml index 0e8d7a5d7b90b..d836b954f6903 100644 --- a/recipes/bioconductor-maizecdf/meta.yaml +++ b/recipes/bioconductor-maizecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "maizecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f9dec9e46688d96daf1e07d4e815afb4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maizecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maizeprobe/meta.yaml b/recipes/bioconductor-maizeprobe/meta.yaml index 5506099f48285..3c8eb2bfe896a 100644 --- a/recipes/bioconductor-maizeprobe/meta.yaml +++ b/recipes/bioconductor-maizeprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "maizeprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ef7ba47de2346b3552621263399c05d1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maizeprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-makecdfenv/meta.yaml b/recipes/bioconductor-makecdfenv/meta.yaml index 1fc6c31d0e941..2271860f8f2bc 100644 --- a/recipes/bioconductor-makecdfenv/meta.yaml +++ b/recipes/bioconductor-makecdfenv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "makecdfenv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4455ab7ea0c109310c0ef051acc9bf44 + md5: b5c8877fd5b09fbb4d3656490fa7eb64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-makecdfenv", max_pin="x.x") }}' requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-malaria.db0/meta.yaml b/recipes/bioconductor-malaria.db0/meta.yaml index b0d07125ccc9e..ddff973edf6fe 100644 --- a/recipes/bioconductor-malaria.db0/meta.yaml +++ b/recipes/bioconductor-malaria.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "malaria.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b8064752fa55d249e89e1c94db04b434 + md5: 6f71b4ac69ae5237f3f5e1337d5073d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-malaria.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-malaria.db0/post-link.sh b/recipes/bioconductor-malaria.db0/post-link.sh index aa5c1fbc028d9..723835d617cfb 100644 --- a/recipes/bioconductor-malaria.db0/post-link.sh +++ b/recipes/bioconductor-malaria.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "malaria.db0-3.17.0" +installBiocDataPackage.sh "malaria.db0-3.18.0" diff --git a/recipes/bioconductor-mammaprintdata/meta.yaml b/recipes/bioconductor-mammaprintdata/meta.yaml index 9f531c2391d37..0ad3e9e516f38 100644 --- a/recipes/bioconductor-mammaprintdata/meta.yaml +++ b/recipes/bioconductor-mammaprintdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "mammaPrintData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfd6915395a6a2adeebac6854f3359c9 + md5: 08b3249a36d5f165a933bfab5eb05a2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mammaprintdata", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, readxl, limma requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mammaprintdata/post-link.sh b/recipes/bioconductor-mammaprintdata/post-link.sh index b1a54fcddb5fa..ee220d325a5a0 100644 --- a/recipes/bioconductor-mammaprintdata/post-link.sh +++ b/recipes/bioconductor-mammaprintdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mammaprintdata-1.36.0" +installBiocDataPackage.sh "mammaprintdata-1.38.0" diff --git a/recipes/bioconductor-manor/meta.yaml b/recipes/bioconductor-manor/meta.yaml index d21c6e9c6b331..0b48ee35d2fea 100644 --- a/recipes/bioconductor-manor/meta.yaml +++ b/recipes/bioconductor-manor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "MANOR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fff1198e00300c326aec0b10f1243e7d + md5: a2d915a1904045acbe371b10102c8512 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-manor", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, bookdown requirements: host: - - 'bioconductor-glad >=2.64.0,<2.65.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' - r-base - libblas - liblapack run: - - 'bioconductor-glad >=2.64.0,<2.65.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-mantelcorr/meta.yaml b/recipes/bioconductor-mantelcorr/meta.yaml index 20ab63e20a1ab..5fe60a98bbc56 100644 --- a/recipes/bioconductor-mantelcorr/meta.yaml +++ b/recipes/bioconductor-mantelcorr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "MantelCorr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f20807432d60061faa0e788a6e98c84 + md5: 7ef5ee0a329a4cf218c340e9289fea32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mantelcorr", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mapkldata/meta.yaml b/recipes/bioconductor-mapkldata/meta.yaml index 50ea4875e03e4..8669aaad8b16f 100644 --- a/recipes/bioconductor-mapkldata/meta.yaml +++ b/recipes/bioconductor-mapkldata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "mAPKLData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d1b511c7be1a423450a153fc118e7cb + md5: ce6399a1c853cb4e78de226347c3dc5d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mapkldata", max_pin="x.x") }}' noarch: generic # Suggests: Biobase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mapkldata/post-link.sh b/recipes/bioconductor-mapkldata/post-link.sh index d7a4cb29b019b..5c4a6533b73dc 100644 --- a/recipes/bioconductor-mapkldata/post-link.sh +++ b/recipes/bioconductor-mapkldata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mapkldata-1.32.0" +installBiocDataPackage.sh "mapkldata-1.34.0" diff --git a/recipes/bioconductor-mapredictdsc/meta.yaml b/recipes/bioconductor-mapredictdsc/meta.yaml index 98832a70410c7..88e0feda89173 100644 --- a/recipes/bioconductor-mapredictdsc/meta.yaml +++ b/recipes/bioconductor-mapredictdsc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "maPredictDSC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6478a774bba2457523926418168a45f2 + md5: b2a491a7c799fcc0efcaed0b3067aa66 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mapredictdsc", max_pin="x.x") }}' noarch: generic # Suggests: parallel requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lungcanceracvssccgeo >=1.36.0,<1.37.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lungcanceracvssccgeo >=1.38.0,<1.39.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-caret - r-class @@ -35,13 +36,13 @@ requirements: - r-mass - r-rocr run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lungcanceracvssccgeo >=1.36.0,<1.37.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lungcanceracvssccgeo >=1.38.0,<1.39.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-caret - r-class diff --git a/recipes/bioconductor-mapscape/meta.yaml b/recipes/bioconductor-mapscape/meta.yaml index 68bec68fe92d6..d0af3af41f6ed 100644 --- a/recipes/bioconductor-mapscape/meta.yaml +++ b/recipes/bioconductor-mapscape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "mapscape" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fb51de837561beef21ffa11f723654f9 + md5: dc197aa43e86dc49fef0d85d2ead252c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mapscape", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-maqcexpression4plex/meta.yaml b/recipes/bioconductor-maqcexpression4plex/meta.yaml index 53bdea96b4749..58945237d3ad0 100644 --- a/recipes/bioconductor-maqcexpression4plex/meta.yaml +++ b/recipes/bioconductor-maqcexpression4plex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "maqcExpression4plex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 761e3e1f398262f4c0cac3cd31979fc7 + md5: 8312b7fbcba763a33630effb8c3b5f10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maqcexpression4plex", max_pin="x.x") }}' noarch: generic # Suggests: oligo, pdInfoBuilder requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maqcexpression4plex/post-link.sh b/recipes/bioconductor-maqcexpression4plex/post-link.sh index fc90732c5d1fd..8a868702a088b 100644 --- a/recipes/bioconductor-maqcexpression4plex/post-link.sh +++ b/recipes/bioconductor-maqcexpression4plex/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "maqcexpression4plex-1.44.0" +installBiocDataPackage.sh "maqcexpression4plex-1.46.0" diff --git a/recipes/bioconductor-maqcsubset/meta.yaml b/recipes/bioconductor-maqcsubset/meta.yaml index 8f3a5ded5021c..4f5f9467649c3 100644 --- a/recipes/bioconductor-maqcsubset/meta.yaml +++ b/recipes/bioconductor-maqcsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "MAQCsubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb3ea654ce6aa3db50c7a39c6d8cab28 + md5: 5757c11a1af2150b8fd17c3a8b8b0c0c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maqcsubset", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, codelink requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maqcsubset/post-link.sh b/recipes/bioconductor-maqcsubset/post-link.sh index 270d828522f4e..2e61448c5748c 100644 --- a/recipes/bioconductor-maqcsubset/post-link.sh +++ b/recipes/bioconductor-maqcsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "maqcsubset-1.38.0" +installBiocDataPackage.sh "maqcsubset-1.40.0" diff --git a/recipes/bioconductor-maqcsubsetilm/meta.yaml b/recipes/bioconductor-maqcsubsetilm/meta.yaml index c1926f58f1dd3..8c1a687bc5053 100644 --- a/recipes/bioconductor-maqcsubsetilm/meta.yaml +++ b/recipes/bioconductor-maqcsubsetilm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "MAQCsubsetILM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4aaeddbd20f73e3f84dc630e9c02e219 + md5: 1c975db69a86cc80e99c5245998ee255 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maqcsubsetilm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-maqcsubsetilm/post-link.sh b/recipes/bioconductor-maqcsubsetilm/post-link.sh index 76cbbf1ec8f5a..20355734efcd0 100644 --- a/recipes/bioconductor-maqcsubsetilm/post-link.sh +++ b/recipes/bioconductor-maqcsubsetilm/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "maqcsubsetilm-1.38.0" +installBiocDataPackage.sh "maqcsubsetilm-1.40.0" diff --git a/recipes/bioconductor-mariner/meta.yaml b/recipes/bioconductor-mariner/meta.yaml index 9e1ea1bdda43a..faa6324855fb2 100644 --- a/recipes/bioconductor-mariner/meta.yaml +++ b/recipes/bioconductor-mariner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "mariner" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e7440b7a29afb6f325512a65653b3b9 + md5: 6ed30878d03b8a17e8e7c4ee17218893 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mariner", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plotgardener >=1.6.0,<1.7.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plotgardener >=1.8.0,<1.9.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-assertthat - r-base @@ -49,19 +50,19 @@ requirements: - r-rlang - 'r-strawr >=0.0.91' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plotgardener >=1.6.0,<1.7.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plotgardener >=1.8.0,<1.9.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-assertthat - r-base diff --git a/recipes/bioconductor-marinerdata/meta.yaml b/recipes/bioconductor-marinerdata/meta.yaml index c1961f6c744f6..1f58a93bd6ba5 100644 --- a/recipes/bioconductor-marinerdata/meta.yaml +++ b/recipes/bioconductor-marinerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "marinerData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88417144bbc4ae0164445918ce73376d + md5: 7875113ebb6baaaed6eb6fc762ba92ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-marinerdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-marinerdata/post-link.sh b/recipes/bioconductor-marinerdata/post-link.sh index ddb0b82fcea0c..a1f63c4a9a63d 100644 --- a/recipes/bioconductor-marinerdata/post-link.sh +++ b/recipes/bioconductor-marinerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "marinerdata-1.0.0" +installBiocDataPackage.sh "marinerdata-1.2.0" diff --git a/recipes/bioconductor-marr/meta.yaml b/recipes/bioconductor-marr/meta.yaml index 5f05cd664dbf4..cb6168d37a922 100644 --- a/recipes/bioconductor-marr/meta.yaml +++ b/recipes/bioconductor-marr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "marr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5034df18a1cb3deb55978997508feea8 + md5: 3b839d77065c34ddb5f5c2a8eee277ea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-marr", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat, covr requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -31,8 +32,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-marray/meta.yaml b/recipes/bioconductor-marray/meta.yaml index b0c13d578a065..d4701902cbd9a 100644 --- a/recipes/bioconductor-marray/meta.yaml +++ b/recipes/bioconductor-marray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "marray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3dc5ce3be06cf55e1e4c95f77f2acce0 + md5: 569b373e346d36964430d249d075cf07 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-marray", max_pin="x.x") }}' noarch: generic # Suggests: tkWidgets requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-martini/meta.yaml b/recipes/bioconductor-martini/meta.yaml index a5c17f5984402..707dd1d27a6ae 100644 --- a/recipes/bioconductor-martini/meta.yaml +++ b/recipes/bioconductor-martini/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "martini" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 400390c31bdbd7cc031fdf235683eb7d + md5: 85e3366daf7ac24c0f50261fafe8b274 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-martini", max_pin="x.x") }}' # Suggests: biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>= 2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>= 0.12.2), knitr, testthat, readr, rmarkdown requirements: host: - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - 'r-igraph >=1.0.1' - r-matrix @@ -30,7 +31,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - 'r-igraph >=1.0.1' - r-matrix diff --git a/recipes/bioconductor-maser/meta.yaml b/recipes/bioconductor-maser/meta.yaml index 831d0c6a9612b..984e5476ff7d0 100644 --- a/recipes/bioconductor-maser/meta.yaml +++ b/recipes/bioconductor-maser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "maser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 052306b8282c5b311639dfa2d5ef7045 + md5: 43be20847a05369476ccdb91cdd6ad4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maser", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr @@ -34,12 +35,12 @@ requirements: - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-masigpro/meta.yaml b/recipes/bioconductor-masigpro/meta.yaml index f932961901201..92ad4b2047ab2 100644 --- a/recipes/bioconductor-masigpro/meta.yaml +++ b/recipes/bioconductor-masigpro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "maSigPro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 712ae9a5e65afe3af9adb7b6b0701938 + md5: ab91a6a10122c6d1f28fee40be32c2b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-masigpro", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass - r-mclust - r-venn run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass - r-mclust diff --git a/recipes/bioconductor-maskbad/meta.yaml b/recipes/bioconductor-maskbad/meta.yaml index f0c5d696b39a6..e7cfd10db732a 100644 --- a/recipes/bioconductor-maskbad/meta.yaml +++ b/recipes/bioconductor-maskbad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "maskBAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b331548e7096b6b3be7c7dec18ef8326 + md5: a5fc8482a4370f32fde7bc2b3e302c77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-maskbad", max_pin="x.x") }}' noarch: generic # Suggests: hgu95av2probe, hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' - r-base test: commands: diff --git a/recipes/bioconductor-massarray/meta.yaml b/recipes/bioconductor-massarray/meta.yaml index 3d6d46c569432..0afae7ac8c0e7 100644 --- a/recipes/bioconductor-massarray/meta.yaml +++ b/recipes/bioconductor-massarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "MassArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10baaf1ef33e244057e4f36061412c28 + md5: 028fea456ce2e5b3820ad6dc0d1989c1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-massarray", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-massir/meta.yaml b/recipes/bioconductor-massir/meta.yaml index 9e0e03f5fb577..dbf9731aa509d 100644 --- a/recipes/bioconductor-massir/meta.yaml +++ b/recipes/bioconductor-massir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "massiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 486b707284622849c02988e6cd5b82f9 + md5: f2dda0fb78f776b416af77100e902b55 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-massir", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster - r-diptest - r-gplots run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-cluster - r-diptest diff --git a/recipes/bioconductor-massspecwavelet/meta.yaml b/recipes/bioconductor-massspecwavelet/meta.yaml index 96df2a5052c6d..3518c50e8a816 100644 --- a/recipes/bioconductor-massspecwavelet/meta.yaml +++ b/recipes/bioconductor-massspecwavelet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "MassSpecWavelet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ebb91cab5b3607ac2c59cd73e6e06c9 + md5: 387636ea7c674fe339c56a8af3458f8a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-massspecwavelet", max_pin="x.x") }}' # Suggests: signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench requirements: host: diff --git a/recipes/bioconductor-mast/meta.yaml b/recipes/bioconductor-mast/meta.yaml index 029f53b7473ce..1dd0a3e36a434 100644 --- a/recipes/bioconductor-mast/meta.yaml +++ b/recipes/bioconductor-mast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MAST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9442a26a462745f9c9f05cdb036cc1df + md5: 5b2d5c6a33243cdf9c2e4440ba4bf1da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mast", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(> 6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater, DelayedArray, HDF5Array, zinbwave, dplyr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-data.table @@ -36,11 +37,11 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-data.table diff --git a/recipes/bioconductor-mastr/meta.yaml b/recipes/bioconductor-mastr/meta.yaml index 812d4bfc3fa77..d13e915d95790 100644 --- a/recipes/bioconductor-mastr/meta.yaml +++ b/recipes/bioconductor-mastr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "mastR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce292ab282a5db42a4c0975bfd326640 + md5: be4cab3fb29097cb5dd34ee7ba1ce228 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mastr", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, BiocStyle, BisqueRNA, clusterProfiler, ComplexHeatmap, depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore, splatter, testthat (>= 3.0.0), UpSetR requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msigdb >=1.8.0,<1.9.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msigdb >=1.10.0,<1.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -39,15 +40,15 @@ requirements: - r-seuratobject - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msigdb >=1.8.0,<1.9.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msigdb >=1.10.0,<1.11.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-matchbox/meta.yaml b/recipes/bioconductor-matchbox/meta.yaml index 987d19e540765..0cb5c684cdaaa 100644 --- a/recipes/bioconductor-matchbox/meta.yaml +++ b/recipes/bioconductor-matchbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "matchBox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e86b03f10e018b4c355da5ff1f8b17d0 + md5: b6e4b10ee38f433d1bce146a089a44ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-matchbox", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-matrixgenerics/meta.yaml b/recipes/bioconductor-matrixgenerics/meta.yaml index 51d5c467ae836..4db7b3d78519a 100644 --- a/recipes/bioconductor-matrixgenerics/meta.yaml +++ b/recipes/bioconductor-matrixgenerics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "MatrixGenerics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91a6ccc193831c76b3806c41b3ceed6d + md5: 18c3a5cc993ca5c2ad48dde1813105e6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-matrixgenerics", max_pin="x.x") }}' noarch: generic # Suggests: Matrix, sparseMatrixStats, SparseArray, DelayedArray, DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0) requirements: diff --git a/recipes/bioconductor-matrixqcvis/meta.yaml b/recipes/bioconductor-matrixqcvis/meta.yaml index 4042891f77548..39bd88b0aa423 100644 --- a/recipes/bioconductor-matrixqcvis/meta.yaml +++ b/recipes/bioconductor-matrixqcvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MatrixQCvis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3c78e12fc1b9c6bda807c330f86197e + md5: 21f91ace512d3afadd5fe42e93ba7fe9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-matrixqcvis", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics (>= 0.37.4), BiocStyle (>= 2.19.2), hexbin (>= 1.28.2), jpeg (>= 0.1-10), knitr (>= 1.33), statmod (>= 1.5.0), testthat (>= 3.0.2) requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-proda >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-proda >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-dplyr >=1.0.5' - 'r-ggplot2 >=3.3.3' @@ -49,14 +50,14 @@ requirements: - 'r-umap >=0.2.7.0' - 'r-upsetr >=1.4.0' run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-proda >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-proda >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-dplyr >=1.0.5' - 'r-ggplot2 >=3.3.3' diff --git a/recipes/bioconductor-matrixrider/meta.yaml b/recipes/bioconductor-matrixrider/meta.yaml index c0e2a75d98583..89be4c1d9d40e 100644 --- a/recipes/bioconductor-matrixrider/meta.yaml +++ b/recipes/bioconductor-matrixrider/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "MatrixRider" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9831760b8e5550b70367da373860cdd9 + md5: 2de2ee8befc7dcf6b84ea6630a0c089f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-matrixrider", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, BiocStyle, JASPAR2014 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-matter/meta.yaml b/recipes/bioconductor-matter/meta.yaml index 37f67677cee07..631bf8eaa0512 100644 --- a/recipes/bioconductor-matter/meta.yaml +++ b/recipes/bioconductor-matter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "matter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9af0c8ea4ebd31da1bb4d27f0e610989 + md5: 08919bc0df5442e0916ee7cffbc23003 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-matter", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-biglm - r-digest @@ -31,9 +32,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-biglm - r-digest @@ -49,8 +50,8 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'A framework for rapid prototyping with file-based data structures' - description: 'Memory-efficient reading, writing, and manipulation of structured binary data as file-based vectors, matrices, arrays, lists, and data frames.' + summary: 'Out-of-memory dense and sparse signal arrays' + description: 'Memory-efficient file-based data structures for dense and sparse vectors, matrices, arrays, and lists with applications to nonuniformly sampled signals and spectra.' extra: identifiers: - biotools:matter diff --git a/recipes/bioconductor-mbamethyl/meta.yaml b/recipes/bioconductor-mbamethyl/meta.yaml index 9df037c318d99..d76d4dc6cc97c 100644 --- a/recipes/bioconductor-mbamethyl/meta.yaml +++ b/recipes/bioconductor-mbamethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MBAmethyl" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c62ade813fcdb70923e320b12b345e16 + md5: 0b6ac0d76525c156606d08bcbf606709 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbamethyl", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mbased/meta.yaml b/recipes/bioconductor-mbased/meta.yaml index 2307cd01cdd85..02ada98f3ea95 100644 --- a/recipes/bioconductor-mbased/meta.yaml +++ b/recipes/bioconductor-mbased/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MBASED" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a182ddefc6e826fc016a735e09a4dda + md5: 441d95c8a2670c6d5fd3488ed33aad2d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbased", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-runit run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-runit test: diff --git a/recipes/bioconductor-mbcb/meta.yaml b/recipes/bioconductor-mbcb/meta.yaml index d4d4d3ad6c293..10a541c33c679 100644 --- a/recipes/bioconductor-mbcb/meta.yaml +++ b/recipes/bioconductor-mbcb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "MBCB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96f8ffc0fec24d84ad88762f060594ca + md5: 51a88491b8d5872a1088def3f6113466 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbcb", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-tcltk2 run: - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-tcltk2 test: diff --git a/recipes/bioconductor-mbecs/meta.yaml b/recipes/bioconductor-mbecs/meta.yaml index 353e54f8d4950..027ca183cf4f5 100644 --- a/recipes/bioconductor-mbecs/meta.yaml +++ b/recipes/bioconductor-mbecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MBECS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ce3a45af4cc4421da87dbb1a2350be7 + md5: 5e7481e4bcd7fc20a2251635324035a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbecs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-cluster - r-dplyr @@ -40,9 +41,9 @@ requirements: - r-tidyr - r-vegan run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-cluster - r-dplyr diff --git a/recipes/bioconductor-mbkmeans/meta.yaml b/recipes/bioconductor-mbkmeans/meta.yaml index f8b3093cd52f8..7d17593365b4e 100644 --- a/recipes/bioconductor-mbkmeans/meta.yaml +++ b/recipes/bioconductor-mbkmeans/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "mbkmeans" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7b6ff2a1ccf521fe1bf7a20e41b88d88 + md5: 1bd55f0f927fea250caa1a8264e3013c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbkmeans", max_pin="x.x") }}' # Suggests: beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-benchmarkme - r-clusterr @@ -37,13 +38,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-benchmarkme - r-clusterr diff --git a/recipes/bioconductor-mbpcr/meta.yaml b/recipes/bioconductor-mbpcr/meta.yaml index 350f2c9b1ecb9..bdcd2d19a5648 100644 --- a/recipes/bioconductor-mbpcr/meta.yaml +++ b/recipes/bioconductor-mbpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "mBPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d80f58ccbe4015bcdc599ba75d2a68d5 + md5: 1d48a3fd5a04c61ce96aa4da34d364a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbpcr", max_pin="x.x") }}' noarch: generic # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gwastools >=1.46.0,<1.47.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-mbqn/meta.yaml b/recipes/bioconductor-mbqn/meta.yaml index 201c9c2424cbf..37d730a8cbee4 100644 --- a/recipes/bioconductor-mbqn/meta.yaml +++ b/recipes/bioconductor-mbqn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "MBQN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af21afa905ec9efb9a8ae56c6c974e10 + md5: e48e4ebcd3b69b82559496b66ca4cf44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbqn", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-paireddata @@ -33,10 +34,10 @@ requirements: - r-rmarkdown - r-xml2 run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-paireddata diff --git a/recipes/bioconductor-mbqtl/meta.yaml b/recipes/bioconductor-mbqtl/meta.yaml index 7bb44f7edfa24..c92f3949b66e7 100644 --- a/recipes/bioconductor-mbqtl/meta.yaml +++ b/recipes/bioconductor-mbqtl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "mbQTL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d840e98993cc26ca1dbb216dacdda443 + md5: 5b8464d079a9297ed19fcdfade113190 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbqtl", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-broom - r-dplyr @@ -32,7 +33,7 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-broom - r-dplyr diff --git a/recipes/bioconductor-mbttest/meta.yaml b/recipes/bioconductor-mbttest/meta.yaml index 5c77e8f2124b3..a9891797e564b 100644 --- a/recipes/bioconductor-mbttest/meta.yaml +++ b/recipes/bioconductor-mbttest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "MBttest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa0087a2a95b5f53df47bea5d6076fd4 + md5: 35c603063456aab63ffa0ebfc67a3c16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mbttest", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics requirements: diff --git a/recipes/bioconductor-mcbiclust/meta.yaml b/recipes/bioconductor-mcbiclust/meta.yaml index c34d3fb25fd94..ba83c329537ca 100644 --- a/recipes/bioconductor-mcbiclust/meta.yaml +++ b/recipes/bioconductor-mcbiclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "MCbiclust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 975f96f64105c1969462273506b9d06e + md5: dd042cb41360eec094ff9596439d3aa6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mcbiclust", max_pin="x.x") }}' noarch: generic # Suggests: gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr, pander, devtools, testthat, GSVA requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-cluster - r-ggally @@ -32,10 +33,10 @@ requirements: - r-scales - r-wgcna run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-cluster - r-ggally diff --git a/recipes/bioconductor-mcsea/meta.yaml b/recipes/bioconductor-mcsea/meta.yaml index 8f97facbb1825..6e571eec95da3 100644 --- a/recipes/bioconductor-mcsea/meta.yaml +++ b/recipes/bioconductor-mcsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "mCSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91864cc204cc545d5bd60196c1176efd + md5: 8bac97f11934f91da5250521a7b26f75 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mcsea", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mcseadata >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mcseadata >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mcseadata >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mcseadata >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-mcseadata/meta.yaml b/recipes/bioconductor-mcseadata/meta.yaml index f8469dde6c5e9..08f1aea183985 100644 --- a/recipes/bioconductor-mcseadata/meta.yaml +++ b/recipes/bioconductor-mcseadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "mCSEAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43b69165fffc6652fc2df2395bd0b8e6 + md5: 11f8150e223a0e8d8fa5b9b8dedaa374 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mcseadata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230717 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mcseadata/post-link.sh b/recipes/bioconductor-mcseadata/post-link.sh index 2eeaf2308191f..eddebf7dac4c4 100644 --- a/recipes/bioconductor-mcseadata/post-link.sh +++ b/recipes/bioconductor-mcseadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mcseadata-1.20.1" +installBiocDataPackage.sh "mcseadata-1.22.0" diff --git a/recipes/bioconductor-mcsurvdata/meta.yaml b/recipes/bioconductor-mcsurvdata/meta.yaml index ec4f53953e076..07bb985fda8c3 100644 --- a/recipes/bioconductor-mcsurvdata/meta.yaml +++ b/recipes/bioconductor-mcsurvdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "mcsurvdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4e4b6fa4d49cfa4588d65cb3a22ab121 + md5: 0299258c7610f3675dc0b9f8e333eefa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mcsurvdata", max_pin="x.x") }}' noarch: generic -# Suggests: knitr +# Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mcsurvdata/post-link.sh b/recipes/bioconductor-mcsurvdata/post-link.sh index f95e358811081..2585fbcb3d43f 100644 --- a/recipes/bioconductor-mcsurvdata/post-link.sh +++ b/recipes/bioconductor-mcsurvdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mcsurvdata-1.18.0" +installBiocDataPackage.sh "mcsurvdata-1.20.0" diff --git a/recipes/bioconductor-mdp/meta.yaml b/recipes/bioconductor-mdp/meta.yaml index b78f40966c9e2..b0c34a1dd0fdb 100644 --- a/recipes/bioconductor-mdp/meta.yaml +++ b/recipes/bioconductor-mdp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "mdp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2ffda81dd0c84bae56391e259a9b8e30 + md5: a947b52acd7f930a3babcdb4e429bb0c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mdp", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, fgsea, BiocManager requirements: diff --git a/recipes/bioconductor-mdqc/meta.yaml b/recipes/bioconductor-mdqc/meta.yaml index db49be2c8f742..1ffa27337522e 100644 --- a/recipes/bioconductor-mdqc/meta.yaml +++ b/recipes/bioconductor-mdqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "mdqc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b3ec385cc5a3e1239228514e209bcc3e + md5: a9dd8adf71b5fe15b4b5b444f0b43110 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mdqc", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mdts/meta.yaml b/recipes/bioconductor-mdts/meta.yaml index d7b9e11c822c9..4f9602a0f22b3 100644 --- a/recipes/bioconductor-mdts/meta.yaml +++ b/recipes/bioconductor-mdts/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MDTS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c9c5c88b0658f84733f792cdd6bdaed + md5: a9ab8fa7a5e9ef7dcdb28fb553b895f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mdts", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-stringr test: diff --git a/recipes/bioconductor-meal/meta.yaml b/recipes/bioconductor-meal/meta.yaml index 247dfcfd6a427..3ab450a08d105 100644 --- a/recipes/bioconductor-meal/meta.yaml +++ b/recipes/bioconductor-meal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "MEAL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9de73f065fd4e5bfad6f5b3d9aea5ea0 + md5: f157edf85ba036b17edb728a44e2e519 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meal", max_pin="x.x") }}' noarch: generic # Suggests: testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-missmethyl >=1.36.0,<1.37.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-ggplot2 >=2.0.0' - r-isva @@ -40,17 +41,17 @@ requirements: - r-smartsva - r-vegan run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-missmethyl >=1.36.0,<1.37.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-ggplot2 >=2.0.0' - r-isva diff --git a/recipes/bioconductor-measurementerror.cor/meta.yaml b/recipes/bioconductor-measurementerror.cor/meta.yaml index 5a6ed80d42dd6..a008cdd80f4d1 100644 --- a/recipes/bioconductor-measurementerror.cor/meta.yaml +++ b/recipes/bioconductor-measurementerror.cor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "MeasurementError.cor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8d6f3c05b7e609ef2150c1bc1a294ea + md5: 7de3f5ca3749a7b1e80fdfa66204a252 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-measurementerror.cor", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-meat/meta.yaml b/recipes/bioconductor-meat/meta.yaml index 3043cdb47180e..084d2922cfced 100644 --- a/recipes/bioconductor-meat/meta.yaml +++ b/recipes/bioconductor-meat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MEAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3f19960d36b1330ef8aee3c8b0922fc + md5: ea3f3041f0bdfab3844cea85f8d28c9b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meat", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base - r-dplyr - 'r-dynamictreecut >=1.63' @@ -33,10 +34,10 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base - r-dplyr - 'r-dynamictreecut >=1.63' diff --git a/recipes/bioconductor-meb/meta.yaml b/recipes/bioconductor-meb/meta.yaml index 74df08e06a995..fbe884a83a68b 100644 --- a/recipes/bioconductor-meb/meta.yaml +++ b/recipes/bioconductor-meb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MEB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d4d4b70c1d2127e1dd18241c6fabde2 + md5: b1785984524fee5b32976a5e768037d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meb", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown,BiocStyle requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-wrswor run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-wrswor diff --git a/recipes/bioconductor-medicagocdf/meta.yaml b/recipes/bioconductor-medicagocdf/meta.yaml index f055eb8e01c78..4f18d4e92ad67 100644 --- a/recipes/bioconductor-medicagocdf/meta.yaml +++ b/recipes/bioconductor-medicagocdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "medicagocdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1fbb2e4c070344d18e65f1b3993867db build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-medicagocdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-medicagoprobe/meta.yaml b/recipes/bioconductor-medicagoprobe/meta.yaml index f508bc9f63561..64886de29099e 100644 --- a/recipes/bioconductor-medicagoprobe/meta.yaml +++ b/recipes/bioconductor-medicagoprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "medicagoprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83b9887ad2ed26c704b0ca7115e5838d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-medicagoprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-medips/meta.yaml b/recipes/bioconductor-medips/meta.yaml index 314a6d555c7ca..fa842250f78ce 100644 --- a/recipes/bioconductor-medips/meta.yaml +++ b/recipes/bioconductor-medips/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "MEDIPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f9d22ca90431583329f7bc0d04937b21 + md5: 088394b1864d37eba7ed1064a9d671e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-medips", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-gtools run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-gtools test: diff --git a/recipes/bioconductor-medipsdata/meta.yaml b/recipes/bioconductor-medipsdata/meta.yaml index 22526db86a800..898fea78b24ec 100644 --- a/recipes/bioconductor-medipsdata/meta.yaml +++ b/recipes/bioconductor-medipsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "MEDIPSData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d6d822abd5a2acc639cad1a270f03a2d + md5: 7b329ecedb2e9911b92ad669856abf2b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-medipsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-medipsdata/post-link.sh b/recipes/bioconductor-medipsdata/post-link.sh index a62231fab4e43..82ae17809dfbd 100644 --- a/recipes/bioconductor-medipsdata/post-link.sh +++ b/recipes/bioconductor-medipsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "medipsdata-1.36.0" +installBiocDataPackage.sh "medipsdata-1.38.0" diff --git a/recipes/bioconductor-medme/meta.yaml b/recipes/bioconductor-medme/meta.yaml index 366e23083231d..83cc34d658330 100644 --- a/recipes/bioconductor-medme/meta.yaml +++ b/recipes/bioconductor-medme/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "MEDME" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5459677fe2fd70028253a9a58f4caf5 + md5: 03868c2e2f04af9c9f33d48cc6abed08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-medme", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-drc - r-mass - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-drc - r-mass diff --git a/recipes/bioconductor-meebodata/meta.yaml b/recipes/bioconductor-meebodata/meta.yaml index d31b64df4acf4..4f4e1ad5b8435 100644 --- a/recipes/bioconductor-meebodata/meta.yaml +++ b/recipes/bioconductor-meebodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "MEEBOdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0eb2ee76322ae64e44bb926769bd1f77 + md5: cd3b9bb8a918c9497903f6274f323904 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meebodata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-meebodata/post-link.sh b/recipes/bioconductor-meebodata/post-link.sh index 7e37c76550466..f406ddac9857c 100644 --- a/recipes/bioconductor-meebodata/post-link.sh +++ b/recipes/bioconductor-meebodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "meebodata-1.38.0" +installBiocDataPackage.sh "meebodata-1.40.0" diff --git a/recipes/bioconductor-megadepth/meta.yaml b/recipes/bioconductor-megadepth/meta.yaml index 6819b6c8c78ef..c3dc6063d66e7 100644 --- a/recipes/bioconductor-megadepth/meta.yaml +++ b/recipes/bioconductor-megadepth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "megadepth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 51770a42690eedccaf6282e0b5dbdf61 + md5: 5fa04f9d4075030126388db419378304 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-megadepth", max_pin="x.x") }}' noarch: generic # Suggests: covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat # SystemRequirements: megadepth () requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-cmdfun - r-dplyr @@ -31,7 +32,7 @@ requirements: - r-readr - r-xfun run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-cmdfun - r-dplyr diff --git a/recipes/bioconductor-melissa/meta.yaml b/recipes/bioconductor-melissa/meta.yaml index 47c67940b57d9..c69b137991ec8 100644 --- a/recipes/bioconductor-melissa/meta.yaml +++ b/recipes/bioconductor-melissa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Melissa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1557389f567dcdd1cc017fc4bd688d16 + md5: 25f975650bec04b62c6e022b11cc33c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-melissa", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-bprmeth >=1.26.0,<1.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-bprmeth >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-assertthat - r-base - r-cowplot @@ -39,9 +40,9 @@ requirements: - r-rocr - r-truncnorm run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-bprmeth >=1.26.0,<1.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-bprmeth >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-assertthat - r-base - r-cowplot diff --git a/recipes/bioconductor-memes/meta.yaml b/recipes/bioconductor-memes/meta.yaml index 7c654b09008a7..eb689687be72c 100644 --- a/recipes/bioconductor-memes/meta.yaml +++ b/recipes/bioconductor-memes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "memes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 637b0a3bf608e7dbdb5b909a53fb1815 + md5: c9b7baebb9608344040a4dc38a05dea3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-memes", max_pin="x.x") }}' noarch: generic # Suggests: cowplot, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr # SystemRequirements: Meme Suite (v5.3.3 or above) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-universalmotif >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-universalmotif >=1.20.0,<1.21.0' - r-base - 'r-cmdfun >=1.0.2' - r-dplyr @@ -42,9 +43,9 @@ requirements: - r-usethis - r-xml2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-universalmotif >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-universalmotif >=1.20.0,<1.21.0' - r-base - 'r-cmdfun >=1.0.2' - r-dplyr diff --git a/recipes/bioconductor-merfishdata/meta.yaml b/recipes/bioconductor-merfishdata/meta.yaml index 7577ff46666b0..70f5bd162ef8c 100644 --- a/recipes/bioconductor-merfishdata/meta.yaml +++ b/recipes/bioconductor-merfishdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.1" %} {% set name = "MerfishData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4e86b95520641c0d3f1b5c938d5a3b7 + md5: 05369f89c4e1a15bdab1ce5174facbe4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-merfishdata", max_pin="x.x") }}' noarch: generic -# Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle +# Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle, DropletUtils requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-merfishdata/post-link.sh b/recipes/bioconductor-merfishdata/post-link.sh index 96590c781dc87..d616f8e059879 100644 --- a/recipes/bioconductor-merfishdata/post-link.sh +++ b/recipes/bioconductor-merfishdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "merfishdata-1.2.0" +installBiocDataPackage.sh "merfishdata-1.4.1" diff --git a/recipes/bioconductor-mergeomics/meta.yaml b/recipes/bioconductor-mergeomics/meta.yaml index a8273f2a04cda..5284a10f7d961 100644 --- a/recipes/bioconductor-mergeomics/meta.yaml +++ b/recipes/bioconductor-mergeomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Mergeomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed07a8df123e4d35ec9671e2cad53bf5 + md5: 1b8f5bc8cf54fa99df988a83c71737d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mergeomics", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-meshdbi/meta.yaml b/recipes/bioconductor-meshdbi/meta.yaml index 2a2268ae1d56d..05e67cd414ef0 100644 --- a/recipes/bioconductor-meshdbi/meta.yaml +++ b/recipes/bioconductor-meshdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "MeSHDbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acde95248b916ed0e3674a2d030c45b5 + md5: edb738bd5c18f7017ebd13bd0cce9d2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meshdbi", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rsqlite test: diff --git a/recipes/bioconductor-meshes/meta.yaml b/recipes/bioconductor-meshes/meta.yaml index c7227ce2fb5dc..860286dd24bc5 100644 --- a/recipes/bioconductor-meshes/meta.yaml +++ b/recipes/bioconductor-meshes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "meshes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f7b0ab25441510c48b40e9ab09a53615 + md5: 90be6eeeb3ced1146ddcba48e2ec6c6e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meshes", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, prettydoc requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' - r-base - r-yulab.utils run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' - r-base - r-yulab.utils test: diff --git a/recipes/bioconductor-meshr/meta.yaml b/recipes/bioconductor-meshr/meta.yaml index b973725c15fa7..529a0bdbb3121 100644 --- a/recipes/bioconductor-meshr/meta.yaml +++ b/recipes/bioconductor-meshr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "meshr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7bcf4253b38df394c838c2cc477f84a9 + md5: 7809b970dabdb3c42112e6b3aad5b75b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meshr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fdrtool - r-knitr @@ -32,11 +33,11 @@ requirements: - r-rmarkdown - r-rsqlite run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fdrtool - r-knitr diff --git a/recipes/bioconductor-meskit/meta.yaml b/recipes/bioconductor-meskit/meta.yaml index efea8c2955c60..df270a05c0104 100644 --- a/recipes/bioconductor-meskit/meta.yaml +++ b/recipes/bioconductor-meskit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MesKit" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eac8c8557107d7d2efca76e50a999af0 + md5: 909ad92f34384c66c0e86f0f13ff7e71 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-meskit", max_pin="x.x") }}' noarch: generic # Suggests: shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), org.Hs.eg.db, clusterProfiler, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-ape >=5.4.1' - r-base - r-circlize @@ -41,11 +42,11 @@ requirements: - r-rcolorbrewer - 'r-tidyr >=1.0.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-ape >=5.4.1' - r-base - r-circlize diff --git a/recipes/bioconductor-messina/meta.yaml b/recipes/bioconductor-messina/meta.yaml index 2a5a2a4501225..48739dc5c9b95 100644 --- a/recipes/bioconductor-messina/meta.yaml +++ b/recipes/bioconductor-messina/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "messina" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 62c9610704259aa1b9f838966beac394 + md5: ad9cfdec37597c8a312b49085f1ff124 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-messina", max_pin="x.x") }}' # Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle requirements: host: diff --git a/recipes/bioconductor-metabcombiner/meta.yaml b/recipes/bioconductor-metabcombiner/meta.yaml index 7b6bcb0515d1d..9b9563bf04b9f 100644 --- a/recipes/bioconductor-metabcombiner/meta.yaml +++ b/recipes/bioconductor-metabcombiner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "metabCombiner" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb2078d2857b0824411b6d7942c469ef + md5: 9840a8f7cdc657e21d3ebc2a7b6b68b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabcombiner", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - 'r-dplyr >=1.0' @@ -31,7 +32,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - 'r-dplyr >=1.0' diff --git a/recipes/bioconductor-metabinr/meta.yaml b/recipes/bioconductor-metabinr/meta.yaml index c7e099f880000..67899dd2e1f85 100644 --- a/recipes/bioconductor-metabinr/meta.yaml +++ b/recipes/bioconductor-metabinr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "metabinR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66c3ea5a3163579c070dde3a0a7fb1f7 + md5: 7080ae8eac49640aeae95bda1185ac7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabinr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) # SystemRequirements: Java (>= 8) diff --git a/recipes/bioconductor-metaboannotation/meta.yaml b/recipes/bioconductor-metaboannotation/meta.yaml index bcedfe552443b..4664b5262cd69 100644 --- a/recipes/bioconductor-metaboannotation/meta.yaml +++ b/recipes/bioconductor-metaboannotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.1" %} {% set name = "MetaboAnnotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ddd0682814407d9262bc9e82c223adb3 + md5: fee181fc1795a1e2bde1d1e551f1a45e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metaboannotation", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, AnnotationHub, microbenchmark, mzR +# Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, microbenchmark, mzR requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-compounddb >=1.4.0,<1.5.0' - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-compounddb >=1.6.0,<1.7.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-compounddb >=1.4.0,<1.5.0' - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-compounddb >=1.6.0,<1.7.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-metabocoreutils/meta.yaml b/recipes/bioconductor-metabocoreutils/meta.yaml index 592a4adbde4b1..a73ae28540ebe 100644 --- a/recipes/bioconductor-metabocoreutils/meta.yaml +++ b/recipes/bioconductor-metabocoreutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MetaboCoreUtils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91404bfbcac731a6ee59e80d777e2148 + md5: e4b834af09aa89158b64b8586d4d15c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabocoreutils", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - r-base run: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - r-base test: commands: diff --git a/recipes/bioconductor-metaboliteidmapping/meta.yaml b/recipes/bioconductor-metaboliteidmapping/meta.yaml index d8785e941a169..e248f2cb8aadb 100644 --- a/recipes/bioconductor-metaboliteidmapping/meta.yaml +++ b/recipes/bioconductor-metaboliteidmapping/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "metaboliteIDmapping" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bd78ec373ce90fac1a10d2c64c462e77 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metaboliteidmapping", max_pin="x.x") }}' noarch: generic # Suggests: magrittr, graphite, dplyr, tidyr, tibble, rappdirs, XML, readxl, stringr, utils, knitr, sets, R.utils, readr, conflicted, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml b/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml index e85a7ad245869..d4c21164ee6d0 100644 --- a/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml +++ b/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "metabolomicsWorkbenchR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5501c9f3300368e1e579ddf3eb89b678 + md5: 7e8485177f5ad463ff6a0f6e573e74fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabolomicsworkbenchr", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, covr, knitr, HDF5Array, rmarkdown, structToolbox, testthat, pmp, grid, png +# Suggests: BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown, structToolbox, testthat, pmp, grid, png requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-struct >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-struct >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-httr - r-jsonlite run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-struct >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-struct >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-httr diff --git a/recipes/bioconductor-metabomxtr/meta.yaml b/recipes/bioconductor-metabomxtr/meta.yaml index 67917cf5d5f8e..1ab86aa0f3f66 100644 --- a/recipes/bioconductor-metabomxtr/meta.yaml +++ b/recipes/bioconductor-metabomxtr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "metabomxtr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9b3776d7ca5080f4c33fffbf74603ca8 + md5: ec247e3fe8099096d1bfcc8fff93f08d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabomxtr", max_pin="x.x") }}' noarch: generic # Suggests: xtable, reshape2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-formula - r-ggplot2 - r-optimx - r-plyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-formula - r-ggplot2 diff --git a/recipes/bioconductor-metabosignal/meta.yaml b/recipes/bioconductor-metabosignal/meta.yaml index d737fef136bbb..01f312d812830 100644 --- a/recipes/bioconductor-metabosignal/meta.yaml +++ b/recipes/bioconductor-metabosignal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.1" %} +{% set version = "1.32.0" %} {% set name = "MetaboSignal" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ff7b743e46475cfa8a60e92bcea0986 + md5: a8f1dc09626a1881461f987e726078bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metabosignal", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - - 'bioconductor-hpar >=1.42.0,<1.43.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-mwastools >=1.24.0,<1.25.0' - - 'bioconductor-mygene >=1.36.0,<1.37.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-hpar >=1.44.0,<1.45.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-mwastools >=1.26.0,<1.27.0' + - 'bioconductor-mygene >=1.38.0,<1.39.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-igraph - r-rcurl run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - - 'bioconductor-hpar >=1.42.0,<1.43.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-mwastools >=1.24.0,<1.25.0' - - 'bioconductor-mygene >=1.36.0,<1.37.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-hpar >=1.44.0,<1.45.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-mwastools >=1.26.0,<1.27.0' + - 'bioconductor-mygene >=1.38.0,<1.39.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-igraph - r-rcurl diff --git a/recipes/bioconductor-metacca/meta.yaml b/recipes/bioconductor-metacca/meta.yaml index 4f5e4e50e1ea6..851175efd2c07 100644 --- a/recipes/bioconductor-metacca/meta.yaml +++ b/recipes/bioconductor-metacca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "metaCCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94d27eb69649e28b07201192f1022a8e + md5: d5be58f253912b275964a681a508234d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metacca", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: diff --git a/recipes/bioconductor-metacyto/meta.yaml b/recipes/bioconductor-metacyto/meta.yaml index b5da01927e8db..e7c7260f307a2 100644 --- a/recipes/bioconductor-metacyto/meta.yaml +++ b/recipes/bioconductor-metacyto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "MetaCyto" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22428db1b2332f3d7fbde4f03fc5ffed + md5: 0cd04a831a226a35bdeb881c03d30193 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metacyto", max_pin="x.x") }}' noarch: generic # Suggests: knitr, dplyr, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' - r-base - r-cluster - r-fastcluster @@ -30,8 +31,8 @@ requirements: - r-metafor - 'r-tidyr >=0.7' run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowsom >=2.8.0,<2.9.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowsom >=2.10.0,<2.11.0' - r-base - r-cluster - r-fastcluster diff --git a/recipes/bioconductor-metagene2/meta.yaml b/recipes/bioconductor-metagene2/meta.yaml index 9fdcbd6880db6..7b828dbbaba57 100644 --- a/recipes/bioconductor-metagene2/meta.yaml +++ b/recipes/bioconductor-metagene2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "metagene2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7b21feb21c30995a96cbec500bb9148a + md5: adef0ffd2a7cec30870a2b66eb2cb4f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metagene2", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr @@ -37,13 +38,13 @@ requirements: - 'r-r6 >=2.0' - r-reshape2 run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-metagenomeseq/meta.yaml b/recipes/bioconductor-metagenomeseq/meta.yaml index f415ce2a68608..73137c6fc52d9 100644 --- a/recipes/bioconductor-metagenomeseq/meta.yaml +++ b/recipes/bioconductor-metagenomeseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.43.0" %} {% set name = "metagenomeSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 639ed9fe16c0bf887c363a66a1e8e5eb + md5: ea0139abb9cbcda1f445b3527e621345 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metagenomeseq", max_pin="x.x") }}' noarch: generic # Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-wrench >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-wrench >=1.20.0,<1.21.0' - r-base - r-foreach - r-glmnet @@ -32,9 +33,9 @@ requirements: - r-matrixstats - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-wrench >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-wrench >=1.20.0,<1.21.0' - r-base - r-foreach - r-glmnet diff --git a/recipes/bioconductor-metagxbreast/meta.yaml b/recipes/bioconductor-metagxbreast/meta.yaml index c75e7b63ed502..969e8d8c535ba 100644 --- a/recipes/bioconductor-metagxbreast/meta.yaml +++ b/recipes/bioconductor-metagxbreast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MetaGxBreast" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38b605d1c36990f9ae722ed9391afb75 + md5: e711302482bca1429de5fe2e5276c788 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metagxbreast", max_pin="x.x") }}' noarch: generic # Suggests: testthat, xtable, tinytex requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metagxbreast/post-link.sh b/recipes/bioconductor-metagxbreast/post-link.sh index f778c7b5da540..e04b480c25fb1 100644 --- a/recipes/bioconductor-metagxbreast/post-link.sh +++ b/recipes/bioconductor-metagxbreast/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metagxbreast-1.20.0" +installBiocDataPackage.sh "metagxbreast-1.22.0" diff --git a/recipes/bioconductor-metagxovarian/meta.yaml b/recipes/bioconductor-metagxovarian/meta.yaml index 7105fb8cdc088..a6cf76c8d62c9 100644 --- a/recipes/bioconductor-metagxovarian/meta.yaml +++ b/recipes/bioconductor-metagxovarian/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MetaGxOvarian" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 180366821492879a0fc25f4b4117b20f + md5: f76dc6c912d3a8936f81509ba6559286 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metagxovarian", max_pin="x.x") }}' noarch: generic # Suggests: testthat, xtable, rmarkdown, knitr, BiocStyle, markdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metagxovarian/post-link.sh b/recipes/bioconductor-metagxovarian/post-link.sh index d364690daf944..a592b878de955 100644 --- a/recipes/bioconductor-metagxovarian/post-link.sh +++ b/recipes/bioconductor-metagxovarian/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metagxovarian-1.20.0" +installBiocDataPackage.sh "metagxovarian-1.22.0" diff --git a/recipes/bioconductor-metagxpancreas/meta.yaml b/recipes/bioconductor-metagxpancreas/meta.yaml index 2bb9483835525..0486ab5f27c80 100644 --- a/recipes/bioconductor-metagxpancreas/meta.yaml +++ b/recipes/bioconductor-metagxpancreas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MetaGxPancreas" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 837617be22e87ee2716a5bd6888bb204 + md5: 0c1764dc18a9a180b2121649c98a26a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metagxpancreas", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown, markdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metagxpancreas/post-link.sh b/recipes/bioconductor-metagxpancreas/post-link.sh index b2264e376b686..325b7237840e4 100644 --- a/recipes/bioconductor-metagxpancreas/post-link.sh +++ b/recipes/bioconductor-metagxpancreas/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metagxpancreas-1.20.0" +installBiocDataPackage.sh "metagxpancreas-1.22.0" diff --git a/recipes/bioconductor-metahdep/build_failure.osx-64.yaml b/recipes/bioconductor-metahdep/build_failure.osx-64.yaml index a39539fdd7101..8f5e1414fd2f4 100644 --- a/recipes/bioconductor-metahdep/build_failure.osx-64.yaml +++ b/recipes/bioconductor-metahdep/build_failure.osx-64.yaml @@ -1,4 +1,4 @@ -recipe_sha: 2edfbb98f63d48d98994d4c4daecfd4678c9619a700efddca7297420a69e54f1 # The commit at which this recipe failed to build. +recipe_sha: 7d681cfa3280b3e2180df68fba6a82a10dab63dfb65f81b7020b5d2b80a134a9 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran @@ -102,3 +102,7 @@ log: |- raise subprocess.CalledProcessError(proc.returncode, _args) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1689833451644/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. +reason: |- + 19:17:50 BIOCONDA INFO (ERR) metahdep.c:471:79: error: incompatible pointer to integer conversion passing 'const char *' to parameter of type 'char' [-Wint-conversion] +category: |- + compiler error diff --git a/recipes/bioconductor-metahdep/meta.yaml b/recipes/bioconductor-metahdep/meta.yaml index 42b9943246328..c8dc23a250052 100644 --- a/recipes/bioconductor-metahdep/meta.yaml +++ b/recipes/bioconductor-metahdep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "metahdep" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3a49994338fecd947fd4e144745b4a39 + md5: 578b66621982372185989aa8559f8293 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metahdep", max_pin="x.x") }}' # Suggests: affyPLM requirements: host: diff --git a/recipes/bioconductor-metams/meta.yaml b/recipes/bioconductor-metams/meta.yaml index 0551920c729ad..af42016d642d6 100644 --- a/recipes/bioconductor-metams/meta.yaml +++ b/recipes/bioconductor-metams/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "metaMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d64ce34b47d681fb1064f1ff93f320ed + md5: c26507515ab859aa42dbea4acc8cacc3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metams", max_pin="x.x") }}' noarch: generic # Suggests: metaMSdata, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-matrix - r-robustbase run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-matrix - r-robustbase diff --git a/recipes/bioconductor-metamsdata/meta.yaml b/recipes/bioconductor-metamsdata/meta.yaml index 7d1d70162c264..b6730e4cfe2c3 100644 --- a/recipes/bioconductor-metamsdata/meta.yaml +++ b/recipes/bioconductor-metamsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "metaMSdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c4408ceda2098402daaa6c94bbd3768 + md5: aa7ca09c8f43104cb85f69fda0a1fc1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metamsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-metamsdata/post-link.sh b/recipes/bioconductor-metamsdata/post-link.sh index c93f33a23616f..6e2a1a56a7ab7 100644 --- a/recipes/bioconductor-metamsdata/post-link.sh +++ b/recipes/bioconductor-metamsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metamsdata-1.36.0" +installBiocDataPackage.sh "metamsdata-1.38.0" diff --git a/recipes/bioconductor-metaneighbor/meta.yaml b/recipes/bioconductor-metaneighbor/meta.yaml index 67b3e6cb1a37b..cdd31dff18139 100644 --- a/recipes/bioconductor-metaneighbor/meta.yaml +++ b/recipes/bioconductor-metaneighbor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MetaNeighbor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d8a02ccc2353f4a830b1a600e6cb070 + md5: 4b42a5bac6ac46bdff32c5cce84e448d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metaneighbor", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2), UpSetR requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-beanplot >=1.2' - r-dplyr @@ -35,8 +36,8 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-beanplot >=1.2' - r-dplyr diff --git a/recipes/bioconductor-metaphor/meta.yaml b/recipes/bioconductor-metaphor/meta.yaml index fb3841cdd3fe7..ee6d1a43d5289 100644 --- a/recipes/bioconductor-metaphor/meta.yaml +++ b/recipes/bioconductor-metaphor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MetaPhOR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd33f344dadc728d1802df7f7596818b + md5: 311e286126427130d127b23a77b3b6f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metaphor", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, kableExtra # SystemRequirements: Cytoscape (>= 3.9.0) for the cytoPath() examples requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-ggplot2 - r-ggrepel @@ -31,8 +32,8 @@ requirements: - r-recordlinkage - r-stringr run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-metapod/meta.yaml b/recipes/bioconductor-metapod/meta.yaml index 81f246e9c0d13..e354996b693d3 100644 --- a/recipes/bioconductor-metapod/meta.yaml +++ b/recipes/bioconductor-metapod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "metapod" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ed81a84b379501af983bb5c25262b63f + md5: 49bf3f5df3f99c0d4068224a8f51eacc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metapod", max_pin="x.x") }}' # Suggests: testthat, knitr, BiocStyle, rmarkdown # SystemRequirements: C++11 requirements: diff --git a/recipes/bioconductor-metapone/meta.yaml b/recipes/bioconductor-metapone/meta.yaml index f011d1814093c..491d13b08b3c4 100644 --- a/recipes/bioconductor-metapone/meta.yaml +++ b/recipes/bioconductor-metapone/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "metapone" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a346aa647de2ac05f8f3494c5fa9c09 + md5: d53938772148968f88fab10130dbc905 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metapone", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - r-fdrtool - r-fields @@ -30,8 +31,8 @@ requirements: - r-ggrepel - r-markdown run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' - r-base - r-fdrtool - r-fields diff --git a/recipes/bioconductor-metascope/meta.yaml b/recipes/bioconductor-metascope/meta.yaml index b0a892aca1284..4e41830dd7494 100644 --- a/recipes/bioconductor-metascope/meta.yaml +++ b/recipes/bioconductor-metascope/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MetaScope" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aef272f5f78bc787f42bd9c47b923cfb + md5: 3e9dbacc12fa3bd332773ffa95325f0b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metascope", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, biomformat, knitr, lintr, plyr, rmarkdown, Rsubread, spelling, sys, testthat, usethis +# Suggests: BiocStyle, biomformat, knitr, lintr, plyr, R.utils, rmarkdown, Rsubread, spelling, sys, testthat, usethis requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -35,20 +36,19 @@ requirements: - r-magrittr - r-matrix - r-qlcmatrix - - r-r.utils - r-readr - r-rlang - r-stringr - r-taxize - r-tidyr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -56,14 +56,13 @@ requirements: - r-magrittr - r-matrix - r-qlcmatrix - - r-r.utils - r-readr - r-rlang - r-stringr - r-taxize - r-tidyr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' @@ -71,6 +70,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data' - description: 'This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is partly an R translation of the PathoScope 2.0 pipeline.' + description: 'This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-metascope/post-link.sh b/recipes/bioconductor-metascope/post-link.sh index f94aeef0d0954..e3bd6b90fb0e0 100644 --- a/recipes/bioconductor-metascope/post-link.sh +++ b/recipes/bioconductor-metascope/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metascope-1.0.0" +installBiocDataPackage.sh "metascope-1.2.0" diff --git a/recipes/bioconductor-metaseq/meta.yaml b/recipes/bioconductor-metaseq/meta.yaml index c229f390a9ea5..564aeea18d8a0 100644 --- a/recipes/bioconductor-metaseq/meta.yaml +++ b/recipes/bioconductor-metaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "metaSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7805af79576c88c0861543ebb4b731a0 + md5: 8c3ee60501395cc86ecda6817d0d5439 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metaseq", max_pin="x.x") }}' requirements: host: - - 'bioconductor-noiseq >=2.44.0,<2.45.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' - r-base - r-rcpp - r-snow - libblas - liblapack run: - - 'bioconductor-noiseq >=2.44.0,<2.45.0' + - 'bioconductor-noiseq >=2.46.0,<2.47.0' - r-base - r-rcpp - r-snow diff --git a/recipes/bioconductor-metcirc/meta.yaml b/recipes/bioconductor-metcirc/meta.yaml index 89b5bb1a95cba..c70232ee98cfa 100644 --- a/recipes/bioconductor-metcirc/meta.yaml +++ b/recipes/bioconductor-metcirc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "MetCirc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 420d7e30089b00444306978ccac47184 + md5: c21a385245acf6911f5c762093ea6e0b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metcirc", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), testthat (>= 2.2.1) requirements: host: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - 'r-amap >=0.8' - r-base - 'r-circlize >=0.3.9' @@ -31,9 +32,9 @@ requirements: - 'r-scales >=0.3.0' - 'r-shiny >=1.0.0' run: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - 'r-amap >=0.8' - r-base - 'r-circlize >=0.3.9' diff --git a/recipes/bioconductor-methimpute/meta.yaml b/recipes/bioconductor-methimpute/meta.yaml index 110306a836ace..65d687e154683 100644 --- a/recipes/bioconductor-methimpute/meta.yaml +++ b/recipes/bioconductor-methimpute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "methimpute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: edb7a53f8b002f4b0d135381af736420 + md5: 7b2a598d7391c33c4ba82639616077e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methimpute", max_pin="x.x") }}' # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table - r-ggplot2 @@ -33,10 +34,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-methinheritsim/meta.yaml b/recipes/bioconductor-methinheritsim/meta.yaml index e17311bc74346..d131c38563f89 100644 --- a/recipes/bioconductor-methinheritsim/meta.yaml +++ b/recipes/bioconductor-methinheritsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "methInheritSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e84fe101c5de73da2e8764b71ec3e467 + md5: c695628dcb686ee7e6a3f4ee134481ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methinheritsim", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-msm run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-msm test: diff --git a/recipes/bioconductor-methped/meta.yaml b/recipes/bioconductor-methped/meta.yaml index 1d52a997eacd3..ab47c7a890944 100644 --- a/recipes/bioconductor-methped/meta.yaml +++ b/recipes/bioconductor-methped/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "MethPed" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b811e3dcc16dd85f75fc300602d99845 + md5: 57b633da5d8548342b0a2071efe3c04d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methped", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, markdown, impute requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-randomforest run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-randomforest test: diff --git a/recipes/bioconductor-methreg/meta.yaml b/recipes/bioconductor-methreg/meta.yaml index 59fcc9250f4b5..639722859e243 100644 --- a/recipes/bioconductor-methreg/meta.yaml +++ b/recipes/bioconductor-methreg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MethReg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 33bbfd93bde253c973cc8324e4475bde + md5: 0c092ea7b8883b6c125e64e16030bca6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methreg", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, downloader, R.utils, doParallel, reshape2, JASPAR2022, TFBSTools, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19 +# Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, downloader, R.utils, doParallel, reshape2, JASPAR2022, TFBSTools, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, openxlsx, data.table, downloader requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sesame >=1.18.0,<1.19.0' - - 'bioconductor-sesamedata >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sesame >=1.20.0,<1.21.0' + - 'bioconductor-sesamedata >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -46,15 +47,15 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sesame >=1.18.0,<1.19.0' - - 'bioconductor-sesamedata >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sesame >=1.20.0,<1.21.0' + - 'bioconductor-sesamedata >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-methrix/meta.yaml b/recipes/bioconductor-methrix/meta.yaml index 5f837225e9e2f..bd7c11532203f 100644 --- a/recipes/bioconductor-methrix/meta.yaml +++ b/recipes/bioconductor-methrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "methrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e0de73ac035291e3328e4157b193997 + md5: 7bdda59fc802fc09d10ca9a4916cfe94 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methrix", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) +# Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.12.4' - r-ggplot2 - r-matrixstats run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.12.4' - r-ggplot2 diff --git a/recipes/bioconductor-methtargetedngs/meta.yaml b/recipes/bioconductor-methtargetedngs/meta.yaml index 6193170be0067..fb49f0aa6445e 100644 --- a/recipes/bioconductor-methtargetedngs/meta.yaml +++ b/recipes/bioconductor-methtargetedngs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "MethTargetedNGS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6777e1517295425bd1b7e6763d58793 + md5: 0bce9edc9682a9ca23653409301d7225 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methtargetedngs", max_pin="x.x") }}' noarch: generic # SystemRequirements: HMMER3 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-gplots - r-seqinr - r-stringr - 'hmmer >=3' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-gplots - r-seqinr diff --git a/recipes/bioconductor-methylaid/meta.yaml b/recipes/bioconductor-methylaid/meta.yaml index 11cefa78cfba2..d6bdffb88c0f7 100644 --- a/recipes/bioconductor-methylaid/meta.yaml +++ b/recipes/bioconductor-methylaid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MethylAid" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8f44cf538be4d026ac332365de6063c + md5: 8e5139726d6384208be410a794ba6388 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylaid", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-gridbase @@ -34,11 +35,11 @@ requirements: - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-gridbase diff --git a/recipes/bioconductor-methylaiddata/meta.yaml b/recipes/bioconductor-methylaiddata/meta.yaml index 2c6f2f3bc4f90..9d93dbaa10899 100644 --- a/recipes/bioconductor-methylaiddata/meta.yaml +++ b/recipes/bioconductor-methylaiddata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "MethylAidData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43ab55538e535cab63f2594898cfbda4 + md5: 95cc72b436067e4a8046564381101e04 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylaiddata", max_pin="x.x") }}' noarch: generic # Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC requirements: host: - - 'bioconductor-methylaid >=1.34.0,<1.35.0' + - 'bioconductor-methylaid >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-methylaid >=1.34.0,<1.35.0' + - 'bioconductor-methylaid >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-methylaiddata/post-link.sh b/recipes/bioconductor-methylaiddata/post-link.sh index bfc7879f10589..05ddd59e85e4c 100644 --- a/recipes/bioconductor-methylaiddata/post-link.sh +++ b/recipes/bioconductor-methylaiddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "methylaiddata-1.32.0" +installBiocDataPackage.sh "methylaiddata-1.34.0" diff --git a/recipes/bioconductor-methylcc/meta.yaml b/recipes/bioconductor-methylcc/meta.yaml index ef779d73a8837..55e496807a54b 100644 --- a/recipes/bioconductor-methylcc/meta.yaml +++ b/recipes/bioconductor-methylcc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "methylCC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f599be86fb37a9d8f95f7e3113facccb + md5: 77566e7338f615ca5305d6e00465908b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylcc", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-flowsorted.blood.450k >=1.38.0,<1.39.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-flowsorted.blood.450k >=1.40.0,<1.41.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-magrittr - r-quadprog run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-flowsorted.blood.450k >=1.38.0,<1.39.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-flowsorted.blood.450k >=1.40.0,<1.41.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-magrittr diff --git a/recipes/bioconductor-methylclock/meta.yaml b/recipes/bioconductor-methylclock/meta.yaml index 981a365aa2e6a..16024462c189f 100644 --- a/recipes/bioconductor-methylclock/meta.yaml +++ b/recipes/bioconductor-methylclock/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "methylclock" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 770a4eeb0cb8da839fe57d6a42e317c3 + md5: b6151e23d6086f38d6489dcc277c81c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylclock", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, GEOquery, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-methylclockdata >=1.8.0,<1.9.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-planet >=1.8.0,<1.9.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-methylclockdata >=1.10.0,<1.11.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-planet >=1.10.0,<1.11.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-devtools - r-dplyr @@ -45,13 +46,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-methylclockdata >=1.8.0,<1.9.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-planet >=1.8.0,<1.9.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-methylclockdata >=1.10.0,<1.11.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-planet >=1.10.0,<1.11.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-devtools - r-dplyr diff --git a/recipes/bioconductor-methylclockdata/meta.yaml b/recipes/bioconductor-methylclockdata/meta.yaml index 0f81c2bd0f5c3..771be08cf1782 100644 --- a/recipes/bioconductor-methylclockdata/meta.yaml +++ b/recipes/bioconductor-methylclockdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "methylclockData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c211da6ed8d39ba8cee6d4d630691bad + md5: 633d9cc6c028025090e12004484fada1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylclockdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-experimenthubdata >=1.26.0,<1.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-experimenthubdata >=1.26.0,<1.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' - r-base - curl - - bioconductor-data-packages>=20230717 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-methylclockdata/post-link.sh b/recipes/bioconductor-methylclockdata/post-link.sh index 744cc5a5c07e4..16f98ea792eb3 100644 --- a/recipes/bioconductor-methylclockdata/post-link.sh +++ b/recipes/bioconductor-methylclockdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "methylclockdata-1.8.1" +installBiocDataPackage.sh "methylclockdata-1.10.0" diff --git a/recipes/bioconductor-methylgsa/meta.yaml b/recipes/bioconductor-methylgsa/meta.yaml index d10d0d4ad8fc6..9858e7286e22e 100644 --- a/recipes/bioconductor-methylgsa/meta.yaml +++ b/recipes/bioconductor-methylgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "methylGSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9287c45585ad0f59e2dc67c738a787e + md5: e802fab6abc1a9bac64bc36dd588c19d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylgsa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, enrichplot requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-missmethyl >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - r-ggplot2 - r-robustrankaggreg - r-shiny - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-missmethyl >=1.36.0,<1.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - r-ggplot2 - r-robustrankaggreg diff --git a/recipes/bioconductor-methylinheritance/meta.yaml b/recipes/bioconductor-methylinheritance/meta.yaml index 6041af6f4b285..c3fcbcbda2b35 100644 --- a/recipes/bioconductor-methylinheritance/meta.yaml +++ b/recipes/bioconductor-methylinheritance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "methylInheritance" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed652748487f26ee71332e443e3f3a80 + md5: 0242605800daea10c810fa356cb2cf0c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylinheritance", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gridextra - r-rebus run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-methylkit >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-methylkit >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gridextra diff --git a/recipes/bioconductor-methylkit/meta.yaml b/recipes/bioconductor-methylkit/meta.yaml index 7582763615f42..05fa1c56fc358 100644 --- a/recipes/bioconductor-methylkit/meta.yaml +++ b/recipes/bioconductor-methylkit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "methylKit" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37ac13b36487394b54e843d5f0b1c4d3 + md5: 5e21ca2558b439a2f542492eeec0f99d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylkit", max_pin="x.x") }}' # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager # SystemRequirements: GNU make requirements: host: - - 'bioconductor-fastseg >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-fastseg >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-data.table >=1.9.6' - r-emdbook @@ -44,17 +45,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-fastseg >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-fastseg >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-data.table >=1.9.6' - r-emdbook diff --git a/recipes/bioconductor-methylmix/meta.yaml b/recipes/bioconductor-methylmix/meta.yaml index 83ed80dadb3c8..80533398aa225 100644 --- a/recipes/bioconductor-methylmix/meta.yaml +++ b/recipes/bioconductor-methylmix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "MethylMix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 752979d4cb82fa14d6408b323f93005f + md5: 4a716254f6aff8e65daf63cdcd939704 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylmix", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-data.table - r-digest @@ -33,8 +34,8 @@ requirements: - r-rcurl - r-rpmm run: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-data.table - r-digest diff --git a/recipes/bioconductor-methylmnm/meta.yaml b/recipes/bioconductor-methylmnm/meta.yaml index 233e752251688..86b480b3cdd61 100644 --- a/recipes/bioconductor-methylmnm/meta.yaml +++ b/recipes/bioconductor-methylmnm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "methylMnM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dfc25779d379687166c7a894b52086eb + md5: 3d6c83c4fa30daea5b1c91e70f67c6b5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylmnm", max_pin="x.x") }}' requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-statmod - libblas - liblapack run: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-statmod build: diff --git a/recipes/bioconductor-methylpipe/meta.yaml b/recipes/bioconductor-methylpipe/meta.yaml index d49eb3e1ee37f..fe35aeaa5f55b 100644 --- a/recipes/bioconductor-methylpipe/meta.yaml +++ b/recipes/bioconductor-methylpipe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "methylPipe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fc26ce4cc91e60ef63712f165615294 + md5: bd41f308a3d5e58c4e05ce38c28f17f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylpipe", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-gplots - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-gplots diff --git a/recipes/bioconductor-methylscaper/meta.yaml b/recipes/bioconductor-methylscaper/meta.yaml index 9ccf2ccb044a2..2dd87a797efc1 100644 --- a/recipes/bioconductor-methylscaper/meta.yaml +++ b/recipes/bioconductor-methylscaper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.4" %} +{% set version = "1.10.0" %} {% set name = "methylscaper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c2bae24f7f0fd7284a2faf5f6fea4f09 + md5: 0fae72e2aac98ec4a55d8aa4343039ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylscaper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-rfast @@ -33,9 +34,9 @@ requirements: - r-shinyfiles - r-shinyjs run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-rfast diff --git a/recipes/bioconductor-methylseekr/meta.yaml b/recipes/bioconductor-methylseekr/meta.yaml index 4c02b0e12be43..49c54a3395fbc 100644 --- a/recipes/bioconductor-methylseekr/meta.yaml +++ b/recipes/bioconductor-methylseekr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "MethylSeekR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9caa87128143195fc74e45aea4c58142 + md5: 02bba9cfe7502e55a26e0ac76ba63457 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylseekr", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-mhsmm >=0.4.4' run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-mhsmm >=0.4.4' test: diff --git a/recipes/bioconductor-methylseqdata/meta.yaml b/recipes/bioconductor-methylseqdata/meta.yaml index 145e934653d1d..136355ee746c8 100644 --- a/recipes/bioconductor-methylseqdata/meta.yaml +++ b/recipes/bioconductor-methylseqdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MethylSeqData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1a6bd69401032cbdba32519c02fdf4c + md5: ded280784f55a6ebec42069160de26ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylseqdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-methylseqdata/post-link.sh b/recipes/bioconductor-methylseqdata/post-link.sh index 7de3f110ab6e7..a095ba9151fb9 100644 --- a/recipes/bioconductor-methylseqdata/post-link.sh +++ b/recipes/bioconductor-methylseqdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "methylseqdata-1.10.0" +installBiocDataPackage.sh "methylseqdata-1.12.0" diff --git a/recipes/bioconductor-methylumi/meta.yaml b/recipes/bioconductor-methylumi/meta.yaml index 422e651866f92..52c8312d6006e 100644 --- a/recipes/bioconductor-methylumi/meta.yaml +++ b/recipes/bioconductor-methylumi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "methylumi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 19a426ce620cab5722a42b3ab54c3ac7 + md5: eb3792c8c9c2a778cf41e9bb7b95232b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylumi", max_pin="x.x") }}' noarch: generic # Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-lattice @@ -42,20 +43,20 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-lattice diff --git a/recipes/bioconductor-metid/meta.yaml b/recipes/bioconductor-metid/meta.yaml index 0fc4c8446b6e2..3b7cbc31f2086 100644 --- a/recipes/bioconductor-metid/meta.yaml +++ b/recipes/bioconductor-metid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MetID" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80066250bcfc764f96ff4f3d3aed3154 + md5: 873920da0ab3c4e6a3bcd9e580097b86 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metid", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) requirements: host: - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - 'r-devtools >=1.13.0' - 'r-igraph >=1.2.1' - 'r-matrix >=1.2-12' - 'r-stringr >=1.3.0' run: - - 'bioconductor-chemminer >=3.52.0,<3.53.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' - r-base - 'r-devtools >=1.13.0' - 'r-igraph >=1.2.1' diff --git a/recipes/bioconductor-metnet/meta.yaml b/recipes/bioconductor-metnet/meta.yaml index e1de4c58763cb..78ede31d4fedc 100644 --- a/recipes/bioconductor-metnet/meta.yaml +++ b/recipes/bioconductor-metnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MetNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67d052b6ddc20ce093c5205bd21113c4 + md5: 0e03ec28e1272f094758907923a0226f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metnet", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genie3 >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genie3 >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bnlearn >=4.3' - 'r-corpcor >=1.6.10' @@ -38,10 +39,10 @@ requirements: - 'r-tibble >=3.0.5' - 'r-tidyr >=1.1.2' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genie3 >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genie3 >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bnlearn >=4.3' - 'r-corpcor >=1.6.10' diff --git a/recipes/bioconductor-mfa/meta.yaml b/recipes/bioconductor-mfa/meta.yaml index 1986448c2f204..5da35eaca5908 100644 --- a/recipes/bioconductor-mfa/meta.yaml +++ b/recipes/bioconductor-mfa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "mfa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a47205412204ffd49737d41b7b78574d + md5: 37fa2e82d83636458e9a20cc72069dcd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mfa", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-coda - r-dplyr @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-coda - r-dplyr diff --git a/recipes/bioconductor-mfuzz/meta.yaml b/recipes/bioconductor-mfuzz/meta.yaml index 3a69ac72e50d2..a85698f9f0ed3 100644 --- a/recipes/bioconductor-mfuzz/meta.yaml +++ b/recipes/bioconductor-mfuzz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.60.0" %} +{% set version = "2.62.0" %} {% set name = "Mfuzz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8997e343fab679b0005f7cb9eb95be1d + md5: 03a765bd452d34b166f85cdfee8063ae build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mfuzz", max_pin="x.x") }}' noarch: generic # Suggests: marray requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-tkwidgets >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-tkwidgets >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' - r-base - r-e1071 test: diff --git a/recipes/bioconductor-mgfm/meta.yaml b/recipes/bioconductor-mgfm/meta.yaml index 1212b35df01a2..7b05b8cea6a81 100644 --- a/recipes/bioconductor-mgfm/meta.yaml +++ b/recipes/bioconductor-mgfm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MGFM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87e2aeabf70fe5c98af8b31fc7eb87a8 + md5: 893a9f574fe4e023d3c4d3b99d58ae78 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgfm", max_pin="x.x") }}' noarch: generic # Suggests: hgu133a.db requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-mgfr/meta.yaml b/recipes/bioconductor-mgfr/meta.yaml index 48dfafef2cb6b..988ffb8e7853e 100644 --- a/recipes/bioconductor-mgfr/meta.yaml +++ b/recipes/bioconductor-mgfr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MGFR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b2461c46ec06a15eb25e35e645a9332 + md5: 73cad34ad523499dbdcfb3746b519b48 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgfr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-mgsa/meta.yaml b/recipes/bioconductor-mgsa/meta.yaml index f3f84f49ee018..18c113cd156d3 100644 --- a/recipes/bioconductor-mgsa/meta.yaml +++ b/recipes/bioconductor-mgsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "mgsa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 29e5cee310a2610a0167f448d39c0206 + md5: 1a0667a9a3b9c3e973a47a49249b08db build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgsa", max_pin="x.x") }}' # Suggests: DBI, RSQLite, GO.db, testthat requirements: host: diff --git a/recipes/bioconductor-mgu74a.db/meta.yaml b/recipes/bioconductor-mgu74a.db/meta.yaml index 5282b2deaa29a..c2dd2b0ae3b6f 100644 --- a/recipes/bioconductor-mgu74a.db/meta.yaml +++ b/recipes/bioconductor-mgu74a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9fb75c159c50e2ae316ee5a8abe1a48c build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74acdf/meta.yaml b/recipes/bioconductor-mgu74acdf/meta.yaml index 790af0f291883..6d1e5d9376af7 100644 --- a/recipes/bioconductor-mgu74acdf/meta.yaml +++ b/recipes/bioconductor-mgu74acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ed6e86398e51c7b0ddca4431797ecbc0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74aprobe/meta.yaml b/recipes/bioconductor-mgu74aprobe/meta.yaml index e82292a4a259d..01606e9b7cee0 100644 --- a/recipes/bioconductor-mgu74aprobe/meta.yaml +++ b/recipes/bioconductor-mgu74aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7fea6d44856203e6293e0cd9fe1ad066 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74av2.db/meta.yaml b/recipes/bioconductor-mgu74av2.db/meta.yaml index b67f4f55511e5..405b9aa9777a8 100644 --- a/recipes/bioconductor-mgu74av2.db/meta.yaml +++ b/recipes/bioconductor-mgu74av2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74av2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3205856d0c7725acded5238415e907bc build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74av2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74av2cdf/meta.yaml b/recipes/bioconductor-mgu74av2cdf/meta.yaml index d066d7b144da8..e72145c2c0482 100644 --- a/recipes/bioconductor-mgu74av2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74av2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74av2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 35e2abb9fbfd68d90dc32a2faae00c95 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74av2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74av2probe/meta.yaml b/recipes/bioconductor-mgu74av2probe/meta.yaml index 0caa9eac2a672..8e2e4ecec00f0 100644 --- a/recipes/bioconductor-mgu74av2probe/meta.yaml +++ b/recipes/bioconductor-mgu74av2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74av2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ac540b0e26b14a411740233b02d3e11c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74av2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74b.db/meta.yaml b/recipes/bioconductor-mgu74b.db/meta.yaml index 7d8d7d5a2a75c..3063cdc54e8e1 100644 --- a/recipes/bioconductor-mgu74b.db/meta.yaml +++ b/recipes/bioconductor-mgu74b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 205577a6e41d56910f221ffb940ee25b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bcdf/meta.yaml b/recipes/bioconductor-mgu74bcdf/meta.yaml index bf1d3d00be458..f44812422b044 100644 --- a/recipes/bioconductor-mgu74bcdf/meta.yaml +++ b/recipes/bioconductor-mgu74bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a1f0f98f29d34a421622447252113e1e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bprobe/meta.yaml b/recipes/bioconductor-mgu74bprobe/meta.yaml index db2bc9262a391..29fd25ee76e40 100644 --- a/recipes/bioconductor-mgu74bprobe/meta.yaml +++ b/recipes/bioconductor-mgu74bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 224d606e6fc87592d387dbaabe5cd353 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bv2.db/meta.yaml b/recipes/bioconductor-mgu74bv2.db/meta.yaml index a686c73cb696c..84c103d1c0982 100644 --- a/recipes/bioconductor-mgu74bv2.db/meta.yaml +++ b/recipes/bioconductor-mgu74bv2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74bv2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4ec0fbed7343f0578ef11e2330d0d12a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74bv2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bv2cdf/meta.yaml b/recipes/bioconductor-mgu74bv2cdf/meta.yaml index 40247022fe1d4..1e5b584de6c4a 100644 --- a/recipes/bioconductor-mgu74bv2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74bv2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bv2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 45c48d11af03633dc10f8682b7ad74c5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74bv2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74bv2probe/meta.yaml b/recipes/bioconductor-mgu74bv2probe/meta.yaml index 3f5bfd9f4b642..2c0bd49a0fabb 100644 --- a/recipes/bioconductor-mgu74bv2probe/meta.yaml +++ b/recipes/bioconductor-mgu74bv2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74bv2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f6a12f88ea3c43a3e885c7e9b3fd03d2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74bv2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74c.db/meta.yaml b/recipes/bioconductor-mgu74c.db/meta.yaml index ae87a17b48e1b..f645da667a7cf 100644 --- a/recipes/bioconductor-mgu74c.db/meta.yaml +++ b/recipes/bioconductor-mgu74c.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74c.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6c4f183e6ed5f0b5735596e7544746ae build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74c.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74ccdf/meta.yaml b/recipes/bioconductor-mgu74ccdf/meta.yaml index 2b1644415aad6..80c910bd5ffb7 100644 --- a/recipes/bioconductor-mgu74ccdf/meta.yaml +++ b/recipes/bioconductor-mgu74ccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74ccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 172e626b0e3072edc65c4efff35fe998 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74ccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cprobe/meta.yaml b/recipes/bioconductor-mgu74cprobe/meta.yaml index 38cf65f888fc5..2e2b2ca35ed51 100644 --- a/recipes/bioconductor-mgu74cprobe/meta.yaml +++ b/recipes/bioconductor-mgu74cprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74cprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 186992992708f0071fd552ef92b9e25c build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74cprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cv2.db/meta.yaml b/recipes/bioconductor-mgu74cv2.db/meta.yaml index 3175d01f69550..997784f9be6fd 100644 --- a/recipes/bioconductor-mgu74cv2.db/meta.yaml +++ b/recipes/bioconductor-mgu74cv2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mgu74cv2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1f860dfbf4400ede54eb30d9a70ec131 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74cv2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cv2cdf/meta.yaml b/recipes/bioconductor-mgu74cv2cdf/meta.yaml index bfe25f12a1f9d..e03108fc7e228 100644 --- a/recipes/bioconductor-mgu74cv2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74cv2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74cv2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9ef62b4b28f97770859db24393a07ed5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74cv2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgu74cv2probe/meta.yaml b/recipes/bioconductor-mgu74cv2probe/meta.yaml index 957ceff230bbe..ca9038a77b902 100644 --- a/recipes/bioconductor-mgu74cv2probe/meta.yaml +++ b/recipes/bioconductor-mgu74cv2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mgu74cv2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0373496c817a1c1a153114047cfa7c5b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgu74cv2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mguatlas5k.db/meta.yaml b/recipes/bioconductor-mguatlas5k.db/meta.yaml index 7f8f9eb126727..22485ecde8e5b 100644 --- a/recipes/bioconductor-mguatlas5k.db/meta.yaml +++ b/recipes/bioconductor-mguatlas5k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mguatlas5k.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 826093fe7228c08962aff36ad89af28e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mguatlas5k.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4104a.db/meta.yaml b/recipes/bioconductor-mgug4104a.db/meta.yaml index 511cc22eba5e0..23f2e33b36284 100644 --- a/recipes/bioconductor-mgug4104a.db/meta.yaml +++ b/recipes/bioconductor-mgug4104a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4104a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7b1cef094a226257cd657ed8d61e9ef1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgug4104a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4120a.db/meta.yaml b/recipes/bioconductor-mgug4120a.db/meta.yaml index c12a333d6504d..5029a19397f6f 100644 --- a/recipes/bioconductor-mgug4120a.db/meta.yaml +++ b/recipes/bioconductor-mgug4120a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4120a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bb57e8b2efe3d038ec2a0ace0313a4e7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgug4120a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4121a.db/meta.yaml b/recipes/bioconductor-mgug4121a.db/meta.yaml index f9b9edd4bd897..f58dbc5d4a23b 100644 --- a/recipes/bioconductor-mgug4121a.db/meta.yaml +++ b/recipes/bioconductor-mgug4121a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4121a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6b5cc321d5175356c383b91e30e120b7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgug4121a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mgug4122a.db/meta.yaml b/recipes/bioconductor-mgug4122a.db/meta.yaml index 11a080bd0e856..f28449f09300b 100644 --- a/recipes/bioconductor-mgug4122a.db/meta.yaml +++ b/recipes/bioconductor-mgug4122a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mgug4122a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5fcdce909ac1c0ccbf06bf6411f6fe52 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgug4122a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mi16cod.db/meta.yaml b/recipes/bioconductor-mi16cod.db/meta.yaml index dcb98323413d3..8fb4d0203848f 100644 --- a/recipes/bioconductor-mi16cod.db/meta.yaml +++ b/recipes/bioconductor-mi16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "mi16cod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f3a8e6f45ce5c298c1b1c5b32bf2630c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mi16cod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mia/meta.yaml b/recipes/bioconductor-mia/meta.yaml index b2031393678e7..919a3676af018 100644 --- a/recipes/bioconductor-mia/meta.yaml +++ b/recipes/bioconductor-mia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "mia" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4e6cd405049a4a4f7890047dd0e3ad9d + md5: 73446335fd354444f38c4e8cf793d520 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mia", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-decontam >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-decontam >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - r-dplyr @@ -46,22 +49,24 @@ requirements: - r-tidyr - r-vegan run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-decontam >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-decontam >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - r-dplyr diff --git a/recipes/bioconductor-miasim/meta.yaml b/recipes/bioconductor-miasim/meta.yaml index 91f6fb97a3046..01006e0284875 100644 --- a/recipes/bioconductor-miasim/meta.yaml +++ b/recipes/bioconductor-miasim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "miaSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36d959599bdaf1bce1bc6f3302022ddc + md5: 0867c6e7b7cae5acbfd6154b8af06d41 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-miasim", max_pin="x.x") }}' noarch: generic -# Suggests: ape, cluster, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy +# Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy requirements: host: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-desolve - r-powerlaw run: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-desolve - r-powerlaw diff --git a/recipes/bioconductor-miaviz/meta.yaml b/recipes/bioconductor-miaviz/meta.yaml index f76a198ae67f3..5d98581a6690d 100644 --- a/recipes/bioconductor-miaviz/meta.yaml +++ b/recipes/bioconductor-miaviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "miaViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12187467cffef6ea27c17e3fce3a336a + md5: 8388770fbcfce7b95040dc84f02938bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-miaviz", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, microbiomeDataSets +# Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, microbiomeDataSets, bluster requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - r-dplyr - r-ggnewscale - r-ggplot2 - 'r-ggraph >=2.0' + - r-ggrepel - r-purrr - r-rlang - r-tibble @@ -45,22 +48,24 @@ requirements: - r-tidytree - r-viridis run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-mia >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-mia >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - r-dplyr - r-ggnewscale - r-ggplot2 - 'r-ggraph >=2.0' + - r-ggrepel - r-purrr - r-rlang - r-tibble diff --git a/recipes/bioconductor-michip/meta.yaml b/recipes/bioconductor-michip/meta.yaml index 91c869251363f..cafafc492b65d 100644 --- a/recipes/bioconductor-michip/meta.yaml +++ b/recipes/bioconductor-michip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "MiChip" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fa83d7ff43b635845b8718f63d52c4c + md5: 28daafdf6588314a9fad7a75b1671c10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-michip", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-microbiome/meta.yaml b/recipes/bioconductor-microbiome/meta.yaml index 97851a11b7c02..1a8d53b4a4491 100644 --- a/recipes/bioconductor-microbiome/meta.yaml +++ b/recipes/bioconductor-microbiome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "microbiome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f6a3ca6428df676e03c3b34d64f4fc88 + md5: 2d185cf8b8bf7d23f295dee1af621a0f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiome", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-compositions - r-dplyr @@ -34,8 +35,8 @@ requirements: - r-tidyr - r-vegan run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-compositions - r-dplyr diff --git a/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml b/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml index 3fdbe1071c43f..4738a600749e6 100644 --- a/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml +++ b/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MicrobiomeBenchmarkData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1116445da1265ebf3e4bf29678bd6cc3 + md5: c6c791669de95bf2dc108798770ea5be build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomebenchmarkdata", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh b/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh index 25fe021fab244..b41c09486c6b4 100644 --- a/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh +++ b/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "microbiomebenchmarkdata-1.2.0" +installBiocDataPackage.sh "microbiomebenchmarkdata-1.4.0" diff --git a/recipes/bioconductor-microbiomedasim/meta.yaml b/recipes/bioconductor-microbiomedasim/meta.yaml index 159e119977f81..1bf6caba4a6b5 100644 --- a/recipes/bioconductor-microbiomedasim/meta.yaml +++ b/recipes/bioconductor-microbiomedasim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "microbiomeDASim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39fb498f8346fa9914285ad4b7790a73 + md5: 9ddf99ab393766f7bcb9dee13b3707f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomedasim", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, devtools requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-ggplot2 - r-mass @@ -32,9 +33,9 @@ requirements: - r-pbapply - r-tmvtnorm run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-ggplot2 - r-mass diff --git a/recipes/bioconductor-microbiomedatasets/meta.yaml b/recipes/bioconductor-microbiomedatasets/meta.yaml index 45bed4d640d18..4fcdb8454b7a9 100644 --- a/recipes/bioconductor-microbiomedatasets/meta.yaml +++ b/recipes/bioconductor-microbiomedatasets/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "microbiomeDataSets" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 084634f8885e50e157bbaef972b7ad8f + md5: 90cd4bb36dafcef8f6eb0e0232afdcd0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomedatasets", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-ape - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-microbiomedatasets/post-link.sh b/recipes/bioconductor-microbiomedatasets/post-link.sh index aa74335043872..a7009b824d2c1 100644 --- a/recipes/bioconductor-microbiomedatasets/post-link.sh +++ b/recipes/bioconductor-microbiomedatasets/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "microbiomedatasets-1.8.0" +installBiocDataPackage.sh "microbiomedatasets-1.10.0" diff --git a/recipes/bioconductor-microbiomeexplorer/meta.yaml b/recipes/bioconductor-microbiomeexplorer/meta.yaml index 046802c402141..87c2c126866f1 100644 --- a/recipes/bioconductor-microbiomeexplorer/meta.yaml +++ b/recipes/bioconductor-microbiomeexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "microbiomeExplorer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a899b212f5888fd3d9b11ee585a8119 + md5: c1e966728a968697ad53fd6405c156c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomeexplorer", max_pin="x.x") }}' noarch: generic # Suggests: V8, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-broom - r-car @@ -54,11 +55,11 @@ requirements: - r-tidyr - r-vegan run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - r-broom - r-car diff --git a/recipes/bioconductor-microbiomemarker/meta.yaml b/recipes/bioconductor-microbiomemarker/meta.yaml index f845014d8b090..6b50c7ac62de1 100644 --- a/recipes/bioconductor-microbiomemarker/meta.yaml +++ b/recipes/bioconductor-microbiomemarker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "microbiomeMarker" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 548c6c090fa44c0a03d1dbdfe4ae4415 + md5: facf2f8071da6049b688fe3d16efb0e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomemarker", max_pin="x.x") }}' noarch: generic # Suggests: testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr requirements: host: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' - - 'bioconductor-ancombc >=2.2.0,<2.3.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' + - 'bioconductor-ancombc >=2.4.0,<2.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-coin @@ -57,23 +58,23 @@ requirements: - r-vegan - r-yaml run: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' - - 'bioconductor-ancombc >=2.2.0,<2.3.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' + - 'bioconductor-ancombc >=2.4.0,<2.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-coin diff --git a/recipes/bioconductor-microbiomeprofiler/meta.yaml b/recipes/bioconductor-microbiomeprofiler/meta.yaml index 0b262d73b3fcf..7a31e5d435166 100644 --- a/recipes/bioconductor-microbiomeprofiler/meta.yaml +++ b/recipes/bioconductor-microbiomeprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "MicrobiomeProfiler" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47b4023245daeb0e51c9aa1e543f1d49 + md5: 47851ff17ed03e5b448a09513c7bf122 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiomeprofiler", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, knitr, prettydoc, testthat (>= 3.0.0) +# Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - r-base - r-config - r-dt @@ -35,8 +36,8 @@ requirements: - r-shinycustomloader - r-shinywidgets run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - r-base - r-config - r-dt diff --git a/recipes/bioconductor-microbiotaprocess/meta.yaml b/recipes/bioconductor-microbiotaprocess/meta.yaml index 509f549b57693..448857a29ab05 100644 --- a/recipes/bioconductor-microbiotaprocess/meta.yaml +++ b/recipes/bioconductor-microbiotaprocess/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "MicrobiotaProcess" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5e400f9a6b55f6e01b6438f36ff42a18 + md5: 104b99004b64b664131ddea6462cbabc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microbiotaprocess", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, corrr, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial +# Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-ggtreeextra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-ggtreeextra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-base - r-cli @@ -34,6 +35,7 @@ requirements: - r-dplyr - r-dtplyr - r-foreach + - 'r-ggfun >=0.1.1' - r-ggplot2 - r-ggrepel - r-ggsignif @@ -51,11 +53,11 @@ requirements: - r-vegan - r-zoo run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-ggtreeextra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-ggtreeextra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-base - r-cli @@ -64,6 +66,7 @@ requirements: - r-dplyr - r-dtplyr - r-foreach + - 'r-ggfun >=0.1.1' - r-ggplot2 - r-ggrepel - r-ggsignif diff --git a/recipes/bioconductor-microrna/meta.yaml b/recipes/bioconductor-microrna/meta.yaml index ee9067d643879..cc92ab37669ca 100644 --- a/recipes/bioconductor-microrna/meta.yaml +++ b/recipes/bioconductor-microrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "microRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 166bcf7edb5ded052551b53db0fe6b9f + md5: 04b7af542581242a8e6ba5d4f19c14ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microrna", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-micrornaome/meta.yaml b/recipes/bioconductor-micrornaome/meta.yaml index cf47ca13893f9..20251ad808f38 100644 --- a/recipes/bioconductor-micrornaome/meta.yaml +++ b/recipes/bioconductor-micrornaome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "microRNAome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04f1271bdd22d4cc2dabd9e8db57e006 + md5: 12d3baf395e82975bbcacfb9ff61a715 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-micrornaome", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, RUnit requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-micrornaome/post-link.sh b/recipes/bioconductor-micrornaome/post-link.sh index 6708b196917f9..2c965f7636c8d 100644 --- a/recipes/bioconductor-micrornaome/post-link.sh +++ b/recipes/bioconductor-micrornaome/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "micrornaome-1.22.0" +installBiocDataPackage.sh "micrornaome-1.24.0" diff --git a/recipes/bioconductor-microstasis/meta.yaml b/recipes/bioconductor-microstasis/meta.yaml index abc37a8a4fdb7..52e1c42705ee5 100644 --- a/recipes/bioconductor-microstasis/meta.yaml +++ b/recipes/bioconductor-microstasis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "microSTASIS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5e65e09dd41f9734e4ce715a6ebf564 + md5: 7b9b67613eb5e6b69918dffc9d4060d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-microstasis", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, gghighlight, knitr, rmarkdown, methods, RefManageR, sessioninfo, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-ggplot2 - r-ggside - r-rlang - r-stringr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-ggplot2 - r-ggside diff --git a/recipes/bioconductor-micsqtl/build.sh b/recipes/bioconductor-micsqtl/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-micsqtl/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-micsqtl/build_failure.linux-64.yaml b/recipes/bioconductor-micsqtl/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3fe5e63aee6a4 --- /dev/null +++ b/recipes/bioconductor-micsqtl/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 48da45ce49c1641d3245866b89ddd5bb41be17df6a5b307fcbb400bb8ebd78e7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + - r-ggplot2 + - r-tca + - r-glue + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-dirmult + - r-nnls + - r-magrittr + - r-purrr + - r-base 4.3.* + - r-ggridges + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested r-tca + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-toast >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-ggpubr + - r-ggplot2 + - r-tca + - r-glue + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-dirmult + - r-nnls + - r-magrittr + - r-purrr + - r-base 4.3.* + - r-ggridges + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested r-tca + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-tca")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-micsqtl/meta.yaml b/recipes/bioconductor-micsqtl/meta.yaml new file mode 100644 index 0000000000000..33eb7aa2e58cf --- /dev/null +++ b/recipes/bioconductor-micsqtl/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.0" %} +{% set name = "MICSQTL" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ec49e08df014da6955d2b6ab7dc77d3b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-micsqtl", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-toast >=1.16.0,<1.17.0' + - r-base + - r-dirmult + - r-ggplot2 + - r-ggpubr + - r-ggridges + - r-glue + - r-magrittr + - r-nnls + - r-purrr + - r-tca + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-toast >=1.16.0,<1.17.0' + - r-base + - r-dirmult + - r-ggplot2 + - r-ggpubr + - r-ggridges + - r-glue + - r-magrittr + - r-nnls + - r-purrr + - r-tca +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)' + description: 'Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-midashla/meta.yaml b/recipes/bioconductor-midashla/meta.yaml index 37868a12e2dfb..99330f8c5b329 100644 --- a/recipes/bioconductor-midashla/meta.yaml +++ b/recipes/bioconductor-midashla/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "midasHLA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 408626a1272bac5201d96f5992d1baab + md5: 7d77f1bda1bff8d67de91e02cb985519 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-midashla", max_pin="x.x") }}' noarch: generic # Suggests: broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 1.1.2) requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-assertthat >=0.2.0' - r-base - 'r-broom >=0.5.1' @@ -38,9 +39,9 @@ requirements: - 'r-stringi >=1.2.4' - 'r-tibble >=2.0.1' run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-assertthat >=0.2.0' - r-base - 'r-broom >=0.5.1' diff --git a/recipes/bioconductor-migsadata/meta.yaml b/recipes/bioconductor-migsadata/meta.yaml index 189ec9574258d..9a6355a9d9d3f 100644 --- a/recipes/bioconductor-migsadata/meta.yaml +++ b/recipes/bioconductor-migsadata/meta.yaml @@ -25,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-milor/meta.yaml b/recipes/bioconductor-milor/meta.yaml index e1011a151d562..85f159f4f472b 100644 --- a/recipes/bioconductor-milor/meta.yaml +++ b/recipes/bioconductor-milor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "miloR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bb65889883141ecec6c2ebc66cae0160 + md5: 9ab9a4a2fe26786cd8fef69354bfa08f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-milor", max_pin="x.x") }}' noarch: generic # Suggests: testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, curl, graphics requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr @@ -48,15 +49,15 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-dplyr diff --git a/recipes/bioconductor-mimager/meta.yaml b/recipes/bioconductor-mimager/meta.yaml index 43bbfc9c7cd82..648f2f64bb6d4 100644 --- a/recipes/bioconductor-mimager/meta.yaml +++ b/recipes/bioconductor-mimager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "mimager" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f6ed0e16875e23c4b287c4a82daaea68 + md5: 2a9eaf36345d24dc2d44a65c1f8640a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mimager", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-gtable - r-scales run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyplm >=1.76.0,<1.77.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyplm >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-gtable diff --git a/recipes/bioconductor-mina/meta.yaml b/recipes/bioconductor-mina/meta.yaml index dfccfbf55bae1..1f816fb2b240f 100644 --- a/recipes/bioconductor-mina/meta.yaml +++ b/recipes/bioconductor-mina/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "mina" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3cfb81237b29c98fd414eadcc05c74d3 + md5: d6578736bef864eef8f89958a849137b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mina", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: diff --git a/recipes/bioconductor-mineica/meta.yaml b/recipes/bioconductor-mineica/meta.yaml index 2e5774e5b900e..4f8e58766912f 100644 --- a/recipes/bioconductor-mineica/meta.yaml +++ b/recipes/bioconductor-mineica/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "MineICA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3bfbe3946133ce2be4c18c146f906f67 + md5: d08aa74cfe4d20f4ad26235e0695d555 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mineica", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - 'bioconductor-lumihumanall.db >=1.22.0,<1.23.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-cluster - r-colorspace @@ -49,17 +50,17 @@ requirements: - r-scales - r-xtable run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - 'bioconductor-lumihumanall.db >=1.22.0,<1.23.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-cluster - r-colorspace diff --git a/recipes/bioconductor-minet/meta.yaml b/recipes/bioconductor-minet/meta.yaml index 5ff3aea1feff8..430543b54eca5 100644 --- a/recipes/bioconductor-minet/meta.yaml +++ b/recipes/bioconductor-minet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.58.0" %} +{% set version = "3.60.0" %} {% set name = "minet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c19e497a170c61859a7f850c18a64829 + md5: 8aaab67519352be115568a301e98ef99 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minet", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-minfi/meta.yaml b/recipes/bioconductor-minfi/meta.yaml index ef3788c157bc2..6ed741d14afee 100644 --- a/recipes/bioconductor-minfi/meta.yaml +++ b/recipes/bioconductor-minfi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "minfi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f2346d9ef5bd96b0715c47402ce585d8 + md5: 3c1998eee0aabbfab3c3796c82339a18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minfi", max_pin="x.x") }}' noarch: generic # Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beanplot - r-data.table @@ -52,25 +53,25 @@ requirements: - r-rcolorbrewer - r-reshape run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beanplot - r-data.table diff --git a/recipes/bioconductor-minfidata/meta.yaml b/recipes/bioconductor-minfidata/meta.yaml index 7168cbc79995f..f41037aeece26 100644 --- a/recipes/bioconductor-minfidata/meta.yaml +++ b/recipes/bioconductor-minfidata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.46.0" %} +{% set version = "0.48.0" %} {% set name = "minfiData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5edb94dae6adb108bd94fdf4e0e8c3d + md5: 1ca7578aeab1a54db146c443870be6e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minfidata", max_pin="x.x") }}' noarch: generic requirements: host: - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-minfidata/post-link.sh b/recipes/bioconductor-minfidata/post-link.sh index a14bd53842e17..7dbdb4780ea5f 100644 --- a/recipes/bioconductor-minfidata/post-link.sh +++ b/recipes/bioconductor-minfidata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "minfidata-0.46.0" +installBiocDataPackage.sh "minfidata-0.48.0" diff --git a/recipes/bioconductor-minfidataepic/meta.yaml b/recipes/bioconductor-minfidataepic/meta.yaml index d65e802545a06..d9429ed793030 100644 --- a/recipes/bioconductor-minfidataepic/meta.yaml +++ b/recipes/bioconductor-minfidataepic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "minfiDataEPIC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f61984902e4c4c2d0c01f375a3533935 + md5: bcb0b01d571c5308e02db4c6b5c0d1ce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minfidataepic", max_pin="x.x") }}' noarch: generic requirements: host: - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base run: - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-minfidataepic/post-link.sh b/recipes/bioconductor-minfidataepic/post-link.sh index 7b5637a02d804..506358fd0d0de 100644 --- a/recipes/bioconductor-minfidataepic/post-link.sh +++ b/recipes/bioconductor-minfidataepic/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "minfidataepic-1.26.0" +installBiocDataPackage.sh "minfidataepic-1.28.0" diff --git a/recipes/bioconductor-minimumdistance/meta.yaml b/recipes/bioconductor-minimumdistance/meta.yaml index 7dbd68965a2b4..46b1638468be4 100644 --- a/recipes/bioconductor-minimumdistance/meta.yaml +++ b/recipes/bioconductor-minimumdistance/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "MinimumDistance" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4a44703f30e7bfa7c4e7b02004a0f4c + md5: ab96e788a4152b80b7a685f3fc8fcd9c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minimumdistance", max_pin="x.x") }}' noarch: generic # Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vanillaice >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vanillaice >=1.64.0,<1.65.0' - r-base - r-data.table - r-ff @@ -39,17 +40,17 @@ requirements: - r-lattice - r-matrixstats run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vanillaice >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vanillaice >=1.64.0,<1.65.0' - r-base - r-data.table - r-ff diff --git a/recipes/bioconductor-minionsummarydata/meta.yaml b/recipes/bioconductor-minionsummarydata/meta.yaml index e8c6a477792c0..f09a52c37ecc6 100644 --- a/recipes/bioconductor-minionsummarydata/meta.yaml +++ b/recipes/bioconductor-minionsummarydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "minionSummaryData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cab7c2dd789ebe23e1c9410bdbc259c6 + md5: 1679c45541b2d76094c3894abe9c011d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-minionsummarydata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-minionsummarydata/post-link.sh b/recipes/bioconductor-minionsummarydata/post-link.sh index cd6445be0f12a..9e9250e8eedd7 100644 --- a/recipes/bioconductor-minionsummarydata/post-link.sh +++ b/recipes/bioconductor-minionsummarydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "minionsummarydata-1.30.0" +installBiocDataPackage.sh "minionsummarydata-1.32.0" diff --git a/recipes/bioconductor-mipp/meta.yaml b/recipes/bioconductor-mipp/meta.yaml index 5f900be73ec9b..50af592ccbaa4 100644 --- a/recipes/bioconductor-mipp/meta.yaml +++ b/recipes/bioconductor-mipp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "MiPP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 79698b2acaac85272c49ff931598336b + md5: ce412e2a72891fcc7969faee078b2be3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mipp", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-mass diff --git a/recipes/bioconductor-miqc/meta.yaml b/recipes/bioconductor-miqc/meta.yaml index 7d4a13b6656fa..6c084decec07f 100644 --- a/recipes/bioconductor-miqc/meta.yaml +++ b/recipes/bioconductor-miqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "miQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 031d41e099bf5babd6b0f8d32d9f0d1e + md5: e1246c2b5dcb83059d6887b35db543a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-miqc", max_pin="x.x") }}' noarch: generic # Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-flexmix - r-ggplot2 run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-flexmix - r-ggplot2 diff --git a/recipes/bioconductor-mira/meta.yaml b/recipes/bioconductor-mira/meta.yaml index 604ac4269053c..93e25f1a9c765 100644 --- a/recipes/bioconductor-mira/meta.yaml +++ b/recipes/bioconductor-mira/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "MIRA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58cb07316068a920e02e241d1bfe8beb + md5: 670cb42f275d260b28e0e2d140cacda2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mira", max_pin="x.x") }}' noarch: generic # Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-mirage/meta.yaml b/recipes/bioconductor-mirage/meta.yaml index 9b622e3b83db0..45a443bde1f58 100644 --- a/recipes/bioconductor-mirage/meta.yaml +++ b/recipes/bioconductor-mirage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "MiRaGE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1ff8ce3f0bd0633b2d4fae52b4eec14 + md5: c86c12c042052eb4d558bdff55e8c47a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirage", max_pin="x.x") }}' noarch: generic # Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager test: diff --git a/recipes/bioconductor-mirbase.db/meta.yaml b/recipes/bioconductor-mirbase.db/meta.yaml index 15bfae93c86f9..a51ede2582bcd 100644 --- a/recipes/bioconductor-mirbase.db/meta.yaml +++ b/recipes/bioconductor-mirbase.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.2.0" %} {% set name = "mirbase.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 316bc12cee8c2dd9240b7fc30cd1619e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirbase.db", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirbaseversions.db/meta.yaml b/recipes/bioconductor-mirbaseversions.db/meta.yaml index 560259e831959..a66ca195291ed 100644 --- a/recipes/bioconductor-mirbaseversions.db/meta.yaml +++ b/recipes/bioconductor-mirbaseversions.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "miRBaseVersions.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,27 +13,28 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9944ab7a474f84a40100c56298f9cb77 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirbaseversions.db", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - r-gtools - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - r-gtools - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mircomp/meta.yaml b/recipes/bioconductor-mircomp/meta.yaml index 9d93697dfe47d..465227f2e2975 100644 --- a/recipes/bioconductor-mircomp/meta.yaml +++ b/recipes/bioconductor-mircomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "miRcomp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c16b1d3d79f266d11691bc93c44c2236 + md5: 06b97d8829ca13b60dd4869a48b684ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mircomp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mircompdata >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mircompdata >=1.32.0,<1.33.0' - r-base - r-kernsmooth run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-mircompdata >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-mircompdata >=1.32.0,<1.33.0' - r-base - r-kernsmooth test: diff --git a/recipes/bioconductor-mircompdata/meta.yaml b/recipes/bioconductor-mircompdata/meta.yaml index 02fc8b1e898c3..95ae5ae333c25 100644 --- a/recipes/bioconductor-mircompdata/meta.yaml +++ b/recipes/bioconductor-mircompdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "miRcompData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df2f1f8eb6489db9c0e242224b47be36 + md5: 0b091222ebe8ac1a3a2c59384931393b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mircompdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mircompdata/post-link.sh b/recipes/bioconductor-mircompdata/post-link.sh index d25f90ae9ebeb..5d104e9b53a6d 100644 --- a/recipes/bioconductor-mircompdata/post-link.sh +++ b/recipes/bioconductor-mircompdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mircompdata-1.30.0" +installBiocDataPackage.sh "mircompdata-1.32.0" diff --git a/recipes/bioconductor-mirintegrator/meta.yaml b/recipes/bioconductor-mirintegrator/meta.yaml index 01a5af4f2e768..e122769fc894f 100644 --- a/recipes/bioconductor-mirintegrator/meta.yaml +++ b/recipes/bioconductor-mirintegrator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "mirIntegrator" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df82dd0262aefe9230e29a27c67f760e + md5: 9ec5789f159dfc3880ce8369af20c27a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirintegrator", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rontotools >=2.28.0,<2.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rontotools >=2.30.0,<2.31.0' - r-base - r-ggplot2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rontotools >=2.28.0,<2.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rontotools >=2.30.0,<2.31.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-mirlab/meta.yaml b/recipes/bioconductor-mirlab/meta.yaml index e61b67c915ad2..02d028c863d44 100644 --- a/recipes/bioconductor-mirlab/meta.yaml +++ b/recipes/bioconductor-mirlab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "miRLAB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 744b41ef84de2faa12cad1caefcae543 + md5: 3347a99a17fc2caade03a35471a79ad0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirlab", max_pin="x.x") }}' noarch: generic # Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown requirements: host: - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-ctc >=1.74.0,<1.75.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-ctc >=1.76.0,<1.77.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-dplyr - r-energy @@ -42,14 +43,14 @@ requirements: - r-rcurl - r-stringr run: - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-ctc >=1.74.0,<1.75.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-ctc >=1.76.0,<1.77.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-dplyr - r-energy diff --git a/recipes/bioconductor-mirna102xgaincdf/meta.yaml b/recipes/bioconductor-mirna102xgaincdf/meta.yaml index 8616bcbf2acdd..c2998928a01d0 100644 --- a/recipes/bioconductor-mirna102xgaincdf/meta.yaml +++ b/recipes/bioconductor-mirna102xgaincdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna102xgaincdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9091a45c2ac15c2de0263743ab334f97 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirna102xgaincdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirna10cdf/meta.yaml b/recipes/bioconductor-mirna10cdf/meta.yaml index b29f31fb1a81c..657e2d588c9fe 100644 --- a/recipes/bioconductor-mirna10cdf/meta.yaml +++ b/recipes/bioconductor-mirna10cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna10cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 814da2a2e298e132f4db0b2e8ab814be build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirna10cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirna10probe/meta.yaml b/recipes/bioconductor-mirna10probe/meta.yaml index cb6bf10f733c7..ad500280b4d55 100644 --- a/recipes/bioconductor-mirna10probe/meta.yaml +++ b/recipes/bioconductor-mirna10probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna10probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8bfa6cdfeee1c563b4881214bd5d4ce1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirna10probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirna20cdf/meta.yaml b/recipes/bioconductor-mirna20cdf/meta.yaml index 7a6ca0f379587..3d81b3981f94a 100644 --- a/recipes/bioconductor-mirna20cdf/meta.yaml +++ b/recipes/bioconductor-mirna20cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mirna20cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 56f7807673ff108427ae7f6bdf85ae1c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirna20cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirnameconverter/meta.yaml b/recipes/bioconductor-mirnameconverter/meta.yaml index ba45c1803c37d..5e214021c777c 100644 --- a/recipes/bioconductor-mirnameconverter/meta.yaml +++ b/recipes/bioconductor-mirnameconverter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "miRNAmeConverter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 159e14aa90692f18e70bd6b8ab4de62e + md5: cfc6563f669ecbc03292cccba919fe05 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirnameconverter", max_pin="x.x") }}' noarch: generic # Suggests: methods, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-mirbaseversions.db >=1.1.0,<1.2.0' - r-base - r-dbi - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-mirbaseversions.db >=1.1.0,<1.2.0' - r-base - r-dbi diff --git a/recipes/bioconductor-mirnapath/meta.yaml b/recipes/bioconductor-mirnapath/meta.yaml index 8c1ceb8ee5cc6..9438bd5588098 100644 --- a/recipes/bioconductor-mirnapath/meta.yaml +++ b/recipes/bioconductor-mirnapath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "miRNApath" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d5b6049d846a3e3d6bfed44c779e70d + md5: 94aad8a3b57b070cb5c559d9d1f14726 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirnapath", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mirnatap.db/meta.yaml b/recipes/bioconductor-mirnatap.db/meta.yaml index 2de40cf5aa5d9..b8f95f3419969 100644 --- a/recipes/bioconductor-mirnatap.db/meta.yaml +++ b/recipes/bioconductor-mirnatap.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.10" %} {% set name = "miRNAtap.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,26 +13,27 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 48010280b68d6f1ddbff3b374132ce0a build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirnatap.db", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-mirnatap >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-mirnatap >=1.36.0,<1.37.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-mirnatap >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-mirnatap >=1.36.0,<1.37.0' - r-base - r-dbi - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirnatap/meta.yaml b/recipes/bioconductor-mirnatap/meta.yaml index df8230d80281b..6a542792493d7 100644 --- a/recipes/bioconductor-mirnatap/meta.yaml +++ b/recipes/bioconductor-mirnatap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "miRNAtap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a8119335b7deb36dd6f674bc005fe77 + md5: f09289c10d9e5e916cc1b95e79bf504f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirnatap", max_pin="x.x") }}' noarch: generic # Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - r-plyr @@ -29,7 +30,7 @@ requirements: - r-sqldf - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - r-plyr diff --git a/recipes/bioconductor-mirnatarget/meta.yaml b/recipes/bioconductor-mirnatarget/meta.yaml index bc6f79cce1728..130d1f40deaf8 100644 --- a/recipes/bioconductor-mirnatarget/meta.yaml +++ b/recipes/bioconductor-mirnatarget/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "miRNATarget" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7418be6b97608cabc13f0812caf9301 + md5: f1988a96af5f0232abfbe507854d49bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirnatarget", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mirnatarget/post-link.sh b/recipes/bioconductor-mirnatarget/post-link.sh index 2dc55d0f7b4f3..cca9ffdc3448c 100644 --- a/recipes/bioconductor-mirnatarget/post-link.sh +++ b/recipes/bioconductor-mirnatarget/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mirnatarget-1.38.0" +installBiocDataPackage.sh "mirnatarget-1.40.0" diff --git a/recipes/bioconductor-mirtarrnaseq/meta.yaml b/recipes/bioconductor-mirtarrnaseq/meta.yaml index c9e30b0034f70..5a9e793f0b0a7 100644 --- a/recipes/bioconductor-mirtarrnaseq/meta.yaml +++ b/recipes/bioconductor-mirtarrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "mirTarRnaSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5293fd7139409c1f97be415ff33cfdb + md5: b8cac8c363bddb02eb97e6009bb91f4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirtarrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE requirements: diff --git a/recipes/bioconductor-missmethyl/meta.yaml b/recipes/bioconductor-missmethyl/meta.yaml index 0d0e59a147311..73c8b2a6314ae 100644 --- a/recipes/bioconductor-missmethyl/meta.yaml +++ b/recipes/bioconductor-missmethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "missMethyl" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,54 +11,55 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14f5ef67dfb35d45507cf6d89aa482b3 + md5: 4773cfc60c545bb0a04dac0b6cc0ac4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-missmethyl", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biasedurn - r-ruv - r-statmod - r-stringr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biasedurn - r-ruv diff --git a/recipes/bioconductor-missrows/meta.yaml b/recipes/bioconductor-missrows/meta.yaml index 202971b260664..95759b50cdab7 100644 --- a/recipes/bioconductor-missrows/meta.yaml +++ b/recipes/bioconductor-missrows/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "missRows" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b83ec2b5bd3f9395ff1ed60e1da40868 + md5: d076124257e06505c39064a9dcddd695 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-missrows", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gtools - r-plyr run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-gtools diff --git a/recipes/bioconductor-mistyr/meta.yaml b/recipes/bioconductor-mistyr/meta.yaml index 4eaa178821c74..ab71622892ea4 100644 --- a/recipes/bioconductor-mistyr/meta.yaml +++ b/recipes/bioconductor-mistyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "mistyR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2e7371ef1a22dcb63add2f2e680deff0 + md5: f21483e1d8c9575d0c27a9fa544cfb3c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mistyr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml, kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0), xgboost requirements: diff --git a/recipes/bioconductor-mitch/meta.yaml b/recipes/bioconductor-mitch/meta.yaml index 906e0da288dcc..0a18ed1cd6dfa 100644 --- a/recipes/bioconductor-mitch/meta.yaml +++ b/recipes/bioconductor-mitch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "mitch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 58be0f0e3a1e2fae1812b39cf31ae3d4 + md5: c21044d7d878482677fcb758acf0a650 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mitch", max_pin="x.x") }}' noarch: generic # Suggests: stringi, testthat (>= 2.1.0) requirements: diff --git a/recipes/bioconductor-mitoclone2/build_failure.osx-64.yaml b/recipes/bioconductor-mitoclone2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..6dc0ac91eab34 --- /dev/null +++ b/recipes/bioconductor-mitoclone2/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 60f475e5bda7669f78635653dbdbbc6ac8818393a7bc525552f7d723c69c6571 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + source download error +log: |2- + tapi: 1100.0.11-h9ce4665_0 conda-forge + tk: 8.6.13-h1abcd95_1 conda-forge + tktable: 2.10-ha166976_5 conda-forge + toml: 0.10.2-pyhd8ed1ab_0 conda-forge + tomlkit: 0.12.3-pyha770c72_0 conda-forge + tzdata: 2023c-h71feb2d_0 conda-forge + xmltodict: 0.13.0-pyhd8ed1ab_0 conda-forge + xz: 5.2.6-h775f41a_0 conda-forge + yaml: 0.2.5-h0d85af4_2 conda-forge + yq: 3.2.3-pyhd8ed1ab_0 conda-forge + zlib: 1.2.13-h8a1eda9_5 conda-forge + zstd: 1.5.5-h829000d_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld + Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-mitoclone2_1703020590195/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2023.11.17-h8857fd0_0 conda-forge + cctools_osx-64: 973.0.1-habff3f6_15 conda-forge + clang: 15.0.7-hac416ee_4 conda-forge + clang-15: 15.0.7-default_h6b1ee41_4 conda-forge + clang_impl_osx-64: 15.0.7-h03d6864_7 conda-forge + clang_osx-64: 15.0.7-hb91bd55_7 conda-forge + clangxx: 15.0.7-default_h6b1ee41_4 conda-forge + clangxx_impl_osx-64: 15.0.7-h2133e9c_7 conda-forge + clangxx_osx-64: 15.0.7-hb91bd55_7 conda-forge + compiler-rt: 15.0.7-ha38d28d_2 conda-forge + compiler-rt_osx-64: 15.0.7-ha38d28d_2 conda-forge + icu: 73.2-hf5e326d_0 conda-forge + ld64_osx-64: 609-h0fd476b_15 conda-forge + libclang-cpp15: 15.0.7-default_h6b1ee41_4 conda-forge + libcxx: 16.0.6-hd57cbcb_0 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm15: 15.0.7-hbedff68_4 conda-forge + libxml2: 2.12.3-hc0ae0f7_0 conda-forge + libzlib: 1.2.13-h8a1eda9_5 conda-forge + llvm-tools: 15.0.7-hbedff68_4 conda-forge + make: 4.3-h22f3db7_1 conda-forge + openssl: 3.2.0-hd75f5a5_1 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1100.0.11-h9ce4665_0 conda-forge + xz: 5.2.6-h775f41a_0 conda-forge + zstd: 1.5.5-h829000d_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + INFO:conda_build.source:Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: mitoClone2_1.8.1_22c58ba6ed.tar.gz + INFO:conda_build.source:Downloading source to cache: mitoClone2_1.8.1_22c58ba6ed.tar.gz + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/mitoClone2_1.8.1.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/mitoClone2_1.8.1.tar.gz + Success + INFO:conda_build.source:Success + Extracting download + Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-mitoclone2/gamma.patch + Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-mitoclone2/gamma.patch with args: + ['-Np1', '-i', '/var/folders/qv/pdh5wsgn0lq3dp77zj602b5c0000gn/T/tmpz0brhpff/gamma.patch.native', '--binary'] + checking file inst/SCITEpkg/findBestTrees.cpp + Hunk #1 succeeded at 55 (offset 2 lines). + Hunk #2 FAILED at 97. + Hunk #3 succeeded at 264 (offset 2 lines). + 1 out of 3 hunks FAILED + checking file inst/SCITEpkg/mcmc.cpp + Hunk #1 FAILED at 41. + Hunk #2 succeeded at 98 (offset 2 lines). + Hunk #3 succeeded at 121 (offset 2 lines). + 1 out of 3 hunks FAILED + checking file inst/SCITEpkg/mcmc.h + Hunk #1 FAILED at 8. + 1 out of 1 hunk FAILED + Warning: failed to download source. If building, will try again after downloading recipe dependencies. + Error was: + Command '['/opt/mambaforge/envs/bioconda/bin/patch', '--no-backup-if-mismatch', '--batch', '-Np1', '-i', '/var/folders/qv/pdh5wsgn0lq3dp77zj602b5c0000gn/T/tmpz0brhpff/gamma.patch.native', '--binary', '--dry-run']' returned non-zero exit status 1. + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2125, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 663, in try_download + raise RuntimeError("Failed to download or patch source. Please see build log for info.") + RuntimeError: Failed to download or patch source. Please see build log for info. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-mitoclone2/meta.yaml b/recipes/bioconductor-mitoclone2/meta.yaml index 099174a4e3d3c..5d35d4e370509 100644 --- a/recipes/bioconductor-mitoclone2/meta.yaml +++ b/recipes/bioconductor-mitoclone2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "mitoClone2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,7 +11,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f92e5f2d2688b3584be28e0aa21b8b90 + md5: 22c58ba6ed0a51f10714551935477355 patches: - gamma.patch build: @@ -19,14 +19,15 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mitoclone2", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, Biostrings, testthat # SystemRequirements: GNU make, PhISCS (optional) requirements: host: - - 'bioconductor-deepsnv >=1.46.0,<1.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-deepsnv >=1.48.0,<1.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-pheatmap @@ -34,10 +35,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-deepsnv >=1.46.0,<1.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-deepsnv >=1.48.0,<1.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-pheatmap diff --git a/recipes/bioconductor-mixomics/meta.yaml b/recipes/bioconductor-mixomics/meta.yaml index a151268aed52f..d86404b99b5ef 100644 --- a/recipes/bioconductor-mixomics/meta.yaml +++ b/recipes/bioconductor-mixomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "6.24.0" %} +{% set version = "6.26.0" %} {% set name = "mixOmics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0002176b6d102e7b6c4e64f8f98b6df9 + md5: d735d1aec6a3576238256244e87031ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mixomics", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-corpcor - r-dplyr @@ -38,7 +39,7 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-corpcor - r-dplyr diff --git a/recipes/bioconductor-mlinterfaces/meta.yaml b/recipes/bioconductor-mlinterfaces/meta.yaml index bf434ef950404..fe32e07d825f8 100644 --- a/recipes/bioconductor-mlinterfaces/meta.yaml +++ b/recipes/bioconductor-mlinterfaces/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.80.0" %} +{% set version = "1.82.0" %} {% set name = "MLInterfaces" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a88e54ac37f4c267ee6c033b1d84a08 + md5: acb5f91abaa05ef8c6b156b2cc7df846 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mlinterfaces", max_pin="x.x") }}' # Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-fpc @@ -45,11 +46,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-fpc diff --git a/recipes/bioconductor-mlp/meta.yaml b/recipes/bioconductor-mlp/meta.yaml index 704803aa1b5d6..2a506c09f0e69 100644 --- a/recipes/bioconductor-mlp/meta.yaml +++ b/recipes/bioconductor-mlp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "MLP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8456e51613e4fca3b957e9d6d0393414 + md5: 5ed5a850807679b4baa1c5d4d88f48d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mlp", max_pin="x.x") }}' noarch: generic # Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz, GOstats, graph, limma, mouse4302.db, reactome.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-gplots run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-gplots test: diff --git a/recipes/bioconductor-mlseq/meta.yaml b/recipes/bioconductor-mlseq/meta.yaml index d9aa91b142ad4..f6a2d8f85b768 100644 --- a/recipes/bioconductor-mlseq/meta.yaml +++ b/recipes/bioconductor-mlseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "MLSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6407c67b3d4879d54a1311c5b2e27f5f + md5: 07ebcff7e7a474bc21b783a6ebc2605b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mlseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, e1071, kernlab requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sseq >=1.38.0,<1.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sseq >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-foreach @@ -37,12 +38,12 @@ requirements: - r-venndiagram - r-xtable run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sseq >=1.38.0,<1.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sseq >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-foreach diff --git a/recipes/bioconductor-mm24kresogen.db/meta.yaml b/recipes/bioconductor-mm24kresogen.db/meta.yaml index fa0455eab640b..13b54d2ee5b24 100644 --- a/recipes/bioconductor-mm24kresogen.db/meta.yaml +++ b/recipes/bioconductor-mm24kresogen.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.5.0" %} {% set name = "mm24kresogen.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 437f5d4bc225ee500af1ecc2d4da472b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mm24kresogen.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml b/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml index 87aa088134e08..316ebba0491be 100644 --- a/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml +++ b/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "MmAgilentDesign026655.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 7ef619bd2c74f22ea4f3c2b2c4131fe9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mmagilentdesign026655.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mmappr2data/meta.yaml b/recipes/bioconductor-mmappr2data/meta.yaml index 178b222d06b81..5d3faebe25bb7 100644 --- a/recipes/bioconductor-mmappr2data/meta.yaml +++ b/recipes/bioconductor-mmappr2data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MMAPPR2data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ea459c418711fc37e694b10789d03ae + md5: 5b4772746766de5c40448c865fa2d60d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mmappr2data", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, roxygen2, seqinr, readr requirements: host: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base run: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mmappr2data/post-link.sh b/recipes/bioconductor-mmappr2data/post-link.sh index 4dd7748e61a2e..6cbdc2a4f1170 100644 --- a/recipes/bioconductor-mmappr2data/post-link.sh +++ b/recipes/bioconductor-mmappr2data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mmappr2data-1.14.0" +installBiocDataPackage.sh "mmappr2data-1.16.0" diff --git a/recipes/bioconductor-mmdiff2/meta.yaml b/recipes/bioconductor-mmdiff2/meta.yaml index 5d7d9ff1f6c61..ad1ed95691e31 100644 --- a/recipes/bioconductor-mmdiff2/meta.yaml +++ b/recipes/bioconductor-mmdiff2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "MMDiff2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59a85253ca552a7e3140890cf5470067 + md5: 6d14e03f2d5842c403a50c41f30c82d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mmdiff2", max_pin="x.x") }}' noarch: generic # Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-locfit - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-locfit diff --git a/recipes/bioconductor-mmdiffbamsubset/meta.yaml b/recipes/bioconductor-mmdiffbamsubset/meta.yaml index 48e87f668f0c6..c8687b937206b 100644 --- a/recipes/bioconductor-mmdiffbamsubset/meta.yaml +++ b/recipes/bioconductor-mmdiffbamsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "MMDiffBamSubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9a590f3dc54a5b5b4e36232ca7e2538 + md5: 0becc66301b49b58a99efa19577ee27c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mmdiffbamsubset", max_pin="x.x") }}' noarch: generic # Suggests: MMDiff2 requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mmdiffbamsubset/post-link.sh b/recipes/bioconductor-mmdiffbamsubset/post-link.sh index c6ea938925a92..41d02cf30eea3 100644 --- a/recipes/bioconductor-mmdiffbamsubset/post-link.sh +++ b/recipes/bioconductor-mmdiffbamsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mmdiffbamsubset-1.36.0" +installBiocDataPackage.sh "mmdiffbamsubset-1.38.0" diff --git a/recipes/bioconductor-mmuphin/meta.yaml b/recipes/bioconductor-mmuphin/meta.yaml index c674a0d4a3eca..40529f7cbcec9 100644 --- a/recipes/bioconductor-mmuphin/meta.yaml +++ b/recipes/bioconductor-mmuphin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MMUPHin" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef1929535164bd5dbb8e6b764a90d141 + md5: 51f094480eb1629226dc1da59902ab32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mmuphin", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter # SystemRequirements: glpk (>= 4.57) requirements: host: - - 'bioconductor-maaslin2 >=1.14.0,<1.15.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' - r-base - r-cowplot - r-dplyr @@ -33,7 +34,7 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-maaslin2 >=1.14.0,<1.15.0' + - 'bioconductor-maaslin2 >=1.16.0,<1.17.0' - r-base - r-cowplot - r-dplyr diff --git a/recipes/bioconductor-mnem/meta.yaml b/recipes/bioconductor-mnem/meta.yaml index 0332f413204d8..10fae6b84f0a8 100644 --- a/recipes/bioconductor-mnem/meta.yaml +++ b/recipes/bioconductor-mnem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "mnem" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: df7fca9a51f7c89a2f846cf070e03341 + md5: 630cb52a48148dc82038613aacb4e834 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mnem", max_pin="x.x") }}' # Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-linnorm >=2.24.0,<2.25.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-linnorm >=2.26.0,<2.27.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-cluster - r-data.table @@ -40,9 +41,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-linnorm >=2.24.0,<2.25.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-linnorm >=2.26.0,<2.27.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-moanin/meta.yaml b/recipes/bioconductor-moanin/meta.yaml index 231bfbbaf8cd4..896119d5f8400 100644 --- a/recipes/bioconductor-moanin/meta.yaml +++ b/recipes/bioconductor-moanin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "moanin" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47abaa04774cc2d70389e1dde355e8b9 + md5: 74f0ff5d927d538a2b41cdc9c1ee9fd9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moanin", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-clusterr - 'r-mass >=1.0.0' @@ -35,11 +36,11 @@ requirements: - r-viridis - r-zoo run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-clusterr - 'r-mass >=1.0.0' diff --git a/recipes/bioconductor-mobilitytransformr/meta.yaml b/recipes/bioconductor-mobilitytransformr/meta.yaml index 59a78638e061e..5d8c9210a5279 100644 --- a/recipes/bioconductor-mobilitytransformr/meta.yaml +++ b/recipes/bioconductor-mobilitytransformr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MobilityTransformR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: feaa92c6a8c2d5c9145dfde034172797 + md5: 1d0f7904be49e25235092248b757df19 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mobilitytransformr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, msdata (>= 0.35.3), knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown requirements: host: - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-metabocoreutils >=1.8.0,<1.9.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base test: commands: diff --git a/recipes/bioconductor-moda/meta.yaml b/recipes/bioconductor-moda/meta.yaml index aa8aa54d1e1ed..f0c112fc22b46 100644 --- a/recipes/bioconductor-moda/meta.yaml +++ b/recipes/bioconductor-moda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MODA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dee62b28e674b74f2ee50a7413256fdb + md5: 5f48d76fbd7f8905725dbd2db1bc6fee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moda", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-amountain >=1.26.0,<1.27.0' + - 'bioconductor-amountain >=1.28.0,<1.29.0' - r-base - r-cluster - r-dynamictreecut @@ -29,7 +30,7 @@ requirements: - r-rcolorbrewer - r-wgcna run: - - 'bioconductor-amountain >=1.26.0,<1.27.0' + - 'bioconductor-amountain >=1.28.0,<1.29.0' - r-base - r-cluster - r-dynamictreecut diff --git a/recipes/bioconductor-modcon/meta.yaml b/recipes/bioconductor-modcon/meta.yaml index 7dc0070ac4bae..b45ecc4ebeb3c 100644 --- a/recipes/bioconductor-modcon/meta.yaml +++ b/recipes/bioconductor-modcon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ModCon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30a6c15c8ebc53114e7f411b9aa54bdc + md5: bdb0634e890917a01325519cf6e53f90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-modcon", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs # SystemRequirements: Perl diff --git a/recipes/bioconductor-modstrings/meta.yaml b/recipes/bioconductor-modstrings/meta.yaml index ace9febb26799..41aab942018f8 100644 --- a/recipes/bioconductor-modstrings/meta.yaml +++ b/recipes/bioconductor-modstrings/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Modstrings" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 005a6307ac499c539b9d7b44d7d85eb2 + md5: 04e7bccc20c165b4d1317e995a0b1de2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-modstrings", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon - r-stringi - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon - r-stringi diff --git a/recipes/bioconductor-moe430a.db/meta.yaml b/recipes/bioconductor-moe430a.db/meta.yaml index b11256886105a..07af16105b075 100644 --- a/recipes/bioconductor-moe430a.db/meta.yaml +++ b/recipes/bioconductor-moe430a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "moe430a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2bcdace3c55437bc8428b99064e486b1 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430acdf/meta.yaml b/recipes/bioconductor-moe430acdf/meta.yaml index a0309689ab273..269ad39177873 100644 --- a/recipes/bioconductor-moe430acdf/meta.yaml +++ b/recipes/bioconductor-moe430acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b03f1295fc483f0d782a4615e8ca0137 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430aprobe/meta.yaml b/recipes/bioconductor-moe430aprobe/meta.yaml index 0229d3b8e3a92..bb37dab84d098 100644 --- a/recipes/bioconductor-moe430aprobe/meta.yaml +++ b/recipes/bioconductor-moe430aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0aa83189d04599a65211d1a2f0a51c8f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430b.db/meta.yaml b/recipes/bioconductor-moe430b.db/meta.yaml index 8580ce349d001..1ca12a8892d3c 100644 --- a/recipes/bioconductor-moe430b.db/meta.yaml +++ b/recipes/bioconductor-moe430b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "moe430b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2d8a80b9d3342fb943087cc327c824e7 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430bcdf/meta.yaml b/recipes/bioconductor-moe430bcdf/meta.yaml index ad821650817a3..e59a11f6dde96 100644 --- a/recipes/bioconductor-moe430bcdf/meta.yaml +++ b/recipes/bioconductor-moe430bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b7112dcf8ccfe4e079ca67ff62046f2e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moe430bprobe/meta.yaml b/recipes/bioconductor-moe430bprobe/meta.yaml index e84ca437bcf8d..cc36302889064 100644 --- a/recipes/bioconductor-moe430bprobe/meta.yaml +++ b/recipes/bioconductor-moe430bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "moe430bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1368e6f4225babe7a693ccd39a3a436a build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moe430bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moex10stprobeset.db/meta.yaml b/recipes/bioconductor-moex10stprobeset.db/meta.yaml index eb27513f5a45b..cfb5fa806324b 100644 --- a/recipes/bioconductor-moex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-moex10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "moex10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b1c12c80a4424e2854beab9dc796cb00 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moex10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml index feb6e978b0de1..224ad7a7dc909 100644 --- a/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "moex10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bc3357b3c77ab7bf1dfb66f5f7da36ec build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moex10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-moexexonprobesetlocation/meta.yaml b/recipes/bioconductor-moexexonprobesetlocation/meta.yaml index 7db924e5850a4..60209c1317491 100644 --- a/recipes/bioconductor-moexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-moexexonprobesetlocation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.0" %} {% set name = "MoExExonProbesetLocation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 07eea205fce2a8cf4585fa7e71fb0057 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moexexonprobesetlocation", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mofa2/meta.yaml b/recipes/bioconductor-mofa2/meta.yaml index 45435aa0c80a0..5040a7de17019 100644 --- a/recipes/bioconductor-mofa2/meta.yaml +++ b/recipes/bioconductor-mofa2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MOFA2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 534a7aee62498651a346619081e8d819 + md5: 0ce3c0d9a65e9e3f18d387af8a86ef6e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mofa2", max_pin="x.x") }}' # Suggests: knitr, testthat, Seurat, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown # SystemRequirements: Python (>=3), numpy, pandas, h5py, scipy, argparse, sklearn, mofapy2 requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-corrplot - r-cowplot @@ -42,10 +43,10 @@ requirements: - r-tidyr - r-uwot run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-corrplot - r-cowplot diff --git a/recipes/bioconductor-mofadata/meta.yaml b/recipes/bioconductor-mofadata/meta.yaml index ba73ea609b4be..3105056f66ed7 100644 --- a/recipes/bioconductor-mofadata/meta.yaml +++ b/recipes/bioconductor-mofadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "MOFAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c3605011c45bfe05471c35727cf9896 + md5: 23e46e209a43d7e62cfd6accc6a6fb44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mofadata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, MultiAssayExperiment, rmarkdown, BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mofadata/post-link.sh b/recipes/bioconductor-mofadata/post-link.sh index d8d3db7951bff..b927a90f23c04 100644 --- a/recipes/bioconductor-mofadata/post-link.sh +++ b/recipes/bioconductor-mofadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mofadata-1.16.1" +installBiocDataPackage.sh "mofadata-1.18.0" diff --git a/recipes/bioconductor-mogamun/meta.yaml b/recipes/bioconductor-mogamun/meta.yaml index 2d1af7529d78f..ec048725b40a6 100644 --- a/recipes/bioconductor-mogamun/meta.yaml +++ b/recipes/bioconductor-mogamun/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MOGAMUN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce6bc4ff332cffdd506ab91cd5246055 + md5: 8e2d5c06b9fc3d7e294b154f7efb83b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogamun", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-igraph - r-runit - r-stringr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-igraph - r-runit diff --git a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml index 6d9d7efb92d10..99400c2a549a3 100644 --- a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml +++ b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.1.0" %} {% set name = "mogene.1.0.st.v1frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b46f76903d0f19b85e8fa30347813ff5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene.1.0.st.v1frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10stprobeset.db/meta.yaml b/recipes/bioconductor-mogene10stprobeset.db/meta.yaml index 150788d2deaab..98460dd552e38 100644 --- a/recipes/bioconductor-mogene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 570d4cf3fcc42d1e9b54237b9e4eb5f7 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml index 9b1a33769b847..b7365dee5c39e 100644 --- a/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9553a8ecefad2baa7241c6b6bb8013f5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10stv1cdf/meta.yaml b/recipes/bioconductor-mogene10stv1cdf/meta.yaml index 1fe199e259fc5..842e7b799689e 100644 --- a/recipes/bioconductor-mogene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-mogene10stv1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mogene10stv1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c0271f5d6493290fc47f041a8c3f925 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene10stv1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene10stv1probe/meta.yaml b/recipes/bioconductor-mogene10stv1probe/meta.yaml index 2c76031f6e705..7df09b6409c4e 100644 --- a/recipes/bioconductor-mogene10stv1probe/meta.yaml +++ b/recipes/bioconductor-mogene10stv1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mogene10stv1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 63cba1e2a0edee9f201267057fddb0fa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene10stv1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene11stprobeset.db/meta.yaml b/recipes/bioconductor-mogene11stprobeset.db/meta.yaml index 1674014284721..d6a7c91a56257 100644 --- a/recipes/bioconductor-mogene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene11stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene11stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1fba63da3f550e814a58c09d24d61cc0 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene11stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml index 68b1d94d06bd2..e973216aa7b66 100644 --- a/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene11sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2a3bf07a4794e2349b7d09368dcb7d18 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene11sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene20stprobeset.db/meta.yaml b/recipes/bioconductor-mogene20stprobeset.db/meta.yaml index ee52a6e528392..d2fae2f15b125 100644 --- a/recipes/bioconductor-mogene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene20stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene20stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a64ddbf33e4f2b96301452e808d0e81a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene20stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml index f852ea0bff57e..192560f9dbc55 100644 --- a/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene20sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e00e56d47bd19169875690e8e2129156 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene20sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene21stprobeset.db/meta.yaml b/recipes/bioconductor-mogene21stprobeset.db/meta.yaml index ca1fbc8d88889..fae2795386efa 100644 --- a/recipes/bioconductor-mogene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene21stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene21stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d6b3c352329b46493a20f6c27db05d43 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene21stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml index 775a5abc82d65..d36ffcbf36338 100644 --- a/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mogene21sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 10aaecc97bf06bfe770496b99612837a build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogene21sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mogsa/meta.yaml b/recipes/bioconductor-mogsa/meta.yaml index 4340dde6e1703..d9ec395d1b4f8 100644 --- a/recipes/bioconductor-mogsa/meta.yaml +++ b/recipes/bioconductor-mogsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "mogsa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 97374d3cdbd264479ec1188d20ddc51f + md5: 177b003a38a7dc7ce3fb238369d1b6e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mogsa", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, org.Hs.eg.db requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-cluster - r-corpcor - r-gplots - r-svd run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base - r-cluster - r-corpcor diff --git a/recipes/bioconductor-moleculeexperiment/meta.yaml b/recipes/bioconductor-moleculeexperiment/meta.yaml index 1aa49271ff42a..995c26bed8b41 100644 --- a/recipes/bioconductor-moleculeexperiment/meta.yaml +++ b/recipes/bioconductor-moleculeexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.2" %} {% set name = "MoleculeExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94c764955d2e47687932b60877afec83 + md5: d8fef705349bc9464ae152cd47bb9a58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moleculeexperiment", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base + - r-cli - r-data.table - 'r-dplyr >=1.1.1' - r-ggplot2 @@ -31,11 +37,15 @@ requirements: - r-purrr - r-rjson - r-rlang - - r-sp - r-terra run: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base + - r-cli - r-data.table - 'r-dplyr >=1.1.1' - r-ggplot2 @@ -44,7 +54,6 @@ requirements: - r-purrr - r-rjson - r-rlang - - r-sp - r-terra test: commands: diff --git a/recipes/bioconductor-moma/meta.yaml b/recipes/bioconductor-moma/meta.yaml index 72b4f034a14c9..82fa380418cee 100644 --- a/recipes/bioconductor-moma/meta.yaml +++ b/recipes/bioconductor-moma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MOMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 375d2de012590d80009625c8bdc11217 + md5: ce4cf6dab5fea53127b5b980756ef5db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moma", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, viper requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-circlize - r-cluster @@ -39,9 +40,9 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-circlize - r-cluster diff --git a/recipes/bioconductor-monalisa/meta.yaml b/recipes/bioconductor-monalisa/meta.yaml index 4fe4192f03b03..a8dbdc4c4bbc7 100644 --- a/recipes/bioconductor-monalisa/meta.yaml +++ b/recipes/bioconductor-monalisa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "monaLisa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,46 +11,47 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e0c35f87fe09e20036c129bc9e1e736 + md5: fc86eb3743fc47252a4420cd850ead9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-monalisa", max_pin="x.x") }}' noarch: generic # Suggests: JASPAR2020, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-circlize - r-glmnet - r-stabs - r-vioplot run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-circlize - r-glmnet diff --git a/recipes/bioconductor-monocle/meta.yaml b/recipes/bioconductor-monocle/meta.yaml index 08bf12a037b44..1877a38efe4cf 100644 --- a/recipes/bioconductor-monocle/meta.yaml +++ b/recipes/bioconductor-monocle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "monocle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 32a002f0d1231c13af5da03fc43f1401 + md5: 8b3a3d5cd2698b4cef4396c388250658 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-monocle", max_pin="x.x") }}' # Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-hsmmsinglecell >=1.20.0,<1.21.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-hsmmsinglecell >=1.22.0,<1.23.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-cluster - r-combinat @@ -54,11 +55,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-hsmmsinglecell >=1.20.0,<1.21.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-hsmmsinglecell >=1.22.0,<1.23.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-cluster - r-combinat diff --git a/recipes/bioconductor-moonlight2r/build.sh b/recipes/bioconductor-moonlight2r/build.sh new file mode 100644 index 0000000000000..497f7b5bdb678 --- /dev/null +++ b/recipes/bioconductor-moonlight2r/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-moonlight2r/meta.yaml b/recipes/bioconductor-moonlight2r/meta.yaml new file mode 100644 index 0000000000000..0bfdabb5af5a6 --- /dev/null +++ b/recipes/bioconductor-moonlight2r/meta.yaml @@ -0,0 +1,108 @@ +{% set version = "1.0.0" %} +{% set name = "Moonlight2R" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 45af1bc580f9231cb2a83eae7517d3b8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moonlight2r", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png +# SystemRequirements: CScapeSomatic +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-circlize + - r-doparallel + - r-dplyr + - r-easypubmed + - r-foreach + - r-fuzzyjoin + - r-gplots + - r-hiver + - r-magrittr + - r-parmigene + - r-purrr + - r-qpdf + - r-randomforest + - r-rcolorbrewer + - r-readr + - r-rismed + - r-seqminer + - r-stringr + - r-tibble + - r-tidyheatmap + - r-tidyr + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-base + - r-circlize + - r-doparallel + - r-dplyr + - r-easypubmed + - r-foreach + - r-fuzzyjoin + - r-gplots + - r-hiver + - r-magrittr + - r-parmigene + - r-purrr + - r-qpdf + - r-randomforest + - r-rcolorbrewer + - r-readr + - r-rismed + - r-seqminer + - r-stringr + - r-tibble + - r-tidyheatmap + - r-tidyr + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] +test: + commands: + - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Identify oncogenes and tumor suppressor genes from omics data' + description: 'The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). We present an updated version of the R/bioconductor package called MoonlightR, namely Moonlight2R, which returns a list of candidate driver genes for specific cancer types on the basis of omics data integration. The Moonlight framework contains a primary layer where gene expression data and information about biological processes are integrated to predict genes called oncogenic mediators, divided into putative tumor suppressors and putative oncogenes. This is done through functional enrichment analyses, gene regulatory networks and upstream regulator analyses to score the importance of well-known biological processes with respect to the studied cancer type. By evaluating the effect of the oncogenic mediators on biological processes or through random forests, the primary layer predicts two putative roles for the oncogenic mediators: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As gene expression data alone is not enough to explain the deregulation of the genes, a second layer of evidence is needed. We have automated the integration of a secondary mutational layer through new functionalities in Moonlight2R. These functionalities analyze mutations in the cancer cohort and classifies these into driver and passenger mutations using the driver mutation prediction tool, CScape-somatic. Those oncogenic mediators with at least one driver mutation are retained as the driver genes. As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, Moonlight2R can be used to discover OCGs and TSGs in the same cancer type. This may for instance help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV). In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + container: + extended-base: true + diff --git a/recipes/bioconductor-moonlightr/meta.yaml b/recipes/bioconductor-moonlightr/meta.yaml index a7f5cc135260a..c20170c048746 100644 --- a/recipes/bioconductor-moonlightr/meta.yaml +++ b/recipes/bioconductor-moonlightr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MoonlightR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6dc98a013d9a14f5fb86143343d1d102 + md5: 2a389ad9b7fe5ffc5e2c47717eb0b4c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-moonlightr", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png +# Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-circlize - r-doparallel @@ -39,13 +40,13 @@ requirements: - r-rcolorbrewer - r-rismed run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinks >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' - r-base - r-circlize - r-doparallel diff --git a/recipes/bioconductor-mosaics/meta.yaml b/recipes/bioconductor-mosaics/meta.yaml index 931647a8ef049..a9598eaacbb9c 100644 --- a/recipes/bioconductor-mosaics/meta.yaml +++ b/recipes/bioconductor-mosaics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "mosaics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e8ea8871c14e28559be2f8ccb77837ff + md5: 0648fcfd9fd595974e0602fbb2a37cac build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mosaics", max_pin="x.x") }}' # Suggests: mosaicsExample # SystemRequirements: Perl requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-lattice - r-mass @@ -35,12 +36,12 @@ requirements: - liblapack - 'perl >=5.6.0' run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-lattice - r-mass diff --git a/recipes/bioconductor-mosaicsexample/meta.yaml b/recipes/bioconductor-mosaicsexample/meta.yaml index 28c25085fd5ee..ff93401dec058 100644 --- a/recipes/bioconductor-mosaicsexample/meta.yaml +++ b/recipes/bioconductor-mosaicsexample/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "mosaicsExample" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbbc0ae50f0d93a64a45efe4bb848a71 + md5: 8852ad56f152a138367e7630b6b21efb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mosaicsexample", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mosaicsexample/post-link.sh b/recipes/bioconductor-mosaicsexample/post-link.sh index 67a72782b8979..b88c16fdb3cce 100644 --- a/recipes/bioconductor-mosaicsexample/post-link.sh +++ b/recipes/bioconductor-mosaicsexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mosaicsexample-1.38.0" +installBiocDataPackage.sh "mosaicsexample-1.40.0" diff --git a/recipes/bioconductor-mosbi/meta.yaml b/recipes/bioconductor-mosbi/meta.yaml index 6651c91f23fc6..4206531beddd4 100644 --- a/recipes/bioconductor-mosbi/meta.yaml +++ b/recipes/bioconductor-mosbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "mosbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b333ac572e9c67bf00a326e4be6cec60 + md5: f34159f8140d9fe59ea7fe2546e9cdce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mosbi", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) # SystemRequirements: C++17, GNU make requirements: host: - - 'bioconductor-fabia >=2.46.0,<2.47.0' - - 'bioconductor-qubic >=1.28.0,<1.29.0' + - 'bioconductor-fabia >=2.48.0,<2.49.0' + - 'bioconductor-qubic >=1.30.0,<1.31.0' - r-akmbiclust - r-base - r-bh @@ -36,8 +37,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-fabia >=2.46.0,<2.47.0' - - 'bioconductor-qubic >=1.28.0,<1.29.0' + - 'bioconductor-fabia >=2.48.0,<2.49.0' + - 'bioconductor-qubic >=1.30.0,<1.31.0' - r-akmbiclust - r-base - r-bh diff --git a/recipes/bioconductor-mosim/meta.yaml b/recipes/bioconductor-mosim/meta.yaml index 045faf97a8da1..b7ae429633a46 100644 --- a/recipes/bioconductor-mosim/meta.yaml +++ b/recipes/bioconductor-mosim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MOSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ece9e267f663dd2ff82200594d6d59fa + md5: 67f131b000a6d50361f61b4a78835d47 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mosim", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 @@ -39,9 +40,9 @@ requirements: - r-tidyr - r-zoo run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-motif2site/meta.yaml b/recipes/bioconductor-motif2site/meta.yaml index 16140537eb5e7..d941340b40832 100644 --- a/recipes/bioconductor-motif2site/meta.yaml +++ b/recipes/bioconductor-motif2site/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "Motif2Site" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 594b23135d3e5f26922687fb1c328655 + md5: e8228f1deb42f2d4b3867a90a6eba14c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motif2site", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass - r-mixtools run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-mass - r-mixtools diff --git a/recipes/bioconductor-motifbreakr/meta.yaml b/recipes/bioconductor-motifbreakr/meta.yaml index d83aaeb709ed2..ac68355c1531a 100644 --- a/recipes/bioconductor-motifbreakr/meta.yaml +++ b/recipes/bioconductor-motifbreakr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.13.7" %} +{% set version = "2.16.0" %} {% set name = "motifbreakR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,49 +11,50 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b47582e0b811ea6ec5a2e46456e1d7db + md5: fd2ed6098a4bade8948f237753404006 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motifbreakr", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifdb >=1.42.0,<1.43.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifdb >=1.44.0,<1.45.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-stringr - r-tfmpvalue run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifdb >=1.42.0,<1.43.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifdb >=1.44.0,<1.45.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrixstats - r-stringr diff --git a/recipes/bioconductor-motifcounter/meta.yaml b/recipes/bioconductor-motifcounter/meta.yaml index a6ee87d58aa3a..a8167142b3b79 100644 --- a/recipes/bioconductor-motifcounter/meta.yaml +++ b/recipes/bioconductor-motifcounter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "motifcounter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 74707d361ecee0670ee22449f0bd3479 + md5: f093ba4ac3fe6bcf19d9d46bfb084290 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motifcounter", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-motifdb/meta.yaml b/recipes/bioconductor-motifdb/meta.yaml index 63e63c09db371..ccbbed4686d7d 100644 --- a/recipes/bioconductor-motifdb/meta.yaml +++ b/recipes/bioconductor-motifdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "MotifDb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 816f2af600528aae335542318f7ead0f + md5: 0aa63f3bc133dc0fa6c8cf88ebae383b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motifdb", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-splitstackshape run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-splitstackshape test: diff --git a/recipes/bioconductor-motifmatchr/meta.yaml b/recipes/bioconductor-motifmatchr/meta.yaml index b18da3e965dc7..77a5618b3748d 100644 --- a/recipes/bioconductor-motifmatchr/meta.yaml +++ b/recipes/bioconductor-motifmatchr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "motifmatchr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cc0571d16d56335905d347e7967a7308 + md5: 23c63cb97f5e359a4fb9e5e6751e037d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motifmatchr", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-matrix - r-rcpp @@ -37,15 +38,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-motifstack/meta.yaml b/recipes/bioconductor-motifstack/meta.yaml index 547e310dd4115..2475f81526c68 100644 --- a/recipes/bioconductor-motifstack/meta.yaml +++ b/recipes/bioconductor-motifstack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.1" %} +{% set version = "1.46.0" %} {% set name = "motifStack" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a907c93e9a990ab341e7ed4ce5a29bc + md5: b3306b32c8722e6d63ee1a37165a572e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motifstack", max_pin="x.x") }}' noarch: generic # Suggests: Cairo, grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-ade4 - r-base - r-ggplot2 - r-htmlwidgets - r-xml run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-ade4 - r-base - r-ggplot2 diff --git a/recipes/bioconductor-mouse.db0/meta.yaml b/recipes/bioconductor-mouse.db0/meta.yaml index 8cdf1d8f11550..ae26bfd28f0fd 100644 --- a/recipes/bioconductor-mouse.db0/meta.yaml +++ b/recipes/bioconductor-mouse.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "mouse.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 132244baa13685fdb259ecaecd9535af + md5: 1ef6bb1d25e53443871e0e8c975b36c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse.db0/post-link.sh b/recipes/bioconductor-mouse.db0/post-link.sh index 7602a0e166383..b17f1a0a17b14 100644 --- a/recipes/bioconductor-mouse.db0/post-link.sh +++ b/recipes/bioconductor-mouse.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mouse.db0-3.17.0" +installBiocDataPackage.sh "mouse.db0-3.18.0" diff --git a/recipes/bioconductor-mouse4302.db/meta.yaml b/recipes/bioconductor-mouse4302.db/meta.yaml index 8fb2201559542..0a61e3af5ee7a 100644 --- a/recipes/bioconductor-mouse4302.db/meta.yaml +++ b/recipes/bioconductor-mouse4302.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mouse4302.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4ecaa53d32faca4199ba712c0e8ee570 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse4302.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302barcodevecs/meta.yaml b/recipes/bioconductor-mouse4302barcodevecs/meta.yaml index f8719b767f2a7..027726e25334e 100644 --- a/recipes/bioconductor-mouse4302barcodevecs/meta.yaml +++ b/recipes/bioconductor-mouse4302barcodevecs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "mouse4302barcodevecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bb60f755fb3fc86b8dbb769bbe6f06c4 + md5: 365757fba17dae1ed483e184d2c9fcdb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse4302barcodevecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302barcodevecs/post-link.sh b/recipes/bioconductor-mouse4302barcodevecs/post-link.sh index 3b8b8dba1b88a..ed7160125db4e 100644 --- a/recipes/bioconductor-mouse4302barcodevecs/post-link.sh +++ b/recipes/bioconductor-mouse4302barcodevecs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mouse4302barcodevecs-1.38.0" +installBiocDataPackage.sh "mouse4302barcodevecs-1.40.0" diff --git a/recipes/bioconductor-mouse4302cdf/meta.yaml b/recipes/bioconductor-mouse4302cdf/meta.yaml index 8ab265eec436f..57eb77636c347 100644 --- a/recipes/bioconductor-mouse4302cdf/meta.yaml +++ b/recipes/bioconductor-mouse4302cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse4302cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bda3463613f958de35c58777db05cec2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse4302cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302frmavecs/meta.yaml b/recipes/bioconductor-mouse4302frmavecs/meta.yaml index f7e7a74083c32..22c8cdff80066 100644 --- a/recipes/bioconductor-mouse4302frmavecs/meta.yaml +++ b/recipes/bioconductor-mouse4302frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.5.0" %} {% set name = "mouse4302frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ec144b381abbe54d696356c1c124e372 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse4302frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse4302probe/meta.yaml b/recipes/bioconductor-mouse4302probe/meta.yaml index c2556746c00f9..6da34b4b12cbc 100644 --- a/recipes/bioconductor-mouse4302probe/meta.yaml +++ b/recipes/bioconductor-mouse4302probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse4302probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7116787a7db241a545e79e419a8cfa0d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse4302probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2.db/meta.yaml b/recipes/bioconductor-mouse430a2.db/meta.yaml index 4a05a16ffe54c..29f8490359d73 100644 --- a/recipes/bioconductor-mouse430a2.db/meta.yaml +++ b/recipes/bioconductor-mouse430a2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mouse430a2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0f1d053517af5f973f3cc49289cca1e5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse430a2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2cdf/meta.yaml b/recipes/bioconductor-mouse430a2cdf/meta.yaml index b120d005cf0e3..e6b2a4871edaf 100644 --- a/recipes/bioconductor-mouse430a2cdf/meta.yaml +++ b/recipes/bioconductor-mouse430a2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse430a2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1114c0415d1200bc21ad205e0830b075 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse430a2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2frmavecs/meta.yaml b/recipes/bioconductor-mouse430a2frmavecs/meta.yaml index b15791ee611b3..885f3133c6c45 100644 --- a/recipes/bioconductor-mouse430a2frmavecs/meta.yaml +++ b/recipes/bioconductor-mouse430a2frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.0" %} {% set name = "mouse430a2frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3bcb8de9182bbb8de5d560748eafa0cc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse430a2frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mouse430a2probe/meta.yaml b/recipes/bioconductor-mouse430a2probe/meta.yaml index b6d9a39038733..9891dca3ac191 100644 --- a/recipes/bioconductor-mouse430a2probe/meta.yaml +++ b/recipes/bioconductor-mouse430a2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mouse430a2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bb3c34477d4fcf03a539772011118795 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mouse430a2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mousechrloc/meta.yaml b/recipes/bioconductor-mousechrloc/meta.yaml index 0be1b73b5ae0c..97f1bb6f99725 100644 --- a/recipes/bioconductor-mousechrloc/meta.yaml +++ b/recipes/bioconductor-mousechrloc/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.1.6" %} {% set name = "mouseCHRLOC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0b81d7391e628cc355af4de3c5585a5f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mousechrloc", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mousefm/meta.yaml b/recipes/bioconductor-mousefm/meta.yaml index 895f5a44886b4..c7958d978dad0 100644 --- a/recipes/bioconductor-mousefm/meta.yaml +++ b/recipes/bioconductor-mousefm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MouseFM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 146c8308ce2ca568d5aed58b37471960 + md5: 02947a619a95abf1ad58bb781953a22d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mousefm", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-curl - r-data.table @@ -38,10 +39,10 @@ requirements: - r-scales - r-tidyr run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-mousegastrulationdata/meta.yaml b/recipes/bioconductor-mousegastrulationdata/meta.yaml index e3a086be85ff4..c6470676bb06c 100644 --- a/recipes/bioconductor-mousegastrulationdata/meta.yaml +++ b/recipes/bioconductor-mousegastrulationdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MouseGastrulationData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 671b5016215ff92409c4aba1f4a59c16 + md5: 4af06fb157942c6cfd9f24494bd7ae1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mousegastrulationdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumpymatrix >=1.8.0,<1.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mousegastrulationdata/post-link.sh b/recipes/bioconductor-mousegastrulationdata/post-link.sh index 8e592cd3fa57a..62b2c9b8a5dae 100644 --- a/recipes/bioconductor-mousegastrulationdata/post-link.sh +++ b/recipes/bioconductor-mousegastrulationdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mousegastrulationdata-1.14.0" +installBiocDataPackage.sh "mousegastrulationdata-1.16.0" diff --git a/recipes/bioconductor-mousethymusageing/meta.yaml b/recipes/bioconductor-mousethymusageing/meta.yaml index ced8a4b35d2a2..0f159f50427ac 100644 --- a/recipes/bioconductor-mousethymusageing/meta.yaml +++ b/recipes/bioconductor-mousethymusageing/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MouseThymusAgeing" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5453bec0eab9aa18f7f438bbfd63c27 + md5: cf1889c22fa9e5ac5899a4d911907a90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mousethymusageing", max_pin="x.x") }}' noarch: generic # Suggests: knitr, scuttle, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mousethymusageing/post-link.sh b/recipes/bioconductor-mousethymusageing/post-link.sh index abdcde4f7eb4f..f63c5f266662c 100644 --- a/recipes/bioconductor-mousethymusageing/post-link.sh +++ b/recipes/bioconductor-mousethymusageing/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mousethymusageing-1.8.0" +installBiocDataPackage.sh "mousethymusageing-1.10.0" diff --git a/recipes/bioconductor-mpedbarray.db/meta.yaml b/recipes/bioconductor-mpedbarray.db/meta.yaml index ae5e294805f59..b919b9c2456b9 100644 --- a/recipes/bioconductor-mpedbarray.db/meta.yaml +++ b/recipes/bioconductor-mpedbarray.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "mpedbarray.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7bcd1fee1554b6f8844c9bf30b7db4ef build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mpedbarray.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mpfe/meta.yaml b/recipes/bioconductor-mpfe/meta.yaml index 22a5c1def59bb..b632910f132e4 100644 --- a/recipes/bioconductor-mpfe/meta.yaml +++ b/recipes/bioconductor-mpfe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "MPFE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9941cf06f60869ff2770e087bf835ab + md5: 4f86c179f9bc43d1e16295df91c07cb8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mpfe", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mpo.db/meta.yaml b/recipes/bioconductor-mpo.db/meta.yaml new file mode 100644 index 0000000000000..1e7309a1611e8 --- /dev/null +++ b/recipes/bioconductor-mpo.db/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.99.7" %} +{% set name = "MPO.db" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1f1b83d5d03d69a82ca2b9e7179b537f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mpo.db", max_pin="x.x") }}' + noarch: generic +# Suggests: rmarkdown, knitr, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + - r-dbi + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - r-base + - r-dbi + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A set of annotation maps describing the Mouse Phenotype Ontology' + description: 'We have developed the human disease ontology R package HDO.db, which provides the semantic relationship between human diseases. Relying on the DOSE and GOSemSim packages we developed, we can carry out disease enrichment and semantic similarity analyses. Many biological studies are achieved through mouse models, and a large number of data indicate the association between genotypes and phenotypes or diseases. The study of model organisms can be transformed into useful knowledge about normal human biology and disease to facilitate treatment and early screening for diseases. Organism-specific genotype-phenotypic associations can be applied to cross-species phenotypic studies to clarify previously unknown phenotypic connections in other species. Using the same principle to diseases can identify genetic associations and even help to identify disease associations that are not obvious. Therefore, as a supplement to HDO.db and DOSE, we developed mouse phenotypic ontology R package MPO.db.' + diff --git a/recipes/bioconductor-mpo.db/post-link.sh b/recipes/bioconductor-mpo.db/post-link.sh new file mode 100644 index 0000000000000..e54b8c62eb857 --- /dev/null +++ b/recipes/bioconductor-mpo.db/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "mpo.db-0.99.7" diff --git a/recipes/bioconductor-mpo.db/pre-unlink.sh b/recipes/bioconductor-mpo.db/pre-unlink.sh new file mode 100644 index 0000000000000..0a46c236ab5a1 --- /dev/null +++ b/recipes/bioconductor-mpo.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MPO.db diff --git a/recipes/bioconductor-mpra/meta.yaml b/recipes/bioconductor-mpra/meta.yaml index feca4df94b4aa..c7695063b2da4 100644 --- a/recipes/bioconductor-mpra/meta.yaml +++ b/recipes/bioconductor-mpra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "mpra" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46586d5c53b2dd30ac5c51ca48ffc54a + md5: ee3c8c16534188d568ee8f0e01afb894 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mpra", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-scales - r-statmod run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-scales - r-statmod diff --git a/recipes/bioconductor-mpranalyze/meta.yaml b/recipes/bioconductor-mpranalyze/meta.yaml index 8bbc71f1d89ef..d750c44c0fcf3 100644 --- a/recipes/bioconductor-mpranalyze/meta.yaml +++ b/recipes/bioconductor-mpranalyze/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MPRAnalyze" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7fefa718bdfc973d4d43150fc54848e0 + md5: 63ae4121bc319692b51499a1b151dffc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mpranalyze", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-progress run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-progress test: diff --git a/recipes/bioconductor-mqmetrics/meta.yaml b/recipes/bioconductor-mqmetrics/meta.yaml index 573e3690b8c3c..22405f3ac0796 100644 --- a/recipes/bioconductor-mqmetrics/meta.yaml +++ b/recipes/bioconductor-mqmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MQmetrics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4519a7303cf121235ab8028b6ed775d + md5: 6c0c8bd3d356ed2db8d6329fd21958d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mqmetrics", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle requirements: diff --git a/recipes/bioconductor-msa/meta.yaml b/recipes/bioconductor-msa/meta.yaml index fdd875fa6c032..d7f0231460388 100644 --- a/recipes/bioconductor-msa/meta.yaml +++ b/recipes/bioconductor-msa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "msa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 261f13d3751fe96b50e9745091278ca0 + md5: 78eba41452ffe497e1a7c72116335b3e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msa", max_pin="x.x") }}' # Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rcpp >=0.11.1' - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rcpp >=0.11.1' build: diff --git a/recipes/bioconductor-msa2dist/meta.yaml b/recipes/bioconductor-msa2dist/meta.yaml index dd53d926e5525..64b19c561480a 100644 --- a/recipes/bioconductor-msa2dist/meta.yaml +++ b/recipes/bioconductor-msa2dist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MSA2dist" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 69cf471088b61e2f4ce253992ace214a + md5: 8a0d1c303af72c93a1810488010c2e6f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msa2dist", max_pin="x.x") }}' # Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-ape - r-base - r-doparallel @@ -40,9 +41,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-ape - r-base - r-doparallel diff --git a/recipes/bioconductor-msbackendmassbank/meta.yaml b/recipes/bioconductor-msbackendmassbank/meta.yaml index e74c7a50c242d..dc48b7c227b93 100644 --- a/recipes/bioconductor-msbackendmassbank/meta.yaml +++ b/recipes/bioconductor-msbackendmassbank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.1" %} {% set name = "MsBackendMassbank" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bbf939d9164027370b91ee2f052dd7af + md5: a929aebecff77108bc62891bc397f057 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msbackendmassbank", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-dbi run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-dbi test: diff --git a/recipes/bioconductor-msbackendmgf/meta.yaml b/recipes/bioconductor-msbackendmgf/meta.yaml index b023175e1c9c3..87335b6ed47d8 100644 --- a/recipes/bioconductor-msbackendmgf/meta.yaml +++ b/recipes/bioconductor-msbackendmgf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MsBackendMgf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 161fa6e31b677cc2e2f9f9a505f7365b + md5: a8b5cc0b0f9c2da6222c217ae8a4c44f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msbackendmgf", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base test: commands: diff --git a/recipes/bioconductor-msbackendmsp/meta.yaml b/recipes/bioconductor-msbackendmsp/meta.yaml index 75f54a1b70ccb..34df8b380d30c 100644 --- a/recipes/bioconductor-msbackendmsp/meta.yaml +++ b/recipes/bioconductor-msbackendmsp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MsBackendMsp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b0c87f4dd11f453f3fdd531640413d4 + md5: 805d831547106b2f232bb9eda75172bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msbackendmsp", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base test: commands: diff --git a/recipes/bioconductor-msbackendrawfilereader/meta.yaml b/recipes/bioconductor-msbackendrawfilereader/meta.yaml index e6d27818945ae..ebd428e4ee072 100644 --- a/recipes/bioconductor-msbackendrawfilereader/meta.yaml +++ b/recipes/bioconductor-msbackendrawfilereader/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "MsBackendRawFileReader" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e2d39d098ace938f7b5e26b18045acc + md5: b933c2e4fbd38b9cc8298a9cb397b5ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msbackendrawfilereader", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat # SystemRequirements: mono-runtime 4.x or higher (including System.Data library) on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft Windows. requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-rawrr >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-rawrr >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-rawrr >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-rawrr >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base test: commands: diff --git a/recipes/bioconductor-msbackendsql/meta.yaml b/recipes/bioconductor-msbackendsql/meta.yaml index 42926a7a93c1d..ebd150923cd74 100644 --- a/recipes/bioconductor-msbackendsql/meta.yaml +++ b/recipes/bioconductor-msbackendsql/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "MsBackendSql" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 750baf1c6b633a31eb5e8ed0ccb74887 + md5: c5d7c6ce9c877e7c0bbbc1b63a71eb70 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msbackendsql", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, msdata, rmarkdown, microbenchmark, mzR requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-data.table - r-dbi - r-progress run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - r-data.table - r-dbi diff --git a/recipes/bioconductor-mscoreutils/meta.yaml b/recipes/bioconductor-mscoreutils/meta.yaml index e47c8407560ae..abc01147f991f 100644 --- a/recipes/bioconductor-mscoreutils/meta.yaml +++ b/recipes/bioconductor-mscoreutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.1" %} {% set name = "MsCoreUtils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e1a918ab120b13cee142f6ae08898d0a + md5: 163cc129bc77ed033c124fed5bf7d9ca build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, norm2, pcaMethods, vsn, Matrix, preprocessCore, missForest + run_exports: '{{ pin_subpackage("bioconductor-mscoreutils", max_pin="x.x") }}' +# Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clue - r-mass @@ -28,7 +29,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clue - r-mass diff --git a/recipes/bioconductor-msd16s/meta.yaml b/recipes/bioconductor-msd16s/meta.yaml index fa6623c0cc230..093763b193ce2 100644 --- a/recipes/bioconductor-msd16s/meta.yaml +++ b/recipes/bioconductor-msd16s/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "msd16s" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 48cc66a74ec0aeff91a4c5217f69c57d + md5: fddb80467192bbe28bb92599941be5d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msd16s", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-metagenomeseq >=1.42.0,<1.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msd16s/post-link.sh b/recipes/bioconductor-msd16s/post-link.sh index eb39e5c656947..62fa20ab286f1 100644 --- a/recipes/bioconductor-msd16s/post-link.sh +++ b/recipes/bioconductor-msd16s/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msd16s-1.20.0" +installBiocDataPackage.sh "msd16s-1.22.0" diff --git a/recipes/bioconductor-msdata/meta.yaml b/recipes/bioconductor-msdata/meta.yaml index 3524f3b40f8d2..a93c158772cf0 100644 --- a/recipes/bioconductor-msdata/meta.yaml +++ b/recipes/bioconductor-msdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.40.0" %} +{% set version = "0.42.0" %} {% set name = "msdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dc6c949e6d593b4220d08511155b9316 + md5: 3ef7fea0866799a767fb8ac2d1da0a16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msdata", max_pin="x.x") }}' noarch: generic # Suggests: xcms, mzR, MSnbase requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msdata/post-link.sh b/recipes/bioconductor-msdata/post-link.sh index 183325d55e1d2..d125e3b63b591 100644 --- a/recipes/bioconductor-msdata/post-link.sh +++ b/recipes/bioconductor-msdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msdata-0.40.0" +installBiocDataPackage.sh "msdata-0.42.0" diff --git a/recipes/bioconductor-msdatahub/meta.yaml b/recipes/bioconductor-msdatahub/meta.yaml index 461800d7ef3c1..2e0d17ac40a1a 100644 --- a/recipes/bioconductor-msdatahub/meta.yaml +++ b/recipes/bioconductor-msdatahub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MsDataHub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c683540dc7f74f68fbd233970fda9a51 + md5: f355465b6b3994491364cbe994e4488d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msdatahub", max_pin="x.x") }}' noarch: generic # Suggests: ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), Spectra, mzR, PSMatch, QFeatures requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base test: commands: diff --git a/recipes/bioconductor-msexperiment/meta.yaml b/recipes/bioconductor-msexperiment/meta.yaml index 23cb602f88adb..13793f29ea8ce 100644 --- a/recipes/bioconductor-msexperiment/meta.yaml +++ b/recipes/bioconductor-msexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "MsExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ef4ff755bcf01849577c7ab9393eb49 + md5: b248141f2ad9d5421d067b7f90a4c87e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msexperiment", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, msdata requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-msfeatures/meta.yaml b/recipes/bioconductor-msfeatures/meta.yaml index 805d24a097fad..f2f78d9cab20a 100644 --- a/recipes/bioconductor-msfeatures/meta.yaml +++ b/recipes/bioconductor-msfeatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MsFeatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3100535245dfbd18aacb93a38a7db53c + md5: 326a08270ef7c22e636f1fed4cf569b6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msfeatures", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown requirements: host: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-msgbsr/meta.yaml b/recipes/bioconductor-msgbsr/meta.yaml index 51513290152d2..945baebb54043 100644 --- a/recipes/bioconductor-msgbsr/meta.yaml +++ b/recipes/bioconductor-msgbsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "msgbsR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 091994f16f89c9151c5f5625d3fcbf23 + md5: 41ae41a9216ffbe0ee9c51a91f89112c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msgbsr", max_pin="x.x") }}' noarch: generic # Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-easyrnaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-easyrnaseq >=2.38.0,<2.39.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-plyr - r-r.utils run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-easyrnaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-easyrnaseq >=2.38.0,<2.39.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-plyr diff --git a/recipes/bioconductor-msigdb/meta.yaml b/recipes/bioconductor-msigdb/meta.yaml index 51c8be04e8ebd..04f7f6cf90356 100644 --- a/recipes/bioconductor-msigdb/meta.yaml +++ b/recipes/bioconductor-msigdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "msigdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1468865f501a46ee6410f5fac54d9441 + md5: eb5822dab5f9ad68cc5a46beaf626de0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msigdb", max_pin="x.x") }}' noarch: generic # Suggests: singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msigdb/post-link.sh b/recipes/bioconductor-msigdb/post-link.sh index 2b9b4297b4376..62fbfe5ec1ef4 100644 --- a/recipes/bioconductor-msigdb/post-link.sh +++ b/recipes/bioconductor-msigdb/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msigdb-1.8.0" +installBiocDataPackage.sh "msigdb-1.10.0" diff --git a/recipes/bioconductor-msimpute/meta.yaml b/recipes/bioconductor-msimpute/meta.yaml index 6a1a8598b3119..3da17fd266353 100644 --- a/recipes/bioconductor-msimpute/meta.yaml +++ b/recipes/bioconductor-msimpute/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "msImpute" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66df74b17cee32a58263c3f8ff86ab65 + md5: 493d744acd5f63e07590f22b2ce0eea2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msimpute", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD # SystemRequirements: python requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-data.table - r-dplyr @@ -35,8 +36,8 @@ requirements: - r-softimpute - r-tidyr run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-mslp/meta.yaml b/recipes/bioconductor-mslp/meta.yaml index b701deb301f74..cffb95da2b231 100644 --- a/recipes/bioconductor-mslp/meta.yaml +++ b/recipes/bioconductor-mslp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "mslp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1ce8ff13dcb84461ad3044da4fa1d95d + md5: 8d78607401143e315c9ad75923a0c9c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mslp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest requirements: host: - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' - r-base - 'r-data.table >=1.13.0' - r-dorng @@ -32,8 +33,8 @@ requirements: - r-proc - r-randomforest run: - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' - r-base - 'r-data.table >=1.13.0' - r-dorng diff --git a/recipes/bioconductor-msmb/meta.yaml b/recipes/bioconductor-msmb/meta.yaml index c0651e7ad2023..75d847b490453 100644 --- a/recipes/bioconductor-msmb/meta.yaml +++ b/recipes/bioconductor-msmb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "MSMB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d9b11ea89215a562d46146b97e3208e + md5: bc2942708f54a40d59ce7e41daff7df0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msmb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle requirements: @@ -27,7 +28,7 @@ requirements: - r-base - r-tibble - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msmb/post-link.sh b/recipes/bioconductor-msmb/post-link.sh index 06758ac01f71c..3244b61f86248 100644 --- a/recipes/bioconductor-msmb/post-link.sh +++ b/recipes/bioconductor-msmb/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msmb-1.18.0" +installBiocDataPackage.sh "msmb-1.20.0" diff --git a/recipes/bioconductor-msmseda/meta.yaml b/recipes/bioconductor-msmseda/meta.yaml index abd89b96a49e9..71435d318c253 100644 --- a/recipes/bioconductor-msmseda/meta.yaml +++ b/recipes/bioconductor-msmseda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "msmsEDA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2cc93eaf5f937a738bcde6c7827142b7 + md5: d2350677044dfea55c25faa434894cb2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msmseda", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-gplots - r-mass - r-rcolorbrewer run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-gplots - r-mass diff --git a/recipes/bioconductor-msmstests/meta.yaml b/recipes/bioconductor-msmstests/meta.yaml index cf1e2f7ba84e2..f842cafcbe067 100644 --- a/recipes/bioconductor-msmstests/meta.yaml +++ b/recipes/bioconductor-msmstests/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "msmsTests" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14ec34cafa4bce236590d54cd072aca8 + md5: 90c08df612ce3e4608ab3b9fa048764a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msmstests", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-msmseda >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-msmseda >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-msmseda >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-msmseda >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base test: commands: diff --git a/recipes/bioconductor-msnbase/meta.yaml b/recipes/bioconductor-msnbase/meta.yaml index 03c1307ba1595..a3dd29afe1be0 100644 --- a/recipes/bioconductor-msnbase/meta.yaml +++ b/recipes/bioconductor-msnbase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.1" %} {% set name = "MSnbase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f68f7e648144f82ce9926ca58b575a23 + md5: 4d3cbd696e9ca193ec9bdc4722f2ac49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msnbase", max_pin="x.x") }}' # Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-digest - r-ggplot2 @@ -46,19 +47,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-digest - r-ggplot2 diff --git a/recipes/bioconductor-msnid/meta.yaml b/recipes/bioconductor-msnid/meta.yaml index e5617ace168c0..2c78af9e2fe61 100644 --- a/recipes/bioconductor-msnid/meta.yaml +++ b/recipes/bioconductor-msnid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MSnID" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be86f620a2146c8c3d84cf9b095b1898 + md5: e0491fe4f99deb1c0128ab4dcde8f3f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msnid", max_pin="x.x") }}' requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msmstests >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msmstests >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-data.table - r-doparallel @@ -49,17 +50,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msmstests >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msmstests >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-msprep/meta.yaml b/recipes/bioconductor-msprep/meta.yaml index 438b4348fd63e..a6f5d896e023c 100644 --- a/recipes/bioconductor-msprep/meta.yaml +++ b/recipes/bioconductor-msprep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MSPrep" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1732ab760da9c7217119d26609efc56 + md5: 65036a0ebe0b1280a2c4666c263a6e5f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msprep", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2) requirements: host: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-crmn - 'r-dplyr >=0.7' @@ -37,11 +38,11 @@ requirements: - r-tidyr - r-vim run: - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-crmn - 'r-dplyr >=0.7' diff --git a/recipes/bioconductor-mspurity/meta.yaml b/recipes/bioconductor-mspurity/meta.yaml index c35428558a1b7..3dcb43f28b697 100644 --- a/recipes/bioconductor-mspurity/meta.yaml +++ b/recipes/bioconductor-mspurity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "msPurity" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0bef4ca96c52c5c6ee0ba8b4a454ec8c + md5: 0a29b8f3eacf707bf9791d50df53083a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mspurity", max_pin="x.x") }}' # Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL requirements: host: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-dbi - r-dbplyr @@ -38,7 +39,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-dbi - r-dbplyr diff --git a/recipes/bioconductor-mspuritydata/meta.yaml b/recipes/bioconductor-mspuritydata/meta.yaml index 93d318ef1d154..52332729fbed8 100644 --- a/recipes/bioconductor-mspuritydata/meta.yaml +++ b/recipes/bioconductor-mspuritydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "msPurityData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 758e960ac371d347930ab01398f27127 + md5: 6c86343515cbb9f81131baa3f25659f0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mspuritydata", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mspuritydata/post-link.sh b/recipes/bioconductor-mspuritydata/post-link.sh index c975c68fe6f81..7b9e5d412b057 100644 --- a/recipes/bioconductor-mspuritydata/post-link.sh +++ b/recipes/bioconductor-mspuritydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mspuritydata-1.28.0" +installBiocDataPackage.sh "mspuritydata-1.30.0" diff --git a/recipes/bioconductor-msqc1/meta.yaml b/recipes/bioconductor-msqc1/meta.yaml index 1ace9e6f47bf7..b1e92a856601d 100644 --- a/recipes/bioconductor-msqc1/meta.yaml +++ b/recipes/bioconductor-msqc1/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "msqc1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eec753dc0f640e28b06685127ac3794e + md5: a95a760a0c0ef5e8053acee1d59170a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msqc1", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2) requirements: @@ -27,7 +28,7 @@ requirements: - r-base - r-lattice - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-msqc1/post-link.sh b/recipes/bioconductor-msqc1/post-link.sh index 61a449edfbb82..7c052c8f8c306 100644 --- a/recipes/bioconductor-msqc1/post-link.sh +++ b/recipes/bioconductor-msqc1/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msqc1-1.28.0" +installBiocDataPackage.sh "msqc1-1.30.0" diff --git a/recipes/bioconductor-msqrob2/meta.yaml b/recipes/bioconductor-msqrob2/meta.yaml index 533a90b1cd280..5084c4368d7b3 100644 --- a/recipes/bioconductor-msqrob2/meta.yaml +++ b/recipes/bioconductor-msqrob2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "msqrob2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47e977ca03352478eee88298fb305024 + md5: b2c0046b0c67c24dd7d94eeb22fea3a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msqrob2", max_pin="x.x") }}' noarch: generic # Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils, covr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-codetools - r-lme4 @@ -33,11 +34,11 @@ requirements: - r-matrix - r-purrr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-codetools - r-lme4 diff --git a/recipes/bioconductor-msquality/meta.yaml b/recipes/bioconductor-msquality/meta.yaml index 1db6c970dcc1b..541bf61068252 100644 --- a/recipes/bioconductor-msquality/meta.yaml +++ b/recipes/bioconductor-msquality/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MsQuality" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c0813d8ece6db8cec01df6ea741da18 + md5: 1d8e2101f472e8fc93bfa275db511982 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msquality", max_pin="x.x") }}' noarch: generic -# Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), msdata (>= 0.32.0), mzR (>= 2.32.0), rmarkdown (>= 2.7), S4Vectors (>= 0.29.17), testthat (>= 2.2.1) +# Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), mzR (>= 2.32.0), rmarkdown (>= 2.7), S4Vectors (>= 0.29.17), testthat (>= 2.2.1) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-msexperiment >=1.2.0,<1.3.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-msdata >=0.42.0,<0.43.0' + - 'bioconductor-msexperiment >=1.4.0,<1.5.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - 'r-ggplot2 >=3.3.5' - 'r-htmlwidgets >=1.5.3' - 'r-plotly >=4.9.4.1' + - 'r-rmzqc >=0.5.0' - 'r-shiny >=1.6.0' - 'r-shinydashboard >=0.7.1' - 'r-stringr >=1.4.0' - 'r-tibble >=3.1.4' - 'r-tidyr >=1.1.3' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-msexperiment >=1.2.0,<1.3.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-spectra >=1.10.0,<1.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-msdata >=0.42.0,<0.43.0' + - 'bioconductor-msexperiment >=1.4.0,<1.5.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' - r-base - 'r-ggplot2 >=3.3.5' - 'r-htmlwidgets >=1.5.3' - 'r-plotly >=4.9.4.1' + - 'r-rmzqc >=0.5.0' - 'r-shiny >=1.6.0' - 'r-shinydashboard >=0.7.1' - 'r-stringr >=1.4.0' diff --git a/recipes/bioconductor-msstats/meta.yaml b/recipes/bioconductor-msstats/meta.yaml index 56e1895593f48..e17bbdfaade32 100644 --- a/recipes/bioconductor-msstats/meta.yaml +++ b/recipes/bioconductor-msstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.8.3" %} +{% set version = "4.10.0" %} {% set name = "MSstats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06dfde9c4e7960e84e1bb35698986b45 + md5: fac3a495f2e627a75b10a9b941d3674d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstats", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, tinytest, covr, markdown requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-checkmate - r-data.table @@ -39,10 +40,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-msstatsbig/build.sh b/recipes/bioconductor-msstatsbig/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msstatsbig/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msstatsbig/meta.yaml b/recipes/bioconductor-msstatsbig/meta.yaml new file mode 100644 index 0000000000000..18aabd0559ba2 --- /dev/null +++ b/recipes/bioconductor-msstatsbig/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.0.0" %} +{% set name = "MSstatsBig" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a53de589b47964296160c6fb8aaeb3b4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsbig", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - r-arrow + - r-base + - r-dbi + - r-dplyr + - r-readr + - r-sparklyr + run: + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - r-arrow + - r-base + - r-dbi + - r-dplyr + - r-readr + - r-sparklyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'MSstats Preprocessing for Larger than Memory Data' + description: 'MSstats package provide tools for preprocessing, summarization and differential analysis of mass spectrometry (MS) proteomics data. Recently, some MS protocols enable acquisition of data sets that result in larger than memory quantitative data. MSstats functions are not able to process such data. MSstatsBig package provides additional converter functions that enable processing larger than memory data sets.' + diff --git a/recipes/bioconductor-msstatsconvert/meta.yaml b/recipes/bioconductor-msstatsconvert/meta.yaml index f8af78a8eb74d..f5eb9823683aa 100644 --- a/recipes/bioconductor-msstatsconvert/meta.yaml +++ b/recipes/bioconductor-msstatsconvert/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.3" %} +{% set version = "1.12.0" %} {% set name = "MSstatsConvert" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c32e16a748d6a0f6fa9d733c3586524 + md5: 1a8b79ba830db5296c2d3f589b398b7f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsconvert", max_pin="x.x") }}' noarch: generic # Suggests: tinytest, covr, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-msstatslip/meta.yaml b/recipes/bioconductor-msstatslip/meta.yaml index 717f277859654..9f580d896931f 100644 --- a/recipes/bioconductor-msstatslip/meta.yaml +++ b/recipes/bioconductor-msstatslip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "MSstatsLiP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b374b82219e6c374a9d8697cf04151ad + md5: 677e775b1c84f40715703064cd74faff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatslip", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatsptm >=2.2.0,<2.3.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatsptm >=2.4.0,<2.5.0' - r-base - r-checkmate - r-data.table @@ -42,10 +43,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatsptm >=2.2.0,<2.3.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatsptm >=2.4.0,<2.5.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-msstatslobd/meta.yaml b/recipes/bioconductor-msstatslobd/meta.yaml index bb59795e8d38a..a464e413da1ea 100644 --- a/recipes/bioconductor-msstatslobd/meta.yaml +++ b/recipes/bioconductor-msstatslobd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MSstatsLOBD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 463905ce41e90270bdf7b7fa3c1098d8 + md5: 1d67c5813cb057b72100d71487c26f64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatslobd", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr requirements: host: diff --git a/recipes/bioconductor-msstatsptm/meta.yaml b/recipes/bioconductor-msstatsptm/meta.yaml index d36bbbe5aa754..6ce348235cd97 100644 --- a/recipes/bioconductor-msstatsptm/meta.yaml +++ b/recipes/bioconductor-msstatsptm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.4" %} +{% set version = "2.4.1" %} {% set name = "MSstatsPTM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 145549a30b3191f757ab605d629686bb + md5: 73b092b7145deaaa579c525e7d243a1e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsptm", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, tinytest, covr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatstmt >=2.8.0,<2.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatstmt >=2.10.0,<2.11.0' - r-base - r-checkmate - r-data.table @@ -37,10 +38,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatstmt >=2.8.0,<2.9.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatstmt >=2.10.0,<2.11.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-msstatsqc/meta.yaml b/recipes/bioconductor-msstatsqc/meta.yaml index 86717ae213a79..fd453766efc47 100644 --- a/recipes/bioconductor-msstatsqc/meta.yaml +++ b/recipes/bioconductor-msstatsqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "MSstatsQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e4777a03d82bbf62a75d8731f5131347 + md5: 9328babd37ae774a13dff37e38088339 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsqc", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown, testthat, RforProteomics requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qcmetrics >=1.38.0,<1.39.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qcmetrics >=1.40.0,<1.41.0' - r-base - r-dplyr - r-ggextra - r-ggplot2 - r-plotly run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qcmetrics >=1.38.0,<1.39.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qcmetrics >=1.40.0,<1.41.0' - r-base - r-dplyr - r-ggextra diff --git a/recipes/bioconductor-msstatsqcgui/meta.yaml b/recipes/bioconductor-msstatsqcgui/meta.yaml index 5f7e42ec22a95..acb4bf4a02184 100644 --- a/recipes/bioconductor-msstatsqcgui/meta.yaml +++ b/recipes/bioconductor-msstatsqcgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MSstatsQCgui" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a9fb31259f2479840addd189193dd56 + md5: 1e648f2226907f737e1d7e71a375f01c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsqcgui", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-msstatsqc >=2.18.0,<2.19.0' + - 'bioconductor-msstatsqc >=2.20.0,<2.21.0' - r-base - r-dplyr - r-ggextra @@ -29,7 +30,7 @@ requirements: - r-plotly - r-shiny run: - - 'bioconductor-msstatsqc >=2.18.0,<2.19.0' + - 'bioconductor-msstatsqc >=2.20.0,<2.21.0' - r-base - r-dplyr - r-ggextra diff --git a/recipes/bioconductor-msstatsshiny/meta.yaml b/recipes/bioconductor-msstatsshiny/meta.yaml index c3a7952dbc3d4..0b5bc563d63a4 100644 --- a/recipes/bioconductor-msstatsshiny/meta.yaml +++ b/recipes/bioconductor-msstatsshiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.3" %} +{% set version = "1.4.1" %} {% set name = "MSstatsShiny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd8ced0fd30746c179d8b8fe12f29b0b + md5: 4eb74ec920d96afc15079226261224f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatsshiny", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0), shinytest2, mockery requirements: host: - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatsptm >=2.2.0,<2.3.0' - - 'bioconductor-msstatstmt >=2.8.0,<2.9.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatsptm >=2.4.0,<2.5.0' + - 'bioconductor-msstatstmt >=2.10.0,<2.11.0' - r-base - r-data.table - r-dplyr @@ -43,11 +44,11 @@ requirements: - r-tidyr - r-uuid run: - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' - - 'bioconductor-msstatsptm >=2.2.0,<2.3.0' - - 'bioconductor-msstatstmt >=2.8.0,<2.9.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - 'bioconductor-msstatsptm >=2.4.0,<2.5.0' + - 'bioconductor-msstatstmt >=2.10.0,<2.11.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-msstatstmt/meta.yaml b/recipes/bioconductor-msstatstmt/meta.yaml index 1959649a11e22..5ea13afd7ae7c 100644 --- a/recipes/bioconductor-msstatstmt/meta.yaml +++ b/recipes/bioconductor-msstatstmt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "MSstatsTMT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d471cc96d18a6910e6ffd312f1b8700 + md5: 73166086fd3882b4771350fde01f37fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msstatstmt", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' - r-base - r-checkmate - r-data.table @@ -31,9 +32,9 @@ requirements: - r-lme4 - r-lmertest run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msstats >=4.8.0,<4.9.0' - - 'bioconductor-msstatsconvert >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msstats >=4.10.0,<4.11.0' + - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' - r-base - r-checkmate - r-data.table diff --git a/recipes/bioconductor-mta10probeset.db/meta.yaml b/recipes/bioconductor-mta10probeset.db/meta.yaml index 0c22dc74a8d66..6e88a7ceb061d 100644 --- a/recipes/bioconductor-mta10probeset.db/meta.yaml +++ b/recipes/bioconductor-mta10probeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mta10probeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 84517c6b354690cd72ccefbe3b39d8e1 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mta10probeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml b/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml index cf5b6d76c6d2c..9a39f45852b4d 100644 --- a/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "mta10transcriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bfd13b16b71ac2cfc82f40f2d102892b build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mta10transcriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mtbls2/meta.yaml b/recipes/bioconductor-mtbls2/meta.yaml index 7787f4fb6f5e9..fb928253ee251 100644 --- a/recipes/bioconductor-mtbls2/meta.yaml +++ b/recipes/bioconductor-mtbls2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "mtbls2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9f3494d399dd599b5e462dba8bd126bb + md5: 820109836c79f398ea5b82f5887b7fea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mtbls2", max_pin="x.x") }}' noarch: generic # Suggests: xcms (>= 3.13.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mtbls2/post-link.sh b/recipes/bioconductor-mtbls2/post-link.sh index a631a19cb959c..0ef2e910328f4 100644 --- a/recipes/bioconductor-mtbls2/post-link.sh +++ b/recipes/bioconductor-mtbls2/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mtbls2-1.30.0" +installBiocDataPackage.sh "mtbls2-1.32.0" diff --git a/recipes/bioconductor-mu11ksuba.db/meta.yaml b/recipes/bioconductor-mu11ksuba.db/meta.yaml index dd83c8e9876a7..b55de485fc588 100644 --- a/recipes/bioconductor-mu11ksuba.db/meta.yaml +++ b/recipes/bioconductor-mu11ksuba.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mu11ksuba.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 73d80611d1eaf8ee1eb37ebc469d97e9 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksuba.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubacdf/meta.yaml b/recipes/bioconductor-mu11ksubacdf/meta.yaml index e838910a4056a..b59ac2145b73a 100644 --- a/recipes/bioconductor-mu11ksubacdf/meta.yaml +++ b/recipes/bioconductor-mu11ksubacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 52fb8ac56435775022fb62f40efafd22 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksubacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubaprobe/meta.yaml b/recipes/bioconductor-mu11ksubaprobe/meta.yaml index 3e8c94ad02544..dcedba4948626 100644 --- a/recipes/bioconductor-mu11ksubaprobe/meta.yaml +++ b/recipes/bioconductor-mu11ksubaprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubaprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 813cd0750cca6ff0cfb696b83286177e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksubaprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubb.db/meta.yaml b/recipes/bioconductor-mu11ksubb.db/meta.yaml index ba344620c6ebd..63bb7d8ea3a05 100644 --- a/recipes/bioconductor-mu11ksubb.db/meta.yaml +++ b/recipes/bioconductor-mu11ksubb.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mu11ksubb.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2b61d911c3595843e80041949cb79b41 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksubb.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubbcdf/meta.yaml b/recipes/bioconductor-mu11ksubbcdf/meta.yaml index 6c076b4d23b69..c998c26278a66 100644 --- a/recipes/bioconductor-mu11ksubbcdf/meta.yaml +++ b/recipes/bioconductor-mu11ksubbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f9691ea74e19dfe57bf6cca6ed396947 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksubbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu11ksubbprobe/meta.yaml b/recipes/bioconductor-mu11ksubbprobe/meta.yaml index 5c19b7e0d066a..8b5ab818deb4d 100644 --- a/recipes/bioconductor-mu11ksubbprobe/meta.yaml +++ b/recipes/bioconductor-mu11ksubbprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubbprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 28d162e18e4e16e3c6db47195d2ea0ac build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu11ksubbprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu15v1.db/meta.yaml b/recipes/bioconductor-mu15v1.db/meta.yaml index 9e51592eede5f..74f2380efbe7e 100644 --- a/recipes/bioconductor-mu15v1.db/meta.yaml +++ b/recipes/bioconductor-mu15v1.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Mu15v1.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e9297b5fe223b046bc65dc6ea0b4376d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu15v1.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksuba.db/meta.yaml b/recipes/bioconductor-mu19ksuba.db/meta.yaml index a87af58bf9b82..35416f946ef4e 100644 --- a/recipes/bioconductor-mu19ksuba.db/meta.yaml +++ b/recipes/bioconductor-mu19ksuba.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mu19ksuba.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c057d8793f2db914a93d2e1f5a3af178 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksuba.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubacdf/meta.yaml b/recipes/bioconductor-mu19ksubacdf/meta.yaml index 9c33eba108be9..795c51c9e9101 100644 --- a/recipes/bioconductor-mu19ksubacdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83a9e7a3bac665b655786e66dbd77848 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksubacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubb.db/meta.yaml b/recipes/bioconductor-mu19ksubb.db/meta.yaml index 30815c0163287..0dcbb94ef24d0 100644 --- a/recipes/bioconductor-mu19ksubb.db/meta.yaml +++ b/recipes/bioconductor-mu19ksubb.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mu19ksubb.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1b177a3b5626c825c91e7c25e0acd897 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksubb.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubbcdf/meta.yaml b/recipes/bioconductor-mu19ksubbcdf/meta.yaml index c8bc3b4ce3fce..f36b278a44c54 100644 --- a/recipes/bioconductor-mu19ksubbcdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 35e5ebcb4cb51950a85c1e3622bb39f0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksubbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubc.db/meta.yaml b/recipes/bioconductor-mu19ksubc.db/meta.yaml index dcddf61bea78a..2a6ec8567e56b 100644 --- a/recipes/bioconductor-mu19ksubc.db/meta.yaml +++ b/recipes/bioconductor-mu19ksubc.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "mu19ksubc.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bef37c9cd01032e9f1fb177a1af8cba4 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksubc.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu19ksubccdf/meta.yaml b/recipes/bioconductor-mu19ksubccdf/meta.yaml index 8e59b4a88c832..a36c87e66abc3 100644 --- a/recipes/bioconductor-mu19ksubccdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e53ef2716f88022e5e41e2cd857fc2a3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu19ksubccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu22v3.db/meta.yaml b/recipes/bioconductor-mu22v3.db/meta.yaml index be15e8d840786..2f51fdab19768 100644 --- a/recipes/bioconductor-mu22v3.db/meta.yaml +++ b/recipes/bioconductor-mu22v3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Mu22v3.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 44aaebe909be9b0108256194c55cf6fb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu22v3.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subacdf/meta.yaml b/recipes/bioconductor-mu6500subacdf/meta.yaml index 0da1ec948f8c1..70ad8c1a4d40a 100644 --- a/recipes/bioconductor-mu6500subacdf/meta.yaml +++ b/recipes/bioconductor-mu6500subacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e72152fc4bae307e3858160e018b7f92 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu6500subacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subbcdf/meta.yaml b/recipes/bioconductor-mu6500subbcdf/meta.yaml index 5d675542693ec..3d1466e9f7e83 100644 --- a/recipes/bioconductor-mu6500subbcdf/meta.yaml +++ b/recipes/bioconductor-mu6500subbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5000bea2a018b4b6ec05cda111438bc1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu6500subbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subccdf/meta.yaml b/recipes/bioconductor-mu6500subccdf/meta.yaml index 4e28b798416fe..7d7b7e16103de 100644 --- a/recipes/bioconductor-mu6500subccdf/meta.yaml +++ b/recipes/bioconductor-mu6500subccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c7cbbe6c70a0a3ae11600ad6c0e540c1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu6500subccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mu6500subdcdf/meta.yaml b/recipes/bioconductor-mu6500subdcdf/meta.yaml index 548d24141b096..33e237d79d7f6 100644 --- a/recipes/bioconductor-mu6500subdcdf/meta.yaml +++ b/recipes/bioconductor-mu6500subdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "mu6500subdcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a614674e8bc60fefd8520dd25d45f8d0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mu6500subdcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mudata/meta.yaml b/recipes/bioconductor-mudata/meta.yaml index b766c63a41b66..bf39d295640fb 100644 --- a/recipes/bioconductor-mudata/meta.yaml +++ b/recipes/bioconductor-mudata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MuData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 389ee9f10c659c43649c72093a748e4a + md5: 10ef702e87a5f0517e59c1ccb96b08dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mudata", max_pin="x.x") }}' noarch: generic # Suggests: HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr, SingleCellMultiModal, CiteFuse, scater requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-mugaexampledata/meta.yaml b/recipes/bioconductor-mugaexampledata/meta.yaml index 3e27f5daa3a80..4141815c412fb 100644 --- a/recipes/bioconductor-mugaexampledata/meta.yaml +++ b/recipes/bioconductor-mugaexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MUGAExampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e9d37ebfc20b7c46c5e0d98528dc188 + md5: b7fe2c7ad41486695fb78263a8c9a854 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mugaexampledata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mugaexampledata/post-link.sh b/recipes/bioconductor-mugaexampledata/post-link.sh index db9219ea03f72..36035835faa9e 100644 --- a/recipes/bioconductor-mugaexampledata/post-link.sh +++ b/recipes/bioconductor-mugaexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mugaexampledata-1.20.0" +installBiocDataPackage.sh "mugaexampledata-1.22.0" diff --git a/recipes/bioconductor-mulcom/meta.yaml b/recipes/bioconductor-mulcom/meta.yaml index 8b1f30c26397a..87516158ebe13 100644 --- a/recipes/bioconductor-mulcom/meta.yaml +++ b/recipes/bioconductor-mulcom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "Mulcom" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 959bad703faed95503f5eca2cf9d5152 + md5: 87375077f62104b18567db2e68a07488 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mulcom", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fields - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fields build: diff --git a/recipes/bioconductor-multiassayexperiment/meta.yaml b/recipes/bioconductor-multiassayexperiment/meta.yaml index 8be82a3ce2582..d65438bca2711 100644 --- a/recipes/bioconductor-multiassayexperiment/meta.yaml +++ b/recipes/bioconductor-multiassayexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "MultiAssayExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62505a73913bf3c40c77e5c33e779c03 + md5: 01844376cd208e33797b236e2e65fd77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multiassayexperiment", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, HDF5Array (>= 1.19.17), knitr, maftools (>= 2.7.10), rmarkdown, R.rsp, RaggedExperiment, UpSetR, survival, survminer, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-tidyr test: diff --git a/recipes/bioconductor-multibac/meta.yaml b/recipes/bioconductor-multibac/meta.yaml index c0d4f723b91c1..56235ddd1ac34 100644 --- a/recipes/bioconductor-multibac/meta.yaml +++ b/recipes/bioconductor-multibac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MultiBaC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4469b7a12aea60b8882fb3bccc5fb9e8 + md5: 5585e9f823074db09f44221063a3e64b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multibac", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, devtools requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' - r-base - r-ggplot2 - r-matrix - r-plotrix run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' - r-base - r-ggplot2 - r-matrix diff --git a/recipes/bioconductor-multiclust/meta.yaml b/recipes/bioconductor-multiclust/meta.yaml index 5cf90fae7abc1..93e1c54ad3fec 100644 --- a/recipes/bioconductor-multiclust/meta.yaml +++ b/recipes/bioconductor-multiclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "multiClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88d9663dab3cbdc5ce296edde7632508 + md5: 86c305cad6c68f0a1850f056dad9615e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multiclust", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery requirements: host: - - 'bioconductor-ctc >=1.74.0,<1.75.0' + - 'bioconductor-ctc >=1.76.0,<1.77.0' - r-amap - r-base - r-cluster @@ -29,7 +30,7 @@ requirements: - r-mclust - r-survival run: - - 'bioconductor-ctc >=1.74.0,<1.75.0' + - 'bioconductor-ctc >=1.76.0,<1.77.0' - r-amap - r-base - r-cluster diff --git a/recipes/bioconductor-multicrispr/meta.yaml b/recipes/bioconductor-multicrispr/meta.yaml index dbcfa4f9022e0..fe725d944bd47 100644 --- a/recipes/bioconductor-multicrispr/meta.yaml +++ b/recipes/bioconductor-multicrispr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.3" %} {% set name = "multicrispr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b9bfeb36b38297c0c222e36950b2423a + md5: d0bbc847e39772348376d944c884290a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multicrispr", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprseek >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - r-assertive + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprseek >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-assertive.base + - r-assertive.files + - r-assertive.numbers + - r-assertive.reflection + - r-assertive.sets - r-base - r-data.table - r-ggplot2 @@ -42,18 +47,22 @@ requirements: - r-tidyr - r-tidyselect run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-crisprseek >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-karyoploter >=1.26.0,<1.27.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - r-assertive + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-crisprseek >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - r-assertive.base + - r-assertive.files + - r-assertive.numbers + - r-assertive.reflection + - r-assertive.sets - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-multidataset/meta.yaml b/recipes/bioconductor-multidataset/meta.yaml index 5766230883d6e..8cbbdbf9d333b 100644 --- a/recipes/bioconductor-multidataset/meta.yaml +++ b/recipes/bioconductor-multidataset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "MultiDataSet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40343f355c0b2c4824b8dbae2d99a46e + md5: 304e6d8ccbb54c446f43f2df5e13f530 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multidataset", max_pin="x.x") }}' noarch: generic # Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel - r-qqman run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-multigsea/meta.yaml b/recipes/bioconductor-multigsea/meta.yaml index aaf5ffda635e0..52e09755c08a2 100644 --- a/recipes/bioconductor-multigsea/meta.yaml +++ b/recipes/bioconductor-multigsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "multiGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 402790b4fd5fe02d3cf9f8c0aec866f3 + md5: 4f22605155c363e634e9a2ca6afae5c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multigsea", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' - 'bioconductor-metaboliteidmapping >=1.0.0,<1.1.0' - r-base - r-dplyr @@ -32,9 +33,9 @@ requirements: - r-rappdirs - r-rlang run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' - 'bioconductor-metaboliteidmapping >=1.0.0,<1.1.0' - r-base - r-dplyr diff --git a/recipes/bioconductor-multihiccompare/meta.yaml b/recipes/bioconductor-multihiccompare/meta.yaml index d6e500783897c..d25d76d5d4fc4 100644 --- a/recipes/bioconductor-multihiccompare/meta.yaml +++ b/recipes/bioconductor-multihiccompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "multiHiCcompare" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d18f5b456ea8b27f8f3646821c85e204 + md5: 04512b7be1f12fa8bfb32a13dbbb408f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multihiccompare", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-aggregation - r-base - r-data.table @@ -35,12 +36,12 @@ requirements: - r-pheatmap - r-qqman run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-aggregation - r-base - r-data.table diff --git a/recipes/bioconductor-multimed/meta.yaml b/recipes/bioconductor-multimed/meta.yaml index e566afa49af3f..0efc3b4e5acb4 100644 --- a/recipes/bioconductor-multimed/meta.yaml +++ b/recipes/bioconductor-multimed/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "MultiMed" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25b04f108f1617d3db68d9aacb8d7451 + md5: 019bc5d7be15d1688b3b5df7b87246f7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multimed", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-multimir/meta.yaml b/recipes/bioconductor-multimir/meta.yaml index e34af927faac8..f62e261c71752 100644 --- a/recipes/bioconductor-multimir/meta.yaml +++ b/recipes/bioconductor-multimir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "multiMiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f6fbcf9e864eee972e452fe334fedb1 + md5: 7102f312557b010d184bac5dea6e5009 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multimir", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dplyr - 'r-purrr >=0.2.2' @@ -30,8 +31,8 @@ requirements: - 'r-tibble >=1.2' - r-xml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dplyr - 'r-purrr >=0.2.2' diff --git a/recipes/bioconductor-multimodalexperiment/meta.yaml b/recipes/bioconductor-multimodalexperiment/meta.yaml index b71a72ef509ec..4e86eba270849 100644 --- a/recipes/bioconductor-multimodalexperiment/meta.yaml +++ b/recipes/bioconductor-multimodalexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "MultimodalExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3edef95bdd0fd57c9c2e7b077aeac135 + md5: 376186ba5972df1b6d4be9dc69253a61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multimodalexperiment", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-multirnaflow/build.sh b/recipes/bioconductor-multirnaflow/build.sh new file mode 100644 index 0000000000000..497f7b5bdb678 --- /dev/null +++ b/recipes/bioconductor-multirnaflow/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multirnaflow/build_failure.linux-64.yaml b/recipes/bioconductor-multirnaflow/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8506b569378e7 --- /dev/null +++ b/recipes/bioconductor-multirnaflow/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: bb62d3b200f33f1ffccfa82f8214efabe8d38de5aa2a4135bccc1e17878148d7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + package r-plot3drgl-1.0.4-r43h6115d3f_0 is excluded by strict repo priority +category: |- + dependency issue diff --git a/recipes/bioconductor-multirnaflow/meta.yaml b/recipes/bioconductor-multirnaflow/meta.yaml new file mode 100644 index 0000000000000..46b7f0655ed98 --- /dev/null +++ b/recipes/bioconductor-multirnaflow/meta.yaml @@ -0,0 +1,89 @@ +{% set version = "1.0.0" %} +{% set name = "MultiRNAflow" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cefc109896f4cb34b4ee6a09ae966f42 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multirnaflow", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocGenerics (>= 0.40.0), BiocStyle, e1071 (>= 1.7.12), knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - 'r-factoextra >=1.0.7' + - 'r-factominer >=2.6' + - 'r-ggalluvial >=0.12.3' + - 'r-ggplot2 >=3.4.0' + - 'r-ggrepel >=0.9.2' + - 'r-ggsci >=2.9' + - 'r-gprofiler2 >=0.2.1' + - 'r-plot3d >=1.4' + - 'r-plot3drgl >=1.0.3' + - 'r-plyr >=1.8.8' + - 'r-rcolorbrewer >=1.1.3' + - 'r-reshape2 >=1.4.4' + - 'r-rlang >=1.1.1' + - 'r-scales >=1.2.1' + - 'r-upsetr >=1.4.0' + run: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - 'r-factoextra >=1.0.7' + - 'r-factominer >=2.6' + - 'r-ggalluvial >=0.12.3' + - 'r-ggplot2 >=3.4.0' + - 'r-ggrepel >=0.9.2' + - 'r-ggsci >=2.9' + - 'r-gprofiler2 >=0.2.1' + - 'r-plot3d >=1.4' + - 'r-plot3drgl >=1.0.3' + - 'r-plyr >=1.8.8' + - 'r-rcolorbrewer >=1.1.3' + - 'r-reshape2 >=1.4.4' + - 'r-rlang >=1.1.1' + - 'r-scales >=1.2.1' + - 'r-upsetr >=1.4.0' + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] +test: + commands: + - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 | file LICENSE' + summary: 'An R package for analysing RNA-seq raw counts with several biological conditions and different time points' + description: 'Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time.' + license_file: LICENSE +extra: + container: + extended-base: true + diff --git a/recipes/bioconductor-multiscan/meta.yaml b/recipes/bioconductor-multiscan/meta.yaml index 9354f244130e1..703917f5a7eb5 100644 --- a/recipes/bioconductor-multiscan/meta.yaml +++ b/recipes/bioconductor-multiscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "multiscan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d181a09f635a8d5f7cca61849e4ac8a2 + md5: 58243690ff05bdbd30da46ea01e409a3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multiscan", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-multiwgcna/build.sh b/recipes/bioconductor-multiwgcna/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-multiwgcna/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multiwgcna/meta.yaml b/recipes/bioconductor-multiwgcna/meta.yaml new file mode 100644 index 0000000000000..b40ef3418752f --- /dev/null +++ b/recipes/bioconductor-multiwgcna/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "multiWGCNA" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b8f70e9496cf73238aa3ba3c08cb81fa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multiwgcna", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan +requirements: + host: + - 'bioconductor-dcanr >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cowplot + - r-data.table + - r-dplyr + - r-flashclust + - r-ggalluvial + - r-ggplot2 + - r-ggrepel + - r-igraph + - r-patchwork + - r-readr + - r-reshape2 + - r-scales + - r-stringr + - r-wgcna + run: + - 'bioconductor-dcanr >=1.18.0,<1.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cowplot + - r-data.table + - r-dplyr + - r-flashclust + - r-ggalluvial + - r-ggplot2 + - r-ggrepel + - r-igraph + - r-patchwork + - r-readr + - r-reshape2 + - r-scales + - r-stringr + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: multiWGCNA + description: 'An R package for deeping mining gene co-expression networks in multi-trait expression data. Provides functions for analyzing, comparing, and visualizing WGCNA networks across conditions. multiWGCNA was designed to handle the common case where there are multiple biologically meaningful sample traits, such as disease vs wildtype across development or anatomical region.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-multtest/meta.yaml b/recipes/bioconductor-multtest/meta.yaml index 97a738c9090aa..2921e8d93355a 100644 --- a/recipes/bioconductor-multtest/meta.yaml +++ b/recipes/bioconductor-multtest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.56.0" %} +{% set version = "2.58.0" %} {% set name = "multtest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2c19179f77fab3d8d805e284334c8a2c + md5: 7d81a8460781f4a86f01a9df5fcf50d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multtest", max_pin="x.x") }}' # Suggests: snow requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-mass - r-survival - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-mass - r-survival diff --git a/recipes/bioconductor-mumosa/meta.yaml b/recipes/bioconductor-mumosa/meta.yaml index 773d5fad68828..8030f8a98140c 100644 --- a/recipes/bioconductor-mumosa/meta.yaml +++ b/recipes/bioconductor-mumosa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "mumosa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,53 +11,54 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 029ee75ea5b608ec5c691437e20a9df8 + md5: 634ea9c4fce9573e5da8297886d4b699 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mumosa", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq requirements: host: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix - r-uwot run: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix diff --git a/recipes/bioconductor-mungesumstats/meta.yaml b/recipes/bioconductor-mungesumstats/meta.yaml index 5b60a43283b23..b1efda96dcf54 100644 --- a/recipes/bioconductor-mungesumstats/meta.yaml +++ b/recipes/bioconductor-mungesumstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.1" %} {% set name = "MungeSumstats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38021189f212fdcf82d1a314142ec7bf + md5: 9164f3e5c8e7612c387b35bff82dc4cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mungesumstats", max_pin="x.x") }}' noarch: generic # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr @@ -39,13 +40,13 @@ requirements: - r-rcurl - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-mus.musculus/meta.yaml b/recipes/bioconductor-mus.musculus/meta.yaml index 9797f1ad64b34..59c522bbcc842 100644 --- a/recipes/bioconductor-mus.musculus/meta.yaml +++ b/recipes/bioconductor-mus.musculus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1" %} {% set name = "Mus.musculus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1b8defe64c2dd308a88d1ac7a4ce04b9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mus.musculus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-muscat/meta.yaml b/recipes/bioconductor-muscat/meta.yaml index 08c28a46c8fc8..9dbac95cfe90b 100644 --- a/recipes/bioconductor-muscat/meta.yaml +++ b/recipes/bioconductor-muscat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "muscat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c076dd82606240da8ce32441aba3a2fa + md5: ee69286717f8d129ce59fb554c1c0994 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-muscat", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, testthat, UpSetR requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variancepartition >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' - r-base - r-blme - r-data.table @@ -48,17 +49,17 @@ requirements: - r-sctransform - r-viridis run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variancepartition >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' - r-base - r-blme - r-data.table diff --git a/recipes/bioconductor-muscdata/meta.yaml b/recipes/bioconductor-muscdata/meta.yaml index f552a704d78c1..9db11d8026d1c 100644 --- a/recipes/bioconductor-muscdata/meta.yaml +++ b/recipes/bioconductor-muscdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "muscData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d39accb42da56f5ca951a6f735f1586a + md5: f34c376f88f97c98d4aac5490b45bc24 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-muscdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, dplyr, DropletUtils, knitr, GEOquery, Matrix, matrixStats, methods, muscat, rmarkdown, R.utils, readxl, scater, scds, Seurat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-muscdata/post-link.sh b/recipes/bioconductor-muscdata/post-link.sh index 1a1accd88b16f..87addac2bf682 100644 --- a/recipes/bioconductor-muscdata/post-link.sh +++ b/recipes/bioconductor-muscdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "muscdata-1.14.0" +installBiocDataPackage.sh "muscdata-1.16.0" diff --git a/recipes/bioconductor-muscle/meta.yaml b/recipes/bioconductor-muscle/meta.yaml index 3f98fbc555ae4..c75199b874840 100644 --- a/recipes/bioconductor-muscle/meta.yaml +++ b/recipes/bioconductor-muscle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.42.0" %} +{% set version = "3.44.0" %} {% set name = "muscle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5f8ece986a6adf5824aa35a420e351f9 + md5: 159745260e624c7aeb3d2e0deeef99ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-muscle", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-musicatk/build_failure.linux-64.yaml b/recipes/bioconductor-musicatk/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..424fa8f85cd80 --- /dev/null +++ b/recipes/bioconductor-musicatk/build_failure.linux-64.yaml @@ -0,0 +1,101 @@ +recipe_sha: add20fc7cb5cb40c6bb4cc7b7f4ec8df2354e950eedc2efb6d70c37d5fb83448 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + ERRO Task processing failed: API error (500): {"message":"write /usr/local/lib/libgoogle_cloud_cpp_dialogflow_cx.so.2.12.0: no space left on device"} +category: |- + compiler error +log: |- + .07:05:52 BIOCONDA INFO (ERR) [Dec 15 07:05:52] SERR [Dec 15 07:05:52] ERRO Task processing failed: API error (500): {"message":"write /usr/local/lib/libgoogle_cloud_cpp_dialogflow_cx.so.2.12.0: no space left on device"} + 07:05:52 BIOCONDA INFO (ERR) [Dec 15 07:05:52] SERR + 07:05:52 BIOCONDA INFO (ERR) [Dec 15 07:05:52] ERRO Task processing failed: Unexpected exit code [1] of container [c84c2e941721 step-698cd8abd9], container preserved + .07:06:42 BIOCONDA INFO (OUT) ........ + 07:06:42 BIOCONDA INFO (ERR) Traceback (most recent call last): + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/bin/mulled-build", line 10, in + 07:06:42 BIOCONDA INFO (ERR) sys.exit(main()) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 414, in main + 07:06:42 BIOCONDA INFO (ERR) sys.exit(mull_targets(targets, **args_to_mull_targets_kwds(args))) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 243, in mull_targets + 07:06:42 BIOCONDA INFO (ERR) ret = involucro_context.exec_command(involucro_args) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 287, in exec_command + 07:06:42 BIOCONDA INFO (ERR) shutil.rmtree('./build') + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 718, in rmtree + 07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(fd, path, onerror) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + 07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(dirfd, fullname, onerror) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + 07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(dirfd, fullname, onerror) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + 07:06:42 BIOCONDA INFO (ERR) _rmtree_safe_fd(dirfd, fullname, onerror) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 675, in _rmtree_safe_fd + 07:06:42 BIOCONDA INFO (ERR) onerror(os.unlink, fullname, sys.exc_info()) + 07:06:42 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 673, in _rmtree_safe_fd + 07:06:42 BIOCONDA INFO (ERR) os.unlink(entry.name, dir_fd=topfd) + 07:06:42 BIOCONDA INFO (ERR) PermissionError: [Errno 13] Permission denied: 'pcre2_set_callout.3' + 07:06:42 BIOCONDA ERROR COMMAND FAILED (exited with 1): mulled-build build-and-test bioconductor-musicatk=1.12.0--r43hdfd78af_0 -n biocontainers --test bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && Rscript -e "library('"'"'musicatk'"'"')"' --channels conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults --involucro-path /opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/involucro + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/pkg_test.py", line 180, in test_package + p = utils.run(cmd, env=env, cwd=d, mask=False, live=live_logs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/utils.py", line 697, in run + raise sp.CalledProcessError(returncode, masked_cmds, output=output) + subprocess.CalledProcessError: Command '['mulled-build', 'build-and-test', 'bioconductor-musicatk=1.12.0--r43hdfd78af_0', '-n', 'biocontainers', '--test', 'bash -c \'/usr/local/env-execute true && . /usr/local/env-activate.sh && Rscript -e "library(\'"\'"\'musicatk\'"\'"\')"\'', '--channels', 'conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults', '--involucro-path', '/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/involucro']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 673, in _rmtree_safe_fd + os.unlink(entry.name, dir_fd=topfd) + PermissionError: [Errno 13] Permission denied: 'pcre2_set_callout.3' + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/bioconda-utils", line 8, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 1114, in main + argh.dispatch_commands([ + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 328, in dispatch_commands + dispatch(parser, *args, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 174, in dispatch + for line in lines: + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 277, in _execute_command + for line in result: + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/argh/dispatching.py", line 260, in _call + result = function(*positional, **keywords) + File "", line 2, in build + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 137, in wrapper + func(*args, **kwargs) + File "", line 2, in build + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 66, in wrapper + func(*args, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/cli.py", line 492, in build + success = build_recipes(recipe_folder, config, recipes, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/build.py", line 421, in build_recipes + res = build(recipe=recipe, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/build.py", line 185, in build + pkg_test.test_package(pkg_path, base_image=base_image, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/pkg_test.py", line 180, in test_package + p = utils.run(cmd, env=env, cwd=d, mask=False, live=live_logs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 827, in __exit__ + self.cleanup() + File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 831, in cleanup + self._rmtree(self.name) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 813, in _rmtree + _shutil.rmtree(name, onerror=onerror) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 718, in rmtree + _rmtree_safe_fd(fd, path, onerror) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + _rmtree_safe_fd(dirfd, fullname, onerror) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + _rmtree_safe_fd(dirfd, fullname, onerror) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd + _rmtree_safe_fd(dirfd, fullname, onerror) + [Previous line repeated 1 more time] + File "/opt/mambaforge/envs/bioconda/lib/python3.8/shutil.py", line 675, in _rmtree_safe_fd + onerror(os.unlink, fullname, sys.exc_info()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 798, in onerror + resetperms(_os.path.dirname(path)) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/tempfile.py", line 794, in resetperms + _os.chmod(path, 0o700) + PermissionError: [Errno 1] Operation not permitted: '/tmp/tmpeaviicao/build/dist/man/man3' + Error: Process completed with exit code 1. diff --git a/recipes/bioconductor-musicatk/meta.yaml b/recipes/bioconductor-musicatk/meta.yaml index 384cee72811a5..3bbcc539d032f 100644 --- a/recipes/bioconductor-musicatk/meta.yaml +++ b/recipes/bioconductor-musicatk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "musicatk" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 23833374b24d85aa3fb37d69c818ad9d + md5: 50869915aff9dd79823e05b4ae163bc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-musicatk", max_pin="x.x") }}' noarch: generic # Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-decomptumor2sig >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-maftools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-decomptumor2sig >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-cluster - r-data.table @@ -67,24 +68,24 @@ requirements: - r-topicmodels - r-uwot run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-decomptumor2sig >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-maftools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-decomptumor2sig >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-maftools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-mutationalpatterns/meta.yaml b/recipes/bioconductor-mutationalpatterns/meta.yaml index d3cfa91018d80..78b54176ec5de 100644 --- a/recipes/bioconductor-mutationalpatterns/meta.yaml +++ b/recipes/bioconductor-mutationalpatterns/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.10.0" %} +{% set version = "3.12.0" %} {% set name = "MutationalPatterns" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e8261046a65aa290c5026e6ab0bfef9 + md5: 6c800e4f89957108a1b4ab1d3a2b4cb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mutationalpatterns", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), ccfindR (>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-cowplot >=0.9.2' - 'r-dplyr >=0.8.3' @@ -44,14 +45,14 @@ requirements: - 'r-tibble >=2.1.3' - 'r-tidyr >=1.0.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-cowplot >=0.9.2' - 'r-dplyr >=0.8.3' diff --git a/recipes/bioconductor-mvcclass/meta.yaml b/recipes/bioconductor-mvcclass/meta.yaml index 7ea5d2273d088..dc8edbb507c49 100644 --- a/recipes/bioconductor-mvcclass/meta.yaml +++ b/recipes/bioconductor-mvcclass/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "MVCClass" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 624849899bde24809fa8df9780da0eb3 + md5: 2ef3331b86ae7981a2ab3323386caf61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mvcclass", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-mvoutdata/meta.yaml b/recipes/bioconductor-mvoutdata/meta.yaml index 9f192cbe3b987..a0a5517d19240 100644 --- a/recipes/bioconductor-mvoutdata/meta.yaml +++ b/recipes/bioconductor-mvoutdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "mvoutData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4a2c65e797ec8403b7657afc81c2714 + md5: abca7ca8ae7729ed8f146d0083aa9757 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mvoutdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mvoutdata/post-link.sh b/recipes/bioconductor-mvoutdata/post-link.sh index c8bac146b0676..c258bd7e17567 100644 --- a/recipes/bioconductor-mvoutdata/post-link.sh +++ b/recipes/bioconductor-mvoutdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mvoutdata-1.36.0" +installBiocDataPackage.sh "mvoutdata-1.38.0" diff --git a/recipes/bioconductor-mwastools/meta.yaml b/recipes/bioconductor-mwastools/meta.yaml index f512e56ccd79b..75f809f1bc281 100644 --- a/recipes/bioconductor-mwastools/meta.yaml +++ b/recipes/bioconductor-mwastools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "MWASTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4a49a058ef4c25ba8756e32251ea6c9 + md5: 4af3f3512a794c7944a27bfad640aa81 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mwastools", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-car @@ -36,11 +37,11 @@ requirements: - r-ppcor - r-rcurl run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-car diff --git a/recipes/bioconductor-mwgcod.db/meta.yaml b/recipes/bioconductor-mwgcod.db/meta.yaml index 4f6b7f79bc085..e5a5c3839be7b 100644 --- a/recipes/bioconductor-mwgcod.db/meta.yaml +++ b/recipes/bioconductor-mwgcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "mwgcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3d6e2af6b05d6e07a212c043dc9d37c4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mwgcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mygene/meta.yaml b/recipes/bioconductor-mygene/meta.yaml index 80b5f1e3c5d32..a48b4d7634c6f 100644 --- a/recipes/bioconductor-mygene/meta.yaml +++ b/recipes/bioconductor-mygene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "mygene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 13074d33fbfe6415400dab10c372bbac + md5: 01ebbd87d5d6b57ca6987eef9c3ae95a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mygene", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-hmisc - 'r-httr >=0.3' @@ -30,8 +31,8 @@ requirements: - r-plyr - r-sqldf run: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-hmisc - 'r-httr >=0.3' diff --git a/recipes/bioconductor-myvariant/meta.yaml b/recipes/bioconductor-myvariant/meta.yaml index 2046e5b7d9672..bfcdcd49ceb7b 100644 --- a/recipes/bioconductor-myvariant/meta.yaml +++ b/recipes/bioconductor-myvariant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "myvariant" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b56b2c182e41681970973e976bb52f7c + md5: 110e5245914806eb225bad404727124f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-myvariant", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-hmisc - r-httr @@ -31,9 +32,9 @@ requirements: - r-magrittr - r-plyr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-hmisc - r-httr diff --git a/recipes/bioconductor-mzid/meta.yaml b/recipes/bioconductor-mzid/meta.yaml index 27c12cc6d0b75..52a34ad7b0de9 100644 --- a/recipes/bioconductor-mzid/meta.yaml +++ b/recipes/bioconductor-mzid/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "mzID" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e92e3ea5ca514f37139a2f9da2ff733 + md5: 8ede9a6260d4b9aa70edd19838e3c80c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mzid", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat requirements: host: - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-doparallel - r-foreach @@ -29,7 +30,7 @@ requirements: - r-plyr - r-xml run: - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-mzr/meta.yaml b/recipes/bioconductor-mzr/meta.yaml index 74feda4882e63..788afdea54a79 100644 --- a/recipes/bioconductor-mzr/meta.yaml +++ b/recipes/bioconductor-mzr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.1" %} +{% set version = "2.36.0" %} {% set name = "mzR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ddbdeebce8ad003ef98a64e98b046dec + md5: aae8b88db5fd49675b653b861702800e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mzr", max_pin="x.x") }}' # Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base - r-ncdf4 - 'r-rcpp >=0.10.1' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base - r-ncdf4 - 'r-rcpp >=0.10.1' diff --git a/recipes/bioconductor-nadfinder/meta.yaml b/recipes/bioconductor-nadfinder/meta.yaml index f2457428ad06a..fef35a4d2ebc1 100644 --- a/recipes/bioconductor-nadfinder/meta.yaml +++ b/recipes/bioconductor-nadfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "NADfinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,50 +11,51 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ed74eabcb223af4a11ffa048cd23d7e + md5: d60f5020a7e46305fafc626c59a11851 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nadfinder", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown requirements: host: - - 'bioconductor-atacseqqc >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-empiricalbrownsmethod >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trackviewer >=1.36.0,<1.37.0' + - 'bioconductor-atacseqqc >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trackviewer >=1.38.0,<1.39.0' - r-base - r-baseline - r-corrplot - r-metap - r-signal run: - - 'bioconductor-atacseqqc >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-empiricalbrownsmethod >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trackviewer >=1.36.0,<1.37.0' + - 'bioconductor-atacseqqc >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trackviewer >=1.38.0,<1.39.0' - r-base - r-baseline - r-corrplot diff --git a/recipes/bioconductor-nanomethviz/meta.yaml b/recipes/bioconductor-nanomethviz/meta.yaml index abe27f2d8f65c..94a584c8be8d5 100644 --- a/recipes/bioconductor-nanomethviz/meta.yaml +++ b/recipes/bioconductor-nanomethviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.1" %} {% set name = "NanoMethViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 708505992439c9c7f2631c9c5f2f6a89 + md5: 5ddef080c0bf460814f94f28ee5f98d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr -# SystemRequirements: C++20 + run_exports: '{{ pin_subpackage("bioconductor-nanomethviz", max_pin="x.x") }}' +# Suggests: BiocStyle, DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr +# SystemRequirements: C++17 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-assertthat - r-base + - r-cli - 'r-cpp11 >=0.2.5' - r-data.table + - r-dbscan - r-dplyr - r-e1071 - r-forcats @@ -47,7 +52,6 @@ requirements: - r-rcpp - r-readr - r-rlang - - r-rsqlite - 'r-scales >=1.2.0' - r-scico - r-stringr @@ -57,19 +61,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-assertthat - r-base + - r-cli - 'r-cpp11 >=0.2.5' - r-data.table + - r-dbscan - r-dplyr - r-e1071 - r-forcats @@ -83,7 +91,6 @@ requirements: - r-rcpp - r-readr - r-rlang - - r-rsqlite - 'r-scales >=1.2.0' - r-scico - r-stringr diff --git a/recipes/bioconductor-nanoporernaseq/meta.yaml b/recipes/bioconductor-nanoporernaseq/meta.yaml index f5e9e177e2c44..262cf057ce809 100644 --- a/recipes/bioconductor-nanoporernaseq/meta.yaml +++ b/recipes/bioconductor-nanoporernaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "NanoporeRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4efdad7f3e17485998405b6d05612ac2 + md5: eca12ebcd403efd53e1b38d5f03f2027 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanoporernaseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments, Rsamtools requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nanoporernaseq/post-link.sh b/recipes/bioconductor-nanoporernaseq/post-link.sh index 3a381b9a76dd7..cb6624b6a8d06 100644 --- a/recipes/bioconductor-nanoporernaseq/post-link.sh +++ b/recipes/bioconductor-nanoporernaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nanoporernaseq-1.10.0" +installBiocDataPackage.sh "nanoporernaseq-1.12.0" diff --git a/recipes/bioconductor-nanostringdiff/meta.yaml b/recipes/bioconductor-nanostringdiff/meta.yaml index e3e58c117163c..ed2b6dc1d1f75 100644 --- a/recipes/bioconductor-nanostringdiff/meta.yaml +++ b/recipes/bioconductor-nanostringdiff/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "NanoStringDiff" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b7337dfd2beccd2c508cd36f6de796d + md5: 3614c5bcf8aeea002875aa005d746092 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanostringdiff", max_pin="x.x") }}' # Suggests: testthat, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-matrixstats - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-matrixstats - r-rcpp diff --git a/recipes/bioconductor-nanostringnctools/meta.yaml b/recipes/bioconductor-nanostringnctools/meta.yaml index fee2b2ae279e2..8e2ae08e86524 100644 --- a/recipes/bioconductor-nanostringnctools/meta.yaml +++ b/recipes/bioconductor-nanostringnctools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "NanoStringNCTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48e7ea143797954a6fdf23341abd5515 + md5: 97985a577c04cc2d7c19d00f2bd8e1d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanostringnctools", max_pin="x.x") }}' noarch: generic # Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggbeeswarm - r-ggiraph @@ -34,11 +35,11 @@ requirements: - r-pheatmap - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggbeeswarm - r-ggiraph diff --git a/recipes/bioconductor-nanotator/meta.yaml b/recipes/bioconductor-nanotator/meta.yaml index 2d617b65005dc..682082bcff49b 100644 --- a/recipes/bioconductor-nanotator/meta.yaml +++ b/recipes/bioconductor-nanotator/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "nanotatoR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 86bdebac66638200c60dbfe387334f08 + md5: e808c68591d98effbfdba4dbac07ac91 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanotator", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, yaml requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-curl - r-dplyr @@ -40,9 +41,9 @@ requirements: - r-xml - r-xml2r run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-curl - r-dplyr diff --git a/recipes/bioconductor-nanotube/meta.yaml b/recipes/bioconductor-nanotube/meta.yaml index d93662dcdc24a..9a1e127227387 100644 --- a/recipes/bioconductor-nanotube/meta.yaml +++ b/recipes/bioconductor-nanotube/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "NanoTube" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f94ce1248e7929f4f278f94de9858fe + md5: 524cdc55bcaf670d538be8f6c2f06c11 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanotube", max_pin="x.x") }}' noarch: generic # Suggests: grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-reshape run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-reshape diff --git a/recipes/bioconductor-nanotubes/meta.yaml b/recipes/bioconductor-nanotubes/meta.yaml index de6c307ed2549..3af73d0c984a9 100644 --- a/recipes/bioconductor-nanotubes/meta.yaml +++ b/recipes/bioconductor-nanotubes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "nanotubes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7d068f3a955216378fe66463811e4adf + md5: ff283cb49c319a357c22e17d2df22715 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nanotubes", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nanotubes/post-link.sh b/recipes/bioconductor-nanotubes/post-link.sh index 0ad8894e1b628..b2fb9f7b15f26 100644 --- a/recipes/bioconductor-nanotubes/post-link.sh +++ b/recipes/bioconductor-nanotubes/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nanotubes-1.16.0" +installBiocDataPackage.sh "nanotubes-1.18.0" diff --git a/recipes/bioconductor-nbamseq/meta.yaml b/recipes/bioconductor-nbamseq/meta.yaml index 89f006c1f15bb..4476179efd3cd 100644 --- a/recipes/bioconductor-nbamseq/meta.yaml +++ b/recipes/bioconductor-nbamseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "NBAMSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 44bb5d716c113a4ffe6ab9e069405889 + md5: 45181f95a38937784da7cbad4d416811 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nbamseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, ggplot2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-mgcv >=1.8-24' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-mgcv >=1.8-24' test: diff --git a/recipes/bioconductor-ncdfflow/meta.yaml b/recipes/bioconductor-ncdfflow/meta.yaml index bb9e9cdff349c..976e9392a7934 100644 --- a/recipes/bioconductor-ncdfflow/meta.yaml +++ b/recipes/bioconductor-ncdfflow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "ncdfFlow" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50a5d7442f7508b50359a6570ef591c2 + md5: 974c454443e3ed6c243aed7395f28911 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ncdfflow", max_pin="x.x") }}' # Suggests: testthat,parallel,flowStats,knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-cpp11 - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bh - r-cpp11 diff --git a/recipes/bioconductor-ncgtw/meta.yaml b/recipes/bioconductor-ncgtw/meta.yaml index 6862f27428261..c74112360f5e6 100644 --- a/recipes/bioconductor-ncgtw/meta.yaml +++ b/recipes/bioconductor-ncgtw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "ncGTW" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0da7500204724de4cd4b4946a37eaec3 + md5: ea33321b03c3751afd04234fd7fbcda3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ncgtw", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-ncigraph/meta.yaml b/recipes/bioconductor-ncigraph/meta.yaml index e250dcc8bb85f..090a8f728c23d 100644 --- a/recipes/bioconductor-ncigraph/meta.yaml +++ b/recipes/bioconductor-ncigraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "NCIgraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d49e4ab0775611fdf993b7a0f677bf3e + md5: ed568ded26dce9e64d5f38606e65c13d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ncigraph", max_pin="x.x") }}' noarch: generic # Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - - r-r.methodss3 + - r-r.oo run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - - r-r.methodss3 + - r-r.oo test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ncigraphdata/meta.yaml b/recipes/bioconductor-ncigraphdata/meta.yaml index 2bf79a205576e..91195f389e417 100644 --- a/recipes/bioconductor-ncigraphdata/meta.yaml +++ b/recipes/bioconductor-ncigraphdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "NCIgraphData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: beb23450c51a8f3bcac07438a25d6f9b + md5: f144169473d42fafb1966986dcf15628 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ncigraphdata", max_pin="x.x") }}' noarch: generic # Suggests: Rgraphviz requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ncigraphdata/post-link.sh b/recipes/bioconductor-ncigraphdata/post-link.sh index 3e382feb2fd73..2c15cc4502b3a 100644 --- a/recipes/bioconductor-ncigraphdata/post-link.sh +++ b/recipes/bioconductor-ncigraphdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ncigraphdata-1.36.0" +installBiocDataPackage.sh "ncigraphdata-1.38.0" diff --git a/recipes/bioconductor-ncrnatools/meta.yaml b/recipes/bioconductor-ncrnatools/meta.yaml index 05b5fdb686ad4..0be79f82b0b3b 100644 --- a/recipes/bioconductor-ncrnatools/meta.yaml +++ b/recipes/bioconductor-ncrnatools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ncRNAtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29e195e74ec13242c94f3ed0b2b0c6d2 + md5: 4e6f2f3809ca2cfe114ecc2c63f1d3dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ncrnatools", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-httr - r-xml2 run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-httr diff --git a/recipes/bioconductor-ndexr/meta.yaml b/recipes/bioconductor-ndexr/meta.yaml index 149ce9b792e32..e78c598266f08 100644 --- a/recipes/bioconductor-ndexr/meta.yaml +++ b/recipes/bioconductor-ndexr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ndexr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4101572e631f965b7ae5bc1d51031ba7 + md5: caa87487f3e0c062aa6b56b1dc6f70a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ndexr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-rcx >=1.4.0,<1.5.0' + - 'bioconductor-rcx >=1.6.0,<1.7.0' - r-base - r-httr - r-jsonlite - r-plyr - r-tidyr run: - - 'bioconductor-rcx >=1.4.0,<1.5.0' + - 'bioconductor-rcx >=1.6.0,<1.7.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-nearbynding/meta.yaml b/recipes/bioconductor-nearbynding/meta.yaml index e1e8b53d6a637..5344eaad1760f 100644 --- a/recipes/bioconductor-nearbynding/meta.yaml +++ b/recipes/bioconductor-nearbynding/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "nearBynding" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c0e19b30364b8df75523fe8a8cf6e85e + md5: 2bcc4459fa78c6327ee2708f06da54db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nearbynding", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown # SystemRequirements: bedtools (>= 2.28.0), Stereogene (>= v2.22), CapR (>= 1.1.1) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-dplyr - r-ggplot2 @@ -41,15 +42,15 @@ requirements: - r-rlang - r-transport run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-nebulosa/meta.yaml b/recipes/bioconductor-nebulosa/meta.yaml index be8b72764b6ab..7ee5a8801e91d 100644 --- a/recipes/bioconductor-nebulosa/meta.yaml +++ b/recipes/bioconductor-nebulosa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Nebulosa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8aa3fd5e95574c3b0023d243302470d4 + md5: e71c21bbda87365578a49f21dd915fa4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nebulosa", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, SeuratObject requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ks @@ -30,8 +31,8 @@ requirements: - r-patchwork - r-seurat run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ks diff --git a/recipes/bioconductor-nempi/meta.yaml b/recipes/bioconductor-nempi/meta.yaml index 1cef818a6c9dd..35ac5c2778196 100644 --- a/recipes/bioconductor-nempi/meta.yaml +++ b/recipes/bioconductor-nempi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "nempi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a75421d6b4a639b46ef0ae5ef181abb2 + md5: 1180e323b8f109079a74702ef7159cda build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nempi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle requirements: host: - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' - r-base - r-e1071 - r-matrixstats @@ -30,8 +31,8 @@ requirements: - r-nnet - r-randomforest run: - - 'bioconductor-epinem >=1.24.0,<1.25.0' - - 'bioconductor-mnem >=1.16.0,<1.17.0' + - 'bioconductor-epinem >=1.26.0,<1.27.0' + - 'bioconductor-mnem >=1.18.0,<1.19.0' - r-base - r-e1071 - r-matrixstats diff --git a/recipes/bioconductor-nestlink/meta.yaml b/recipes/bioconductor-nestlink/meta.yaml index 3dfa79d67adb0..7547790cc430c 100644 --- a/recipes/bioconductor-nestlink/meta.yaml +++ b/recipes/bioconductor-nestlink/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "NestLink" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae3c598105a6b4fc40e3ce4ad0bf1e99 + md5: 11cd94f5bd8b38cf261ae3346a283e81 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nestlink", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat, specL, lattice, scales requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-gplots >=3.0' - 'r-protviz >=0.4' run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - 'r-gplots >=3.0' - 'r-protviz >=0.4' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nestlink/post-link.sh b/recipes/bioconductor-nestlink/post-link.sh index 70a917bc106e7..e4c21fc4a1132 100644 --- a/recipes/bioconductor-nestlink/post-link.sh +++ b/recipes/bioconductor-nestlink/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nestlink-1.16.0" +installBiocDataPackage.sh "nestlink-1.18.0" diff --git a/recipes/bioconductor-netactivity/meta.yaml b/recipes/bioconductor-netactivity/meta.yaml index 451a5f24248ea..78e371d72f461 100644 --- a/recipes/bioconductor-netactivity/meta.yaml +++ b/recipes/bioconductor-netactivity/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "NetActivity" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3937c60ef36d7b14327a8b1c5f803cf + md5: 3493b441d888adf6d3a089936bbeafd6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netactivity", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse requirements: host: - - 'bioconductor-airway >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-netactivitydata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-airway >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-netactivitydata >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-airway >=1.20.0,<1.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-netactivitydata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-airway >=1.22.0,<1.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-netactivitydata >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-netactivitydata/meta.yaml b/recipes/bioconductor-netactivitydata/meta.yaml index 99d3fc99db88e..eb4cf6502a8c5 100644 --- a/recipes/bioconductor-netactivitydata/meta.yaml +++ b/recipes/bioconductor-netactivitydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "NetActivityData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43f1651effd619c45926094b7f6df44b + md5: a3805046d14d13afc30a0f082952f200 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netactivitydata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-netactivitydata/post-link.sh b/recipes/bioconductor-netactivitydata/post-link.sh index 0092bdf08ff5e..945e66b43cd20 100644 --- a/recipes/bioconductor-netactivitydata/post-link.sh +++ b/recipes/bioconductor-netactivitydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "netactivitydata-1.2.0" +installBiocDataPackage.sh "netactivitydata-1.4.0" diff --git a/recipes/bioconductor-netboost/meta.yaml b/recipes/bioconductor-netboost/meta.yaml index f7474534850b3..827401588e5f8 100644 --- a/recipes/bioconductor-netboost/meta.yaml +++ b/recipes/bioconductor-netboost/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "netboost" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 290c4fcdcc62163c74e30ff61011cba2 + md5: d21f645a3fe85c35ff9b9127bce1fbca build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: knitr, markdown, rmarkdown + run_exports: '{{ pin_subpackage("bioconductor-netboost", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown # SystemRequirements: GNU make, Bash, Perl, Gzip requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-colorspace - r-dynamictreecut @@ -33,8 +34,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-base - r-colorspace - r-dynamictreecut diff --git a/recipes/bioconductor-netdx/meta.yaml b/recipes/bioconductor-netdx/meta.yaml index 5ccaf70bd86f4..4c60cf23c5c53 100644 --- a/recipes/bioconductor-netdx/meta.yaml +++ b/recipes/bioconductor-netdx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "netDx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ce730cb8934c6792d800eb5f32559f9 + md5: 6fdc48ce518c74e0261acee84948ce26 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netdx", max_pin="x.x") }}' noarch: generic # Suggests: curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3, clusterExperiment, netSmooth, scater requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bigmemory - r-combinat @@ -44,12 +45,12 @@ requirements: - r-rocr - r-rtsne run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bigmemory - r-combinat diff --git a/recipes/bioconductor-nethet/meta.yaml b/recipes/bioconductor-nethet/meta.yaml index a3a9f0c858646..fa9f00d135eb1 100644 --- a/recipes/bioconductor-nethet/meta.yaml +++ b/recipes/bioconductor-nethet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "nethet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e0364a3984a014bf2108f461a2021433 + md5: 35bc35cf08904b721563aa54e486cc95 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nethet", max_pin="x.x") }}' # Suggests: knitr, xtable, BiocStyle, testthat requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-compquadform - r-genenet @@ -38,8 +39,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-compquadform - r-genenet diff --git a/recipes/bioconductor-netomics/meta.yaml b/recipes/bioconductor-netomics/meta.yaml index a27e24166b1ef..b64d798252c5b 100644 --- a/recipes/bioconductor-netomics/meta.yaml +++ b/recipes/bioconductor-netomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "netOmics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37282b31aeb12e9b3af18911b8dd523d + md5: 8ab3cf60546da2beea2e9c3630340c12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netomics", max_pin="x.x") }}' noarch: generic # Suggests: mixOmics, timeOmics, tidyverse, BiocStyle, testthat, covr, rmarkdown, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-randomwalkrestartmh >=1.20.0,<1.21.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-randomwalkrestartmh >=1.22.0,<1.23.0' - r-base - r-dplyr - r-ggplot2 @@ -35,10 +36,10 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-randomwalkrestartmh >=1.20.0,<1.21.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-randomwalkrestartmh >=1.22.0,<1.23.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-netpathminer/meta.yaml b/recipes/bioconductor-netpathminer/meta.yaml index 5828131271fee..50aca74364875 100644 --- a/recipes/bioconductor-netpathminer/meta.yaml +++ b/recipes/bioconductor-netpathminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "NetPathMiner" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76776ce19013b746222cfb08237367b2 + md5: 91cc0601961f682fcf1a2bed61eb6438 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netpathminer", max_pin="x.x") }}' # Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle # SystemRequirements: libxml2, libSBML (>= 5.5) requirements: host: - r-base - - r-igraph + - 'r-igraph >=1.0' - libblas - liblapack - libxml2 run: - r-base - - r-igraph + - 'r-igraph >=1.0' - libxml2 build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-netprior/meta.yaml b/recipes/bioconductor-netprior/meta.yaml index dd14ef112ba9b..146dd2bda1f80 100644 --- a/recipes/bioconductor-netprior/meta.yaml +++ b/recipes/bioconductor-netprior/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "netprioR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 582d959f00a6f534f0cf141a80168936 + md5: 7e4023edbe230057c85ae74d90f59fd1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netprior", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, pander requirements: diff --git a/recipes/bioconductor-netresponse/meta.yaml b/recipes/bioconductor-netresponse/meta.yaml index 12cd8aed603e9..c0beb901e67b0 100644 --- a/recipes/bioconductor-netresponse/meta.yaml +++ b/recipes/bioconductor-netresponse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "netresponse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16f0c62907c79eb5d346ae329345310f + md5: 990c864cea311427d5af5f854edf4041 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netresponse", max_pin="x.x") }}' # Suggests: knitr requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-igraph @@ -36,11 +37,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-ggplot2 - r-igraph diff --git a/recipes/bioconductor-netsam/meta.yaml b/recipes/bioconductor-netsam/meta.yaml index 4e91e0438b0a1..7bdf23012be6b 100644 --- a/recipes/bioconductor-netsam/meta.yaml +++ b/recipes/bioconductor-netsam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "NetSAM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd6a61494b69858daa7ea594754eff4a + md5: 8248bae56028b8d8ee872cb007cbd7f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netsam", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - 'r-dbi >=0.5-1' - 'r-doparallel >=1.0.10' @@ -34,9 +35,9 @@ requirements: - 'r-survival >=2.37-7' - 'r-wgcna >=1.34.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base - 'r-dbi >=0.5-1' - 'r-doparallel >=1.0.10' diff --git a/recipes/bioconductor-netsmooth/meta.yaml b/recipes/bioconductor-netsmooth/meta.yaml index eaf08ae7dc387..8ba8209e5b286 100644 --- a/recipes/bioconductor-netsmooth/meta.yaml +++ b/recipes/bioconductor-netsmooth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "netSmooth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 515bd1a10da3b5db97cce11ba66d0171 + md5: 074a02c5cf8d32c2111268513d8404c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netsmooth", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot requirements: host: - - 'bioconductor-clusterexperiment >=2.20.0,<2.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-clusterexperiment >=2.22.0,<2.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-data.table - r-entropy - r-matrix run: - - 'bioconductor-clusterexperiment >=2.20.0,<2.21.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-clusterexperiment >=2.22.0,<2.23.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-netzoor/meta.yaml b/recipes/bioconductor-netzoor/meta.yaml index c94a5fb6ffe30..6091f5648d7f6 100644 --- a/recipes/bioconductor-netzoor/meta.yaml +++ b/recipes/bioconductor-netzoor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "netZooR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab5dcac5e4394525a93ba72131f0f222 + md5: 2f4adb3763df2df201212073e34bab10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-netzoor", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, pkgdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pandar >=1.32.0,<1.33.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-yarn >=1.26.0,<1.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pandar >=1.34.0,<1.35.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-yarn >=1.28.0,<1.29.0' - r-assertthat - r-base - r-data.table @@ -53,15 +54,15 @@ requirements: - r-vegan - r-viridislite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-pandar >=1.32.0,<1.33.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-yarn >=1.26.0,<1.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-pandar >=1.34.0,<1.35.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-yarn >=1.28.0,<1.29.0' - r-assertthat - r-base - r-data.table diff --git a/recipes/bioconductor-neve2006/meta.yaml b/recipes/bioconductor-neve2006/meta.yaml index 0103cfa7e4a8c..42228ba33d521 100644 --- a/recipes/bioconductor-neve2006/meta.yaml +++ b/recipes/bioconductor-neve2006/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "Neve2006" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77132d53a223319770a7abcf21d8e202 + md5: 1feec2f09bac8c69ba9df5ea29e7e08c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-neve2006", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-neve2006/post-link.sh b/recipes/bioconductor-neve2006/post-link.sh index 427f48443403c..24e05c66b69e3 100644 --- a/recipes/bioconductor-neve2006/post-link.sh +++ b/recipes/bioconductor-neve2006/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "neve2006-0.38.0" +installBiocDataPackage.sh "neve2006-0.40.0" diff --git a/recipes/bioconductor-newwave/build.sh b/recipes/bioconductor-newwave/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-newwave/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-newwave/meta.yaml b/recipes/bioconductor-newwave/meta.yaml new file mode 100644 index 0000000000000..72507f5c6eb2b --- /dev/null +++ b/recipes/bioconductor-newwave/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.12.0" %} +{% set name = "NewWave" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ed222f643c357c84a7eb8534aa7b3a91 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-newwave", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr +requirements: + host: + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-sharedobject >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-irlba + - r-matrix + run: + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-sharedobject >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-irlba + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Negative binomial model for scRNA-seq' + description: 'A model designed for dimensionality reduction and batch effect removal for scRNA-seq data. It is designed to be massively parallelizable using shared objects that prevent memory duplication, and it can be used with different mini-batch approaches in order to reduce time consumption. It assumes a negative binomial distribution for the data with a dispersion parameter that can be both commonwise across gene both genewise.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-ngscopydata/meta.yaml b/recipes/bioconductor-ngscopydata/meta.yaml index 9646ebf7b1a92..68de821e7a0fb 100644 --- a/recipes/bioconductor-ngscopydata/meta.yaml +++ b/recipes/bioconductor-ngscopydata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "NGScopyData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2d29d8d5f08328e350974da855da611 + md5: 0ba77cf672a331e4c9dd90b26f41b5c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ngscopydata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ngscopydata/post-link.sh b/recipes/bioconductor-ngscopydata/post-link.sh index 192efa48a1bee..362855219f4b3 100644 --- a/recipes/bioconductor-ngscopydata/post-link.sh +++ b/recipes/bioconductor-ngscopydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ngscopydata-1.20.0" +installBiocDataPackage.sh "ngscopydata-1.22.0" diff --git a/recipes/bioconductor-ngsreports/meta.yaml b/recipes/bioconductor-ngsreports/meta.yaml index ea350d3c66571..185ed58b5bdcb 100644 --- a/recipes/bioconductor-ngsreports/meta.yaml +++ b/recipes/bioconductor-ngsreports/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.4" %} +{% set version = "2.4.0" %} {% set name = "ngsReports" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3fa618125cffae2c7a1059bc9caacf86 + md5: c2d8c1f7a1869275420e05125fb1b420 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ngsreports", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, Cairo, knitr, testthat, truncnorm requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-checkmate - 'r-dplyr >=1.1.0' @@ -47,8 +48,8 @@ requirements: - 'r-tidyselect >=0.2.3' - r-zoo run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-checkmate - 'r-dplyr >=1.1.0' diff --git a/recipes/bioconductor-nipalsmcia/build.sh b/recipes/bioconductor-nipalsmcia/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-nipalsmcia/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nipalsmcia/meta.yaml b/recipes/bioconductor-nipalsmcia/meta.yaml new file mode 100644 index 0000000000000..bfba119094b74 --- /dev/null +++ b/recipes/bioconductor-nipalsmcia/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "nipalsMCIA" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0558d05ea61523c6fcaed9d8ed9b0ded +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nipalsmcia", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - 'r-ggplot2 >=3.0.0' + - r-pracma + - r-rlang + - r-rspectra + - r-scales + run: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - 'r-ggplot2 >=3.0.0' + - r-pracma + - r-rlang + - r-rspectra + - r-scales +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Multiple Co-Inertia Analysis via the NIPALS Method' + description: 'Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the Nonlinear Iterative Partial Least Squares method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple options for row- and table-level preprocessing, and speeds up computation of variance explained. Vignettes detail application to bulk- and single cell- multi-omics studies.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-nnnorm/meta.yaml b/recipes/bioconductor-nnnorm/meta.yaml index 5f6340ae54b8f..ed154d75e8173 100644 --- a/recipes/bioconductor-nnnorm/meta.yaml +++ b/recipes/bioconductor-nnnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.64.0" %} +{% set version = "2.66.0" %} {% set name = "nnNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32948108dfc1ce0d1a90c589af10149a + md5: f6e41106fc2afb44568c00dce1a36670 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nnnorm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-nnet run: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-nnet test: diff --git a/recipes/bioconductor-nnsvg/meta.yaml b/recipes/bioconductor-nnsvg/meta.yaml index 7720cd36de4a1..b04d39476984c 100644 --- a/recipes/bioconductor-nnsvg/meta.yaml +++ b/recipes/bioconductor-nnsvg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "nnSVG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 226c134290d6643df454277b54b5d067 + md5: 4af169b12d944eff8ee9d9e3063ff5ea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nnsvg", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-brisc - r-matrix - r-matrixstats run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-brisc - r-matrix diff --git a/recipes/bioconductor-noiseq/meta.yaml b/recipes/bioconductor-noiseq/meta.yaml index 6dae72b652d48..675fe63b421b6 100644 --- a/recipes/bioconductor-noiseq/meta.yaml +++ b/recipes/bioconductor-noiseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "NOISeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 546e44e3bd29e9fe3a4d2d35d7eb04c1 + md5: e7ea859871f96aa68269efa3a1e7dd46 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-noiseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - 'r-matrix >=1.2' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - 'r-matrix >=1.2' test: diff --git a/recipes/bioconductor-nondetects/meta.yaml b/recipes/bioconductor-nondetects/meta.yaml index 7c27d12de272e..05ea32239f1d2 100644 --- a/recipes/bioconductor-nondetects/meta.yaml +++ b/recipes/bioconductor-nondetects/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "nondetects" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9b56e99e728154927bb62fb6c6120d0c + md5: 6507efbde0bbb76f863c731bcc8464bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nondetects", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-htqpcr >=1.54.0,<1.55.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-htqpcr >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-arm - r-base - r-mvtnorm run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-htqpcr >=1.54.0,<1.55.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-htqpcr >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-arm - r-base - r-mvtnorm diff --git a/recipes/bioconductor-norce/meta.yaml b/recipes/bioconductor-norce/meta.yaml index cbd2329e19012..8aea0cd7dd50e 100644 --- a/recipes/bioconductor-norce/meta.yaml +++ b/recipes/bioconductor-norce/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "NoRCE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eda53dbedd3a44f4b5416f2f3d2f77f0 + md5: 8e3a1a53f9c68bc68ab881bd49e28ecb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-norce", max_pin="x.x") }}' noarch: generic # Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,markdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-dbi - r-dbplyr @@ -49,20 +50,20 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-dbi - r-dbplyr diff --git a/recipes/bioconductor-normalize450k/meta.yaml b/recipes/bioconductor-normalize450k/meta.yaml index d362f6a7ca9da..d3980f100fdc2 100644 --- a/recipes/bioconductor-normalize450k/meta.yaml +++ b/recipes/bioconductor-normalize450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "normalize450K" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09d6b4499a0f70e1071d1ddd963cc7f4 + md5: f5ea0fdcbdd43103b5ee941c96fe43fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-normalize450k", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - r-base - r-quadprog run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - r-base - r-quadprog test: diff --git a/recipes/bioconductor-normalyzerde/meta.yaml b/recipes/bioconductor-normalyzerde/meta.yaml index b7b48ad46e2ee..73ac8ed4eadf9 100644 --- a/recipes/bioconductor-normalyzerde/meta.yaml +++ b/recipes/bioconductor-normalyzerde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "NormalyzerDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef1878f963a1376db00cfcdb34c8f6f9 + md5: e55d57346b59dbd8b317a263e4b413b0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-normalyzerde", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-ape - r-base - r-car @@ -33,14 +34,12 @@ requirements: - r-ggplot2 - r-mass - r-matrixstats - - r-raster - - r-rcmdrmisc run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-ape - r-base - r-car @@ -48,8 +47,6 @@ requirements: - r-ggplot2 - r-mass - r-matrixstats - - r-raster - - r-rcmdrmisc test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-normqpcr/meta.yaml b/recipes/bioconductor-normqpcr/meta.yaml index 78f8d1ce11160..79afa3c7882ff 100644 --- a/recipes/bioconductor-normqpcr/meta.yaml +++ b/recipes/bioconductor-normqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "NormqPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 26722c237731e8a7ed2dcb5f6babb676 + md5: 379e7395ad03c0d57dffa7331748e253 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-normqpcr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-readqpcr >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-readqpcr >=1.48.0,<1.49.0' - r-base - r-qpcr - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-readqpcr >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-readqpcr >=1.48.0,<1.49.0' - r-base - r-qpcr - r-rcolorbrewer diff --git a/recipes/bioconductor-normr/meta.yaml b/recipes/bioconductor-normr/meta.yaml index 36cea3b30c3a2..7e2b0dacc4662 100644 --- a/recipes/bioconductor-normr/meta.yaml +++ b/recipes/bioconductor-normr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "normr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3d9b6c8514fcac077afbb985ba09d65b + md5: 06d294d5935656789cc44341eca46620 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-normr", max_pin="x.x") }}' # Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown # SystemRequirements: C++11 requirements: host: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-rcpp >=0.11' - libblas - liblapack run: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-rcpp >=0.11' build: diff --git a/recipes/bioconductor-norway981.db/meta.yaml b/recipes/bioconductor-norway981.db/meta.yaml index fc706e5452c15..71d94b527398a 100644 --- a/recipes/bioconductor-norway981.db/meta.yaml +++ b/recipes/bioconductor-norway981.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Norway981.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 85367390919bba9018438585e59fbb87 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-norway981.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nparc/meta.yaml b/recipes/bioconductor-nparc/meta.yaml index 77f43f2b02960..0c5bebf6db5c1 100644 --- a/recipes/bioconductor-nparc/meta.yaml +++ b/recipes/bioconductor-nparc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "NPARC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d5e6e63e7bc6f5681ae1e3e763b7aaa + md5: b49f408fb60e58d3c62cfd2d5d4809cb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nparc", max_pin="x.x") }}' noarch: generic # Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-broom - r-dplyr @@ -30,7 +31,7 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-broom - r-dplyr diff --git a/recipes/bioconductor-npgsea/meta.yaml b/recipes/bioconductor-npgsea/meta.yaml index e539c18eeb5e9..908e3b860253b 100644 --- a/recipes/bioconductor-npgsea/meta.yaml +++ b/recipes/bioconductor-npgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "npGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be25afa3330016c8a304b773601defd1 + md5: 82d2208fe4478a1d5423940daa7128be build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-npgsea", max_pin="x.x") }}' noarch: generic # Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-ntw/meta.yaml b/recipes/bioconductor-ntw/meta.yaml index 2b28a78d7b9b5..61ef8840dc598 100644 --- a/recipes/bioconductor-ntw/meta.yaml +++ b/recipes/bioconductor-ntw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "NTW" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a724372ec6201f37b22c2c5cc507483 + md5: c64df447dfa43cbb3bf97922655ff516 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ntw", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-nucleosim/meta.yaml b/recipes/bioconductor-nucleosim/meta.yaml index a7e44a2b153f8..3bfd2f9382492 100644 --- a/recipes/bioconductor-nucleosim/meta.yaml +++ b/recipes/bioconductor-nucleosim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "nucleoSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54387b881dbc7f4ed750081a7d444f1f + md5: b1b994c654ce500e414a8a7caea5162f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nucleosim", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-nucler/meta.yaml b/recipes/bioconductor-nucler/meta.yaml index 2be954587e6bf..340e91083a435 100644 --- a/recipes/bioconductor-nucler/meta.yaml +++ b/recipes/bioconductor-nucler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "nucleR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 033fb6cde8087be9add9a70235e27fb0 + md5: 854586c378515ad6e2eefe2e1a09f394 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nucler", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dplyr - r-ggplot2 - r-magrittr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-nucpos/meta.yaml b/recipes/bioconductor-nucpos/meta.yaml index 0f6d76078c045..4bc66b50e3842 100644 --- a/recipes/bioconductor-nucpos/meta.yaml +++ b/recipes/bioconductor-nucpos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "nuCpos" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d825e3c5513f7be0367edf8e72f114d9 + md5: b029b2678c784645c2198f00093bd923 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nucpos", max_pin="x.x") }}' noarch: generic # Suggests: NuPoP, Biostrings, testthat requirements: diff --git a/recipes/bioconductor-nugohs1a520180.db/meta.yaml b/recipes/bioconductor-nugohs1a520180.db/meta.yaml index 2e57f0de3efb1..b418a0f7208e0 100644 --- a/recipes/bioconductor-nugohs1a520180.db/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f83701b35b07e69e1ad503b546bb5eaf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugohs1a520180.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugohs1a520180cdf/meta.yaml b/recipes/bioconductor-nugohs1a520180cdf/meta.yaml index f624518fc2b88..f90749d9e7a72 100644 --- a/recipes/bioconductor-nugohs1a520180cdf/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aa152658a4a801cc0edb552a98aee841 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugohs1a520180cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugohs1a520180probe/meta.yaml b/recipes/bioconductor-nugohs1a520180probe/meta.yaml index 8134389eb12fd..f0bd987761f56 100644 --- a/recipes/bioconductor-nugohs1a520180probe/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6acf20ac4a799eaae97d0a64426d6ac3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugohs1a520180probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugomm1a520177.db/meta.yaml b/recipes/bioconductor-nugomm1a520177.db/meta.yaml index ca4aef5adf082..7be86d928b24d 100644 --- a/recipes/bioconductor-nugomm1a520177.db/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 99f69ea2cbb80a79bedee99e3d726e50 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugomm1a520177.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugomm1a520177cdf/meta.yaml b/recipes/bioconductor-nugomm1a520177cdf/meta.yaml index 749c80d468182..6e57813681d86 100644 --- a/recipes/bioconductor-nugomm1a520177cdf/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fc60c2018580decaea30f09de55142fb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugomm1a520177cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nugomm1a520177probe/meta.yaml b/recipes/bioconductor-nugomm1a520177probe/meta.yaml index 7bf4085f23db2..1d994b823856e 100644 --- a/recipes/bioconductor-nugomm1a520177probe/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7fa974389ad2be6ebda8810496221a9b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nugomm1a520177probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nullranges/meta.yaml b/recipes/bioconductor-nullranges/meta.yaml index be1686768f962..61ea19b4a06cf 100644 --- a/recipes/bioconductor-nullranges/meta.yaml +++ b/recipes/bioconductor-nullranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.0" %} {% set name = "nullranges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 57d37d766de72195faa55f893e79debc + md5: 6ee32a46c332cfeefa89ebc2b32608bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nullranges", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, purrr, magrittr, tidyr, cobalt, DiagrammeR, tidySummarizedExperiment requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 @@ -35,12 +36,12 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-nullrangesdata/meta.yaml b/recipes/bioconductor-nullrangesdata/meta.yaml index 9d383cbff145a..357383664f328 100644 --- a/recipes/bioconductor-nullrangesdata/meta.yaml +++ b/recipes/bioconductor-nullrangesdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "nullrangesData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54631ad9bc1a63e3c981cb9df919a1a4 + md5: c8b4cf63d70a2577251c03c093c014b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nullrangesdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nullrangesdata/post-link.sh b/recipes/bioconductor-nullrangesdata/post-link.sh index caa8f21cc6151..56c49a53ff303 100644 --- a/recipes/bioconductor-nullrangesdata/post-link.sh +++ b/recipes/bioconductor-nullrangesdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nullrangesdata-1.6.0" +installBiocDataPackage.sh "nullrangesdata-1.8.0" diff --git a/recipes/bioconductor-nupop/meta.yaml b/recipes/bioconductor-nupop/meta.yaml index 34a784ea5862f..95a7ccb26204e 100644 --- a/recipes/bioconductor-nupop/meta.yaml +++ b/recipes/bioconductor-nupop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.1" %} +{% set version = "2.10.0" %} {% set name = "NuPoP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f8fd1ab74555d543f34738389d28587 + md5: 65372d828848fa588584e42324762643 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nupop", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: diff --git a/recipes/bioconductor-nxtirfdata/meta.yaml b/recipes/bioconductor-nxtirfdata/meta.yaml index d90d0eb06de8b..60c0e2b69d5f7 100644 --- a/recipes/bioconductor-nxtirfdata/meta.yaml +++ b/recipes/bioconductor-nxtirfdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "NxtIRFdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 49c677044a8e671562fec6f64533b284 + md5: 3d9c35f12650fe6e2eb413224b3590dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-nxtirfdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-r.utils run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-r.utils - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-nxtirfdata/post-link.sh b/recipes/bioconductor-nxtirfdata/post-link.sh index 839225414a35a..bc8f830b35b74 100644 --- a/recipes/bioconductor-nxtirfdata/post-link.sh +++ b/recipes/bioconductor-nxtirfdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nxtirfdata-1.6.0" +installBiocDataPackage.sh "nxtirfdata-1.8.0" diff --git a/recipes/bioconductor-obmiti/meta.yaml b/recipes/bioconductor-obmiti/meta.yaml index 0cfaa078750e0..a995f44ec42d3 100644 --- a/recipes/bioconductor-obmiti/meta.yaml +++ b/recipes/bioconductor-obmiti/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ObMiTi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 679880ec1082c72dc04b91c7c43b86d1 + md5: 0510665a5231cd3109d19478e4aadbd9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-obmiti", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors, devtools, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-obmiti/post-link.sh b/recipes/bioconductor-obmiti/post-link.sh index 739594a5416ea..03b4d1416cd34 100644 --- a/recipes/bioconductor-obmiti/post-link.sh +++ b/recipes/bioconductor-obmiti/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "obmiti-1.8.0" +installBiocDataPackage.sh "obmiti-1.10.0" diff --git a/recipes/bioconductor-occugene/meta.yaml b/recipes/bioconductor-occugene/meta.yaml index 18d0068dc24ec..f5f74d87be869 100644 --- a/recipes/bioconductor-occugene/meta.yaml +++ b/recipes/bioconductor-occugene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "occugene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c3bc7c5109e680763202f69c7a35abce + md5: 264da1422714d735ac474b414e57a2a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-occugene", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-ocplus/meta.yaml b/recipes/bioconductor-ocplus/meta.yaml index 2edb915b101ae..5dd736c909f68 100644 --- a/recipes/bioconductor-ocplus/meta.yaml +++ b/recipes/bioconductor-ocplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "OCplus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1c461ba3d6b8e3310af4f823f80061c + md5: 8093ec3c635bc4ba57d27f42c6c85c48 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ocplus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-interp run: - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-interp test: diff --git a/recipes/bioconductor-oct4/meta.yaml b/recipes/bioconductor-oct4/meta.yaml index d331169780dbd..14a38304a08b0 100644 --- a/recipes/bioconductor-oct4/meta.yaml +++ b/recipes/bioconductor-oct4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "oct4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 733c8377b6b7065265506a938f1c7c09 + md5: 1b6bbc6300c74c038689c7fb5b7d5eb2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oct4", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-oct4/post-link.sh b/recipes/bioconductor-oct4/post-link.sh index c58332df2a32d..b3235662475f3 100644 --- a/recipes/bioconductor-oct4/post-link.sh +++ b/recipes/bioconductor-oct4/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "oct4-1.16.0" +installBiocDataPackage.sh "oct4-1.18.0" diff --git a/recipes/bioconductor-octad.db/meta.yaml b/recipes/bioconductor-octad.db/meta.yaml index e249cf73495ec..a4fa56d807f6c 100644 --- a/recipes/bioconductor-octad.db/meta.yaml +++ b/recipes/bioconductor-octad.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "octad.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 242e1f3e5df68b1ccbc324eaf3924797 + md5: ef8723031fea32015ee26dbf30d2c8ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-octad.db", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-octad.db/post-link.sh b/recipes/bioconductor-octad.db/post-link.sh index c9d4883ad95ce..2b1a3295db9c8 100644 --- a/recipes/bioconductor-octad.db/post-link.sh +++ b/recipes/bioconductor-octad.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "octad.db-1.2.0" +installBiocDataPackage.sh "octad.db-1.4.0" diff --git a/recipes/bioconductor-octad/meta.yaml b/recipes/bioconductor-octad/meta.yaml index 4b05424e89677..5247c0dddb66c 100644 --- a/recipes/bioconductor-octad/meta.yaml +++ b/recipes/bioconductor-octad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "octad" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16534514ddcf3ab39f87e15eb20527dd + md5: 65dcd54e4646d61afcfb9afc90108ba4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-octad", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-octad.db >=1.2.0,<1.3.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-octad.db >=1.4.0,<1.5.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -45,18 +46,18 @@ requirements: - r-reshape2 - r-rfast run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-octad.db >=1.2.0,<1.3.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-octad.db >=1.4.0,<1.5.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-odseq/meta.yaml b/recipes/bioconductor-odseq/meta.yaml index 80bde4e87ab53..15f186744d094 100644 --- a/recipes/bioconductor-odseq/meta.yaml +++ b/recipes/bioconductor-odseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "odseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 28a91ac69eb76e788013a765301cb90d + md5: 5eac4befb045c1d0531b13501f3aa880 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-odseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr(>= 1.11) requirements: host: - - 'bioconductor-kebabs >=1.34.0,<1.35.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-kebabs >=1.36.0,<1.37.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - 'r-mclust >=5.1' run: - - 'bioconductor-kebabs >=1.34.0,<1.35.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-kebabs >=1.36.0,<1.37.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - 'r-mclust >=5.1' test: diff --git a/recipes/bioconductor-ogre/meta.yaml b/recipes/bioconductor-ogre/meta.yaml index d41487802403a..31154fe4bd61b 100644 --- a/recipes/bioconductor-ogre/meta.yaml +++ b/recipes/bioconductor-ogre/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "OGRE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8573ec05b2170c32440425eaa57567a7 + md5: cff18fd2eda3eb1e67e9f7739fb9e773 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ogre", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11) requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-data.table @@ -39,13 +40,13 @@ requirements: - r-shinyfiles - r-tidyr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-data.table diff --git a/recipes/bioconductor-oligo/meta.yaml b/recipes/bioconductor-oligo/meta.yaml index d9592d51fb19e..b3a0210da009e 100644 --- a/recipes/bioconductor-oligo/meta.yaml +++ b/recipes/bioconductor-oligo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.1" %} +{% set version = "1.66.0" %} {% set name = "oligo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0e40f8ea848ec94333feb3fc9d0cd7ac + md5: 3ba99dedbe0ebca2fcaa81a400777469 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oligo", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-dbi >=0.3.1' - r-ff @@ -35,14 +36,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-dbi >=0.3.1' - r-ff diff --git a/recipes/bioconductor-oligoclasses/meta.yaml b/recipes/bioconductor-oligoclasses/meta.yaml index da8d8b7d73f58..f580b7d23a33d 100644 --- a/recipes/bioconductor-oligoclasses/meta.yaml +++ b/recipes/bioconductor-oligoclasses/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "oligoClasses" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81ef026f64df521596ed8f336cf7c139 + md5: 379f1364d7159e2456c9310556e990e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oligoclasses", max_pin="x.x") }}' noarch: generic # Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm requirements: host: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-dbi @@ -36,14 +37,14 @@ requirements: - r-foreach - r-rsqlite run: - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-oligodata/meta.yaml b/recipes/bioconductor-oligodata/meta.yaml index f462620f0a2bb..3359689fb98fc 100644 --- a/recipes/bioconductor-oligodata/meta.yaml +++ b/recipes/bioconductor-oligodata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.8.0" %} {% set name = "oligoData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9625cfd4b31bb575c4029a0632a7ee12 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oligodata", max_pin="x.x") }}' noarch: generic # Suggests: pd.hg.u95av2, pd.huex.1.0.st.v2, pd.mapping50k.xba240, pd.hg18.60mer.expr, pd.2006.07.18.hg18.refseq.promoter, pd.hugene.1.0.st.v1 requirements: host: - - 'bioconductor-oligo >=1.64.0,<1.65.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' - r-base run: - - 'bioconductor-oligo >=1.64.0,<1.65.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-olin/meta.yaml b/recipes/bioconductor-olin/meta.yaml index 800c3a8724560..90100d3abd625 100644 --- a/recipes/bioconductor-olin/meta.yaml +++ b/recipes/bioconductor-olin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "OLIN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 78861856588cb82ace6edbe1ab39c8f7 + md5: 3a6ce43e9272204280a346c20012f710 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-olin", max_pin="x.x") }}' noarch: generic # Suggests: convert requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-locfit run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-locfit test: diff --git a/recipes/bioconductor-olingui/meta.yaml b/recipes/bioconductor-olingui/meta.yaml index dfc53412fb04a..229943f4192e8 100644 --- a/recipes/bioconductor-olingui/meta.yaml +++ b/recipes/bioconductor-olingui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "OLINgui" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ae51f7c642bee5c4fd8e3734d838a59 + md5: 5f960cc922153099a7b7a6e7ee939d9f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-olingui", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-olin >=1.78.0,<1.79.0' - - 'bioconductor-tkwidgets >=1.78.0,<1.79.0' - - 'bioconductor-widgettools >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-olin >=1.80.0,<1.81.0' + - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' + - 'bioconductor-widgettools >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-olin >=1.78.0,<1.79.0' - - 'bioconductor-tkwidgets >=1.78.0,<1.79.0' - - 'bioconductor-widgettools >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' + - 'bioconductor-olin >=1.80.0,<1.81.0' + - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' + - 'bioconductor-widgettools >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-omada/meta.yaml b/recipes/bioconductor-omada/meta.yaml index e0436b7414617..009cfe955a23d 100644 --- a/recipes/bioconductor-omada/meta.yaml +++ b/recipes/bioconductor-omada/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.0" %} +{% set version = "1.4.0" %} {% set name = "omada" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 86be333cce02f3ba85831756d5f599ff + md5: d214fdb20c51cbce86bf1d34c59cb84b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omada", max_pin="x.x") }}' # Suggests: rmarkdown, knitr, testthat requirements: host: - r-base - - 'r-clustercrit >=1.2.8' - 'r-clvalid >=0.7' - 'r-dicer >=0.6.0' - 'r-dplyr >=1.0.7' - 'r-fpc >=2.2-9' + - 'r-genieclust >=1.1.3' - 'r-ggplot2 >=3.3.5' - 'r-glmnet >=4.1.3' - 'r-kernlab >=0.9-29' @@ -36,11 +37,11 @@ requirements: - liblapack run: - r-base - - 'r-clustercrit >=1.2.8' - 'r-clvalid >=0.7' - 'r-dicer >=0.6.0' - 'r-dplyr >=1.0.7' - 'r-fpc >=2.2-9' + - 'r-genieclust >=1.1.3' - 'r-ggplot2 >=3.3.5' - 'r-glmnet >=4.1.3' - 'r-kernlab >=0.9-29' diff --git a/recipes/bioconductor-omadb/meta.yaml b/recipes/bioconductor-omadb/meta.yaml index 9191ab18d378e..2f326296a255a 100644 --- a/recipes/bioconductor-omadb/meta.yaml +++ b/recipes/bioconductor-omadb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "OmaDB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9bd7ca3376459757a00128152fde6617 + md5: 4bfced261f7429c6e881e05dc45ec0d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omadb", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-ape - r-base - 'r-httr >=1.2.1' - r-jsonlite - 'r-plyr >=1.8.4' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-ape - r-base - 'r-httr >=1.2.1' diff --git a/recipes/bioconductor-omicade4/meta.yaml b/recipes/bioconductor-omicade4/meta.yaml index 11202dcd1613b..d1459a945c810 100644 --- a/recipes/bioconductor-omicade4/meta.yaml +++ b/recipes/bioconductor-omicade4/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "omicade4" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a22d04cdab97b81511ff76f4a8ca34fa + md5: ed6de2f603d54a9ad262ff62784818a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicade4", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-made4 >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-made4 >=1.76.0,<1.77.0' - r-ade4 - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-made4 >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-made4 >=1.76.0,<1.77.0' - r-ade4 - r-base test: diff --git a/recipes/bioconductor-omiccircos/meta.yaml b/recipes/bioconductor-omiccircos/meta.yaml index 30c9f1733d7fc..38a85dda1eaff 100644 --- a/recipes/bioconductor-omiccircos/meta.yaml +++ b/recipes/bioconductor-omiccircos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "OmicCircos" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82db65a2a816bf1811423176dc23a908 + md5: 7d77b9a00853d3e6fec869012ce33daf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omiccircos", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base test: commands: diff --git a/recipes/bioconductor-omicplotr/meta.yaml b/recipes/bioconductor-omicplotr/meta.yaml index 43d68b9cf96ad..f4321b6264bdd 100644 --- a/recipes/bioconductor-omicplotr/meta.yaml +++ b/recipes/bioconductor-omicplotr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "omicplotR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2399395b2b761fa04cdb0370398db8ee + md5: 1ab1c2e82c98f8086b4dba4f65a613e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicplotr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' - r-base - r-compositions - r-dt @@ -32,7 +33,7 @@ requirements: - r-vegan - r-zcompositions run: - - 'bioconductor-aldex2 >=1.32.0,<1.33.0' + - 'bioconductor-aldex2 >=1.34.0,<1.35.0' - r-base - r-compositions - r-dt diff --git a/recipes/bioconductor-omicrexposome/meta.yaml b/recipes/bioconductor-omicrexposome/meta.yaml index 1fdf6a1e7b990..b6b78aeaefd18 100644 --- a/recipes/bioconductor-omicrexposome/meta.yaml +++ b/recipes/bioconductor-omicrexposome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.2" %} {% set name = "omicRexposome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 764e526f71b89b0846d239fc3b963904 + md5: 3b7a896124164c0dd282c91c79d2db00 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicrexposome", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-omicade4 >=1.40.0,<1.41.0' - - 'bioconductor-rexposome >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-omicade4 >=1.42.0,<1.43.0' + - 'bioconductor-rexposome >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 - r-ggrepel @@ -37,13 +38,13 @@ requirements: - r-smartsva - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-omicade4 >=1.40.0,<1.41.0' - - 'bioconductor-rexposome >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-omicade4 >=1.42.0,<1.43.0' + - 'bioconductor-rexposome >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-omicspca/meta.yaml b/recipes/bioconductor-omicspca/meta.yaml index 962db73ce6c27..3dfa436153af2 100644 --- a/recipes/bioconductor-omicspca/meta.yaml +++ b/recipes/bioconductor-omicspca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "OMICsPCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72c763d94cf3a24deaa8a3a84913ee53 + md5: d115069df9bde574c2439532f584f19a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicspca", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-helloranges >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-omicspcadata >=1.18.0,<1.19.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-helloranges >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-omicspcadata >=1.20.0,<1.21.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-cluster - r-clvalid @@ -48,12 +49,12 @@ requirements: - r-rmarkdown - r-tidyr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-helloranges >=1.26.0,<1.27.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-omicspcadata >=1.18.0,<1.19.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-helloranges >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-omicspcadata >=1.20.0,<1.21.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-cluster - r-clvalid diff --git a/recipes/bioconductor-omicspcadata/meta.yaml b/recipes/bioconductor-omicspcadata/meta.yaml index ed5731bde2f4d..463dedac14b20 100644 --- a/recipes/bioconductor-omicspcadata/meta.yaml +++ b/recipes/bioconductor-omicspcadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "OMICsPCAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 058c8440badd8afe17e693d3055fbf23 + md5: ba3167fdf846cb80aea07162b88c9b73 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicspcadata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, kableExtra, rmarkdown requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-omicspcadata/post-link.sh b/recipes/bioconductor-omicspcadata/post-link.sh index 2275b7d5f9fd8..ca5c61ccc8b1f 100644 --- a/recipes/bioconductor-omicspcadata/post-link.sh +++ b/recipes/bioconductor-omicspcadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "omicspcadata-1.18.0" +installBiocDataPackage.sh "omicspcadata-1.20.0" diff --git a/recipes/bioconductor-omicsprint/meta.yaml b/recipes/bioconductor-omicsprint/meta.yaml index 6db33b6e24e67..43008f464b26c 100644 --- a/recipes/bioconductor-omicsprint/meta.yaml +++ b/recipes/bioconductor-omicsprint/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "omicsPrint" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bde78492e675b58b7797c253a972330a + md5: 4e45c908441cedfc0dac097c558e61f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicsprint", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass - r-matrixstats run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-mass - r-matrixstats diff --git a/recipes/bioconductor-omicsviewer/build_failure.linux-64.yaml b/recipes/bioconductor-omicsviewer/build_failure.linux-64.yaml index 860b1ad27b912..42c095bbef5d2 100644 --- a/recipes/bioconductor-omicsviewer/build_failure.linux-64.yaml +++ b/recipes/bioconductor-omicsviewer/build_failure.linux-64.yaml @@ -1,8 +1,11 @@ -recipe_sha: a7735e832a66d80dfff55fe542bfee9b6a353575cd5dbf9ce52813c0ecb6eeb4 # The commit at which this recipe failed to build. +recipe_sha: 239d6bdc75a778a6447bf4fc3495c2f506b1d9b087b303660bddf9344473faef # The commit at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + r-flatxml 0.1.1 would require r-base >=4.2,<4.3.0a0, which conflicts with any installable versions previously reported; +category: |- + dependency issue log: |- - - Encountered problems while solving: - - - package bioconductor-summarizedexperiment-1.30.2-r43hdfd78af_0 requires bioconductor-genomicranges >=1.52.0,<1.53.0, but none of the providers can be installed + - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires bioconductor-delayedarray >=0.28.0,<0.29.0, but none of the providers can be installed - Leaving build/test directories: @@ -25,48 +28,49 @@ log: |- File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve raise RuntimeError("Solver could not find solution." error_string) RuntimeError: Solver could not find solution.Mamba failed to solve: - - r-rcolorbrewer - - r-plotly - - bioconductor-biobase >=2.60.0,<2.61.0 - - r-shinythemes - - r-shinyjs - - r-shinycssloaders - r-ggplot2 - - r-shinybusy - r-matrixstats - - r-openxlsx - - r-rsqlite - - r-shiny - - bioconductor-s4vectors >=0.38.0,<0.39.0 - - bioconductor-fgsea >=1.26.0,<1.27.0 + - r-fastmatch - r-psych - - r-flatxml - - r-survminer - - r-base 4.3.* + - r-rsqlite + - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - r-rocr - - r-stringr - - r-survival - - r-fastmatch - - r-beeswarm + - r-survminer - r-matrix - - r-dt - - r-shinywidgets - - r-reshape2 - - r-ggseqlogo - - r-httr - - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-shinybusy - r-htmlwidgets + - r-rcolorbrewer + - bioconductor-fgsea >=1.28.0,<1.29.0 - r-networkd3 + - r-dt + - r-shinyjs + - r-plotly + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-ggseqlogo - r-curl + - r-flatxml + - r-shinythemes + - r-httr + - r-shinywidgets + - r-reshape2 + - r-shiny + - r-base 4.3.* + - r-openxlsx + - r-stringr + - bioconductor-biobase >=2.62.0,<2.63.0 + - r-shinycssloaders + - r-survival + - r-beeswarm with channels: + - file:///opt/host-conda-bld - conda-forge - bioconda - defaults The reported errors are: - Encountered problems while solving: - - - package bioconductor-summarizedexperiment-1.30.2-r43hdfd78af_0 requires bioconductor-genomicranges >=1.52.0,<1.53.0, but none of the providers can be installed + - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires bioconductor-delayedarray >=0.28.0,<0.29.0, but none of the providers can be installed - During handling of the above exception, another exception occurred: @@ -100,5 +104,5 @@ log: |- actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-summarizedexperiment==1.30.2=r43hdfd78af_0"), MatchSpec("bioconductor-genomicranges[version='>=1.52.0,<1.53.0']")} + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-summarizedexperiment==1.32.0=r43hdfd78af_0"), MatchSpec("bioconductor-delayedarray[version='>=0.28.0,<0.29.0']")} # Last 100 lines of the build log. diff --git a/recipes/bioconductor-omicsviewer/meta.yaml b/recipes/bioconductor-omicsviewer/meta.yaml index b457e664d14ce..bc96b7d767299 100644 --- a/recipes/bioconductor-omicsviewer/meta.yaml +++ b/recipes/bioconductor-omicsviewer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "omicsViewer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba3a9dc8fda84db3bbfd024389c9d4e6 + md5: 7d650ff242a133610199a574a29abfde build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicsviewer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, unittest requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beeswarm - r-curl @@ -55,10 +56,10 @@ requirements: - r-survival - r-survminer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-beeswarm - r-curl diff --git a/recipes/bioconductor-omixer/meta.yaml b/recipes/bioconductor-omixer/meta.yaml index be9e560a6cb29..5a6e3c4aa6eb1 100644 --- a/recipes/bioconductor-omixer/meta.yaml +++ b/recipes/bioconductor-omixer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Omixer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71204a8a366fca0179c7c8d8df4e476f + md5: 6360569495c662f2c34c86dbd7387f4a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omixer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, magick, testthat requirements: diff --git a/recipes/bioconductor-omnipathr/meta.yaml b/recipes/bioconductor-omnipathr/meta.yaml index 20fac42c22e3a..e3b362d4d7544 100644 --- a/recipes/bioconductor-omnipathr/meta.yaml +++ b/recipes/bioconductor-omnipathr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.0" %} +{% set version = "3.10.1" %} {% set name = "OmnipathR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,14 +11,15 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5026627a035e201129c1765133a2c3e4 + md5: c51296b40e8d580f14dc3ff6839495f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omnipathr", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, biomaRt, bookdown, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, smoof, supraHex, testthat +# Suggests: BiocStyle, biomaRt, bookdown, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, sigmajs, smoof, supraHex, testthat requirements: host: - r-base @@ -26,12 +27,13 @@ requirements: - r-crayon - r-curl - r-digest - - r-dplyr + - 'r-dplyr >=1.1.0' - r-httr - r-igraph - r-jsonlite - r-later - r-logger + - r-lubridate - r-magrittr - r-progress - r-purrr @@ -41,6 +43,7 @@ requirements: - r-rlang - r-rmarkdown - r-rvest + - r-stringi - r-stringr - r-tibble - r-tidyr @@ -54,12 +57,13 @@ requirements: - r-crayon - r-curl - r-digest - - r-dplyr + - 'r-dplyr >=1.1.0' - r-httr - r-igraph - r-jsonlite - r-later - r-logger + - r-lubridate - r-magrittr - r-progress - r-purrr @@ -69,6 +73,7 @@ requirements: - r-rlang - r-rmarkdown - r-rvest + - r-stringi - r-stringr - r-tibble - r-tidyr diff --git a/recipes/bioconductor-ompbam/meta.yaml b/recipes/bioconductor-ompbam/meta.yaml index 211fce60b8a72..87ebc1481b424 100644 --- a/recipes/bioconductor-ompbam/meta.yaml +++ b/recipes/bioconductor-ompbam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ompBAM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 118828a1b81d93cb734b85dfa7dea65c + md5: 9e9d31ddcad0b4bb4acb30ad970a0cd5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ompbam", max_pin="x.x") }}' # Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-onassisjavalibs/meta.yaml b/recipes/bioconductor-onassisjavalibs/meta.yaml index aa33d15402a43..d2c32d35b58e1 100644 --- a/recipes/bioconductor-onassisjavalibs/meta.yaml +++ b/recipes/bioconductor-onassisjavalibs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "OnassisJavaLibs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32a85e21248ac13de54dfee722eee3f1 + md5: 88d86bc7e7d339146ba7ea689c2d8080 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-onassisjavalibs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr # SystemRequirements: Java (>= 1.8) @@ -29,7 +30,7 @@ requirements: - r-base - r-rjava - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' - openjdk test: commands: diff --git a/recipes/bioconductor-onassisjavalibs/post-link.sh b/recipes/bioconductor-onassisjavalibs/post-link.sh index c9c7f57e98503..2e98dfca3f0c9 100644 --- a/recipes/bioconductor-onassisjavalibs/post-link.sh +++ b/recipes/bioconductor-onassisjavalibs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "onassisjavalibs-1.22.0" +installBiocDataPackage.sh "onassisjavalibs-1.24.0" diff --git a/recipes/bioconductor-oncomix/meta.yaml b/recipes/bioconductor-oncomix/meta.yaml index 403e8e73f96ce..e3d50be1cdf3e 100644 --- a/recipes/bioconductor-oncomix/meta.yaml +++ b/recipes/bioconductor-oncomix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "oncomix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 366323b113f34a562f6a3fe523595cb0 + md5: dd6381604152d7cb96f7c592e8f82ab7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oncomix", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, RMySQL requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel - r-mclust - r-rcolorbrewer run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-oncoscanr/meta.yaml b/recipes/bioconductor-oncoscanr/meta.yaml index 3479ba987b17b..84d19dea331fa 100644 --- a/recipes/bioconductor-oncoscanr/meta.yaml +++ b/recipes/bioconductor-oncoscanr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "oncoscanR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80e05d30297850d138e26ad1ccc9f51c + md5: 48aee6850c94c299417e75cf74418b01 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oncoscanr", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-magrittr - r-readr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-magrittr - r-readr diff --git a/recipes/bioconductor-oncoscore/meta.yaml b/recipes/bioconductor-oncoscore/meta.yaml index b8102697059ad..f85345b846e04 100644 --- a/recipes/bioconductor-oncoscore/meta.yaml +++ b/recipes/bioconductor-oncoscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "OncoScore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62b68dec725d2a79df4d45eb05fbfe86 + md5: 5b61a8738f91d4c8ff214b38878a8564 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oncoscore", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, knitr, testthat, requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-oncosimulr/build.sh b/recipes/bioconductor-oncosimulr/build.sh index 8723af305997a..ac78ea511ccf4 100644 --- a/recipes/bioconductor-oncosimulr/build.sh +++ b/recipes/bioconductor-oncosimulr/build.sh @@ -11,4 +11,4 @@ CXX14=$CXX" > ~/.R/Makevars if [[ $OSTYPE == "darwin"* ]]; then sed -i.bak "s/OncoSimulR.so/OncoSimulR.dylib/g" src/install.libs.R fi -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-oncosimulr/meta.yaml b/recipes/bioconductor-oncosimulr/meta.yaml index 1a46c55588f7a..daa4bec2d291d 100644 --- a/recipes/bioconductor-oncosimulr/meta.yaml +++ b/recipes/bioconductor-oncosimulr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.2.0" %} +{% set version = "4.4.0" %} {% set name = "OncoSimulR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 741c17927e4a7a2022f6d757602e3c72 + md5: 9b908040a100f075d4f2493ec3c1fa85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oncosimulr", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-car - r-data.table @@ -37,8 +38,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-car - r-data.table diff --git a/recipes/bioconductor-onlinefdr/meta.yaml b/recipes/bioconductor-onlinefdr/meta.yaml index 2ad6e39347b96..24c6eefdc5faf 100644 --- a/recipes/bioconductor-onlinefdr/meta.yaml +++ b/recipes/bioconductor-onlinefdr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "onlineFDR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f9a9d661fcecba747e4229d4e6cf920 + md5: 1fcb84d6fd99c3f48d43c07adc29f256 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-onlinefdr", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, covr requirements: host: diff --git a/recipes/bioconductor-ontoproc/meta.yaml b/recipes/bioconductor-ontoproc/meta.yaml index b8b5cfba1fd90..ebdd3376d7bee 100644 --- a/recipes/bioconductor-ontoproc/meta.yaml +++ b/recipes/bioconductor-ontoproc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ontoProc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b292bc23074c04cfed8987658c6cafc + md5: 157cb78951de651c6be909aef51480a5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ontoproc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-dt @@ -37,13 +38,13 @@ requirements: - r-ontologyplot - r-shiny run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-ontoprocdata/meta.yaml b/recipes/bioconductor-ontoprocdata/meta.yaml index d71b56dc9f9ba..b0247d4b82b11 100644 --- a/recipes/bioconductor-ontoprocdata/meta.yaml +++ b/recipes/bioconductor-ontoprocdata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.9901" %} {% set name = "ontoProcData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d4160c1fc853db468ce73c7fe62ca00f build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ontoprocdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), AnnotationHub, utils, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-opencyto/meta.yaml b/recipes/bioconductor-opencyto/meta.yaml index 2e2d3584c5621..6c2923914d7d3 100644 --- a/recipes/bioconductor-opencyto/meta.yaml +++ b/recipes/bioconductor-opencyto/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "openCyto" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fabe8dc6a63062ffd1b3fefadeb787b5 + md5: 04a62bb1960f008fc218686296a3118d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-opencyto", max_pin="x.x") }}' # Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-bh - r-cpp11 @@ -37,15 +38,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-flowclust >=3.38.0,<3.39.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowviz >=1.64.0,<1.65.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-ncdfflow >=2.46.0,<2.47.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-flowclust >=3.40.0,<3.41.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - r-bh - r-cpp11 diff --git a/recipes/bioconductor-openprimer/meta.yaml b/recipes/bioconductor-openprimer/meta.yaml index d0e580bce2926..e7ebaf881fc1c 100644 --- a/recipes/bioconductor-openprimer/meta.yaml +++ b/recipes/bioconductor-openprimer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "openPrimeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 105634c21aebdcf44ef3c0151664e343 + md5: e3fe2285d832b192c7054a36e2aedc6b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-openprimer", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) # SystemRequirements: MAFFT (>= 7.305), OligoArrayAux (>= 3.8), ViennaRNA (>= 2.4.1), MELTING (>= 5.1.1), Pandoc (>= 1.12.3) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-ape >=3.5' - r-base - 'r-digest >=0.6.9' @@ -52,12 +53,12 @@ requirements: - 'r-xml >=3.98-1.4' - 'mafft >=7.305' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'r-ape >=3.5' - r-base - 'r-digest >=0.6.9' diff --git a/recipes/bioconductor-openprimerui/meta.yaml b/recipes/bioconductor-openprimerui/meta.yaml index 99cb97ce36f13..c0bfddd6d19af 100644 --- a/recipes/bioconductor-openprimerui/meta.yaml +++ b/recipes/bioconductor-openprimerui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "openPrimeRui" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 365ce6ca2bb48726abf97ca874a6f6da + md5: 11cb9510b6a6ecdbc8df2d5c2497d029 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-openprimerui", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.13) requirements: host: - - 'bioconductor-openprimer >=1.22.0,<1.23.0' + - 'bioconductor-openprimer >=1.24.0,<1.25.0' - r-base - 'r-dt >=0.2' - 'r-rmarkdown >=1.0' @@ -29,7 +30,7 @@ requirements: - 'r-shinybs >=0.61' - 'r-shinyjs >=0.9' run: - - 'bioconductor-openprimer >=1.22.0,<1.23.0' + - 'bioconductor-openprimer >=1.24.0,<1.25.0' - r-base - 'r-dt >=0.2' - 'r-rmarkdown >=1.0' diff --git a/recipes/bioconductor-openstats/meta.yaml b/recipes/bioconductor-openstats/meta.yaml index 73794c3fe60c9..f78c9bcdf4b49 100644 --- a/recipes/bioconductor-openstats/meta.yaml +++ b/recipes/bioconductor-openstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "OpenStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7930395c0dc75c56e7f67cfef6526ac1 + md5: 0e8a0fcd25ca1377c5bce5068bfaabff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-openstats", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown requirements: diff --git a/recipes/bioconductor-operonhumanv3.db/meta.yaml b/recipes/bioconductor-operonhumanv3.db/meta.yaml index e859629198e93..c1bf73b30fa4b 100644 --- a/recipes/bioconductor-operonhumanv3.db/meta.yaml +++ b/recipes/bioconductor-operonhumanv3.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "OperonHumanV3.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 648da5d4d63c6c8327f6035ee09f2b65 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-operonhumanv3.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-opossom/meta.yaml b/recipes/bioconductor-opossom/meta.yaml index 368d85fca06ae..131a22582ed1a 100644 --- a/recipes/bioconductor-opossom/meta.yaml +++ b/recipes/bioconductor-opossom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "oposSOM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d0e76bf961fef11d0ae091eec82824b + md5: a5660824c13db2ae8bf7b79aa7c529f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-opossom", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-ape - r-base - r-fastica @@ -38,9 +39,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-ape - r-base - r-fastica diff --git a/recipes/bioconductor-oppar/meta.yaml b/recipes/bioconductor-oppar/meta.yaml index dabd8ae7baf3b..9546c106c3853 100644 --- a/recipes/bioconductor-oppar/meta.yaml +++ b/recipes/bioconductor-oppar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "oppar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa9223b057764734655c8cdbbe8dc740 + md5: 21adf37b9236cf860009e709f63d5e30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oppar", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-oppti/meta.yaml b/recipes/bioconductor-oppti/meta.yaml index 8a401c37715a6..ceb9efd135c77 100644 --- a/recipes/bioconductor-oppti/meta.yaml +++ b/recipes/bioconductor-oppti/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "oppti" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee66d8bc8d637cf14d5724387ffd3894 + md5: 8f995db99b66e966a96b8ce150c956a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oppti", max_pin="x.x") }}' noarch: generic # Suggests: markdown requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-devtools - r-ggplot2 @@ -31,7 +32,7 @@ requirements: - r-rcolorbrewer - r-reshape run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-devtools - r-ggplot2 diff --git a/recipes/bioconductor-optimalflow/meta.yaml b/recipes/bioconductor-optimalflow/meta.yaml index c7ba7fd84a780..992876df6f621 100644 --- a/recipes/bioconductor-optimalflow/meta.yaml +++ b/recipes/bioconductor-optimalflow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "optimalFlow" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fff3df9b484a19d62f4c06e763a554ea + md5: c66127dc23a70fdcfd651543ea596329 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-optimalflow", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, magick requirements: host: - - 'bioconductor-flowmeans >=1.60.0,<1.61.0' - - 'bioconductor-optimalflowdata >=1.12.0,<1.13.0' + - 'bioconductor-flowmeans >=1.62.0,<1.63.0' + - 'bioconductor-optimalflowdata >=1.14.0,<1.15.0' - r-base - r-dbscan - r-doparallel @@ -36,8 +37,8 @@ requirements: - r-robustbase - r-transport run: - - 'bioconductor-flowmeans >=1.60.0,<1.61.0' - - 'bioconductor-optimalflowdata >=1.12.0,<1.13.0' + - 'bioconductor-flowmeans >=1.62.0,<1.63.0' + - 'bioconductor-optimalflowdata >=1.14.0,<1.15.0' - r-base - r-dbscan - r-doparallel diff --git a/recipes/bioconductor-optimalflowdata/meta.yaml b/recipes/bioconductor-optimalflowdata/meta.yaml index 4b1bf0bf2330b..d65bee9574e4b 100644 --- a/recipes/bioconductor-optimalflowdata/meta.yaml +++ b/recipes/bioconductor-optimalflowdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "optimalFlowData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: daba5d6a8b8fdde9d58fed555c569ad5 + md5: 790ea8af88ecf90abafdef9a7c4abb08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-optimalflowdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, magick requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-optimalflowdata/post-link.sh b/recipes/bioconductor-optimalflowdata/post-link.sh index a58d0484a9929..0a5ec1a8c8c2a 100644 --- a/recipes/bioconductor-optimalflowdata/post-link.sh +++ b/recipes/bioconductor-optimalflowdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "optimalflowdata-1.12.0" +installBiocDataPackage.sh "optimalflowdata-1.14.0" diff --git a/recipes/bioconductor-opweight/meta.yaml b/recipes/bioconductor-opweight/meta.yaml index 82f1af5964129..cd88a4afed9cd 100644 --- a/recipes/bioconductor-opweight/meta.yaml +++ b/recipes/bioconductor-opweight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "OPWeight" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a33f46eeb9e69082fdd9a89cb7a5f23c + md5: 83d9a0007e617f317f9424a4c228c50a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-opweight", max_pin="x.x") }}' noarch: generic # Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-mass - r-tibble run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-mass - r-tibble diff --git a/recipes/bioconductor-orderedlist/meta.yaml b/recipes/bioconductor-orderedlist/meta.yaml index d4fc2fe472c0a..6be59704a0e91 100644 --- a/recipes/bioconductor-orderedlist/meta.yaml +++ b/recipes/bioconductor-orderedlist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "OrderedList" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 352cb6d578f4aa28920229c8844fe469 + md5: d8239906b10a2630dc25ab749903a511 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orderedlist", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-twilight >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-twilight >=1.78.0,<1.79.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-twilight >=1.76.0,<1.77.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-twilight >=1.78.0,<1.79.0' - r-base test: commands: diff --git a/recipes/bioconductor-orfhunter/meta.yaml b/recipes/bioconductor-orfhunter/meta.yaml index 67b3d4b0cdee9..239909d4356a3 100644 --- a/recipes/bioconductor-orfhunter/meta.yaml +++ b/recipes/bioconductor-orfhunter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ORFhunteR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de379db06acbc82ad053e95517675ebf + md5: c9e57a998b0746df96e6d173d75fd032 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orfhunter", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-peptides @@ -33,9 +34,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-peptides diff --git a/recipes/bioconductor-orfik/meta.yaml b/recipes/bioconductor-orfik/meta.yaml index a443240ae3bdb..3a5075e7dd6ce 100644 --- a/recipes/bioconductor-orfik/meta.yaml +++ b/recipes/bioconductor-orfik/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ORFik" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 712d98a9513f8a55085f3269902744f2 + md5: 80a8144faafb88fcd9745dcfce492512 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orfik", max_pin="x.x") }}' # Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biomartr - 'r-cowplot >=1.0.0' + - r-curl - 'r-data.table >=1.11.8' + - r-downloader - 'r-fst >=0.9.2' - 'r-ggplot2 >=2.2.1' - 'r-gridextra >=2.3' @@ -47,30 +50,35 @@ requirements: - r-jsonlite - r-r.utils - 'r-rcpp >=1.0.0' + - r-rcurl + - r-withr + - r-xml - 'r-xml2 >=1.2.0' - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biomartr - 'r-cowplot >=1.0.0' + - r-curl - 'r-data.table >=1.11.8' + - r-downloader - 'r-fst >=0.9.2' - 'r-ggplot2 >=2.2.1' - 'r-gridextra >=2.3' @@ -78,6 +86,9 @@ requirements: - r-jsonlite - r-r.utils - 'r-rcpp >=1.0.0' + - r-rcurl + - r-withr + - r-xml - 'r-xml2 >=1.2.0' build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-org.ag.eg.db/meta.yaml b/recipes/bioconductor-org.ag.eg.db/meta.yaml index 1051e8dd1d8c4..6a62269c6da3b 100644 --- a/recipes/bioconductor-org.ag.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ag.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Ag.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb3e06ad1afc3c386367a239e559f342 + md5: a67c309f5472338fd47fe43ff20ce2e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.ag.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ag.eg.db/post-link.sh b/recipes/bioconductor-org.ag.eg.db/post-link.sh index b668057bfacd7..914a57fe474f6 100644 --- a/recipes/bioconductor-org.ag.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ag.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ag.eg.db-3.17.0" +installBiocDataPackage.sh "org.ag.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.at.tair.db/meta.yaml b/recipes/bioconductor-org.at.tair.db/meta.yaml index 23f5054e0fde6..6ed40899b87cc 100644 --- a/recipes/bioconductor-org.at.tair.db/meta.yaml +++ b/recipes/bioconductor-org.at.tair.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.At.tair.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 568e09bfbf9b86a9120b52ca6eb47879 + md5: 5d6161b859de99eaeadebc0e03ae9c68 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.at.tair.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.at.tair.db/post-link.sh b/recipes/bioconductor-org.at.tair.db/post-link.sh index 96929528fea52..4fbdf92ea3f91 100644 --- a/recipes/bioconductor-org.at.tair.db/post-link.sh +++ b/recipes/bioconductor-org.at.tair.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.at.tair.db-3.17.0" +installBiocDataPackage.sh "org.at.tair.db-3.18.0" diff --git a/recipes/bioconductor-org.bt.eg.db/meta.yaml b/recipes/bioconductor-org.bt.eg.db/meta.yaml index a83cc489b9227..c0fef6c777d07 100644 --- a/recipes/bioconductor-org.bt.eg.db/meta.yaml +++ b/recipes/bioconductor-org.bt.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Bt.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13b2350bb7e6219a25caea3a4038f104 + md5: 23fd8017323c86930c50d596204bad54 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.bt.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.bt.eg.db/post-link.sh b/recipes/bioconductor-org.bt.eg.db/post-link.sh index 6b094edee61d3..cd489eb184530 100644 --- a/recipes/bioconductor-org.bt.eg.db/post-link.sh +++ b/recipes/bioconductor-org.bt.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.bt.eg.db-3.17.0" +installBiocDataPackage.sh "org.bt.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.ce.eg.db/meta.yaml b/recipes/bioconductor-org.ce.eg.db/meta.yaml index dc4e0188f33c5..495acc87d6521 100644 --- a/recipes/bioconductor-org.ce.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ce.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Ce.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8884864a691574d7640b2059a8d6613b + md5: 441a5efb4649a1201b5552b14c1f1cef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.ce.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ce.eg.db/post-link.sh b/recipes/bioconductor-org.ce.eg.db/post-link.sh index 7f5644e45824a..2bdc66737e6a1 100644 --- a/recipes/bioconductor-org.ce.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ce.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ce.eg.db-3.17.0" +installBiocDataPackage.sh "org.ce.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.cf.eg.db/meta.yaml b/recipes/bioconductor-org.cf.eg.db/meta.yaml index dc71863d364c4..67f62fb8f70c8 100644 --- a/recipes/bioconductor-org.cf.eg.db/meta.yaml +++ b/recipes/bioconductor-org.cf.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Cf.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 594a306e7ac757df56e9563163168713 + md5: 038d08c046a81218a31ff8db0877dd15 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.cf.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.cf.eg.db/post-link.sh b/recipes/bioconductor-org.cf.eg.db/post-link.sh index 1f27db3f27775..06faa06376c83 100644 --- a/recipes/bioconductor-org.cf.eg.db/post-link.sh +++ b/recipes/bioconductor-org.cf.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.cf.eg.db-3.17.0" +installBiocDataPackage.sh "org.cf.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.dm.eg.db/meta.yaml b/recipes/bioconductor-org.dm.eg.db/meta.yaml index b16f5f34268f6..f5b192c04a705 100644 --- a/recipes/bioconductor-org.dm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dm.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Dm.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a680c3ea7320013c7ab1181d11e2177 + md5: 92577ed3bc5d76b78905169eebfebe7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.dm.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.dm.eg.db/post-link.sh b/recipes/bioconductor-org.dm.eg.db/post-link.sh index e5724e3adb8e1..d0c3e58bb8bf4 100644 --- a/recipes/bioconductor-org.dm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dm.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.dm.eg.db-3.17.0" +installBiocDataPackage.sh "org.dm.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.dr.eg.db/meta.yaml b/recipes/bioconductor-org.dr.eg.db/meta.yaml index 794990e882fae..38cae1002a138 100644 --- a/recipes/bioconductor-org.dr.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dr.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Dr.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03edb42214f27a93743dfc57200cddbb + md5: cfea28c45f2f34c675975eacbe861a5f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.dr.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.dr.eg.db/post-link.sh b/recipes/bioconductor-org.dr.eg.db/post-link.sh index 565224b42083a..f65f46693b80e 100644 --- a/recipes/bioconductor-org.dr.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dr.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.dr.eg.db-3.17.0" +installBiocDataPackage.sh "org.dr.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.eck12.eg.db/meta.yaml b/recipes/bioconductor-org.eck12.eg.db/meta.yaml index d2bfbf47153ea..496eac6758b52 100644 --- a/recipes/bioconductor-org.eck12.eg.db/meta.yaml +++ b/recipes/bioconductor-org.eck12.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.EcK12.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 676642eb784017bf9f82711274f8987e + md5: 50d3d3ca9efec212eae3a920b00750a3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.eck12.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.eck12.eg.db/post-link.sh b/recipes/bioconductor-org.eck12.eg.db/post-link.sh index 9d039702bf9a3..ebfed362951d8 100644 --- a/recipes/bioconductor-org.eck12.eg.db/post-link.sh +++ b/recipes/bioconductor-org.eck12.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.eck12.eg.db-3.17.0" +installBiocDataPackage.sh "org.eck12.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml b/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml index 40bfe1dfaf5fe..d251c5b30c35e 100644 --- a/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.EcSakai.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 135a50e2604715a7c5f1c2a36bddf691 + md5: 3f26ffa55ce30fc8caa64f826207ac61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.ecsakai.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh b/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh index 1190bbfee42ac..8ec1c9f68fb4b 100644 --- a/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ecsakai.eg.db-3.17.0" +installBiocDataPackage.sh "org.ecsakai.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.gg.eg.db/meta.yaml b/recipes/bioconductor-org.gg.eg.db/meta.yaml index cbb9dabfd6da5..4e11232145408 100644 --- a/recipes/bioconductor-org.gg.eg.db/meta.yaml +++ b/recipes/bioconductor-org.gg.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Gg.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 292b22ea846c6c184528e92ab4a53247 + md5: 4ebcbfb0baeee3332a2a07aeae2402a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.gg.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.gg.eg.db/post-link.sh b/recipes/bioconductor-org.gg.eg.db/post-link.sh index 14fb60f9390bb..19ca51f5ad61d 100644 --- a/recipes/bioconductor-org.gg.eg.db/post-link.sh +++ b/recipes/bioconductor-org.gg.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.gg.eg.db-3.17.0" +installBiocDataPackage.sh "org.gg.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index d2144f7ab5e8c..2aaffdc1eb4a7 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Hs.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1015fd071ab69055865940ef6e205f4 + md5: e1f74b9d0c541b5678a0d88f6a8ec847 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.hs.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.hs.eg.db/post-link.sh b/recipes/bioconductor-org.hs.eg.db/post-link.sh index 3a9f65c1b9409..88931ccb51392 100644 --- a/recipes/bioconductor-org.hs.eg.db/post-link.sh +++ b/recipes/bioconductor-org.hs.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.hs.eg.db-3.17.0" +installBiocDataPackage.sh "org.hs.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.mm.eg.db/meta.yaml b/recipes/bioconductor-org.mm.eg.db/meta.yaml index 62b1b53e60da6..9d5b8774b3b7a 100644 --- a/recipes/bioconductor-org.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mm.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Mm.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b2124d1ef7c0936bb4ecfcbd2a979b8 + md5: bd95e1ff46f764fff51acc60b249fe95 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.mm.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.mm.eg.db/post-link.sh b/recipes/bioconductor-org.mm.eg.db/post-link.sh index 498545f19ed05..ea3b970a24917 100644 --- a/recipes/bioconductor-org.mm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.mm.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.mm.eg.db-3.17.0" +installBiocDataPackage.sh "org.mm.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.mmu.eg.db/meta.yaml b/recipes/bioconductor-org.mmu.eg.db/meta.yaml index 1af50dabafd7f..408a76b274591 100644 --- a/recipes/bioconductor-org.mmu.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mmu.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Mmu.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d59c3d744ec7def892edacf12c99b869 + md5: 45a35940d0d1ab91b2b262a8666afa53 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.mmu.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.mmu.eg.db/post-link.sh b/recipes/bioconductor-org.mmu.eg.db/post-link.sh index f4810f44dd65f..017b895a9759c 100644 --- a/recipes/bioconductor-org.mmu.eg.db/post-link.sh +++ b/recipes/bioconductor-org.mmu.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.mmu.eg.db-3.17.0" +installBiocDataPackage.sh "org.mmu.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.mxanthus.db/meta.yaml b/recipes/bioconductor-org.mxanthus.db/meta.yaml index f5df60ed94e1b..558a2aefd9d12 100644 --- a/recipes/bioconductor-org.mxanthus.db/meta.yaml +++ b/recipes/bioconductor-org.mxanthus.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.27" %} {% set name = "org.Mxanthus.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,27 +13,28 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e493814c41401de383b4f6e0f3d39619 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.mxanthus.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, RUnit, clusterProfiler, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.pt.eg.db/meta.yaml b/recipes/bioconductor-org.pt.eg.db/meta.yaml index 05faf04d070c0..b98e9dd870761 100644 --- a/recipes/bioconductor-org.pt.eg.db/meta.yaml +++ b/recipes/bioconductor-org.pt.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Pt.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3c4135532486951e94ed5d182030217 + md5: d6672365e68ece6415e2736f40bf096c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.pt.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.pt.eg.db/post-link.sh b/recipes/bioconductor-org.pt.eg.db/post-link.sh index 03ab6fa472388..9bcd0492d2c7f 100644 --- a/recipes/bioconductor-org.pt.eg.db/post-link.sh +++ b/recipes/bioconductor-org.pt.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.pt.eg.db-3.17.0" +installBiocDataPackage.sh "org.pt.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.rn.eg.db/meta.yaml b/recipes/bioconductor-org.rn.eg.db/meta.yaml index 670d3c8303da1..aa8ee6cf68f8d 100644 --- a/recipes/bioconductor-org.rn.eg.db/meta.yaml +++ b/recipes/bioconductor-org.rn.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Rn.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf40322d9b95075d75777ec63a797198 + md5: 1ff92cec0fc2cbd5b3055d1153526ce3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.rn.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.rn.eg.db/post-link.sh b/recipes/bioconductor-org.rn.eg.db/post-link.sh index 73d94ea033353..58dd4a7343f2b 100644 --- a/recipes/bioconductor-org.rn.eg.db/post-link.sh +++ b/recipes/bioconductor-org.rn.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.rn.eg.db-3.17.0" +installBiocDataPackage.sh "org.rn.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.sc.sgd.db/meta.yaml b/recipes/bioconductor-org.sc.sgd.db/meta.yaml index f93e10ad3af11..278039220b5c7 100644 --- a/recipes/bioconductor-org.sc.sgd.db/meta.yaml +++ b/recipes/bioconductor-org.sc.sgd.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Sc.sgd.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0fd2fcd421007a5b9bd7bc2f5874ae3 + md5: cd83de7109be623e7a294a47ca65f160 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.sc.sgd.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.sc.sgd.db/post-link.sh b/recipes/bioconductor-org.sc.sgd.db/post-link.sh index d98eb50cfefb3..ad3c38e6e585e 100644 --- a/recipes/bioconductor-org.sc.sgd.db/post-link.sh +++ b/recipes/bioconductor-org.sc.sgd.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.sc.sgd.db-3.17.0" +installBiocDataPackage.sh "org.sc.sgd.db-3.18.0" diff --git a/recipes/bioconductor-org.ss.eg.db/meta.yaml b/recipes/bioconductor-org.ss.eg.db/meta.yaml index b016e212ce8c3..6e7b63562d155 100644 --- a/recipes/bioconductor-org.ss.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ss.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Ss.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9f8354c9869e86a610ad30f51eb533b + md5: f9b32c76d23f9195df7a7eb6529f3340 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.ss.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ss.eg.db/post-link.sh b/recipes/bioconductor-org.ss.eg.db/post-link.sh index b54a6e63afd13..5696d4ac5b715 100644 --- a/recipes/bioconductor-org.ss.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ss.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ss.eg.db-3.17.0" +installBiocDataPackage.sh "org.ss.eg.db-3.18.0" diff --git a/recipes/bioconductor-org.xl.eg.db/meta.yaml b/recipes/bioconductor-org.xl.eg.db/meta.yaml index 70fb5c04244ff..48b5a78fe55b9 100644 --- a/recipes/bioconductor-org.xl.eg.db/meta.yaml +++ b/recipes/bioconductor-org.xl.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "org.Xl.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ce9e0dc3566a220f5c12b70ffb2538c + md5: bbea76a4373d8b51048029b83c591aca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-org.xl.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.xl.eg.db/post-link.sh b/recipes/bioconductor-org.xl.eg.db/post-link.sh index f6af33a8d689b..d079ec990a1cf 100644 --- a/recipes/bioconductor-org.xl.eg.db/post-link.sh +++ b/recipes/bioconductor-org.xl.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.xl.eg.db-3.17.0" +installBiocDataPackage.sh "org.xl.eg.db-3.18.0" diff --git a/recipes/bioconductor-organism.dplyr/meta.yaml b/recipes/bioconductor-organism.dplyr/meta.yaml index c3360180e94ae..2ccba681f13c0 100644 --- a/recipes/bioconductor-organism.dplyr/meta.yaml +++ b/recipes/bioconductor-organism.dplyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.1" %} {% set name = "Organism.dplyr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d89fd354e720e5b09282fa271367efe3 + md5: b16c25c3ee5abafa1007a9c7bd731801 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-organism.dplyr", max_pin="x.x") }}' noarch: generic -# Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, BiocStyle, ggplot2 +# Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-dbplyr @@ -37,14 +38,14 @@ requirements: - r-rsqlite - r-tibble run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-dbplyr diff --git a/recipes/bioconductor-organismdbi/meta.yaml b/recipes/bioconductor-organismdbi/meta.yaml index 7e0477602eab8..3424eb8e53508 100644 --- a/recipes/bioconductor-organismdbi/meta.yaml +++ b/recipes/bioconductor-organismdbi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "OrganismDbi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b63d172cafa48c26622cff0fa0a338a + md5: 3d6c3ba042e4e0b6ecf5fa27fc344a82 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-organismdbi", max_pin="x.x") }}' noarch: generic # Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-dbi run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-biocmanager - r-dbi diff --git a/recipes/bioconductor-orthogene/meta.yaml b/recipes/bioconductor-orthogene/meta.yaml index 6856abd424938..5fb52c90803da 100644 --- a/recipes/bioconductor-orthogene/meta.yaml +++ b/recipes/bioconductor-orthogene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "orthogene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e4dcc64a91b436e77b287eb1c94ed801 + md5: f3597fa7ce02e2e32ee6cebb20f67c08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orthogene", max_pin="x.x") }}' noarch: generic # Suggests: rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-babelgene - r-base - r-data.table @@ -37,8 +38,8 @@ requirements: - r-patchwork - r-repmis run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-babelgene - r-base - r-data.table diff --git a/recipes/bioconductor-orthology.eg.db/meta.yaml b/recipes/bioconductor-orthology.eg.db/meta.yaml index c01f01405c677..b4bceecfb8d50 100644 --- a/recipes/bioconductor-orthology.eg.db/meta.yaml +++ b/recipes/bioconductor-orthology.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "Orthology.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90c181057a638413afc54bb11071a42e + md5: 1e53a6a144a5074544cbe166ad241012 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orthology.eg.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-orthology.eg.db/post-link.sh b/recipes/bioconductor-orthology.eg.db/post-link.sh index 9de63532c30a8..62dc891778772 100644 --- a/recipes/bioconductor-orthology.eg.db/post-link.sh +++ b/recipes/bioconductor-orthology.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "orthology.eg.db-3.17.0" +installBiocDataPackage.sh "orthology.eg.db-3.18.0" diff --git a/recipes/bioconductor-orthos/build.sh b/recipes/bioconductor-orthos/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-orthos/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-orthos/meta.yaml b/recipes/bioconductor-orthos/meta.yaml new file mode 100644 index 0000000000000..638a68a53caf2 --- /dev/null +++ b/recipes/bioconductor-orthos/meta.yaml @@ -0,0 +1,81 @@ +{% set version = "1.0.1" %} +{% set name = "orthos" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c35d515c0e956e4207b00db662192707 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orthos", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-orthosdata >=1.0.0,<1.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-colorspace + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-ggpubr + - r-ggrepel + - r-ggsci + - r-keras + - r-plyr + - r-reticulate + - r-rlang + - r-tensorflow + - r-tidyr + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-orthosdata >=1.0.0,<1.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-colorspace + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-ggpubr + - r-ggrepel + - r-ggsci + - r-keras + - r-plyr + - r-reticulate + - r-rlang + - r-tensorflow + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: '`orthos` is an R package for variance decomposition using conditional variational auto-encoders' + description: '`orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large database of contrasts (derived from ARCHS4, https://maayanlab.cloud/archs4/) to identify similar experiments. `orthos` furthermore provides plotting functions to visualize the results of such a search for similar contrasts.' + license_file: LICENSE + diff --git a/recipes/bioconductor-orthosdata/meta.yaml b/recipes/bioconductor-orthosdata/meta.yaml new file mode 100644 index 0000000000000..8aca3fc0ed845 --- /dev/null +++ b/recipes/bioconductor-orthosdata/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "orthosData" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7970587455fa5197daf1f6b640b7f688 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-orthosdata", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, ggplot2, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-stringr + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-stringr + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Data for the orthos package' + description: '`orthosData` is the companion ExperimentData package to the `orthos` R package for mechanistic studies using differential gene expression experiments. It provides functions for retrieval from ExperimentHub and local caching of the models and datasets used internally in orthos.' + license_file: LICENSE + diff --git a/recipes/bioconductor-orthosdata/post-link.sh b/recipes/bioconductor-orthosdata/post-link.sh new file mode 100644 index 0000000000000..5c3cfd2f32ffc --- /dev/null +++ b/recipes/bioconductor-orthosdata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "orthosdata-1.0.0" diff --git a/recipes/bioconductor-orthosdata/pre-unlink.sh b/recipes/bioconductor-orthosdata/pre-unlink.sh new file mode 100644 index 0000000000000..78d90840ebfb5 --- /dev/null +++ b/recipes/bioconductor-orthosdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ orthosData diff --git a/recipes/bioconductor-osat/meta.yaml b/recipes/bioconductor-osat/meta.yaml index a41d9a8ef09cc..8b31b07c069f0 100644 --- a/recipes/bioconductor-osat/meta.yaml +++ b/recipes/bioconductor-osat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "OSAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41b946e0e889d7756364cff5f9a3386e + md5: 64bba183cfa8a211960d891cb5ee3ddb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-osat", max_pin="x.x") }}' noarch: generic # Suggests: xtable, Biobase requirements: diff --git a/recipes/bioconductor-oscope/meta.yaml b/recipes/bioconductor-oscope/meta.yaml index a5f1f62cfab43..d854e94085c0f 100644 --- a/recipes/bioconductor-oscope/meta.yaml +++ b/recipes/bioconductor-oscope/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "Oscope" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fdee060dfcb4bd73e1e89a377abe73e + md5: 96a8fc6730b6d493d352d74032c4b3d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oscope", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' - r-base - r-cluster - r-testthat run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' - r-base - r-cluster - r-testthat diff --git a/recipes/bioconductor-otubase/build_failure.linux-64.yaml b/recipes/bioconductor-otubase/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ffb92d761f8f5 --- /dev/null +++ b/recipes/bioconductor-otubase/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 2466376a66b53bb6cdb3dff2c8ae7300a0ed3b25e36f88bb855a119a89b9d177 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [] 1.2s + conda-forge/linux-64 + conda-forge/noarch + bioconda/linux-64 100% + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gbioconda/linux-64 + [] 1.3s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.4s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 100% + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 + [] 1.5s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.6s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/noarch + [] 1.7s + conda-forge/linux-64 + conda-forge/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.8s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gconda-forge/noarch + [] 1.9s + conda-forge/linux-64 + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[0Gpkgs/r/noarch + pkgs/r/linux-64 + [] 2.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.4s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.5s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.6s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.7s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.8s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.9s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s + [2K[1A[2K[0Gconda-forge/linux-64 + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.6MB/s 0.0s + opt/conda/conda-bld/noarch 922.0 B @ 18.8MB/s 0.0s + [?25hTraceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test + environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, + File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env + display_actions(actions, index) + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions + actions['LINK'] = [index[d] for d in actions['LINK']] + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in + actions['LINK'] = [index[d] for d in actions['LINK']] + KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-otubase/meta.yaml b/recipes/bioconductor-otubase/meta.yaml index d46aa09d35d25..51975ccd38e1e 100644 --- a/recipes/bioconductor-otubase/meta.yaml +++ b/recipes/bioconductor-otubase/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "OTUbase" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ff077bed280afa9c1460747ad4bb96b + md5: 612c0f07995eb5cc0f753eb6750e5216 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-otubase", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-vegan run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-vegan test: diff --git a/recipes/bioconductor-outrider/meta.yaml b/recipes/bioconductor-outrider/meta.yaml index 1a290b5564a2c..7fb41ce9d207b 100644 --- a/recipes/bioconductor-outrider/meta.yaml +++ b/recipes/bioconductor-outrider/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "OUTRIDER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e41d4122f3ed2b2b7fbc9e73d0f5341 + md5: 92609d3ce486cdf55004d26887a9494d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-outrider", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bbmisc - r-data.table @@ -48,15 +49,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bbmisc - r-data.table diff --git a/recipes/bioconductor-outsplice/meta.yaml b/recipes/bioconductor-outsplice/meta.yaml index b8d74daa973f8..88b5efe5ba59d 100644 --- a/recipes/bioconductor-outsplice/meta.yaml +++ b/recipes/bioconductor-outsplice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "OutSplice" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 216bb720d2a43d5d264f25733e0dd546 + md5: 7a55735983a79681a2bbcd567c9f0c53 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-outsplice", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-repitools >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-repitools >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-repitools >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-repitools >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-oveseg/meta.yaml b/recipes/bioconductor-oveseg/meta.yaml index 6334a2389e884..9f062d2d0697a 100644 --- a/recipes/bioconductor-oveseg/meta.yaml +++ b/recipes/bioconductor-oveseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "OVESEG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3cc11546cd7fdf569be32319bbac34b4 + md5: 2a1ac203dcd19e6c511d4bcefa0cee45 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-oveseg", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-fdrtool - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-fdrtool - r-rcpp diff --git a/recipes/bioconductor-paa/meta.yaml b/recipes/bioconductor-paa/meta.yaml index 7c378000470d1..e433b71cba99c 100644 --- a/recipes/bioconductor-paa/meta.yaml +++ b/recipes/bioconductor-paa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "PAA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4be8a4102d0386d6a8ef5e446e538bd7 + md5: 4968ea3bfbaa5edd0e6d00dcbe93a6d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-paa", max_pin="x.x") }}' # Suggests: BiocStyle, RUnit, BiocGenerics, vsn # SystemRequirements: C++ software package Random Jungle requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-e1071 - r-gplots @@ -35,8 +36,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-e1071 - r-gplots diff --git a/recipes/bioconductor-packfinder/meta.yaml b/recipes/bioconductor-packfinder/meta.yaml index e097de4cffde0..f973e5d16efa5 100644 --- a/recipes/bioconductor-packfinder/meta.yaml +++ b/recipes/bioconductor-packfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "packFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1b5c25374c50cdd102cea61cf7739ce + md5: 8c2f41158644b4d04136910e0ce39af8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-packfinder", max_pin="x.x") }}' noarch: generic # Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-kmer run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-ape - r-base - r-kmer diff --git a/recipes/bioconductor-padma/meta.yaml b/recipes/bioconductor-padma/meta.yaml index a2324e45cd0db..b61afc3f54526 100644 --- a/recipes/bioconductor-padma/meta.yaml +++ b/recipes/bioconductor-padma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "padma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f47e277f616547846880f0f924f63e66 + md5: 126a8aec3057f8ccc5a435c5435adfc0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-padma", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot requirements: host: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-factominer run: - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-factominer test: diff --git a/recipes/bioconductor-padog/meta.yaml b/recipes/bioconductor-padog/meta.yaml index 9351472072933..a248a46b7416c 100644 --- a/recipes/bioconductor-padog/meta.yaml +++ b/recipes/bioconductor-padog/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "PADOG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2791538f9d0ad24c3373a42e750db060 + md5: ca2c1e477f0ef2d2be1eaf52570dd8c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-padog", max_pin="x.x") }}' noarch: generic # Suggests: doParallel, parallel requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-keggdzpathwaysgeo >=1.38.0,<1.39.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dorng - r-foreach - r-gsa - r-nlme run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-keggdzpathwaysgeo >=1.38.0,<1.39.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-dorng - r-foreach diff --git a/recipes/bioconductor-paeg1acdf/meta.yaml b/recipes/bioconductor-paeg1acdf/meta.yaml index f318eb8326b9d..83f68341ac443 100644 --- a/recipes/bioconductor-paeg1acdf/meta.yaml +++ b/recipes/bioconductor-paeg1acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "paeg1acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 73af974112051db0f715518393e84726 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-paeg1acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-paeg1aprobe/meta.yaml b/recipes/bioconductor-paeg1aprobe/meta.yaml index a274b700708aa..52fa2ca8579b2 100644 --- a/recipes/bioconductor-paeg1aprobe/meta.yaml +++ b/recipes/bioconductor-paeg1aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "paeg1aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 493fa1fc7b92a78c8114b65038113c42 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-paeg1aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pagerank/meta.yaml b/recipes/bioconductor-pagerank/meta.yaml index 88a28aebda42f..fadcf0f1bd68e 100644 --- a/recipes/bioconductor-pagerank/meta.yaml +++ b/recipes/bioconductor-pagerank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "pageRank" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95bbea12ddfe8b6f3e526c78defd4eaf + md5: 05578860ad3f7021d25c6c07953218ea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pagerank", max_pin="x.x") }}' noarch: generic # Suggests: bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools, GenomicFeatures, annotate requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - r-base - r-igraph run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - r-base - r-igraph test: diff --git a/recipes/bioconductor-pairadise/meta.yaml b/recipes/bioconductor-pairadise/meta.yaml index 076065bb143ad..da305a20a0c68 100644 --- a/recipes/bioconductor-pairadise/meta.yaml +++ b/recipes/bioconductor-pairadise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "PAIRADISE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a974fbe1fda2aafd380d6faac180347a + md5: 2a3889d2380363b7a9b0ee3c75ef0891 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pairadise", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-nloptr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-nloptr diff --git a/recipes/bioconductor-paircompviz/meta.yaml b/recipes/bioconductor-paircompviz/meta.yaml index 242d9a92a6680..1a78dfad94d52 100644 --- a/recipes/bioconductor-paircompviz/meta.yaml +++ b/recipes/bioconductor-paircompviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "paircompviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eca876e3442dd83dc7e355080a6e5af6 + md5: e9c57c7305e15062d9258019fed12f3e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-paircompviz", max_pin="x.x") }}' noarch: generic # Suggests: multcomp, reshape, rpart, plyr, xtable requirements: host: - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-pairedgsea/meta.yaml b/recipes/bioconductor-pairedgsea/meta.yaml index 31d687a75a195..f5f6ebb5140ba 100644 --- a/recipes/bioconductor-pairedgsea/meta.yaml +++ b/recipes/bioconductor-pairedgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "pairedGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f8f47e26a85154c5df37d0729db4c24d + md5: 591cbbc31b4eab5064ef39c4b8133fa5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pairedgsea", max_pin="x.x") }}' noarch: generic # Suggests: writexl, readxl, readr, rhdf5, msigdbr, plotly, testthat (>= 3.0.0), knitr, rmarkdown, covr, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-aggregation - r-base - r-ggplot2 run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dexseq >=1.46.0,<1.47.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-aggregation - r-base - r-ggplot2 diff --git a/recipes/bioconductor-pairkat/meta.yaml b/recipes/bioconductor-pairkat/meta.yaml index 8bdd341e56c06..88e9611ce00c4 100644 --- a/recipes/bioconductor-pairkat/meta.yaml +++ b/recipes/bioconductor-pairkat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "pairkat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 548c23a7fea8eec39dc6fd06b283ec76 + md5: 030b0f4ea6e9f71adf6769ca9b16cae0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pairkat", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, dplyr requirements: host: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-compquadform - r-data.table @@ -30,8 +31,8 @@ requirements: - r-magrittr - r-tibble run: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-compquadform - r-data.table diff --git a/recipes/bioconductor-pandar/meta.yaml b/recipes/bioconductor-pandar/meta.yaml index 66cf2a539d820..b750dee69940d 100644 --- a/recipes/bioconductor-pandar/meta.yaml +++ b/recipes/bioconductor-pandar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "pandaR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eae276fe37e113e2e860952b2004645c + md5: 203422d8a9df096677530f57bffe9e9c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pandar", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-ggplot2 - r-hexbin @@ -32,8 +33,8 @@ requirements: - r-reshape - r-runit run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-ggplot2 - r-hexbin diff --git a/recipes/bioconductor-panelcn.mops/meta.yaml b/recipes/bioconductor-panelcn.mops/meta.yaml index d436c6ae205e2..a1f76cb47c1ad 100644 --- a/recipes/bioconductor-panelcn.mops/meta.yaml +++ b/recipes/bioconductor-panelcn.mops/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "panelcn.mops" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a9626de33823bb9f8a22e83136a5ade8 + md5: c40de00a870c4b693e6312b7d2110b96 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panelcn.mops", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, RUnit, BiocGenerics requirements: host: - - 'bioconductor-cn.mops >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-cn.mops >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-cn.mops >=1.46.0,<1.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-cn.mops >=1.48.0,<1.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-panomir/meta.yaml b/recipes/bioconductor-panomir/meta.yaml index ca9c1e393db04..0ded484f43400 100644 --- a/recipes/bioconductor-panomir/meta.yaml +++ b/recipes/bioconductor-panomir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "PanomiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3aa1e186fd1ce598777d57f08c4e00e9 + md5: a8f96cdc267551107e69e8cb260a05c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panomir", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dplyr - r-forcats @@ -36,11 +37,11 @@ requirements: - r-tibble - r-withr run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-dplyr - r-forcats diff --git a/recipes/bioconductor-panp/meta.yaml b/recipes/bioconductor-panp/meta.yaml index cbfbb7effa540..88b59b7b344ae 100644 --- a/recipes/bioconductor-panp/meta.yaml +++ b/recipes/bioconductor-panp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "panp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f0193664c739a413e0bc97960f3e859d + md5: 1cc532873dbc4e2cde6c04ca995545db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panp", max_pin="x.x") }}' noarch: generic # Suggests: gcrma requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-panr/meta.yaml b/recipes/bioconductor-panr/meta.yaml index d4f06ff44235b..5a1a71d18d317 100644 --- a/recipes/bioconductor-panr/meta.yaml +++ b/recipes/bioconductor-panr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "PANR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a76063c60e0a92870203aa9b907281e1 + md5: accc5472b6656e95d885960d9f1ecee3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panr", max_pin="x.x") }}' noarch: generic # Suggests: snow requirements: host: - - 'bioconductor-reder >=2.4.0,<2.5.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' - r-base - r-igraph - r-mass - r-pvclust run: - - 'bioconductor-reder >=2.4.0,<2.5.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' - r-base - r-igraph - r-mass diff --git a/recipes/bioconductor-panther.db/meta.yaml b/recipes/bioconductor-panther.db/meta.yaml index 9d0ca87b10175..9f4277d05f21e 100644 --- a/recipes/bioconductor-panther.db/meta.yaml +++ b/recipes/bioconductor-panther.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.11" %} +{% set version = "1.0.12" %} {% set name = "PANTHER.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 561f6b164b27f6dc4287f0d7fd6bb8b3 + md5: edafd1c94f2f1cf3975f525fae7a9b83 build: - number: 4 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panther.db", max_pin="x.x") }}' noarch: generic # Suggests: RUnit,knitr,BiocStyle,rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-panther.db/post-link.sh b/recipes/bioconductor-panther.db/post-link.sh index b4e3a5abb373c..6801e59a4e786 100644 --- a/recipes/bioconductor-panther.db/post-link.sh +++ b/recipes/bioconductor-panther.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "panther.db-1.0.11" +installBiocDataPackage.sh "panther.db-1.0.12" diff --git a/recipes/bioconductor-panviz/meta.yaml b/recipes/bioconductor-panviz/meta.yaml index 6720e043d4792..96a8028875a67 100644 --- a/recipes/bioconductor-panviz/meta.yaml +++ b/recipes/bioconductor-panviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "PanViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a17196e1176705982077a84a995f6340 + md5: 5d5ced4ee7d68f57367aed30633f29e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-panviz", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, networkD3, requirements: diff --git a/recipes/bioconductor-parathyroidse/meta.yaml b/recipes/bioconductor-parathyroidse/meta.yaml index afd868a5c35f1..a43c027d7671f 100644 --- a/recipes/bioconductor-parathyroidse/meta.yaml +++ b/recipes/bioconductor-parathyroidse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "parathyroidSE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 055bda4d4376fcdec3bce484ec634117 + md5: e4d06f888feb4015273e20b14f8ee37a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-parathyroidse", max_pin="x.x") }}' noarch: generic # Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-parathyroidse/post-link.sh b/recipes/bioconductor-parathyroidse/post-link.sh index 0216c73790017..170c351577c93 100644 --- a/recipes/bioconductor-parathyroidse/post-link.sh +++ b/recipes/bioconductor-parathyroidse/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "parathyroidse-1.38.0" +installBiocDataPackage.sh "parathyroidse-1.40.0" diff --git a/recipes/bioconductor-pareg/build.sh b/recipes/bioconductor-pareg/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pareg/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pareg/meta.yaml b/recipes/bioconductor-pareg/meta.yaml new file mode 100644 index 0000000000000..b98c62126d92e --- /dev/null +++ b/recipes/bioconductor-pareg/meta.yaml @@ -0,0 +1,97 @@ +{% set version = "1.6.0" %} +{% set name = "pareg" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fef96a7ed5d753b6729186f4870f4283 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pareg", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, plotROC, PRROC, mgsa, topGO, msigdbr, betareg, fgsea, ComplexHeatmap, GGally, ggsignif, circlize, enrichplot, ggnewscale, tidyverse, cowplot, ggfittext, simplifyEnrichment, GSEABenchmarkeR, BiocParallel, ggupset, latex2exp, org.Hs.eg.db, GO.db +requirements: + host: + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - r-base + - r-devtools + - r-dofuture + - r-dorng + - r-dplyr + - r-foreach + - r-future + - r-ggplot2 + - r-ggraph + - r-ggrepel + - r-glue + - r-hms + - r-igraph + - r-keras + - r-logger + - r-magrittr + - r-matrix + - r-nloptr + - r-progress + - r-proxy + - r-purrr + - r-reticulate + - r-rlang + - r-stringr + - 'r-tensorflow >=2.2.0' + - 'r-tfprobability >=0.10.0' + - r-tibble + - r-tidygraph + - r-tidyr + run: + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - r-base + - r-devtools + - r-dofuture + - r-dorng + - r-dplyr + - r-foreach + - r-future + - r-ggplot2 + - r-ggraph + - r-ggrepel + - r-glue + - r-hms + - r-igraph + - r-keras + - r-logger + - r-magrittr + - r-matrix + - r-nloptr + - r-progress + - r-proxy + - r-purrr + - r-reticulate + - r-rlang + - r-stringr + - 'r-tensorflow >=2.2.0' + - 'r-tfprobability >=0.10.0' + - r-tibble + - r-tidygraph + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Pathway enrichment using a regularized regression approach' + description: 'Compute pathway enrichment scores while accounting for term-term relations. This package uses a regularized multiple linear regression to regress differential expression p-values obtained from multi-condition experiments on a pathway membership matrix. By doing so, it is able to incorporate additional biological knowledge into the enrichment analysis and to estimate pathway enrichment scores more robustly.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-parglms/meta.yaml b/recipes/bioconductor-parglms/meta.yaml index 72f49afd8f4d5..ddeebc825c183 100644 --- a/recipes/bioconductor-parglms/meta.yaml +++ b/recipes/bioconductor-parglms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "parglms" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0e74c1ca871ba837fb9329207a55c3e4 + md5: 0d6a2dc756389064b9be38e755e1a24b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-parglms", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges, gwascat, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-batchjobs - r-doparallel - r-foreach run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-batchjobs - r-doparallel diff --git a/recipes/bioconductor-parody/meta.yaml b/recipes/bioconductor-parody/meta.yaml index 87ce03a669d80..c39b7ed701f61 100644 --- a/recipes/bioconductor-parody/meta.yaml +++ b/recipes/bioconductor-parody/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "parody" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e329e9fd1626c3d05bd1f2cf7208f5cf + md5: b466cc7b30f33e1854daac921ec9dc87 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-parody", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, testthat, rmarkdown requirements: diff --git a/recipes/bioconductor-partcnv/build.sh b/recipes/bioconductor-partcnv/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-partcnv/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-partcnv/meta.yaml b/recipes/bioconductor-partcnv/meta.yaml new file mode 100644 index 0000000000000..b464c8fbd145d --- /dev/null +++ b/recipes/bioconductor-partcnv/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "partCNV" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e004f2129cbb1fe1e84e33cf223c06f6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-partcnv", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, rmarkdown, knitr, IRanges, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + - r-data.table + - r-depmixs4 + - r-magrittr + - r-seurat + run: + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + - r-data.table + - r-depmixs4 + - r-magrittr + - r-seurat +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Infer locally aneuploid cells using single cell RNA-seq data' + description: 'This package uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH).' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + diff --git a/recipes/bioconductor-partheenmetadata.db/meta.yaml b/recipes/bioconductor-partheenmetadata.db/meta.yaml index 6da9a7770c14e..174c5d3e8a5fe 100644 --- a/recipes/bioconductor-partheenmetadata.db/meta.yaml +++ b/recipes/bioconductor-partheenmetadata.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "PartheenMetaData.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1c9fd27e13a341b9aba9a235a67ce978 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-partheenmetadata.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pasilla/meta.yaml b/recipes/bioconductor-pasilla/meta.yaml index d1e60b9363b9a..cbe7571ac3d4a 100644 --- a/recipes/bioconductor-pasilla/meta.yaml +++ b/recipes/bioconductor-pasilla/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "pasilla" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a6abc62e6e4ddde42ee0269256ac8342 + md5: e1fbdd57136d8a29edd1e0164dc2412e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pasilla", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, BiocStyle, knitr +# Suggests: rmarkdown, BiocStyle, knitr, roxygen2 requirements: host: - - 'bioconductor-dexseq >=1.46.0,<1.47.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-dexseq >=1.46.0,<1.47.0' + - 'bioconductor-dexseq >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pasilla/post-link.sh b/recipes/bioconductor-pasilla/post-link.sh index 409a42d31ba3b..d7bfc5e712bc6 100644 --- a/recipes/bioconductor-pasilla/post-link.sh +++ b/recipes/bioconductor-pasilla/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pasilla-1.28.0" +installBiocDataPackage.sh "pasilla-1.30.0" diff --git a/recipes/bioconductor-pasillabamsubset/meta.yaml b/recipes/bioconductor-pasillabamsubset/meta.yaml index 1d6f3c2d878d3..a7095742aa73c 100644 --- a/recipes/bioconductor-pasillabamsubset/meta.yaml +++ b/recipes/bioconductor-pasillabamsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "pasillaBamSubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c80a6afcfb87c88e88e8c3c69e66e71 + md5: 8fd05eac2d37650e157871908cbaf306 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pasillabamsubset", max_pin="x.x") }}' noarch: generic # Suggests: pasilla requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pasillabamsubset/post-link.sh b/recipes/bioconductor-pasillabamsubset/post-link.sh index 70c9fa4bf3d2e..6e8d22f6eff32 100644 --- a/recipes/bioconductor-pasillabamsubset/post-link.sh +++ b/recipes/bioconductor-pasillabamsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pasillabamsubset-0.38.0" +installBiocDataPackage.sh "pasillabamsubset-0.40.0" diff --git a/recipes/bioconductor-pasillatranscriptexpr/meta.yaml b/recipes/bioconductor-pasillatranscriptexpr/meta.yaml index 28e7132908a6c..befc4ad24b21e 100644 --- a/recipes/bioconductor-pasillatranscriptexpr/meta.yaml +++ b/recipes/bioconductor-pasillatranscriptexpr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "PasillaTranscriptExpr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d5e8ec6f9ba14ca8da1565b8a2b0bac + md5: 7d1d8c852fff7d80c11e8ab79dae7487 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pasillatranscriptexpr", max_pin="x.x") }}' noarch: generic # Suggests: rtracklayer, BiocStyle, knitr, testthat requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pasillatranscriptexpr/post-link.sh b/recipes/bioconductor-pasillatranscriptexpr/post-link.sh index 8d9070d95d4c1..4bb80603c4361 100644 --- a/recipes/bioconductor-pasillatranscriptexpr/post-link.sh +++ b/recipes/bioconductor-pasillatranscriptexpr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pasillatranscriptexpr-1.28.0" +installBiocDataPackage.sh "pasillatranscriptexpr-1.30.0" diff --git a/recipes/bioconductor-past/meta.yaml b/recipes/bioconductor-past/meta.yaml index 519ae97444a6b..a2f50e875b09f 100644 --- a/recipes/bioconductor-past/meta.yaml +++ b/recipes/bioconductor-past/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "PAST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56e17729beeb8a5cbbed7c1a4bdce03a + md5: 9af26fa0c8f74a586f23905b9b2408c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-past", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-dplyr @@ -33,10 +34,10 @@ requirements: - r-iterators - r-rlang run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-path2ppi/meta.yaml b/recipes/bioconductor-path2ppi/meta.yaml index 165179a2c5498..0153df53f02fd 100644 --- a/recipes/bioconductor-path2ppi/meta.yaml +++ b/recipes/bioconductor-path2ppi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "Path2PPI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98206bf5ffb337ead19023c0370d1abd + md5: 4fcd4d73b05e2167ecdfb79aadfe8722 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-path2ppi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle requirements: diff --git a/recipes/bioconductor-pathifier/meta.yaml b/recipes/bioconductor-pathifier/meta.yaml index 6d2ce71cd171d..818306e1cb392 100644 --- a/recipes/bioconductor-pathifier/meta.yaml +++ b/recipes/bioconductor-pathifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "pathifier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ec39c0e53442653e330922de4718ebde + md5: 344576d367c4da46c28918be3de3f65e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathifier", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-pathnet/meta.yaml b/recipes/bioconductor-pathnet/meta.yaml index cfc4a76e93bd0..a65c695e30d6d 100644 --- a/recipes/bioconductor-pathnet/meta.yaml +++ b/recipes/bioconductor-pathnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "PathNet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34979e84ad0538dcde4f4651440e271c + md5: 13ca247b602840ebfaea9f1e9a5839aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathnet", max_pin="x.x") }}' noarch: generic # Suggests: PathNetData, RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-pathnetdata/meta.yaml b/recipes/bioconductor-pathnetdata/meta.yaml index e043fc729b5d1..cea53f8bb3615 100644 --- a/recipes/bioconductor-pathnetdata/meta.yaml +++ b/recipes/bioconductor-pathnetdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "PathNetData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20449e0dcf262e4f6c1f7e2521a00370 + md5: d72e955b33c92f1703ae072ec788c1d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathnetdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pathnetdata/post-link.sh b/recipes/bioconductor-pathnetdata/post-link.sh index fb162ea9a115b..c51f9a25a4d1a 100644 --- a/recipes/bioconductor-pathnetdata/post-link.sh +++ b/recipes/bioconductor-pathnetdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pathnetdata-1.36.0" +installBiocDataPackage.sh "pathnetdata-1.38.0" diff --git a/recipes/bioconductor-pathostat/meta.yaml b/recipes/bioconductor-pathostat/meta.yaml index 091743b6f0830..adc375d616f15 100644 --- a/recipes/bioconductor-pathostat/meta.yaml +++ b/recipes/bioconductor-pathostat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "PathoStat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ea0b93420abe012159eb546e13e1c6b + md5: fd391aaf46df86a1608019bd2454d67f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathostat", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, testthat requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-ape - r-base - r-corpcor @@ -52,12 +53,12 @@ requirements: - r-webshot - r-xml run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-ape - r-base - r-corpcor diff --git a/recipes/bioconductor-pathrender/meta.yaml b/recipes/bioconductor-pathrender/meta.yaml index be81c5a910394..8f6884f8bfe86 100644 --- a/recipes/bioconductor-pathrender/meta.yaml +++ b/recipes/bioconductor-pathrender/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "pathRender" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16706f4d1fe0a7f576b59b689c67d608 + md5: 0796d30e763067880a67ed2435d2ac26 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathrender", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-cmap >=1.15.0,<1.16.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - 'bioconductor-cmap >=1.15.0,<1.16.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-rcolorbrewer test: diff --git a/recipes/bioconductor-pathview/meta.yaml b/recipes/bioconductor-pathview/meta.yaml index fe5c87f5c51fc..939a3d3b6bded 100644 --- a/recipes/bioconductor-pathview/meta.yaml +++ b/recipes/bioconductor-pathview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "pathview" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d7f0911b44b34964b38a1e16e2dc7f90 + md5: 5e17ceee29bb13083a2b11be28edacb0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathview", max_pin="x.x") }}' noarch: generic # Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-png - r-xml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-png - r-xml diff --git a/recipes/bioconductor-pathwaypca/meta.yaml b/recipes/bioconductor-pathwaypca/meta.yaml index becc41189d541..caaad95452bb9 100644 --- a/recipes/bioconductor-pathwaypca/meta.yaml +++ b/recipes/bioconductor-pathwaypca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "pathwayPCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a75a06c3b8dd34524470a4bc72221e9 + md5: 100ae90b68c015f8e344da1d3a2a4863 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathwaypca", max_pin="x.x") }}' noarch: generic # Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse requirements: diff --git a/recipes/bioconductor-paxtoolsr/meta.yaml b/recipes/bioconductor-paxtoolsr/meta.yaml index 6b4a2e63d594a..230c75036cd40 100644 --- a/recipes/bioconductor-paxtoolsr/meta.yaml +++ b/recipes/bioconductor-paxtoolsr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "paxtoolsr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c281fec96db1800644742f7e19d1c17 + md5: 2ed785fb7d7859ff53d143baba8ff73d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-paxtoolsr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, formatR, rmarkdown, RColorBrewer, foreach, doSNOW, parallel, org.Hs.eg.db, clusterProfiler # SystemRequirements: Java (>= 1.6) diff --git a/recipes/bioconductor-pcaexplorer/meta.yaml b/recipes/bioconductor-pcaexplorer/meta.yaml index 1c2db1a771ac3..9c16c5e3fce55 100644 --- a/recipes/bioconductor-pcaexplorer/meta.yaml +++ b/recipes/bioconductor-pcaexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.26.1" %} +{% set version = "2.28.0" %} {% set name = "pcaExplorer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd855f02c1ab744f8e2ab682bae0df19 + md5: 622f43cef60e783c51d59ed8624019d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcaexplorer", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-base64enc - r-dt @@ -53,18 +54,18 @@ requirements: - r-threejs - r-tidyr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-base64enc - r-dt diff --git a/recipes/bioconductor-pcamethods/meta.yaml b/recipes/bioconductor-pcamethods/meta.yaml index 38c796c6de0cb..daa71eb6ce889 100644 --- a/recipes/bioconductor-pcamethods/meta.yaml +++ b/recipes/bioconductor-pcamethods/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.92.0" %} +{% set version = "1.94.0" %} {% set name = "pcaMethods" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 265adae0e55769ebc4294914cb26b6db + md5: a989ad925a9852f55eb5e4d16d1529d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcamethods", max_pin="x.x") }}' # Suggests: matrixStats, lattice, ggplot2 # SystemRequirements: Rcpp requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-mass - 'r-rcpp >=0.11.3' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-mass - 'r-rcpp >=0.11.3' diff --git a/recipes/bioconductor-pcan/meta.yaml b/recipes/bioconductor-pcan/meta.yaml index d9970c2c400cd..47cee63d9eee6 100644 --- a/recipes/bioconductor-pcan/meta.yaml +++ b/recipes/bioconductor-pcan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "PCAN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 33693be38c25d3ebb5ebb1bc7069a724 + md5: 94596d43854d98aee2e6da198147772b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcan", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-pcatools/meta.yaml b/recipes/bioconductor-pcatools/meta.yaml index 1e4eac16f8ce3..eabd07294dc9a 100644 --- a/recipes/bioconductor-pcatools/meta.yaml +++ b/recipes/bioconductor-pcatools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "PCAtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f6cda4da875b51f599a56738386685b + md5: 316c693617402890169745a37dfaead6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcatools", max_pin="x.x") }}' # Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - r-base - r-bh - r-cowplot @@ -39,11 +40,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - r-base - r-bh - r-cowplot diff --git a/recipes/bioconductor-pchicdata/meta.yaml b/recipes/bioconductor-pchicdata/meta.yaml index 983a1d3ca9aff..ab00c43103068 100644 --- a/recipes/bioconductor-pchicdata/meta.yaml +++ b/recipes/bioconductor-pchicdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "PCHiCdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7048c278620231f478014314a1a16e74 + md5: 8791902075a44ae03c0366150aa3f61e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pchicdata", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-chicago >=1.28.0,<1.29.0' + - 'bioconductor-chicago >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-chicago >=1.28.0,<1.29.0' + - 'bioconductor-chicago >=1.30.0,<1.31.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pchicdata/post-link.sh b/recipes/bioconductor-pchicdata/post-link.sh index 03b0822345427..3ab10ccd183c5 100644 --- a/recipes/bioconductor-pchicdata/post-link.sh +++ b/recipes/bioconductor-pchicdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pchicdata-1.28.0" +installBiocDataPackage.sh "pchicdata-1.30.0" diff --git a/recipes/bioconductor-pcxn/meta.yaml b/recipes/bioconductor-pcxn/meta.yaml index 1d620be98fc79..ae4e85ca7141e 100644 --- a/recipes/bioconductor-pcxn/meta.yaml +++ b/recipes/bioconductor-pcxn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "pcxn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e984b3bb93ac67438338e968c76556fe + md5: bc66fe53111b80e8978344ddc59eff6f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcxn", max_pin="x.x") }}' noarch: generic # Suggests: igraph, annotate, org.Hs.eg.db requirements: host: - - 'bioconductor-pcxndata >=2.22.0,<2.23.0' + - 'bioconductor-pcxndata >=2.24.0,<2.25.0' - r-base - r-pheatmap run: - - 'bioconductor-pcxndata >=2.22.0,<2.23.0' + - 'bioconductor-pcxndata >=2.24.0,<2.25.0' - r-base - r-pheatmap test: diff --git a/recipes/bioconductor-pcxndata/meta.yaml b/recipes/bioconductor-pcxndata/meta.yaml index a2411936baeab..edbfeb11dbe00 100644 --- a/recipes/bioconductor-pcxndata/meta.yaml +++ b/recipes/bioconductor-pcxndata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "pcxnData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0d340cd964638e91faf2181216c06159 + md5: 7814b1a6f5dbd08e71df1e92ea4328f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pcxndata", max_pin="x.x") }}' noarch: generic # Suggests: pcxn requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pcxndata/post-link.sh b/recipes/bioconductor-pcxndata/post-link.sh index fba32530b08c6..2ff975463bbe2 100644 --- a/recipes/bioconductor-pcxndata/post-link.sh +++ b/recipes/bioconductor-pcxndata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pcxndata-2.22.0" +installBiocDataPackage.sh "pcxndata-2.24.0" diff --git a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml index 7d05a2bb3b616..d5211fafad4a4 100644 --- a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml +++ b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.4" %} {% set name = "pd.081229.hg18.promoter.medip.hx1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f3c240fa0d4503e94047be5ee323856b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.081229.hg18.promoter.medip.hx1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml index bf32a1b76db93..608d949b2763d 100644 --- a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.8.1" %} {% set name = "pd.2006.07.18.hg18.refseq.promoter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 00838332d75b82d212078a9957f495df build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.2006.07.18.hg18.refseq.promoter", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml index 4d04d0a6c9cc7..fa0edeb2bdc22 100644 --- a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.2006.07.18.mm8.refseq.promoter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 084b0a6759fd96d1bc775dd4c66c42b0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.2006.07.18.mm8.refseq.promoter", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml index 2f905ead37d08..fc6ff228ae8d5 100644 --- a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.2006.10.31.rn34.refseq.promoter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ab5bb767ad29b213e5a969a5fc51ee7d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.2006.10.31.rn34.refseq.promoter", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ag/meta.yaml b/recipes/bioconductor-pd.ag/meta.yaml index 40eb2c4d96f2c..28b10f01dcf8b 100644 --- a/recipes/bioconductor-pd.ag/meta.yaml +++ b/recipes/bioconductor-pd.ag/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ag" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 21fb288536568ff010ad4847b671f9d6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ag", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml b/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml index a57f85a752c91..626b8d0f92db1 100644 --- a/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.aragene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ff87a0793fd4b713c4a45b6c1d4a4977 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.aragene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml b/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml index 56468db0c0fb1..5393c826fa919 100644 --- a/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.aragene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 828ad790eb2495e396d7fcd9bcbf9133 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.aragene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.atdschip.tiling/meta.yaml b/recipes/bioconductor-pd.atdschip.tiling/meta.yaml index 033ae995d48ad..998de9d485df6 100644 --- a/recipes/bioconductor-pd.atdschip.tiling/meta.yaml +++ b/recipes/bioconductor-pd.atdschip.tiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "pd.atdschip.tiling" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a38ac90ece38e2e9f980966194865fe0 + md5: a81ffdc7dfb8eb04e09ec133db77d0d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.atdschip.tiling", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - 'r-rsqlite >=0.10.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - 'r-rsqlite >=0.10.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.atdschip.tiling/post-link.sh b/recipes/bioconductor-pd.atdschip.tiling/post-link.sh index 7f8b5f2fb87ff..3b973708641a2 100644 --- a/recipes/bioconductor-pd.atdschip.tiling/post-link.sh +++ b/recipes/bioconductor-pd.atdschip.tiling/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pd.atdschip.tiling-0.38.0" +installBiocDataPackage.sh "pd.atdschip.tiling-0.40.0" diff --git a/recipes/bioconductor-pd.ath1.121501/meta.yaml b/recipes/bioconductor-pd.ath1.121501/meta.yaml index 3b73d0a793e9b..994ab7c1fec7b 100644 --- a/recipes/bioconductor-pd.ath1.121501/meta.yaml +++ b/recipes/bioconductor-pd.ath1.121501/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ath1.121501" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d7ed8640f0deac552e0083a091e72a72 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ath1.121501", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.barley1/meta.yaml b/recipes/bioconductor-pd.barley1/meta.yaml index fa7241a0434e7..de7dce84ec276 100644 --- a/recipes/bioconductor-pd.barley1/meta.yaml +++ b/recipes/bioconductor-pd.barley1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.barley1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b8d11f5ad42e75f7a91931b46d449c1a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.barley1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml index 6b8ebc175bfd3..4d35be7142cfe 100644 --- a/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bovgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6e9747d13aee7825722562ccc49ad35f build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.bovgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml index cfc6be91851e0..8ff60cbe49df0 100644 --- a/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bovgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 342246c0a76755fcca458cd723b3e98e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.bovgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bovine/meta.yaml b/recipes/bioconductor-pd.bovine/meta.yaml index 3aad529bd54ad..74ee2b7d78929 100644 --- a/recipes/bioconductor-pd.bovine/meta.yaml +++ b/recipes/bioconductor-pd.bovine/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bovine" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6c7026dba53b54b547b1f1e135d043b3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.bovine", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.bsubtilis/meta.yaml b/recipes/bioconductor-pd.bsubtilis/meta.yaml index cb55649e8b54a..a22e19c9d4fdf 100644 --- a/recipes/bioconductor-pd.bsubtilis/meta.yaml +++ b/recipes/bioconductor-pd.bsubtilis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.bsubtilis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2261d8b0ec178beb432d71eafd90ec9a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.bsubtilis", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml index 2d25076d471e1..be8e5256dd995 100644 --- a/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cangene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a39d6378193e3f7d31a7210f6766eaf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cangene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml index 99d7bd3b258ba..a37c378d3bfbc 100644 --- a/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cangene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 946074601e7bee72f3b3dd6ae6b3bc33 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cangene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.canine.2/meta.yaml b/recipes/bioconductor-pd.canine.2/meta.yaml index 34721787008bd..41ddf9797e74f 100644 --- a/recipes/bioconductor-pd.canine.2/meta.yaml +++ b/recipes/bioconductor-pd.canine.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.canine.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bc918d1953a3c7ac7168b60a53405a93 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.canine.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.canine/meta.yaml b/recipes/bioconductor-pd.canine/meta.yaml index 888a7d729b6b8..e825b40089dc5 100644 --- a/recipes/bioconductor-pd.canine/meta.yaml +++ b/recipes/bioconductor-pd.canine/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.canine" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5b40fe9e40d0b7f36d338e413d121ba7 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.canine", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.celegans/meta.yaml b/recipes/bioconductor-pd.celegans/meta.yaml index cdd01dc0395d6..c905fedbbd292 100644 --- a/recipes/bioconductor-pd.celegans/meta.yaml +++ b/recipes/bioconductor-pd.celegans/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.celegans" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b90ea2e071522bb340c103a1c8270205 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.celegans", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.charm.hg18.example/meta.yaml b/recipes/bioconductor-pd.charm.hg18.example/meta.yaml index eb3462223a211..86ae0af9f5bd9 100644 --- a/recipes/bioconductor-pd.charm.hg18.example/meta.yaml +++ b/recipes/bioconductor-pd.charm.hg18.example/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.4" %} {% set name = "pd.charm.hg18.example" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e201d4281a23c202f57bae1135e226b4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.charm.hg18.example", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chicken/meta.yaml b/recipes/bioconductor-pd.chicken/meta.yaml index ad15c7b0268ee..8a7c80e514a6c 100644 --- a/recipes/bioconductor-pd.chicken/meta.yaml +++ b/recipes/bioconductor-pd.chicken/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chicken" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: af79b6d0910621910e72ea374499e5eb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.chicken", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml index 9f9eb85707463..566afb7f346b2 100644 --- a/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chigene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e37cb047678fabb1801109d4efd16773 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.chigene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml index ad75c72b6f078..8db3bb63df879 100644 --- a/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chigene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bec602b45961607f5a4571977d54e015 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.chigene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml b/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml index 03db8e8c462f9..839f379c0b0a9 100644 --- a/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chogene.2.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 641718e3d172838185a200bac3d32433 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.chogene.2.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml b/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml index ae06030e3c7d1..5a6d320121240 100644 --- a/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.chogene.2.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ed25825e58a514cdde70b961bce9b4d7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.chogene.2.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.citrus/meta.yaml b/recipes/bioconductor-pd.citrus/meta.yaml index 3252ab6e7afaa..ff50b6ed856a3 100644 --- a/recipes/bioconductor-pd.citrus/meta.yaml +++ b/recipes/bioconductor-pd.citrus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.citrus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dee9b3298b84e7dd5152f48ad449b15a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.citrus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.d.human/meta.yaml b/recipes/bioconductor-pd.clariom.d.human/meta.yaml index a81580f52c92e..69c689cf4964b 100644 --- a/recipes/bioconductor-pd.clariom.d.human/meta.yaml +++ b/recipes/bioconductor-pd.clariom.d.human/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.d.human" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9d3505af53cc7c99980f29c527f0f37d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.d.human", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml index 5379cb80b4589..aa251a19d8271 100644 --- a/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.human.ht" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 90f910bea1b1aeb550a3f1bdd91d1a06 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.human.ht", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.human/meta.yaml b/recipes/bioconductor-pd.clariom.s.human/meta.yaml index 9513c52802345..883abafec76d4 100644 --- a/recipes/bioconductor-pd.clariom.s.human/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.human/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.human" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 797afe8a6a8041453a34ced3cce34884 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.human", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml index f2d3116b4cf5f..01a66173dfb16 100644 --- a/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.mouse.ht" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9cb6f77cf9666a0d54e1eacb904fd57c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.mouse.ht", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml b/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml index 6ec762255afa7..6339960068e70 100644 --- a/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.mouse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e3e4ce2b22a78faf525dd6c0c0b2a42d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.mouse", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml index c24c95ff7c0bc..057c509ee1c90 100644 --- a/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.rat.ht" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: be901eb9e8830f3e5bedf154189a3743 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.rat.ht", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.clariom.s.rat/meta.yaml b/recipes/bioconductor-pd.clariom.s.rat/meta.yaml index 36fe6e688e28b..92289bca2dfa0 100644 --- a/recipes/bioconductor-pd.clariom.s.rat/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.rat/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.rat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: be464b3eaea8eb8bdbcca6047fce4dea build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.rat", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cotton/meta.yaml b/recipes/bioconductor-pd.cotton/meta.yaml index a8d90c4caaaa5..b086689a2b42f 100644 --- a/recipes/bioconductor-pd.cotton/meta.yaml +++ b/recipes/bioconductor-pd.cotton/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cotton" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 78c408902bcefb8c695119767534b393 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cotton", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml index 3669b80f76118..63fe0e2e116cf 100644 --- a/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyngene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 784fac6cc92a0fe46dae32c9b737812a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cyngene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml index 55402f20e119c..ee76fadc3b263 100644 --- a/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyngene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a6217267e3e08a15f70c600918c7d4f6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cyngene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml index 0a8b22e70c70b..9862258a4d044 100644 --- a/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyrgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 63228c07d3d16d6c62e9c0e83f10a855 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cyrgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml index 38e8eeda3855f..e0cf4deb6049c 100644 --- a/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cyrgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dbe3bb580b96aaddcc597de45159320d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cyrgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.cytogenetics.array/meta.yaml b/recipes/bioconductor-pd.cytogenetics.array/meta.yaml index 4b79cff1b026a..cc6d19032f9c6 100644 --- a/recipes/bioconductor-pd.cytogenetics.array/meta.yaml +++ b/recipes/bioconductor-pd.cytogenetics.array/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.cytogenetics.array" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8c359ff56a9a558d370dc9a6a54218e0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.cytogenetics.array", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml b/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml index 39c4aa15c6cd8..00cff01593c5b 100644 --- a/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drogene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 67f92a97a5b78a95693edfdd32b67e93 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.drogene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml b/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml index 24c8e44762b4f..3f2c2a0e4aea8 100644 --- a/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drogene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5c63236ea91390d49dbabea63a48f0a2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.drogene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drosgenome1/meta.yaml b/recipes/bioconductor-pd.drosgenome1/meta.yaml index f642da5de5c9d..e6a9cb0bbd747 100644 --- a/recipes/bioconductor-pd.drosgenome1/meta.yaml +++ b/recipes/bioconductor-pd.drosgenome1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drosgenome1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 59c1a37a7d6a43fc70ff8756bf1195ef build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.drosgenome1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.drosophila.2/meta.yaml b/recipes/bioconductor-pd.drosophila.2/meta.yaml index da85a23a63ad9..ce040c054161a 100644 --- a/recipes/bioconductor-pd.drosophila.2/meta.yaml +++ b/recipes/bioconductor-pd.drosophila.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.drosophila.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ddb821e35e722af8dcf0807c6da4fac1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.drosophila.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.e.coli.2/meta.yaml b/recipes/bioconductor-pd.e.coli.2/meta.yaml index b6c8de0807693..65befa3aa9ca4 100644 --- a/recipes/bioconductor-pd.e.coli.2/meta.yaml +++ b/recipes/bioconductor-pd.e.coli.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.e.coli.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9176faa60a0c252a815b2a74d2f63dd4 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.e.coli.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ecoli.asv2/meta.yaml b/recipes/bioconductor-pd.ecoli.asv2/meta.yaml index 77f423303b8d9..9bff540ced298 100644 --- a/recipes/bioconductor-pd.ecoli.asv2/meta.yaml +++ b/recipes/bioconductor-pd.ecoli.asv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ecoli.asv2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d789ddf5a178a9a50c5587ee3ab294a4 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ecoli.asv2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ecoli/meta.yaml b/recipes/bioconductor-pd.ecoli/meta.yaml index 735960ab3f2ee..faee4d2687af3 100644 --- a/recipes/bioconductor-pd.ecoli/meta.yaml +++ b/recipes/bioconductor-pd.ecoli/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ecoli" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 077e91b2567a32780305f0fb6b126fe9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ecoli", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml b/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml index 01ce29cf5e66c..dea66c5327058 100644 --- a/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.elegene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b6110c58d5964703c7117e5e0668c901 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.elegene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml b/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml index b0c35c061c975..cf32b4ff695a2 100644 --- a/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.elegene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1dbe166ea347a5a7e240db925d2081c7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.elegene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml index 0d4b8edc223b8..2ec09700424d3 100644 --- a/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.equgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3448f36fdb899f04702be37ffab4c4c7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.equgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml index 1fa43fce2724e..f5976ac239916 100644 --- a/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.equgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bed32525513ce25f14d433ce805e7d6c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.equgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml index 28de8519985b6..fcc901394bc1c 100644 --- a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml +++ b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.feinberg.hg18.me.hx1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b6eeaf79671bab6f597965009516ce57 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.feinberg.hg18.me.hx1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml index 53ddd0a4744fd..941ef51cff169 100644 --- a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml +++ b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.3" %} {% set name = "pd.feinberg.mm8.me.hx1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7332102b69fc9ee087f52d3cdc311d00 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.feinberg.mm8.me.hx1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.7-1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml index 4b73bb1bf19c8..96ca01bb821b7 100644 --- a/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.felgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b7ac0a5cbde5f248aac5d0a7422bd88d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.felgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml index cd2d1ae2be574..aa2ec52c8c490 100644 --- a/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.felgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 734807a7f3608f6c44c76df7eee04c99 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.felgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml b/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml index 400177cbda04e..aac9805b9a463 100644 --- a/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.fingene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b79e4f8a52cad3b62e32401bbe74603d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.fingene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml b/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml index 9d7da08a16f50..543282bb74fc8 100644 --- a/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.fingene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 29030b14a0e8f8073874fb694a8c0c09 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.fingene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml b/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml index 3822c217acbf6..a9f3b15e3ee6d 100644 --- a/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml +++ b/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.genomewidesnp.5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d02255c861e82fca6a7445ada0c69e5d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.genomewidesnp.5", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml b/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml index 7f1c3bc2d2fbd..b6b0437fd72fd 100644 --- a/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml +++ b/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.genomewidesnp.6" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6e5369234e251c763f4f6c0220fbcb0c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.genomewidesnp.6", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml index c4286326c613f..d1840016e0d28 100644 --- a/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.guigene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 29fe31499931836af72ddd0c7d06acfa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.guigene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml index 189178fecf6df..6c1aedcc5bf9d 100644 --- a/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.guigene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aa3e0389c596a3676322104de5ad2358 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.guigene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hc.g110/meta.yaml b/recipes/bioconductor-pd.hc.g110/meta.yaml index 930ada7cf2017..dce97b5d9dd19 100644 --- a/recipes/bioconductor-pd.hc.g110/meta.yaml +++ b/recipes/bioconductor-pd.hc.g110/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hc.g110" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5c5418c588ed28e2fa088c7952c48b91 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hc.g110", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.focus/meta.yaml b/recipes/bioconductor-pd.hg.focus/meta.yaml index d8c330ad4bc2e..07333501d804f 100644 --- a/recipes/bioconductor-pd.hg.focus/meta.yaml +++ b/recipes/bioconductor-pd.hg.focus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.focus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a89f344ae7ff8061a8e7968f155f4bcf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.focus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml b/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml index 3f747cf51c252..7c7d03a5cbfbd 100644 --- a/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133.plus.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8a87aa63c04e84266962bdde5226c06c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133.plus.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133a.2/meta.yaml b/recipes/bioconductor-pd.hg.u133a.2/meta.yaml index 506d65b0d49ac..aa934add79651 100644 --- a/recipes/bioconductor-pd.hg.u133a.2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a7941473bf081831fad4f4412023d9ee build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133a.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml b/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml index 9d54bcf7d86db..966e51ee906c8 100644 --- a/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a.tag" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e090383098d6e1062b290889fba065d5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133a.tag", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133a/meta.yaml b/recipes/bioconductor-pd.hg.u133a/meta.yaml index 92258642e435e..fd20c37e93ead 100644 --- a/recipes/bioconductor-pd.hg.u133a/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 05b4521f65ab294a5040a0c60198d22c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u133b/meta.yaml b/recipes/bioconductor-pd.hg.u133b/meta.yaml index 792faa79356bb..4bfe9bab4a6e3 100644 --- a/recipes/bioconductor-pd.hg.u133b/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c5eac82ad7480571b9f2b442b4a8faa6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u219/meta.yaml b/recipes/bioconductor-pd.hg.u219/meta.yaml index 03cab68e7f700..f55dc3f703be2 100644 --- a/recipes/bioconductor-pd.hg.u219/meta.yaml +++ b/recipes/bioconductor-pd.hg.u219/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u219" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dab073d315af47ff3001c72a6d1e7972 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u219", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95a/meta.yaml b/recipes/bioconductor-pd.hg.u95a/meta.yaml index 0942bd87f9d52..e66160602d507 100644 --- a/recipes/bioconductor-pd.hg.u95a/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a9ad7d6a085e0e3ed7623902e7810da0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95av2/meta.yaml b/recipes/bioconductor-pd.hg.u95av2/meta.yaml index 67a80141c2fe7..95848bb127f5f 100644 --- a/recipes/bioconductor-pd.hg.u95av2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95av2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95av2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3a4182b529bc07ec91277a95b1462468 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95av2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95b/meta.yaml b/recipes/bioconductor-pd.hg.u95b/meta.yaml index 5c34719af06f1..8d252d62d20d3 100644 --- a/recipes/bioconductor-pd.hg.u95b/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a7f10f91e920e191c5009fac8ca79c24 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95c/meta.yaml b/recipes/bioconductor-pd.hg.u95c/meta.yaml index e56011d16a928..b498166f902ea 100644 --- a/recipes/bioconductor-pd.hg.u95c/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95c/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95c" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 85655bf7a9ecd7aaa867e05899c5e3e4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95c", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95d/meta.yaml b/recipes/bioconductor-pd.hg.u95d/meta.yaml index 3dacf5a5cc3c1..ee978c70f173e 100644 --- a/recipes/bioconductor-pd.hg.u95d/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95d/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95d" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 946701ecfc9cccb46aaeb57a4d6fe1c5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95d", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg.u95e/meta.yaml b/recipes/bioconductor-pd.hg.u95e/meta.yaml index cdac7d0b9bab1..51b85127f3579 100644 --- a/recipes/bioconductor-pd.hg.u95e/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95e/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95e" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9295e2fd1b4be6ff58477ea5a5de45ee build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95e", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml b/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml index fcd4a33ca8f27..c94697cfd3954 100644 --- a/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml +++ b/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hg18.60mer.expr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ee8d3813f74edce4e796933aa63999fb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hg18.60mer.expr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml index 209d6f26bb27b..f8c8caeeabca3 100644 --- a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml +++ b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.hg.u133.plus.pm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5b1c3dd0ab3f8b21154982c197512a7c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ht.hg.u133.plus.pm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml b/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml index a599fd6dbd8db..10d4330dd368f 100644 --- a/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml +++ b/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.hg.u133a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 80a82f43083f95e1e9f5e2e2da2e288e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ht.hg.u133a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ht.mg.430a/meta.yaml b/recipes/bioconductor-pd.ht.mg.430a/meta.yaml index d40943fa17101..0ffa3f528e690 100644 --- a/recipes/bioconductor-pd.ht.mg.430a/meta.yaml +++ b/recipes/bioconductor-pd.ht.mg.430a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.mg.430a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 65ea4fae22d21ad70998ba3ea034dcc0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ht.mg.430a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hta.2.0/meta.yaml b/recipes/bioconductor-pd.hta.2.0/meta.yaml index 96fc7cc93730e..7e82318382efb 100644 --- a/recipes/bioconductor-pd.hta.2.0/meta.yaml +++ b/recipes/bioconductor-pd.hta.2.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.2" %} {% set name = "pd.hta.2.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8e13f85ece49c38da73eaf7b2247f5f0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hta.2.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hu6800/meta.yaml b/recipes/bioconductor-pd.hu6800/meta.yaml index 7dc594ce3fabe..9cb8265192e77 100644 --- a/recipes/bioconductor-pd.hu6800/meta.yaml +++ b/recipes/bioconductor-pd.hu6800/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.hu6800" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9a3a3edde6d6f31b9e90dc32aa68875d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hu6800", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml b/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml index a741e0a6c9308..92f4d90dcf4f9 100644 --- a/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml +++ b/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.huex.1.0.st.v2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f4c4836c53447890b75b012efbdef3e9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.huex.1.0.st.v2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml index 64e47c869f52a..a6b0f80043946 100644 --- a/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.1.0.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8cb24c351aee5bf216180e4b19742506 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.1.0.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml index ea64270d668c8..bc8bf2b9c2ee4 100644 --- a/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.1.1.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7a17ee4f7d258792be1d21be7d03deb0 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.1.1.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml b/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml index 409673e5b749a..aded0828efe02 100644 --- a/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.2.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e484209aa0c2a839c3445d91c1a799ce build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.2.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml b/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml index b4e55987dadbe..4ba83c112fde7 100644 --- a/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.2.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 164227f10b87f87059e4ae27b40f5238 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.2.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.maize/meta.yaml b/recipes/bioconductor-pd.maize/meta.yaml index 08e4a585a46d8..6acdd12194b41 100644 --- a/recipes/bioconductor-pd.maize/meta.yaml +++ b/recipes/bioconductor-pd.maize/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.maize" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a1689518c8525d3dfa97e870f90b7a7b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.maize", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml b/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml index 6ad3366094538..d662313ff247e 100644 --- a/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml +++ b/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping250k.nsp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2786d00e1d621a9c415a599b4afe838b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mapping250k.nsp", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping250k.sty/meta.yaml b/recipes/bioconductor-pd.mapping250k.sty/meta.yaml index 04ae6d0f76244..431d2f563a670 100644 --- a/recipes/bioconductor-pd.mapping250k.sty/meta.yaml +++ b/recipes/bioconductor-pd.mapping250k.sty/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping250k.sty" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0db5992855eaf9b8f61f8bc2e57ef347 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mapping250k.sty", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml b/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml index 8453b2010cf8c..22b5b5394c56e 100644 --- a/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml +++ b/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping50k.hind240" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 83615dcb01eb381f0c69e07504809094 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mapping50k.hind240", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml b/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml index f0ac8da648f4f..351f1e536040b 100644 --- a/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml +++ b/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping50k.xba240" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eb0f9250fe0d7b590ca9938fee88f2e7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mapping50k.xba240", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.margene.1.0.st/meta.yaml b/recipes/bioconductor-pd.margene.1.0.st/meta.yaml index 586b5883ac30e..6300298e4726a 100644 --- a/recipes/bioconductor-pd.margene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.margene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.margene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f670b192e4b453f13bb7cae154b5de42 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.margene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.margene.1.1.st/meta.yaml b/recipes/bioconductor-pd.margene.1.1.st/meta.yaml index 55ffdd6dfda0f..4a7d544a718bf 100644 --- a/recipes/bioconductor-pd.margene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.margene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.margene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: efd71aeb9c5ab36c2ddeccf9cb66ddec build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.margene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml index 8a0d04ac3eb19..408d867813d22 100644 --- a/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.medgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2a0048ccd5310ec5c45bb691f3c25885 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.medgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml index fe0bca8c284d1..f519411548246 100644 --- a/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.medgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d96894cfea509734af62110311100142 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.medgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.medicago/meta.yaml b/recipes/bioconductor-pd.medicago/meta.yaml index 26b8b1490b8c2..769fa2b2e172b 100644 --- a/recipes/bioconductor-pd.medicago/meta.yaml +++ b/recipes/bioconductor-pd.medicago/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.medicago" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0e3f00777919374619a9dc8244167068 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.medicago", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74a/meta.yaml b/recipes/bioconductor-pd.mg.u74a/meta.yaml index 60ac7a18bc7dc..e94ef1d820d7e 100644 --- a/recipes/bioconductor-pd.mg.u74a/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a855c7d2b80e9b8f9bbc1a3f83aca799 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74av2/meta.yaml b/recipes/bioconductor-pd.mg.u74av2/meta.yaml index 82a3f943a5f07..12c4b3403f631 100644 --- a/recipes/bioconductor-pd.mg.u74av2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74av2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74av2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 01c6e4da9c2ad0f1939482284dd5b421 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74av2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74b/meta.yaml b/recipes/bioconductor-pd.mg.u74b/meta.yaml index b8d715cc903d5..d3a265d3115ec 100644 --- a/recipes/bioconductor-pd.mg.u74b/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 47bb81abaceba6dfaab3e0987f28706c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74bv2/meta.yaml b/recipes/bioconductor-pd.mg.u74bv2/meta.yaml index d89e472d6734b..3cba6e2bcbf62 100644 --- a/recipes/bioconductor-pd.mg.u74bv2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74bv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74bv2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dbb6cd5b16bd5cafbf654744bc2d5c5c build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74bv2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74c/meta.yaml b/recipes/bioconductor-pd.mg.u74c/meta.yaml index b6d655fdb12b2..d34eec569ed78 100644 --- a/recipes/bioconductor-pd.mg.u74c/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74c/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74c" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 01f10eae99481f03d1d5a6a2c2f01733 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74c", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mg.u74cv2/meta.yaml b/recipes/bioconductor-pd.mg.u74cv2/meta.yaml index db3aa3aef3958..dded57370137e 100644 --- a/recipes/bioconductor-pd.mg.u74cv2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74cv2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74cv2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b60943b90b95a24fcf93f8c245fd88be build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74cv2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.1.0/meta.yaml b/recipes/bioconductor-pd.mirna.1.0/meta.yaml index 63eacb6291fbd..cc8a6f4292057 100644 --- a/recipes/bioconductor-pd.mirna.1.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.1.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.1.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8dfeb82a9da6d6f73e5fb716a2867a34 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.1.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.2.0/meta.yaml b/recipes/bioconductor-pd.mirna.2.0/meta.yaml index 569cf51670331..39fb38a4ddbc3 100644 --- a/recipes/bioconductor-pd.mirna.2.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.2.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.2.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: aab53cbc62fbd7727ca0303aeb1dca13 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.2.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.3.0/meta.yaml b/recipes/bioconductor-pd.mirna.3.0/meta.yaml index 6e83b6b7f4847..1fa7ec6d77b92 100644 --- a/recipes/bioconductor-pd.mirna.3.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.3.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.3.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1265f1969c618b3b5121e6a77ba57009 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.3.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.3.1/meta.yaml b/recipes/bioconductor-pd.mirna.3.1/meta.yaml index e968576995635..5efcf883ca1ee 100644 --- a/recipes/bioconductor-pd.mirna.3.1/meta.yaml +++ b/recipes/bioconductor-pd.mirna.3.1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.8.1" %} {% set name = "pd.mirna.3.1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 296b3584ee5e9416c9018353d3e29c6c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.3.1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-rsqlite >=0.11.1' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mirna.4.0/meta.yaml b/recipes/bioconductor-pd.mirna.4.0/meta.yaml index 14517e4896b52..a3ad36ee6f9cf 100644 --- a/recipes/bioconductor-pd.mirna.4.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.4.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.4.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cae1a18c02aaa20a2f05172103e9d938 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.4.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.moe430a/meta.yaml b/recipes/bioconductor-pd.moe430a/meta.yaml index 70887f8731119..e9ab0dd8f57dd 100644 --- a/recipes/bioconductor-pd.moe430a/meta.yaml +++ b/recipes/bioconductor-pd.moe430a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.moe430a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f9a7cb62140e42c2a82177548a1c73fb build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.moe430a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.moe430b/meta.yaml b/recipes/bioconductor-pd.moe430b/meta.yaml index 2cfad28753931..72a0e356ab58c 100644 --- a/recipes/bioconductor-pd.moe430b/meta.yaml +++ b/recipes/bioconductor-pd.moe430b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.moe430b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c19d2ee5e7e87703cf73afa33a5f3156 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.moe430b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml index 14aee2e8a08a6..d83f930bddeed 100644 --- a/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.moex.1.0.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 57427e63b2d44258c12d796eada1897b build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.moex.1.0.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml index e452a31afec54..890fc6f4cb1c6 100644 --- a/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.1.0.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c3767385af3b9a120c777adb6d6e3364 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.1.0.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml index c541512b2793c..09713fc997bd3 100644 --- a/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.1.1.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3d6c5d29e4d8a0b0152e109b68f82c37 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.1.1.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml b/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml index 0cd167f8e7dea..9c9a7d684131a 100644 --- a/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.2.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 71326d6bd85de02490171696f923d053 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.2.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml b/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml index aef43e3a54ceb..499af455820e9 100644 --- a/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.2.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2c7fc5644eae98359cb945ff16d072a2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.2.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mouse430.2/meta.yaml b/recipes/bioconductor-pd.mouse430.2/meta.yaml index 6064430c2092b..205b87d6bbb36 100644 --- a/recipes/bioconductor-pd.mouse430.2/meta.yaml +++ b/recipes/bioconductor-pd.mouse430.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mouse430.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7f37397a57b06d15101ef86fa6242ca4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mouse430.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mouse430a.2/meta.yaml b/recipes/bioconductor-pd.mouse430a.2/meta.yaml index e3e97c992a487..328c8998bd334 100644 --- a/recipes/bioconductor-pd.mouse430a.2/meta.yaml +++ b/recipes/bioconductor-pd.mouse430a.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mouse430a.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0c28f564a1fa23f59c936d42c156796d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mouse430a.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mta.1.0/meta.yaml b/recipes/bioconductor-pd.mta.1.0/meta.yaml index e0a52461a85e0..7deeae0d5bdfb 100644 --- a/recipes/bioconductor-pd.mta.1.0/meta.yaml +++ b/recipes/bioconductor-pd.mta.1.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mta.1.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0f737b4f1f1353733e56e2df637f554b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mta.1.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mu11ksuba/meta.yaml b/recipes/bioconductor-pd.mu11ksuba/meta.yaml index 6d8393f88932e..94eb4e26e996d 100644 --- a/recipes/bioconductor-pd.mu11ksuba/meta.yaml +++ b/recipes/bioconductor-pd.mu11ksuba/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mu11ksuba" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 56be58b3f444ccb9572dc4c3882964b2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mu11ksuba", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.mu11ksubb/meta.yaml b/recipes/bioconductor-pd.mu11ksubb/meta.yaml index 250416e090676..11001e1c78fc9 100644 --- a/recipes/bioconductor-pd.mu11ksubb/meta.yaml +++ b/recipes/bioconductor-pd.mu11ksubb/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.mu11ksubb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c45b0ebe777b99cec38499826cc1b457 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.mu11ksubb", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml b/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml index 0ceee2111c0df..104d2cb3a3b15 100644 --- a/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml +++ b/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "pd.nugo.hs1a520180" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 88a836472f0f9aab2e1d54e4bad7d6af build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.nugo.hs1a520180", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml b/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml index 4492a301ca5b0..3114b806849f1 100644 --- a/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml +++ b/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "pd.nugo.mm1a520177" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5cd64895eaddaf4cae1c48db9468c079 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.nugo.mm1a520177", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml index d4123ffc506a8..0127427f2b795 100644 --- a/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ovigene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 88cfedfe10dd357539305051a69d31a1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ovigene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml index 04d4af36fef2b..1c6bc4fd9fc71 100644 --- a/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.ovigene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d6158cacd32a1892975fddd8dc8bb3f2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ovigene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.pae.g1a/meta.yaml b/recipes/bioconductor-pd.pae.g1a/meta.yaml index 4d4d8c40e7ec4..78b855cedb8e9 100644 --- a/recipes/bioconductor-pd.pae.g1a/meta.yaml +++ b/recipes/bioconductor-pd.pae.g1a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.pae.g1a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d96462eb35c63b30772bccae2a27a8cd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.pae.g1a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml b/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml index 6f3fd0d8d595d..5db40654cc0d4 100644 --- a/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml +++ b/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.plasmodium.anopheles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ae55b1451ceaed951f68213c0433f3d0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.plasmodium.anopheles", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.poplar/meta.yaml b/recipes/bioconductor-pd.poplar/meta.yaml index 725ba844d814a..56d765944b6ab 100644 --- a/recipes/bioconductor-pd.poplar/meta.yaml +++ b/recipes/bioconductor-pd.poplar/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.poplar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c33b7528e5a47654aeacf61b71058a8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.poplar", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.porcine/meta.yaml b/recipes/bioconductor-pd.porcine/meta.yaml index 82c47a2bdff34..3c508d25653f1 100644 --- a/recipes/bioconductor-pd.porcine/meta.yaml +++ b/recipes/bioconductor-pd.porcine/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.porcine" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5df404babadb1d6faef73e249c819a72 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.porcine", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml index a9f0bf892744a..60c46a620aa02 100644 --- a/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.porgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 203fc56b0e2904fa7063c4a325e038f1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.porgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml index 430150b714537..d719ca62d0871 100644 --- a/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.porgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3a31d325861925a7428241207c461a1d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.porgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml index 2fc33f0100628..2d107b381b133 100644 --- a/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rabgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7f1e33f4767a4c4653bdaff2b79989a0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rabgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml index 364c9cedad143..4695d505632f7 100644 --- a/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rabgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2492695661309f5e6628612685460ee5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rabgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rae230a/meta.yaml b/recipes/bioconductor-pd.rae230a/meta.yaml index 9ed5fd10cc095..663454610c8b4 100644 --- a/recipes/bioconductor-pd.rae230a/meta.yaml +++ b/recipes/bioconductor-pd.rae230a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rae230a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fa4a1c29d3457b1db82b1010c5f72412 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rae230a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rae230b/meta.yaml b/recipes/bioconductor-pd.rae230b/meta.yaml index f83f7dcb76548..46e25943b634f 100644 --- a/recipes/bioconductor-pd.rae230b/meta.yaml +++ b/recipes/bioconductor-pd.rae230b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rae230b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 10e2e70bb7538119127cd65f636f93b6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rae230b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml index b7e51f74b747a..519e76f5d2ad1 100644 --- a/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.raex.1.0.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e2160b549f63ffcc9222d88d82d4d393 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.raex.1.0.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml index fd93c7e228cab..83bbe9f667204 100644 --- a/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.1.0.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 122cb69603e705218d01d70f48e90cad build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.1.0.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml index d5b1e4f5f14b0..7acf2c90841f4 100644 --- a/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.1.1.st.v1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7301ab6472849395ccb800c39807e969 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.1.1.st.v1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml b/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml index fe928c01c0ba1..d353b093c0f97 100644 --- a/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.2.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 37157b09f009fef368b54e47711c313b build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.2.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml b/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml index e57d364d6bd4e..97f536d4fe7f2 100644 --- a/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.2.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 53adfa5ff2c7e466da83b807dbc7b237 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.2.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rat230.2/meta.yaml b/recipes/bioconductor-pd.rat230.2/meta.yaml index 2e706cdde08a6..b9a674841bfcf 100644 --- a/recipes/bioconductor-pd.rat230.2/meta.yaml +++ b/recipes/bioconductor-pd.rat230.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rat230.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 286b1a7868ef6c795ebeb6dd8a5d5920 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rat230.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml index 6ea3f356da10a..9200e31904ff5 100644 --- a/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rcngene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c7c5ef4d4f5ed92d9130d77a99a0685 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rcngene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml index 7f3111b1fbbf6..d5109147ee4f8 100644 --- a/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rcngene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9781549447d90b5423e820fff5cc6273 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rcngene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rg.u34a/meta.yaml b/recipes/bioconductor-pd.rg.u34a/meta.yaml index 377e2433efbcc..814b06a1e7993 100644 --- a/recipes/bioconductor-pd.rg.u34a/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34a/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34a" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ac3a6cc203dabb8faab85b97f1a7ae3c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rg.u34a", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rg.u34b/meta.yaml b/recipes/bioconductor-pd.rg.u34b/meta.yaml index 3e06011a43a95..3bd194cf18f4d 100644 --- a/recipes/bioconductor-pd.rg.u34b/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34b/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34b" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 757966b66795d388c7169816d31977ad build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rg.u34b", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rg.u34c/meta.yaml b/recipes/bioconductor-pd.rg.u34c/meta.yaml index 58acea111a8eb..0be8eaeea6991 100644 --- a/recipes/bioconductor-pd.rg.u34c/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34c/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34c" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bc9cb7b208972ac2901235bdabdee5b2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rg.u34c", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml index 0a72cd95d1d5f..0b394c279d5fa 100644 --- a/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rhegene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6469add6928e663529df4df98fcdd7a8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rhegene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml index dc6fc4ec8900f..9f7b2da4be891 100644 --- a/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rhegene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4f63424ab52283a95731767dce6623cd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rhegene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rhesus/meta.yaml b/recipes/bioconductor-pd.rhesus/meta.yaml index e760022f0a205..168eb0a7c0836 100644 --- a/recipes/bioconductor-pd.rhesus/meta.yaml +++ b/recipes/bioconductor-pd.rhesus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rhesus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 51efcfe1384ac956ff93bf0530965054 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rhesus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rice/meta.yaml b/recipes/bioconductor-pd.rice/meta.yaml index b9ce05cd1da4f..cc3172d469287 100644 --- a/recipes/bioconductor-pd.rice/meta.yaml +++ b/recipes/bioconductor-pd.rice/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rice" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9c456981b3d0b99a96ac6c71e3eb7c8a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rice", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml index 29985fdc1fa4f..6d55e5903b9cc 100644 --- a/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rjpgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 066f5dbacc1110e42ce4d457ad3b9306 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rjpgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml index d72c006ebbc88..f1cce02ab6f8c 100644 --- a/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rjpgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 265503774b15e0f4e71ac53a276a80f2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rjpgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rn.u34/meta.yaml b/recipes/bioconductor-pd.rn.u34/meta.yaml index fce938a21f5ae..7ba2751df2778 100644 --- a/recipes/bioconductor-pd.rn.u34/meta.yaml +++ b/recipes/bioconductor-pd.rn.u34/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rn.u34" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1728c547f1383bffab330796505119ec build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rn.u34", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rta.1.0/meta.yaml b/recipes/bioconductor-pd.rta.1.0/meta.yaml index 8fbd60597c1f6..96549451b50b6 100644 --- a/recipes/bioconductor-pd.rta.1.0/meta.yaml +++ b/recipes/bioconductor-pd.rta.1.0/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.2" %} {% set name = "pd.rta.1.0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 90752a892a103c7fe4cd6c86e61a61db build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rta.1.0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml index 14e2235bfc16b..1377c31afcc2c 100644 --- a/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rusgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0b9b00fee58ef211e041395052344483 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rusgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml index 3461cf3b2f6c9..ce4353bf56c14 100644 --- a/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.rusgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 228837c2de4a4b106806cb7f384564fa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.rusgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.s.aureus/meta.yaml b/recipes/bioconductor-pd.s.aureus/meta.yaml index c900149e19766..7bb76e909c429 100644 --- a/recipes/bioconductor-pd.s.aureus/meta.yaml +++ b/recipes/bioconductor-pd.s.aureus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.s.aureus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f173ae6e4316aaa2eafbde92d5868a5a build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.s.aureus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.soybean/meta.yaml b/recipes/bioconductor-pd.soybean/meta.yaml index 010526d295f82..9a179dc85bbc3 100644 --- a/recipes/bioconductor-pd.soybean/meta.yaml +++ b/recipes/bioconductor-pd.soybean/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.soybean" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6dbe167be9d40c1d9096485afb4525f0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.soybean", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml b/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml index 072fa4b68f2a2..a347597e89b5a 100644 --- a/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.soygene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b264df0648ec35d04f91e0ef8e26ac95 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.soygene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml b/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml index e8615e564f1ec..a1729ed3dabec 100644 --- a/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.soygene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4a911a4a4b5de927fe6239e500a2993f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.soygene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.sugar.cane/meta.yaml b/recipes/bioconductor-pd.sugar.cane/meta.yaml index ea2c076dbe86a..1ac46bfb035b6 100644 --- a/recipes/bioconductor-pd.sugar.cane/meta.yaml +++ b/recipes/bioconductor-pd.sugar.cane/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.sugar.cane" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bd7eb8b1a1c9ac77359358a5347330fb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.sugar.cane", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.tomato/meta.yaml b/recipes/bioconductor-pd.tomato/meta.yaml index 499efa24cc9b0..f934a7a17e110 100644 --- a/recipes/bioconductor-pd.tomato/meta.yaml +++ b/recipes/bioconductor-pd.tomato/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.tomato" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ce78f6ee43d72e017608413dd4d50580 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.tomato", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.u133.x3p/meta.yaml b/recipes/bioconductor-pd.u133.x3p/meta.yaml index bd1109ab7bf75..8831a79d5d391 100644 --- a/recipes/bioconductor-pd.u133.x3p/meta.yaml +++ b/recipes/bioconductor-pd.u133.x3p/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.u133.x3p" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e3f343e32273667f851e26d7b8a7a5db build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.u133.x3p", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.vitis.vinifera/meta.yaml b/recipes/bioconductor-pd.vitis.vinifera/meta.yaml index e5fa0473c18b9..65c61d4bfd7fd 100644 --- a/recipes/bioconductor-pd.vitis.vinifera/meta.yaml +++ b/recipes/bioconductor-pd.vitis.vinifera/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.vitis.vinifera" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 104a8ac33a9baa25a61f953679795696 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.vitis.vinifera", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.wheat/meta.yaml b/recipes/bioconductor-pd.wheat/meta.yaml index 7528bceb33c0b..2880ec9932dab 100644 --- a/recipes/bioconductor-pd.wheat/meta.yaml +++ b/recipes/bioconductor-pd.wheat/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.wheat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 38a7183c8d3b874cf62391a9e9169bb9 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.wheat", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.x.laevis.2/meta.yaml b/recipes/bioconductor-pd.x.laevis.2/meta.yaml index 4d9af187348ba..85c3ad7eb268f 100644 --- a/recipes/bioconductor-pd.x.laevis.2/meta.yaml +++ b/recipes/bioconductor-pd.x.laevis.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.x.laevis.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 32416957e3cdc11ad4dbfcd9141ff113 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.x.laevis.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.x.tropicalis/meta.yaml b/recipes/bioconductor-pd.x.tropicalis/meta.yaml index 55d5ba4d4b85f..6670ccd4bafab 100644 --- a/recipes/bioconductor-pd.x.tropicalis/meta.yaml +++ b/recipes/bioconductor-pd.x.tropicalis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.x.tropicalis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 79a4de91831e4b0153495e12b9c6e8d3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.x.tropicalis", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.xenopus.laevis/meta.yaml b/recipes/bioconductor-pd.xenopus.laevis/meta.yaml index 279aa750ba211..95dc899a279f5 100644 --- a/recipes/bioconductor-pd.xenopus.laevis/meta.yaml +++ b/recipes/bioconductor-pd.xenopus.laevis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.xenopus.laevis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6d5c2c9e8e3891770b1c6e9dcd823c0d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.xenopus.laevis", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.yeast.2/meta.yaml b/recipes/bioconductor-pd.yeast.2/meta.yaml index aa48be6c21621..26d834b6f5f33 100644 --- a/recipes/bioconductor-pd.yeast.2/meta.yaml +++ b/recipes/bioconductor-pd.yeast.2/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.yeast.2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 780f5139ee9cda46c9e38122538ce129 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.yeast.2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.yg.s98/meta.yaml b/recipes/bioconductor-pd.yg.s98/meta.yaml index 31794da957b8a..9747d83c970c7 100644 --- a/recipes/bioconductor-pd.yg.s98/meta.yaml +++ b/recipes/bioconductor-pd.yg.s98/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.yg.s98" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: caec3e8f29918f078b2dc7c76f4a74e2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.yg.s98", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml index 49fea51353521..3bb4402a2e409 100644 --- a/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.zebgene.1.0.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 54fcf757b8069e95dd7e2f3ff74ae050 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.zebgene.1.0.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml index bfb5ed075f4bc..bb23b5798ea1e 100644 --- a/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.zebgene.1.1.st" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d87028cd9024bc33be518635cf2f48fc build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.zebgene.1.1.st", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pd.zebrafish/meta.yaml b/recipes/bioconductor-pd.zebrafish/meta.yaml index fe16ec6bb090a..c747bdcc950f4 100644 --- a/recipes/bioconductor-pd.zebrafish/meta.yaml +++ b/recipes/bioconductor-pd.zebrafish/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "pd.zebrafish" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,32 +13,33 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 101f09a9d9304d1d8fbcc7f4812897b1 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pd.zebrafish", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pdatk/build_failure.linux-64.yaml b/recipes/bioconductor-pdatk/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8c604002d4745 --- /dev/null +++ b/recipes/bioconductor-pdatk/build_failure.linux-64.yaml @@ -0,0 +1,10 @@ +recipe_sha: 635aae6bed8d84cc4ff74353dbdc5a5f9128c7c2618b5cb2c1d55e0a4340da36 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + /opt/conda/conda-bld/bioconductor-pdatk_1702300846111/test_tmp/run_test.sh: line 7: -e: command not found +category: |- + test failure +log: |- + 13:26:37 BIOCONDA INFO (OUT) export SRC_DIR=/opt/conda/conda-bld/bioconductor-pdatk_1702300846111/test_tmp + 13:26:37 BIOCONDA INFO (OUT) + -e 'library('\''PDATK'\'')' + 13:26:37 BIOCONDA INFO (OUT) /opt/conda/conda-bld/bioconductor-pdatk_1702300846111/test_tmp/run_test.sh: line 7: -e: command not found diff --git a/recipes/bioconductor-pdatk/meta.yaml b/recipes/bioconductor-pdatk/meta.yaml index a10c49dde85f7..e154475d539d2 100644 --- a/recipes/bioconductor-pdatk/meta.yaml +++ b/recipes/bioconductor-pdatk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "PDATK" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ffb59256d71d12b3fea031e2936445a + md5: 7593f074493a9b3123e757f9f265d05c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pdatk", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr, HDF5Array requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-genefu >=2.32.0,<2.33.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-piano >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-survcomp >=1.50.0,<1.51.0' - - 'bioconductor-switchbox >=1.36.0,<1.37.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-genefu >=2.34.0,<2.35.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-piano >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-survcomp >=1.52.0,<1.53.0' + - 'bioconductor-switchbox >=1.38.0,<1.39.0' - r-base - r-caret - r-clusterrepro @@ -52,18 +53,18 @@ requirements: - r-survminer - r-verification run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusclusterplus >=1.64.0,<1.65.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-genefu >=2.32.0,<2.33.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-piano >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-survcomp >=1.50.0,<1.51.0' - - 'bioconductor-switchbox >=1.36.0,<1.37.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-genefu >=2.34.0,<2.35.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-piano >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-survcomp >=1.52.0,<1.53.0' + - 'bioconductor-switchbox >=1.38.0,<1.39.0' - r-base - r-caret - r-clusterrepro @@ -84,11 +85,11 @@ requirements: - r-verification test: commands: - - 'R -e "library(''{{ name }}'')"' + - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Pancreatic Ductal Adenocarcinoma Tool-Kit' - description: 'Pancreatic ductal adenocarcinoma (PDA) has a relatively poor prognosis and is one of the most lethal cancers. Molecular classification of gene expression profiles holds the potential to identify meaningful subtypes which can inform therapeutic strategy in the clinical setting. The Pancreatic Cancer Adenocarcinoma Tool-Kit (PDATK) provides an S4 class-based interface for performing unsupervised subtype discovery, cross-cohort meta-clustering, gene-expression-based classification, and subsequent survival analysis to identify prognostically useful subtypes in pancreatic cancer and beyond. Two novel methods, Consensus Subtypes in Pancreatic Cancer (CSPC) and Pancreatic Cancer Overall Survival Predictor (PCOSP) are included for consensus-based meta-clustering and overall-survival prediction, respectively. Additionally, four published subtype classifiers and three published prognostic gene signatures are included to allow users to easily recreate published results, apply existing classifiers to new data, and benchmark the relative performance of new methods. The use of existing Bioconductor classes as input to all PDATK classes and methods enables integration with existing Bioconductor datasets, including the 21 pancreatic cancer patient cohorts available in the MetaGxPancreas data package. PDATK has been used to replicate results from Sandhu et al (2019) and an additional paper is in the works using CSPC to validate subtypes from the included published classifiers, both of which use the data available in MetaGxPancreas. The inclusion of subtype centroids and prognostic gene signatures from these and other publications will enable researchers and clinicians to classify novel patient gene expression data, allowing the direct clinical application of the classifiers included in PDATK. Overall, PDATK provides a rich set of tools to identify and validate useful prognostic and molecular subtypes based on gene-expression data, benchmark new classifiers against existing ones, and apply discovered classifiers on novel patient data to inform clinical decision making.' + description: 'Pancreatic ductal adenocarcinoma (PDA) has a relatively poor prognosis and is one of the most lethal cancers. Molecular classification of gene expression profiles holds the potential to identify meaningful subtypes which can inform therapeutic strategy in the clinical setting. The Pancreatic Cancer Adenocarcinoma Tool-Kit (PDATK) provides an S4 class-based interface for performing unsupervised subtype discovery, cross-cohort meta-clustering, gene-expression-based classification, and subsequent survival analysis to identify prognostically useful subtypes in pancreatic cancer and beyond. Two novel methods, Consensus Subtypes in Pancreatic Cancer (CSPC) and Pancreatic Cancer Overall Survival Predictor (PCOSP) are included for consensus-based meta-clustering and overall-survival prediction, respectively. Additionally, four published subtype classifiers and three published prognostic gene signatures are included to allow users to easily recreate published results, apply existing classifiers to new data, and benchmark the relative performance of new methods. The use of existing Bioconductor classes as input to all PDATK classes and methods enables integration with existing Bioconductor datasets, including the 21 pancreatic cancer patient cohorts available in the MetaGxPancreas data package. PDATK has been used to replicate results from Sandhu et al (2019) [https://doi.org/10.1200/cci.18.00102] and an additional paper is in the works using CSPC to validate subtypes from the included published classifiers, both of which use the data available in MetaGxPancreas. The inclusion of subtype centroids and prognostic gene signatures from these and other publications will enable researchers and clinicians to classify novel patient gene expression data, allowing the direct clinical application of the classifiers included in PDATK. Overall, PDATK provides a rich set of tools to identify and validate useful prognostic and molecular subtypes based on gene-expression data, benchmark new classifiers against existing ones, and apply discovered classifiers on novel patient data to inform clinical decision making.' license_file: LICENSE diff --git a/recipes/bioconductor-pdinfobuilder/meta.yaml b/recipes/bioconductor-pdinfobuilder/meta.yaml index eab66da1b8744..b94711d5f3961 100644 --- a/recipes/bioconductor-pdinfobuilder/meta.yaml +++ b/recipes/bioconductor-pdinfobuilder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "pdInfoBuilder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46f59ac69b5b94cc24cdb49cc12d28ac + md5: 67c0c8df22f95792e50c1e6c4b6eba2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pdinfobuilder", max_pin="x.x") }}' requirements: host: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' - libblas - liblapack run: - - 'bioconductor-affxparser >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affxparser >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' diff --git a/recipes/bioconductor-peacoqc/meta.yaml b/recipes/bioconductor-peacoqc/meta.yaml index a6054ffe7608f..2a019595f29fb 100644 --- a/recipes/bioconductor-peacoqc/meta.yaml +++ b/recipes/bioconductor-peacoqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "PeacoQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35cce4a53dfc774f2606eed22e09da17 + md5: fa296e0522b97273b692874b5ec23b97 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-peacoqc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - r-base - r-circlize - r-ggplot2 - r-gridextra - r-plyr run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-flowworkspace >=4.12.0,<4.13.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-peakpanther/meta.yaml b/recipes/bioconductor-peakpanther/meta.yaml index cc70a7e482192..d56a1978bcd39 100644 --- a/recipes/bioconductor-peakpanther/meta.yaml +++ b/recipes/bioconductor-peakpanther/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "peakPantheR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 654760a5537dfdc83125d3cd253f2124 + md5: 9753434861181af826b86fbc734b5850 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-peakpanther", max_pin="x.x") }}' noarch: generic # Suggests: testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-bslib - 'r-doparallel >=1.0.11' @@ -39,8 +40,8 @@ requirements: - 'r-stringr >=1.2.0' - 'r-xml >=3.98.1.10' run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-bslib - 'r-doparallel >=1.0.11' diff --git a/recipes/bioconductor-peca/meta.yaml b/recipes/bioconductor-peca/meta.yaml index 1884e5ed624c3..5605c4a16cf73 100644 --- a/recipes/bioconductor-peca/meta.yaml +++ b/recipes/bioconductor-peca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "PECA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 658444c729d969dfd2f1a3edd43d3966 + md5: 43aed7fc555cb6ccbf70335add80f6dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-peca", max_pin="x.x") }}' noarch: generic # Suggests: SpikeIn requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rots >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rots >=1.30.0,<1.31.0' - r-aroma.affymetrix - r-aroma.core - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rots >=1.28.0,<1.29.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rots >=1.30.0,<1.31.0' - r-aroma.affymetrix - r-aroma.core - r-base diff --git a/recipes/bioconductor-peco/meta.yaml b/recipes/bioconductor-peco/meta.yaml index 4a1b3d0fa6fe4..42ee30969da6a 100644 --- a/recipes/bioconductor-peco/meta.yaml +++ b/recipes/bioconductor-peco/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "peco" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47a4083ee1746cc79c437205b7eae854 + md5: 9a15c75c989ee10da1fb0ead1bbac99f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-peco", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-circular @@ -32,9 +33,9 @@ requirements: - r-foreach - 'r-genlasso >=1.4' run: - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-circular diff --git a/recipes/bioconductor-pedbarrayv10.db/meta.yaml b/recipes/bioconductor-pedbarrayv10.db/meta.yaml index d2a77ef59a613..1c9fa8f5fbffa 100644 --- a/recipes/bioconductor-pedbarrayv10.db/meta.yaml +++ b/recipes/bioconductor-pedbarrayv10.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "pedbarrayv10.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 25acc3bfee229015ecca1c7d688e5168 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pedbarrayv10.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pedbarrayv9.db/meta.yaml b/recipes/bioconductor-pedbarrayv9.db/meta.yaml index faf9c5826fd37..1d5180b7a344c 100644 --- a/recipes/bioconductor-pedbarrayv9.db/meta.yaml +++ b/recipes/bioconductor-pedbarrayv9.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "pedbarrayv9.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: da4b2f9c0a672e0c9ee53f017bacaff7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pedbarrayv9.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pengls/meta.yaml b/recipes/bioconductor-pengls/meta.yaml index c1a75c82cf20b..641c32b81fdc8 100644 --- a/recipes/bioconductor-pengls/meta.yaml +++ b/recipes/bioconductor-pengls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "pengls" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bb111f7ec56fb1ce6cf319a56dbc3042 + md5: 7b4703b0839f4e46a97e208289a69345 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pengls", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown,testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-glmnet - r-nlme run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-glmnet - r-nlme diff --git a/recipes/bioconductor-pepdat/meta.yaml b/recipes/bioconductor-pepdat/meta.yaml index 89df237ee40a3..e632c11c7cf5c 100644 --- a/recipes/bioconductor-pepdat/meta.yaml +++ b/recipes/bioconductor-pepdat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "pepDat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c0f8c749db61b37d83728109a2e08df + md5: 4ce373369604b54b15e5992ebe9355b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pepdat", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pepdat/post-link.sh b/recipes/bioconductor-pepdat/post-link.sh index f398190520806..18087b8b14b2d 100644 --- a/recipes/bioconductor-pepdat/post-link.sh +++ b/recipes/bioconductor-pepdat/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pepdat-1.20.0" +installBiocDataPackage.sh "pepdat-1.22.0" diff --git a/recipes/bioconductor-pepsnmr/meta.yaml b/recipes/bioconductor-pepsnmr/meta.yaml index 4720727dca64f..58ea6cbaff257 100644 --- a/recipes/bioconductor-pepsnmr/meta.yaml +++ b/recipes/bioconductor-pepsnmr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "PepsNMR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80a3c52dea0ca605a0988a664215b1a8 + md5: afd34a264a3af86ad7aec1d6163b0aab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pepsnmr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData requirements: diff --git a/recipes/bioconductor-pepsnmrdata/meta.yaml b/recipes/bioconductor-pepsnmrdata/meta.yaml index ece4231e32bf7..bc0e5911ad73c 100644 --- a/recipes/bioconductor-pepsnmrdata/meta.yaml +++ b/recipes/bioconductor-pepsnmrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "PepsNMRData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98f84b07316d8ec6aab7c64862c695d2 + md5: 96fc9090499b4460f72fb85a0428b357 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pepsnmrdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, rmarkdown, BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pepsnmrdata/post-link.sh b/recipes/bioconductor-pepsnmrdata/post-link.sh index f40152b399244..31aa57da37b58 100644 --- a/recipes/bioconductor-pepsnmrdata/post-link.sh +++ b/recipes/bioconductor-pepsnmrdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pepsnmrdata-1.18.0" +installBiocDataPackage.sh "pepsnmrdata-1.20.0" diff --git a/recipes/bioconductor-pepstat/meta.yaml b/recipes/bioconductor-pepstat/meta.yaml index 553e2eb03cf16..63ce17507e1e1 100644 --- a/recipes/bioconductor-pepstat/meta.yaml +++ b/recipes/bioconductor-pepstat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "pepStat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da35a44e27569b966515d3baa63da1c1 + md5: 031af81c6bcac97b7262d978bfda2392 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pepstat", max_pin="x.x") }}' noarch: generic # Suggests: pepDat, Pviz, knitr, shiny requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-data.table - r-fields - r-ggplot2 - r-plyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-data.table - r-fields diff --git a/recipes/bioconductor-pepxmltab/meta.yaml b/recipes/bioconductor-pepxmltab/meta.yaml index 967fd5813d88b..44ccd49357088 100644 --- a/recipes/bioconductor-pepxmltab/meta.yaml +++ b/recipes/bioconductor-pepxmltab/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "pepXMLTab" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eae67a9f54e44fbce148fb9e5077fdd0 + md5: 71d6bcb41c5a79bc2cfdd375c6468250 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pepxmltab", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-periodicdna/meta.yaml b/recipes/bioconductor-periodicdna/meta.yaml index 8ec4ccf2ef572..d85c082208a88 100644 --- a/recipes/bioconductor-periodicdna/meta.yaml +++ b/recipes/bioconductor-periodicdna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "periodicDNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb823cba035d96f14027fc949ba7df9b + md5: 60036578bc6ec2c45d1c4b57ae96ad03 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-periodicdna", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-ggplot2 - r-magrittr - r-zoo run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-ggplot2 diff --git a/recipes/bioconductor-pfam.db/meta.yaml b/recipes/bioconductor-pfam.db/meta.yaml index 34aaa02a5dce7..d5113df6b0741 100644 --- a/recipes/bioconductor-pfam.db/meta.yaml +++ b/recipes/bioconductor-pfam.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "PFAM.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 729496d021868b74cbecfd156066d0e9 + md5: f98f5d1e5d335e6bbf1ea6426cde67bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pfam.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pfam.db/post-link.sh b/recipes/bioconductor-pfam.db/post-link.sh index 97165541e6661..c837f5c6d710e 100644 --- a/recipes/bioconductor-pfam.db/post-link.sh +++ b/recipes/bioconductor-pfam.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pfam.db-3.17.0" +installBiocDataPackage.sh "pfam.db-3.18.0" diff --git a/recipes/bioconductor-pfamanalyzer/meta.yaml b/recipes/bioconductor-pfamanalyzer/meta.yaml index 6f220cb9fcb37..d17c3a7853043 100644 --- a/recipes/bioconductor-pfamanalyzer/meta.yaml +++ b/recipes/bioconductor-pfamanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "pfamAnalyzeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d3921913adbae5d53442475b60ee78d + md5: 20159a7f365760efda4827ae6fff80d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pfamanalyzer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-pgca/meta.yaml b/recipes/bioconductor-pgca/meta.yaml index 408fa2cd1793b..bccdf859ffd7e 100644 --- a/recipes/bioconductor-pgca/meta.yaml +++ b/recipes/bioconductor-pgca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "pgca" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3285cff9d2bd68e50c1f8d51f61e22e0 + md5: 43c58c5b347ebf060a9e6afdc8aa8e93 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pgca", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: diff --git a/recipes/bioconductor-phantasus/meta.yaml b/recipes/bioconductor-phantasus/meta.yaml index f7b71859045be..12893d324c41d 100644 --- a/recipes/bioconductor-phantasus/meta.yaml +++ b/recipes/bioconductor-phantasus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.2" %} +{% set version = "1.22.2" %} {% set name = "phantasus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 010a7126b3a72bf9c3a89e45cd789d23 + md5: 84c6e2dce18e76a3268130cdd236ba59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phantasus", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-assertthat - r-base - r-ccapp @@ -48,13 +50,14 @@ requirements: - r-stringr - r-svglite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-assertthat - r-base - r-ccapp diff --git a/recipes/bioconductor-phantasuslite/build.sh b/recipes/bioconductor-phantasuslite/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-phantasuslite/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-phantasuslite/meta.yaml b/recipes/bioconductor-phantasuslite/meta.yaml new file mode 100644 index 0000000000000..8f7dc38016eeb --- /dev/null +++ b/recipes/bioconductor-phantasuslite/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "phantasusLite" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5fe0e101ac53a89dd49e077d5fb4c07d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phantasuslite", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery +requirements: + host: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-rhdf5client >=1.24.0,<1.25.0' + - r-base + - r-data.table + - r-httr + - r-stringr + run: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-rhdf5client >=1.24.0,<1.25.0' + - r-base + - r-data.table + - r-httr + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Loading and annotation RNA-Seq counts matrices' + description: 'PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.' + license_file: LICENSE + diff --git a/recipes/bioconductor-pharmacogx/meta.yaml b/recipes/bioconductor-pharmacogx/meta.yaml index fe20c276b51b7..b3ec539112cf6 100644 --- a/recipes/bioconductor-pharmacogx/meta.yaml +++ b/recipes/bioconductor-pharmacogx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.4.0" %} +{% set version = "3.6.0" %} {% set name = "PharmacoGx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a5db5607c2e34052f84c04aae7a19ca + md5: a786bf3c0ace641195cfb3b00823cda3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pharmacogx", max_pin="x.x") }}' # Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-catools @@ -43,13 +44,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-catools diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml index 1f87007d434f7..d94d17575001b 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.2" %} {% set name = "phastCons100way.UCSC.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 65aa706a567f7e328dbba0095f995cf1 build: - number: 13 + number: 14 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phastcons100way.ucsc.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml index 0f97e217028b1..bfb7828fb7da6 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.1" %} {% set name = "phastCons100way.UCSC.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 878c757f9270b3410d11e4e4a4213c8e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phastcons100way.ucsc.hg38", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml index 26e57dffe6ed9..c1311660034c3 100644 --- a/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "phastCons30way.UCSC.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 754faee8463bc494c502540cb8f6ea8d build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phastcons30way.ucsc.hg38", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml b/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml index f874908947d57..1cd646da27c64 100644 --- a/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml +++ b/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.16.0" %} {% set name = "phastCons35way.UCSC.mm39" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 83fc2a2265bc341b6a00064a1286b5bc build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phastcons35way.ucsc.mm39", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml index 2fc48c1d9f445..8584071542d60 100644 --- a/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.7.1" %} {% set name = "phastCons7way.UCSC.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c2d87446b022c166c1c325ea2aef521d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phastcons7way.ucsc.hg38", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phemd/meta.yaml b/recipes/bioconductor-phemd/meta.yaml index 323cf23e779a4..ea542cdc06cb2 100644 --- a/recipes/bioconductor-phemd/meta.yaml +++ b/recipes/bioconductor-phemd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "phemd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f2f4325b02cd7c6b4c96b69de58ec50a + md5: 8cefd4ddfea1dd2deb007acb6cebfb7a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phemd", max_pin="x.x") }}' noarch: generic -# Suggests: knitr +# Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-destiny >=3.14.0,<3.15.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-destiny >=3.16.0,<3.17.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-cowplot @@ -46,13 +47,13 @@ requirements: - r-transport - r-vgam run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-destiny >=3.14.0,<3.15.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-destiny >=3.16.0,<3.17.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-cowplot diff --git a/recipes/bioconductor-phenogeneranker/meta.yaml b/recipes/bioconductor-phenogeneranker/meta.yaml index b423258bb8175..930e12d2e9963 100644 --- a/recipes/bioconductor-phenogeneranker/meta.yaml +++ b/recipes/bioconductor-phenogeneranker/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "PhenoGeneRanker" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c54470bf5e606eb9b28ba81ac9250305 + md5: a6530ed180fae6b4250bc56d3de24e19 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phenogeneranker", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-phenomis/meta.yaml b/recipes/bioconductor-phenomis/meta.yaml index 02939aac0a470..7d1a1238da6ff 100644 --- a/recipes/bioconductor-phenomis/meta.yaml +++ b/recipes/bioconductor-phenomis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "phenomis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 68bcdad2f28989d9cf025744aa994e91 + md5: 6fc3be4aed9fead1f2038fb3d2837854 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phenomis", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biodb >=1.8.0,<1.9.0' - - 'bioconductor-biodbchebi >=1.6.0,<1.7.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' + - 'bioconductor-biodbchebi >=1.8.0,<1.9.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-futile.logger @@ -44,14 +45,14 @@ requirements: - r-tidyr - r-venndiagram run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biodb >=1.8.0,<1.9.0' - - 'bioconductor-biodbchebi >=1.6.0,<1.7.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biodb >=1.10.0,<1.11.0' + - 'bioconductor-biodbchebi >=1.8.0,<1.9.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-futile.logger diff --git a/recipes/bioconductor-phenopath/meta.yaml b/recipes/bioconductor-phenopath/meta.yaml index 2079195f58ac1..bc3a0995ad613 100644 --- a/recipes/bioconductor-phenopath/meta.yaml +++ b/recipes/bioconductor-phenopath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "phenopath" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d5602a76199cdbdc31210788b9569c72 + md5: 1bbbcb87efbf78aa39ee07851d27f498 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phenopath", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -30,7 +31,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-phenotest/meta.yaml b/recipes/bioconductor-phenotest/meta.yaml index ed39526f9108c..58b9a36220404 100644 --- a/recipes/bioconductor-phenotest/meta.yaml +++ b/recipes/bioconductor-phenotest/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "phenoTest" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cedbc33a7165cbb547d8bf62db8de022 + md5: 20bd295654c25854160e8a1aad42d8e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phenotest", max_pin="x.x") }}' noarch: generic # Suggests: GSEABase, GO.db requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-heatplus >=3.8.0,<3.9.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-heatplus >=3.10.0,<3.11.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-bma - r-ellipse @@ -42,17 +43,17 @@ requirements: - r-survival - r-xtable run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-heatplus >=3.8.0,<3.9.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-heatplus >=3.10.0,<3.11.0' - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-bma - r-ellipse diff --git a/recipes/bioconductor-phenstat/meta.yaml b/recipes/bioconductor-phenstat/meta.yaml index 0da5e272bc69f..c766d7ff7dc15 100644 --- a/recipes/bioconductor-phenstat/meta.yaml +++ b/recipes/bioconductor-phenstat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "PhenStat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73057858116719f9411fe66000677aa2 + md5: f28cba815b5f6e8b3350c926d1d05907 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phenstat", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-car - r-corrplot @@ -37,7 +38,7 @@ requirements: - r-reshape - r-smoothwin run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-car - r-corrplot diff --git a/recipes/bioconductor-philr/meta.yaml b/recipes/bioconductor-philr/meta.yaml index afea06135912c..225cd7a47bc4c 100644 --- a/recipes/bioconductor-philr/meta.yaml +++ b/recipes/bioconductor-philr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "philr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16ca92ff095dc3125adfee5cc63a6177 + md5: d55e931af78335bd6378fba38c5f54a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-philr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-base - r-ggplot2 - r-phangorn - r-tidyr run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-base - r-ggplot2 diff --git a/recipes/bioconductor-phipdata/meta.yaml b/recipes/bioconductor-phipdata/meta.yaml index b34c62b91219d..2c96fe878d6dc 100644 --- a/recipes/bioconductor-phipdata/meta.yaml +++ b/recipes/bioconductor-phipdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "PhIPData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac34fb97c8b145805e1e0d3b876c21e8 + md5: fdb81e6f685727bbbe4584f42ca33797 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phipdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli test: diff --git a/recipes/bioconductor-phosphonormalizer/meta.yaml b/recipes/bioconductor-phosphonormalizer/meta.yaml index 4a77350d28cf3..83fa2d9b82923 100644 --- a/recipes/bioconductor-phosphonormalizer/meta.yaml +++ b/recipes/bioconductor-phosphonormalizer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "phosphonormalizer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f61fb102338add2c5407d1cf9ea82feb + md5: b0146ac595b90e20d854404e6fa427bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phosphonormalizer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-phosr/meta.yaml b/recipes/bioconductor-phosr/meta.yaml index f7e0eec29e307..c27015e7252dc 100644 --- a/recipes/bioconductor-phosr/meta.yaml +++ b/recipes/bioconductor-phosr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "PhosR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 378bad4ffeacf7daaac34ba1f3dfafb7 + md5: 49f34b9174257536ac2a912530d69d10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phosr", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dendextend @@ -47,12 +48,12 @@ requirements: - r-stringi - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-dendextend diff --git a/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml b/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml index 8ff0e9d94e577..891cac36e766a 100644 --- a/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml +++ b/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.16.0" %} {% set name = "phyloP35way.UCSC.mm39" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2c34eef5f20eace04efd47673cdf1062 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phylop35way.ucsc.mm39", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phyloprofile/meta.yaml b/recipes/bioconductor-phyloprofile/meta.yaml index 0cece8597d94a..c9851553e3706 100644 --- a/recipes/bioconductor-phyloprofile/meta.yaml +++ b/recipes/bioconductor-phyloprofile/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.5" %} +{% set version = "1.16.0" %} {% set name = "PhyloProfile" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd16fd6e4d6e6ed690b6780e2b381508 + md5: 96200a149b95297ba34dee53963493a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phyloprofile", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biodist >=1.72.0,<1.73.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-omadb >=2.16.0,<2.17.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biodist >=1.74.0,<1.75.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-omadb >=2.18.0,<2.19.0' - r-ape - r-base - r-colourpicker @@ -40,17 +41,19 @@ requirements: - r-rcurl - r-shiny - r-shinybs + - r-shinycssloaders - r-shinyfiles - r-shinyjs + - r-stringr - r-xml2 - r-yaml - r-zoo run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biodist >=1.72.0,<1.73.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-omadb >=2.16.0,<2.17.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biodist >=1.74.0,<1.75.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-omadb >=2.18.0,<2.19.0' - r-ape - r-base - r-colourpicker @@ -65,8 +68,10 @@ requirements: - r-rcurl - r-shiny - r-shinybs + - r-shinycssloaders - r-shinyfiles - r-shinyjs + - r-stringr - r-xml2 - r-yaml - r-zoo diff --git a/recipes/bioconductor-phyloprofiledata/meta.yaml b/recipes/bioconductor-phyloprofiledata/meta.yaml index 4cf4ebb33acf0..f08883286f7df 100644 --- a/recipes/bioconductor-phyloprofiledata/meta.yaml +++ b/recipes/bioconductor-phyloprofiledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "PhyloProfileData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3be065a86910a062e9b63540157ff949 + md5: 68dda32e9151c0aba4eb5b29c0313f83 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phyloprofiledata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-phyloprofiledata/post-link.sh b/recipes/bioconductor-phyloprofiledata/post-link.sh index 967b824fdd6e4..7f47b649e3562 100644 --- a/recipes/bioconductor-phyloprofiledata/post-link.sh +++ b/recipes/bioconductor-phyloprofiledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "phyloprofiledata-1.14.0" +installBiocDataPackage.sh "phyloprofiledata-1.16.0" diff --git a/recipes/bioconductor-phyloseq/meta.yaml b/recipes/bioconductor-phyloseq/meta.yaml index 1da612a78b6e4..816a5356e24c3 100644 --- a/recipes/bioconductor-phyloseq/meta.yaml +++ b/recipes/bioconductor-phyloseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "phyloseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c159f15cbf12ce81298c1b4d1d1fe43b + md5: 335dc9dedba529ce34669dd881127e7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-phyloseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58), knitr (>= 1.16), magrittr (>= 1.5), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - 'r-ade4 >=1.7-4' - 'r-ape >=5.0' - r-base @@ -39,11 +40,11 @@ requirements: - 'r-scales >=0.4.0' - 'r-vegan >=2.5' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomformat >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - 'r-ade4 >=1.7-4' - 'r-ape >=5.0' - r-base diff --git a/recipes/bioconductor-pi/meta.yaml b/recipes/bioconductor-pi/meta.yaml index 8a863f41dee2c..13cad610cab01 100644 --- a/recipes/bioconductor-pi/meta.yaml +++ b/recipes/bioconductor-pi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "Pi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b09c5d11dc5ba832eb809dc6d0009913 + md5: cb989f0e8a3a1ab90a4a319c860ef602 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pi", max_pin="x.x") }}' noarch: generic # Suggests: foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr, rtracklayer, ggbio, Gviz, data.tree, jsonlite requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-suprahex >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-suprahex >=1.40.0,<1.41.0' - r-base - r-caret - r-dnet @@ -49,11 +50,11 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-suprahex >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-suprahex >=1.40.0,<1.41.0' - r-base - r-caret - r-dnet diff --git a/recipes/bioconductor-piano/meta.yaml b/recipes/bioconductor-piano/meta.yaml index 53acfc159e0f9..947eddd07883a 100644 --- a/recipes/bioconductor-piano/meta.yaml +++ b/recipes/bioconductor-piano/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "piano" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1dce4336105325c4f7200406542ba3fe + md5: 84b0ce2cca9fb11110bd82113e066e82 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-piano", max_pin="x.x") }}' noarch: generic # Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-dt - r-gplots @@ -37,10 +38,10 @@ requirements: - r-shinyjs - r-visnetwork run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-dt - r-gplots diff --git a/recipes/bioconductor-pickgene/meta.yaml b/recipes/bioconductor-pickgene/meta.yaml index e320a7ba7ddca..2ac35c4ab1be0 100644 --- a/recipes/bioconductor-pickgene/meta.yaml +++ b/recipes/bioconductor-pickgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "pickgene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 70c09c4cc929410aca20e9a4c1aae523 + md5: 250b3649eff783447f1d2c34f67bf3ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pickgene", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-pics/meta.yaml b/recipes/bioconductor-pics/meta.yaml index 7ba57e9eb4425..29900a517454a 100644 --- a/recipes/bioconductor-pics/meta.yaml +++ b/recipes/bioconductor-pics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "PICS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: efd0dc25199e80b8b905bc5cb4043400 + md5: 04ed3fdb7f1db15654e9974438495e43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pics", max_pin="x.x") }}' # Suggests: rtracklayer, parallel, knitr +# SystemRequirements: gsl requirements: host: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - libblas - liblapack + - gsl run: - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base + - gsl build: - {{ compiler('c') }} - automake diff --git a/recipes/bioconductor-pig.db0/meta.yaml b/recipes/bioconductor-pig.db0/meta.yaml index 04e11d645142e..15e8ede99ee85 100644 --- a/recipes/bioconductor-pig.db0/meta.yaml +++ b/recipes/bioconductor-pig.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "pig.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d4ea227fc9495dc815bb3ad2387a7e26 + md5: 85aaccdbdb969825957db45db3fb7801 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pig.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pig.db0/post-link.sh b/recipes/bioconductor-pig.db0/post-link.sh index 0b4239037a5b6..ccf6ee98e3660 100644 --- a/recipes/bioconductor-pig.db0/post-link.sh +++ b/recipes/bioconductor-pig.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pig.db0-3.17.0" +installBiocDataPackage.sh "pig.db0-3.18.0" diff --git a/recipes/bioconductor-pigengene/meta.yaml b/recipes/bioconductor-pigengene/meta.yaml index c0adf6351ca07..6200d1de33d16 100644 --- a/recipes/bioconductor-pigengene/meta.yaml +++ b/recipes/bioconductor-pigengene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "Pigengene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e8dfb7f626a2cf129ffce0986a6ee6c9 + md5: 2d7b090a6d6fad6cf62c987970663167 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pigengene", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, AnnotationDbi, energy requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - 'r-bnlearn >=4.7' - 'r-c50 >=0.1.2' @@ -44,15 +45,15 @@ requirements: - 'r-pheatmap >=1.0.8' - r-wgcna run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - 'r-bnlearn >=4.7' - 'r-c50 >=0.1.2' diff --git a/recipes/bioconductor-ping/meta.yaml b/recipes/bioconductor-ping/meta.yaml index 90020f35dd6a7..05e5b3f99f186 100644 --- a/recipes/bioconductor-ping/meta.yaml +++ b/recipes/bioconductor-ping/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "PING" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c30c9725a93000736ebb0e890f6efc44 + md5: 703e11e3d890a3cf2b48c15d4c76ea87 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ping", max_pin="x.x") }}' # Suggests: parallel, ShortRead, rtracklayer requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pics >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pics >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pics >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pics >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fda build: diff --git a/recipes/bioconductor-pipecomp/meta.yaml b/recipes/bioconductor-pipecomp/meta.yaml index 2133ccf7b66c8..f2a38e18004db 100644 --- a/recipes/bioconductor-pipecomp/meta.yaml +++ b/recipes/bioconductor-pipecomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "pipeComp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a2b7cb51586dade4ebeaa1d1d85c06f + md5: ccc688331233bccee84104cbbb9b5d81 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pipecomp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-aricode - r-base - r-circlize @@ -49,13 +50,13 @@ requirements: - r-uwot - r-viridislite run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-aricode - r-base - r-circlize diff --git a/recipes/bioconductor-pipeframe/meta.yaml b/recipes/bioconductor-pipeframe/meta.yaml index 33725a2823fd5..eab0329b0160a 100644 --- a/recipes/bioconductor-pipeframe/meta.yaml +++ b/recipes/bioconductor-pipeframe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "pipeFrame" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75006944af02f9c62b4e851fca8e0e0e + md5: 142f8d049aa03cec36050c2b0ccc87d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pipeframe", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-digest - r-magrittr - r-rmarkdown - r-visnetwork run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-digest - r-magrittr diff --git a/recipes/bioconductor-planet/meta.yaml b/recipes/bioconductor-planet/meta.yaml index ff48e269b2eae..3b2c110ad4fd1 100644 --- a/recipes/bioconductor-planet/meta.yaml +++ b/recipes/bioconductor-planet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "planet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cee64675bce4d388dd7f348ff68900d1 + md5: dbd74bc4dd3583d6ebbd871b251ecd6d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-planet", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown requirements: @@ -37,6 +38,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Placental DNA methylation analysis tools' - description: 'This package contains R functions to infer additional biological variables to supplemental DNA methylation analysis of placental data. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data. The package comes with an example processed placental dataset.' + description: 'This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' diff --git a/recipes/bioconductor-planttfhunter/meta.yaml b/recipes/bioconductor-planttfhunter/meta.yaml index 2ab1ade95a55c..2d4836f3fc65b 100644 --- a/recipes/bioconductor-planttfhunter/meta.yaml +++ b/recipes/bioconductor-planttfhunter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "planttfhunter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 95ba952e191581983529908ece129c54 + md5: 94bf35ef27114ae40bdd4be243dfb8fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-planttfhunter", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0) # SystemRequirements: HMMER requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml b/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml index 4d28ad9cf4a33..5ce91658cfd34 100644 --- a/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml +++ b/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "plasmodiumanophelescdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 54c5c326977d6358c40cacf34cb2aca2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plasmodiumanophelescdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml b/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml index a02c4b7775cd5..7a007c04ba9cd 100644 --- a/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml +++ b/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "plasmodiumanophelesprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 281683dab923168c2eedb7b08c528935 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plasmodiumanophelesprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-plasmut/build.sh b/recipes/bioconductor-plasmut/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-plasmut/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plasmut/meta.yaml b/recipes/bioconductor-plasmut/meta.yaml new file mode 100644 index 0000000000000..7af4ecae4a8c9 --- /dev/null +++ b/recipes/bioconductor-plasmut/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.0" %} +{% set name = "plasmut" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8681d905157c0cbb8b46e48cbe4ecde9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plasmut", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) +requirements: + host: + - r-base + - r-dplyr + - r-tibble + run: + - r-base + - r-dplyr + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic' + description: 'A Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.' + diff --git a/recipes/bioconductor-plgem/meta.yaml b/recipes/bioconductor-plgem/meta.yaml index 4b7ee6e985e04..2bc338a763d0a 100644 --- a/recipes/bioconductor-plgem/meta.yaml +++ b/recipes/bioconductor-plgem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "plgem" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 384f0e272bf6bca492d6b6fa3b10bbc6 + md5: caa3e3fe048da49643b34bde9fcb834a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plgem", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-plier/meta.yaml b/recipes/bioconductor-plier/meta.yaml index 7efe1ff38926d..55b9c161f346c 100644 --- a/recipes/bioconductor-plier/meta.yaml +++ b/recipes/bioconductor-plier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "plier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3ada0e5da50940e184dd56e4f15c2aac + md5: f16a09bf8bccc7f5596d55ed0577a593 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plier", max_pin="x.x") }}' requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-plogo2/meta.yaml b/recipes/bioconductor-plogo2/meta.yaml index 47f580c06cbc6..0b50bf78d9598 100644 --- a/recipes/bioconductor-plogo2/meta.yaml +++ b/recipes/bioconductor-plogo2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "PloGO2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c885f0334d65006c9d06c9670f337b8 + md5: a9d28e5ed4822c97721db2c841ce3eec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plogo2", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' - r-base - r-httr - r-lattice - r-openxlsx - r-xtable run: - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' - r-base - r-httr - r-lattice diff --git a/recipes/bioconductor-plotgardener/meta.yaml b/recipes/bioconductor-plotgardener/meta.yaml index 2862ea7a65f6a..e7cb36e9c2ed0 100644 --- a/recipes/bioconductor-plotgardener/meta.yaml +++ b/recipes/bioconductor-plotgardener/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.1" %} {% set name = "plotgardener" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 08318dcfcb24afd0efc11e1cd81dd7a6 + md5: 7459452ce71af8384d3df8340a7c3db0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plotgardener", max_pin="x.x") }}' # Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, GenomeInfoDb, GenomicRanges, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' - r-base - r-curl - r-data.table @@ -36,8 +39,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-plyranges >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-plotgardenerdata/meta.yaml b/recipes/bioconductor-plotgardenerdata/meta.yaml index a575a778f4be1..9a02df7d187eb 100644 --- a/recipes/bioconductor-plotgardenerdata/meta.yaml +++ b/recipes/bioconductor-plotgardenerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "plotgardenerData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82519e095b0f464cd59388d4146d21db + md5: 96055b11818bd59c0c91977b34973608 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plotgardenerdata", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-plotgardenerdata/post-link.sh b/recipes/bioconductor-plotgardenerdata/post-link.sh index 40c8cd63e1efd..44e9cf40f78cf 100644 --- a/recipes/bioconductor-plotgardenerdata/post-link.sh +++ b/recipes/bioconductor-plotgardenerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "plotgardenerdata-1.6.0" +installBiocDataPackage.sh "plotgardenerdata-1.8.0" diff --git a/recipes/bioconductor-plotgrouper/meta.yaml b/recipes/bioconductor-plotgrouper/meta.yaml index 1d887cfbba08c..c6e6e6c5bff30 100644 --- a/recipes/bioconductor-plotgrouper/meta.yaml +++ b/recipes/bioconductor-plotgrouper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "plotGrouper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5bfb2cb4a73da0fa5aaa637ca56e2f99 + md5: aca262974325a32b1d28d58d28e4e012 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plotgrouper", max_pin="x.x") }}' noarch: generic # Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-plpe/meta.yaml b/recipes/bioconductor-plpe/meta.yaml index 4da5eb67c552d..5818330d03f6a 100644 --- a/recipes/bioconductor-plpe/meta.yaml +++ b/recipes/bioconductor-plpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "PLPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a03620bea737c30691c47836a5a62e2f + md5: 1a4887a4c08676e0ce69331caacc297e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plpe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lpe >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lpe >=1.76.0,<1.77.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-lpe >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-lpe >=1.76.0,<1.77.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-plyinteractions/build.sh b/recipes/bioconductor-plyinteractions/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-plyinteractions/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plyinteractions/meta.yaml b/recipes/bioconductor-plyinteractions/meta.yaml new file mode 100644 index 0000000000000..19e57bfea4e2f --- /dev/null +++ b/recipes/bioconductor-plyinteractions/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.0.0" %} +{% set name = "plyinteractions" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e072613b18768f43d832eaa32354bbc9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plyinteractions", max_pin="x.x") }}' + noarch: generic +# Suggests: tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings, BiocParallel, scales, HiContactsData, rtracklayer, BiocStyle, covr, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), RefManageR +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-dplyr + - r-rlang + - r-tibble + - r-tidyselect + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-dplyr + - r-rlang + - r-tibble + - r-tidyselect +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Extending tidy verbs to genomic interactions' + description: 'Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.' + diff --git a/recipes/bioconductor-plyranges/meta.yaml b/recipes/bioconductor-plyranges/meta.yaml index cee8917eb76bc..b8bbe45eb1171 100644 --- a/recipes/bioconductor-plyranges/meta.yaml +++ b/recipes/bioconductor-plyranges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "plyranges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1afddfe644bc0efd5e2af427d1d9e9e1 + md5: 23b74165be3c4a855e6a49d8c0f1bab1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plyranges", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0), HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr, ggplot2 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-magrittr - 'r-rlang >=0.2.0' - 'r-tidyselect >=1.0.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-magrittr diff --git a/recipes/bioconductor-pmm/meta.yaml b/recipes/bioconductor-pmm/meta.yaml index 9c766f9eaa537..370e01487e660 100644 --- a/recipes/bioconductor-pmm/meta.yaml +++ b/recipes/bioconductor-pmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "pmm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bb0cdf8f45d20c01984eb90fdf84c93a + md5: 43957004fa9664b15f4bca34f7ea975e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pmm", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-pmp/meta.yaml b/recipes/bioconductor-pmp/meta.yaml index 815b949774a12..ffe645d75fd11 100644 --- a/recipes/bioconductor-pmp/meta.yaml +++ b/recipes/bioconductor-pmp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "pmp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ae759e61d37da021af27182c987264a7 + md5: 07feec54f330f10904aae29238f79369 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pmp", max_pin="x.x") }}' noarch: generic # Suggests: testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra, magick requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-matrixstats - r-missforest - r-reshape2 run: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-matrixstats diff --git a/recipes/bioconductor-pocrcannotation.db/meta.yaml b/recipes/bioconductor-pocrcannotation.db/meta.yaml index 1da24ace53dd7..0918cbf3fda7b 100644 --- a/recipes/bioconductor-pocrcannotation.db/meta.yaml +++ b/recipes/bioconductor-pocrcannotation.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "POCRCannotation.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: da1d4dacc5fffb9c5dfea55649974aa5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pocrcannotation.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-podcall/meta.yaml b/recipes/bioconductor-podcall/meta.yaml index fd7ab13b42a15..9e63932878f83 100644 --- a/recipes/bioconductor-podcall/meta.yaml +++ b/recipes/bioconductor-podcall/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "PoDCall" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f8244df4ed33630558e25e740b18b3b + md5: e079c4df0c773e27d396662c928ac51b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-podcall", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: @@ -53,6 +54,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Positive Droplet Calling for DNA Methylation Droplet Digital PCR' - description: 'Reads files exported from ''QuantaSoft'' containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.' + description: 'Reads files exported from ''QX Manager or QuantaSoft'' containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-podkat/meta.yaml b/recipes/bioconductor-podkat/meta.yaml index 25dd36027bbcf..9678b6fcdff8a 100644 --- a/recipes/bioconductor-podkat/meta.yaml +++ b/recipes/bioconductor-podkat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "podkat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2d1ac828841d66fe3450803679df6c97 + md5: b06fbdc3f282bde5ec8df0d062d3ecb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-podkat", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-matrix - 'r-rcpp >=0.11.1' - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-matrix - 'r-rcpp >=0.11.1' diff --git a/recipes/bioconductor-pogos/meta.yaml b/recipes/bioconductor-pogos/meta.yaml index f09afba07cf48..426527de50e5d 100644 --- a/recipes/bioconductor-pogos/meta.yaml +++ b/recipes/bioconductor-pogos/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "pogos" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7a5e5764a5fdd26c7864e71e8dfab96d + md5: 14955bb127999aaa92633bc1ce3a1227 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pogos", max_pin="x.x") }}' noarch: generic # Suggests: knitr, DT, ontologyPlot, testthat, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-ontoproc >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ontoproc >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - 'r-httr >=1.3.1' - 'r-rjson >=0.2.15' - r-shiny run: - - 'bioconductor-ontoproc >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ontoproc >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - 'r-httr >=1.3.1' diff --git a/recipes/bioconductor-polyester/meta.yaml b/recipes/bioconductor-polyester/meta.yaml index daebb81f896f5..7fa24f5ce3bc9 100644 --- a/recipes/bioconductor-polyester/meta.yaml +++ b/recipes/bioconductor-polyester/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "polyester" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6737b2c8ec5c8b1415e784d632e0840c + md5: acc47ee29fb9c22fb1ad4bbfafe8fd4d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-polyester", max_pin="x.x") }}' noarch: generic # Suggests: knitr, ballgown, markdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-logspline run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-logspline test: diff --git a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml index a963c8fbefadf..bd986aeb518f3 100644 --- a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml +++ b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "PolyPhen.Hsapiens.dbSNP131" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,24 +13,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 763e9cd4afd97b36f7e659f5454ef61f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-polyphen.hsapiens.dbsnp131", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-poma/meta.yaml b/recipes/bioconductor-poma/meta.yaml index df2809ab82fee..fffe40d372e0b 100644 --- a/recipes/bioconductor-poma/meta.yaml +++ b/recipes/bioconductor-poma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "POMA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acdda87011b0add03854dc75df78fe2b + md5: 89690c830c8b6120d4d436f05e34f4eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-poma", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, ggraph, knitr, patchwork, plotly, tidyverse, testthat (>= 2.3.2) requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mixomics >=6.24.0,<6.25.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-caret @@ -45,13 +46,13 @@ requirements: - r-uwot - r-vegan run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mixomics >=6.24.0,<6.25.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-broom - r-caret diff --git a/recipes/bioconductor-poplarcdf/meta.yaml b/recipes/bioconductor-poplarcdf/meta.yaml index e498d9b89ead7..abe70a10b697e 100644 --- a/recipes/bioconductor-poplarcdf/meta.yaml +++ b/recipes/bioconductor-poplarcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "poplarcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 556e7f8f6f76436552d8044ef29279cb build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-poplarcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-poplarprobe/meta.yaml b/recipes/bioconductor-poplarprobe/meta.yaml index fbe45b20cc09b..8844ecc8570be 100644 --- a/recipes/bioconductor-poplarprobe/meta.yaml +++ b/recipes/bioconductor-poplarprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "poplarprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 87a608cd86084a06973a88e9b51f799a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-poplarprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-porcine.db/meta.yaml b/recipes/bioconductor-porcine.db/meta.yaml index 3baabe5d742c9..345d8a9eba876 100644 --- a/recipes/bioconductor-porcine.db/meta.yaml +++ b/recipes/bioconductor-porcine.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "porcine.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4a86b3e696d267dca673b4e9276d6368 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-porcine.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.ss.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.ss.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.ss.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.ss.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-porcinecdf/meta.yaml b/recipes/bioconductor-porcinecdf/meta.yaml index d05d5a922f835..11979dc62adb7 100644 --- a/recipes/bioconductor-porcinecdf/meta.yaml +++ b/recipes/bioconductor-porcinecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "porcinecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 32a60b93829c06a935895fab0a469228 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-porcinecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-porcineprobe/meta.yaml b/recipes/bioconductor-porcineprobe/meta.yaml index 35c05fe4ea718..5d0f2c7ddf24a 100644 --- a/recipes/bioconductor-porcineprobe/meta.yaml +++ b/recipes/bioconductor-porcineprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "porcineprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5ac483b6329a012d4c9954e3dee8869e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-porcineprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-powertcr/meta.yaml b/recipes/bioconductor-powertcr/meta.yaml index 56035aad2d4fb..8df9efbe126d8 100644 --- a/recipes/bioconductor-powertcr/meta.yaml +++ b/recipes/bioconductor-powertcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "powerTCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1ea8721802f5c9366953c388f888d67 + md5: 6033da999bfcba4c2e80a45e358c3855 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-powertcr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-powsc/meta.yaml b/recipes/bioconductor-powsc/meta.yaml index 34d53c13d6475..9d658ab0472af 100644 --- a/recipes/bioconductor-powsc/meta.yaml +++ b/recipes/bioconductor-powsc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "POWSC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68f052aeb186749e50a9f2bbb5cbe3f6 + md5: e2ed51f94e9a1b37aa91fe74a007f4d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-powsc", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-pheatmap - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-pheatmap diff --git a/recipes/bioconductor-ppcseq/meta.yaml b/recipes/bioconductor-ppcseq/meta.yaml index 0603999607703..bb0514df5b5e6 100644 --- a/recipes/bioconductor-ppcseq/meta.yaml +++ b/recipes/bioconductor-ppcseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ppcseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dc7a246fc82400b73aa46ba102e9e3ee + md5: 5a95706ac4269643dd1eb6efd4bccb67 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ppcseq", max_pin="x.x") }}' # Suggests: knitr, testthat, BiocStyle, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-benchmarkme - 'r-bh >=1.66.0' - r-dplyr - r-foreach - - r-furrr - - r-future <1.33 - r-ggplot2 - r-lifecycle - r-magrittr - r-purrr - 'r-rcpp >=0.12.0' - 'r-rcppeigen >=0.3.3.3.0' + - 'r-rcppparallel >=5.0.1' - r-rlang - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.0.0' + - 'r-rstantools >=2.1.1' - 'r-stanheaders >=2.18.0' - r-tibble - r-tidybayes @@ -45,23 +45,22 @@ requirements: - libblas - liblapack run: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-benchmarkme - 'r-bh >=1.66.0' - r-dplyr - r-foreach - - r-furrr - - r-future <1.33 - r-ggplot2 - r-lifecycle - r-magrittr - r-purrr - 'r-rcpp >=0.12.0' - 'r-rcppeigen >=0.3.3.3.0' + - 'r-rcppparallel >=5.0.1' - r-rlang - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.0.0' + - 'r-rstantools >=2.1.1' - 'r-stanheaders >=2.18.0' - r-tibble - r-tidybayes diff --git a/recipes/bioconductor-ppinfer/meta.yaml b/recipes/bioconductor-ppinfer/meta.yaml index ad0b1aad6d7d1..a413c32921519 100644 --- a/recipes/bioconductor-ppinfer/meta.yaml +++ b/recipes/bioconductor-ppinfer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "PPInfer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5157ef584ef792c5ff0cb55de3da9eba + md5: f6b346ab6e0c90b546825aa50fb52b59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ppinfer", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-yeastexpdata >=0.46.0,<0.47.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-yeastexpdata >=0.48.0,<0.49.0' - r-base - r-ggplot2 - r-httr - r-igraph - r-kernlab run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-yeastexpdata >=0.46.0,<0.47.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-yeastexpdata >=0.48.0,<0.49.0' - r-base - r-ggplot2 - r-httr diff --git a/recipes/bioconductor-pqsfinder/meta.yaml b/recipes/bioconductor-pqsfinder/meta.yaml index 112d56bf8879b..d89644da4851d 100644 --- a/recipes/bioconductor-pqsfinder/meta.yaml +++ b/recipes/bioconductor-pqsfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "pqsfinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 498ce0ee8270dbdff5c63f84e4c8717d + md5: c1201a86985850d5ace97c629e2d4864 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pqsfinder", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi # SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.78.0' - 'r-rcpp >=0.12.3' - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-bh >=1.78.0' - 'r-rcpp >=0.12.3' diff --git a/recipes/bioconductor-pram/meta.yaml b/recipes/bioconductor-pram/meta.yaml index b198a21d7c48a..6e6332cc06696 100644 --- a/recipes/bioconductor-pram/meta.yaml +++ b/recipes/bioconductor-pram/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "pram" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8737ac32a1a9f2e17fded29baf810970 + md5: 129a8e2cbbf4abab07038d3b7899c58e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pram", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-data.table >=1.11.8' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-data.table >=1.11.8' test: diff --git a/recipes/bioconductor-prebs/meta.yaml b/recipes/bioconductor-prebs/meta.yaml index e7ba1de006868..8be0337f23ffe 100644 --- a/recipes/bioconductor-prebs/meta.yaml +++ b/recipes/bioconductor-prebs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "prebs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c460d482da9e9b3357490dc60b494517 + md5: 847264218e6725926f1b56aacd09b541 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prebs", max_pin="x.x") }}' noarch: generic # Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rpa >=1.56.0,<1.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rpa >=1.58.0,<1.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rpa >=1.56.0,<1.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rpa >=1.58.0,<1.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-prebsdata/meta.yaml b/recipes/bioconductor-prebsdata/meta.yaml index 2f4e2bf53fa33..1b3a2dde647b4 100644 --- a/recipes/bioconductor-prebsdata/meta.yaml +++ b/recipes/bioconductor-prebsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "prebsdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 96c0666ea91a4bd5b5c8dbc584f873b3 + md5: a1c6aee2732035357adc3e2cb99d6bcc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prebsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prebsdata/post-link.sh b/recipes/bioconductor-prebsdata/post-link.sh index 34de2b2ebc061..816d1ef0dbdd3 100644 --- a/recipes/bioconductor-prebsdata/post-link.sh +++ b/recipes/bioconductor-prebsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prebsdata-1.36.0" +installBiocDataPackage.sh "prebsdata-1.38.0" diff --git a/recipes/bioconductor-precisetad/meta.yaml b/recipes/bioconductor-precisetad/meta.yaml index c11fc03892901..47324c027359e 100644 --- a/recipes/bioconductor-precisetad/meta.yaml +++ b/recipes/bioconductor-precisetad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "preciseTAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d90370e884f035d71c774706abf96f2 + md5: 5e6495261bf370abf46d979aace7f363 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-precisetad", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rcgh >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rcgh >=1.32.0,<1.33.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-cluster @@ -39,10 +40,10 @@ requirements: - r-prroc - r-randomforest run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rcgh >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rcgh >=1.32.0,<1.33.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-cluster diff --git a/recipes/bioconductor-precisetadhub/meta.yaml b/recipes/bioconductor-precisetadhub/meta.yaml index b9aadfa5e8254..d4dc0c0f45d28 100644 --- a/recipes/bioconductor-precisetadhub/meta.yaml +++ b/recipes/bioconductor-precisetadhub/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "preciseTADhub" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e0da7747a2ae263545ef3e426701fd6 + md5: bff4bbf0a4ac1abf21ff72ad4346795c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-precisetadhub", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown, BiocStyle, preciseTAD requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-precisetadhub/post-link.sh b/recipes/bioconductor-precisetadhub/post-link.sh index e29d34389daa1..ff7494e2c8d04 100644 --- a/recipes/bioconductor-precisetadhub/post-link.sh +++ b/recipes/bioconductor-precisetadhub/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "precisetadhub-1.8.0" +installBiocDataPackage.sh "precisetadhub-1.10.0" diff --git a/recipes/bioconductor-preda/meta.yaml b/recipes/bioconductor-preda/meta.yaml index f930ab14e4aaf..2c12240a90381 100644 --- a/recipes/bioconductor-preda/meta.yaml +++ b/recipes/bioconductor-preda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "PREDA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9660d5fd5b0221d82953b8bf43e631e7 + md5: 6f051dc3182b2d70715d84a12e39dd57 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-preda", max_pin="x.x") }}' noarch: generic # Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-lokern >=1.0.9' run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-lokern >=1.0.9' test: diff --git a/recipes/bioconductor-predasampledata/meta.yaml b/recipes/bioconductor-predasampledata/meta.yaml index 58b45e3f02932..1d617501f624f 100644 --- a/recipes/bioconductor-predasampledata/meta.yaml +++ b/recipes/bioconductor-predasampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.40.0" %} +{% set version = "0.42.0" %} {% set name = "PREDAsampledata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 478b0cd1f601998cfefcca0fdf60eb3d + md5: 5acce57384c00a56d658281ba4fa57e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-predasampledata", max_pin="x.x") }}' noarch: generic # Suggests: hgu133plus2.db, hgu133plus2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preda >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preda >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preda >=1.46.0,<1.47.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preda >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-predasampledata/post-link.sh b/recipes/bioconductor-predasampledata/post-link.sh index 52ddf15f66bff..abc7050325f76 100644 --- a/recipes/bioconductor-predasampledata/post-link.sh +++ b/recipes/bioconductor-predasampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "predasampledata-0.40.0" +installBiocDataPackage.sh "predasampledata-0.42.0" diff --git a/recipes/bioconductor-preprocesscore/build.sh b/recipes/bioconductor-preprocesscore/build.sh index 203597e1fddf9..c1d13421f5f1e 100644 --- a/recipes/bioconductor-preprocesscore/build.sh +++ b/recipes/bioconductor-preprocesscore/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --configure-args="--disable-threading" --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-preprocesscore/meta.yaml b/recipes/bioconductor-preprocesscore/meta.yaml index 9237faa672b3e..d43ce20f0865a 100644 --- a/recipes/bioconductor-preprocesscore/meta.yaml +++ b/recipes/bioconductor-preprocesscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.1" %} +{% set version = "1.64.0" %} {% set name = "preprocessCore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ef397708852e43e7b3fb42dfe9194d4 + md5: 2116c6363074b59becdaf7a1e88caf91 build: number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-preprocesscore", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-primeviewcdf/meta.yaml b/recipes/bioconductor-primeviewcdf/meta.yaml index ddd2fcbf84023..352d7095f852b 100644 --- a/recipes/bioconductor-primeviewcdf/meta.yaml +++ b/recipes/bioconductor-primeviewcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "primeviewcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 71e39a59a5907e9b8a8dba58d36eee50 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-primeviewcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-primeviewprobe/meta.yaml b/recipes/bioconductor-primeviewprobe/meta.yaml index 9f3a51a54987e..73bf4d160c889 100644 --- a/recipes/bioconductor-primeviewprobe/meta.yaml +++ b/recipes/bioconductor-primeviewprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "primeviewprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 87cc56a8da4fb742ab1558ce1d3d26cc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-primeviewprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-primirtss/meta.yaml b/recipes/bioconductor-primirtss/meta.yaml index 8c7d1f158dfb0..7ba8ad1cb4071 100644 --- a/recipes/bioconductor-primirtss/meta.yaml +++ b/recipes/bioconductor-primirtss/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "primirTSS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dfadad951f97d12b55332c5eff234d6 + md5: ead295f564f0e3c4c9d9c8bfa568e745 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-primirtss", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - 'bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - 'r-dplyr >=0.7.6' - 'r-purrr >=0.2.5' @@ -42,18 +43,18 @@ requirements: - 'r-tibble >=1.4.2' - 'r-tidyr >=0.8.1' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - 'bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - 'r-dplyr >=0.7.6' - 'r-purrr >=0.2.5' diff --git a/recipes/bioconductor-prince/meta.yaml b/recipes/bioconductor-prince/meta.yaml index a2cef262d826a..f898336ea68c0 100644 --- a/recipes/bioconductor-prince/meta.yaml +++ b/recipes/bioconductor-prince/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "PrInCE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4341628e51ae0ee0129c0d8036bab10d + md5: 98e7e0b9a7e620e0e4ab55436b5c289b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prince", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - 'r-dplyr >=0.7.4' - 'r-forecast >=8.2' @@ -39,8 +40,8 @@ requirements: - 'r-tester >=0.1.7' - 'r-tidyr >=0.8.99' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - 'r-dplyr >=0.7.4' - 'r-forecast >=8.2' diff --git a/recipes/bioconductor-proactiv/meta.yaml b/recipes/bioconductor-proactiv/meta.yaml index b3149a802a75b..475fc41ef36eb 100644 --- a/recipes/bioconductor-proactiv/meta.yaml +++ b/recipes/bioconductor-proactiv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "proActiv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4681528e213cee2381e40f66ba06a214 + md5: 3aaa83b78fb2e017358c24ab185506ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proactiv", max_pin="x.x") }}' noarch: generic # Suggests: testthat, rmarkdown, knitr, Rtsne, gridExtra requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -40,16 +41,16 @@ requirements: - r-scales - r-tibble run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-probamr/meta.yaml b/recipes/bioconductor-probamr/meta.yaml index 52604dbff010f..2afdefe586872 100644 --- a/recipes/bioconductor-probamr/meta.yaml +++ b/recipes/bioconductor-probamr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "proBAMr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e55435900db79ff363dd274ae7abc343 + md5: 0b5a894a54fb0d56f940b75e025c0d47 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-probamr", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-process/meta.yaml b/recipes/bioconductor-process/meta.yaml index 6d3f897f897f6..3d680a0f15bea 100644 --- a/recipes/bioconductor-process/meta.yaml +++ b/recipes/bioconductor-process/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "PROcess" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 605613c9cdcffbaf4c7d332e93e66937 + md5: 9a9b6e6d31c1c45fb08e1f7cf00f0170 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-process", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-icens >=1.72.0,<1.73.0' + - 'bioconductor-icens >=1.74.0,<1.75.0' - r-base run: - - 'bioconductor-icens >=1.72.0,<1.73.0' + - 'bioconductor-icens >=1.74.0,<1.75.0' - r-base test: commands: diff --git a/recipes/bioconductor-procoil/meta.yaml b/recipes/bioconductor-procoil/meta.yaml index 679fe920302b5..c05235fe4603e 100644 --- a/recipes/bioconductor-procoil/meta.yaml +++ b/recipes/bioconductor-procoil/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "procoil" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d4ab86952e13fcb2719019f2f21c40d8 + md5: 5536c056587bff646a606dec3437fa5d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-procoil", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-kebabs >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-kebabs >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-kebabs >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-kebabs >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-proda/meta.yaml b/recipes/bioconductor-proda/meta.yaml index 95ef3bb8a2674..5a6afff59963e 100644 --- a/recipes/bioconductor-proda/meta.yaml +++ b/recipes/bioconductor-proda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "proDA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7900e3d2213cb542d3095140fe54bda3 + md5: 906f58f351f6a657aafcb3f6a670cc9f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proda", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr, tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-extradistr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-extradistr test: diff --git a/recipes/bioconductor-prodata/meta.yaml b/recipes/bioconductor-prodata/meta.yaml index f64eac848efe7..8b8c68696cd5a 100644 --- a/recipes/bioconductor-prodata/meta.yaml +++ b/recipes/bioconductor-prodata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ProData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a4c17dd4a55240fdeab52f3301e19f6 + md5: 73f3449db86899c83d61173f6bd02a79 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prodata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prodata/post-link.sh b/recipes/bioconductor-prodata/post-link.sh index 966db4c8593cf..fd3bd80e9d246 100644 --- a/recipes/bioconductor-prodata/post-link.sh +++ b/recipes/bioconductor-prodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prodata-1.38.0" +installBiocDataPackage.sh "prodata-1.40.0" diff --git a/recipes/bioconductor-profileplyr/meta.yaml b/recipes/bioconductor-profileplyr/meta.yaml index 080c30cc6af96..760ca42727502 100644 --- a/recipes/bioconductor-profileplyr/meta.yaml +++ b/recipes/bioconductor-profileplyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "profileplyr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3975e32d9f4494ea85312b1a009ac8ce + md5: bc6ac2ac1050660a2cb45a11ebbd1a67 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-profileplyr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown, png, Cairo requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-enrichedheatmap >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgreat >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-soggi >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgreat >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-soggi >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base @@ -54,25 +55,25 @@ requirements: - r-tidyr - r-tiff run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-enrichedheatmap >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgreat >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-soggi >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgreat >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-soggi >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base diff --git a/recipes/bioconductor-profilescoredist/meta.yaml b/recipes/bioconductor-profilescoredist/meta.yaml index bedbfef8f41f1..7be23f4741047 100644 --- a/recipes/bioconductor-profilescoredist/meta.yaml +++ b/recipes/bioconductor-profilescoredist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "profileScoreDist" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61e62770ee189714e138987ad490fb96 + md5: 59d0f0bd369e20aa7be8352e5cf46830 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-profilescoredist", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, MotifDb requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-progeny/meta.yaml b/recipes/bioconductor-progeny/meta.yaml index cbb4a9c2e9064..b6dfccddd3534 100644 --- a/recipes/bioconductor-progeny/meta.yaml +++ b/recipes/bioconductor-progeny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "progeny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bdb55828f59d804d05e3bddb43c20367 + md5: 9798ea9424f4115b980496038619f009 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-progeny", max_pin="x.x") }}' noarch: generic # Suggests: airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' - r-base - r-dplyr - r-ggplot2 @@ -31,8 +32,8 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-decoupler >=2.6.0,<2.7.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-decoupler >=2.8.0,<2.9.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-projectr/meta.yaml b/recipes/bioconductor-projectr/meta.yaml index a6ff976b635cf..b84111fbdebb1 100644 --- a/recipes/bioconductor-projectr/meta.yaml +++ b/recipes/bioconductor-projectr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "projectR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,53 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef6439c75fc8aa471312a4a03dde8dfb + md5: 7351d9a1c593186a6adb189ebd3ff9d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-projectr", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap +# Suggests: BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools, rmarkdown, knitr, rmarkdown, ComplexHeatmap, gplots requirements: host: - - 'bioconductor-cogaps >=3.19.0,<3.20.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-cluster + - r-cowplot - r-dplyr - r-ggalluvial - r-ggplot2 + - r-ggrepel + - r-matrix + - r-matrixmodels - r-nmf - r-rcolorbrewer - r-reshape2 - r-rocr - r-scales + - r-tsne + - r-umap - r-viridis run: - - 'bioconductor-cogaps >=3.19.0,<3.20.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-cluster + - r-cowplot - r-dplyr - r-ggalluvial - r-ggplot2 + - r-ggrepel + - r-matrix + - r-matrixmodels - r-nmf - r-rcolorbrewer - r-reshape2 - r-rocr - r-scales + - r-tsne + - r-umap - r-viridis test: commands: diff --git a/recipes/bioconductor-proloc/meta.yaml b/recipes/bioconductor-proloc/meta.yaml index 9a4fbacdab1db..230e1d8a522c7 100644 --- a/recipes/bioconductor-proloc/meta.yaml +++ b/recipes/bioconductor-proloc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.1" %} +{% set version = "1.42.0" %} {% set name = "pRoloc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4300b0c722aeef0f0fd76d37bcb56149 + md5: 309ce5a09f91050bdf916ab18389d7a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proloc", max_pin="x.x") }}' # Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-mlinterfaces >=1.80.0,<1.81.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-caret - r-class @@ -56,12 +57,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-mlinterfaces >=1.80.0,<1.81.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-caret - r-class diff --git a/recipes/bioconductor-prolocdata/meta.yaml b/recipes/bioconductor-prolocdata/meta.yaml index caef916fdfc2a..fb5d1764fc6b7 100644 --- a/recipes/bioconductor-prolocdata/meta.yaml +++ b/recipes/bioconductor-prolocdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "pRolocdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3cf7b5644c6af5a158d0291d9b597cd2 + md5: 8aafd04221b21588077788ec79272e1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prolocdata", max_pin="x.x") }}' noarch: generic # Suggests: pRoloc (>= 1.13.8), testthat, SummarizedExperiment requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prolocdata/post-link.sh b/recipes/bioconductor-prolocdata/post-link.sh index bc590e3d40f51..58c959a4f2622 100644 --- a/recipes/bioconductor-prolocdata/post-link.sh +++ b/recipes/bioconductor-prolocdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prolocdata-1.38.0" +installBiocDataPackage.sh "prolocdata-1.40.0" diff --git a/recipes/bioconductor-prolocgui/meta.yaml b/recipes/bioconductor-prolocgui/meta.yaml index 654796709e1ee..92ba43b5a6797 100644 --- a/recipes/bioconductor-prolocgui/meta.yaml +++ b/recipes/bioconductor-prolocgui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "pRolocGUI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9696984952c5868c1550fbb89db5eb6d + md5: a9947bbed5501a1c2c68f7c35364c1da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prolocgui", max_pin="x.x") }}' noarch: generic # Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-proloc >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-proloc >=1.42.0,<1.43.0' - r-base - r-colorspace - r-colourpicker @@ -39,10 +40,10 @@ requirements: - r-shinyjs - r-shinywidgets run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-proloc >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-proloc >=1.42.0,<1.43.0' - r-base - r-colorspace - r-colourpicker diff --git a/recipes/bioconductor-promise/build_failure.linux-64.yaml b/recipes/bioconductor-promise/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..cf404d42c073a --- /dev/null +++ b/recipes/bioconductor-promise/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5b781e0fa5e8b6eb7b4e980f15193540530dbd5b63b9a1fb5db07f32907673c6 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.2s + conda-forge/linux-64 + conda-forge/noarch + bioconda/linux-64 + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gbioconda/linux-64 + [] 1.3s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 + pkgs/main/noarch + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.4s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/linux-64 100% + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/main/linux-64 + [] 1.5s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.6s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch [2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0G[] 1.7s + conda-forge/linux-64 + conda-forge/noarch + pkgs/main/noarch + pkgs/r/linux-64 + pkgs/r/noarch 100%[2K[1A[2K[1A[2K[1A[2K[1A[2K[1A[2K[0Gpkgs/r/noarch + pkgs/main/noarch + [] 1.8s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0G[] 1.9s + conda-forge/linux-64 + conda-forge/noarch 100% + pkgs/r/linux-64 [2K[1A[2K[1A[2K[1A[2K[0Gconda-forge/noarch + pkgs/r/linux-64 + [] 2.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 2.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.6s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.7s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.8s + conda-forge/linux-64 [2K[1A[2K[0G[] 3.9s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.0s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.1s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.2s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.3s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.4s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.5s + conda-forge/linux-64 [2K[1A[2K[0G[] 4.6s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.7s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.8s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 4.9s + conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s + conda-forge/linux-64 100%[2K[1A[2K[0Gconda-forge/linux-64 + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.2MB/s 0.0s + opt/conda/conda-bld/noarch 748.0 B @ 15.0MB/s 0.0s + [?25hTraceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test + environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, + File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1052, in create_env + display_actions(actions, index) + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in display_actions + actions['LINK'] = [index[d] for d in actions['LINK']] + File "/opt/conda/lib/python3.8/site-packages/conda/exports.py", line 204, in + actions['LINK'] = [index[d] for d in actions['LINK']] + KeyError: Dist(channel='conda-forge', dist_name='python-3.12.1-hab00c5b_0_cpython', name='python', fmt='.conda', version='3.12.1', build_string='hab00c5b_0_cpython', build_number=0, base_url=None, platform=None) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-promise/meta.yaml b/recipes/bioconductor-promise/meta.yaml index aeac8a19e26de..17795839b7288 100644 --- a/recipes/bioconductor-promise/meta.yaml +++ b/recipes/bioconductor-promise/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "PROMISE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89f8708d951f68b7e63c5cb57cc4b182 + md5: ad7b8b2fcd0ba52ad47eb9ff23097a4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-promise", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' - r-base test: commands: diff --git a/recipes/bioconductor-proper/meta.yaml b/recipes/bioconductor-proper/meta.yaml index 0aa0c569bc782..4bb762b00bf39 100644 --- a/recipes/bioconductor-proper/meta.yaml +++ b/recipes/bioconductor-proper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "PROPER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95670318c035e13983013b9802b91a8e + md5: 6f91ce4b3f5feee476a991fc1072c521 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,DESeq2,DSS,knitr requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base test: commands: diff --git a/recipes/bioconductor-props/meta.yaml b/recipes/bioconductor-props/meta.yaml index e22e75404825b..31a4de48bbbe6 100644 --- a/recipes/bioconductor-props/meta.yaml +++ b/recipes/bioconductor-props/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "PROPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00746ca2b4edfa8b4d462491b777039f + md5: 20b285908014c5e85775518ea72349c0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-props", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-bnlearn - r-reshape2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-bnlearn - r-reshape2 diff --git a/recipes/bioconductor-prostar/meta.yaml b/recipes/bioconductor-prostar/meta.yaml index 1946540dc3a1b..7833b98683be8 100644 --- a/recipes/bioconductor-prostar/meta.yaml +++ b/recipes/bioconductor-prostar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.1" %} +{% set version = "1.34.3" %} {% set name = "Prostar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 24a2213ce5e4ff844a53fdc1453d5abe + md5: ab3095af56a61bfe4fe81279dffcae21 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostar", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, BiocManager, testthat, shinyTree, knitr, colourpicker, gtools, XML, R.utils, RColorBrewer, DT, shinyWidgets, sass, rclipboard +# Suggests: BiocStyle, BiocManager, testthat requirements: host: - - 'bioconductor-dapar >=1.32.0,<1.33.0' - - 'bioconductor-dapardata >=1.30.0,<1.31.0' + - 'bioconductor-dapar >=1.34.0,<1.35.0' + - 'bioconductor-dapardata >=1.32.0,<1.33.0' - r-base + - r-colourpicker - r-data.table + - r-dt - r-future - r-ggplot2 - r-gplots + - r-gtools - r-highcharter - r-htmlwidgets + - r-knitr - r-later - r-promises + - r-r.utils + - r-rclipboard + - r-rcolorbrewer - r-rhandsontable + - r-sass - r-shiny - r-shinyace - r-shinybs @@ -40,22 +49,33 @@ requirements: - r-shinyjqui - r-shinyjs - r-shinythemes + - r-shinytree + - r-shinywidgets - r-tibble - r-vioplot - r-webshot + - r-xml run: - - 'bioconductor-dapar >=1.32.0,<1.33.0' - - 'bioconductor-dapardata >=1.30.0,<1.31.0' + - 'bioconductor-dapar >=1.34.0,<1.35.0' + - 'bioconductor-dapardata >=1.32.0,<1.33.0' - r-base + - r-colourpicker - r-data.table + - r-dt - r-future - r-ggplot2 - r-gplots + - r-gtools - r-highcharter - r-htmlwidgets + - r-knitr - r-later - r-promises + - r-r.utils + - r-rclipboard + - r-rcolorbrewer - r-rhandsontable + - r-sass - r-shiny - r-shinyace - r-shinybs @@ -63,9 +83,12 @@ requirements: - r-shinyjqui - r-shinyjs - r-shinythemes + - r-shinytree + - r-shinywidgets - r-tibble - r-vioplot - r-webshot + - r-xml test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancercamcap/meta.yaml b/recipes/bioconductor-prostatecancercamcap/meta.yaml index 4d29f05598ac7..b01bd5c2727ae 100644 --- a/recipes/bioconductor-prostatecancercamcap/meta.yaml +++ b/recipes/bioconductor-prostatecancercamcap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "prostateCancerCamcap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff2a0d04db22bce6d2d1722e718edeb5 + md5: 5a27ee47f07162569e5e1e06ffd69886 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostatecancercamcap", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancercamcap/post-link.sh b/recipes/bioconductor-prostatecancercamcap/post-link.sh index f05e7e90c4971..884e3a7cda119 100644 --- a/recipes/bioconductor-prostatecancercamcap/post-link.sh +++ b/recipes/bioconductor-prostatecancercamcap/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancercamcap-1.28.0" +installBiocDataPackage.sh "prostatecancercamcap-1.30.0" diff --git a/recipes/bioconductor-prostatecancergrasso/meta.yaml b/recipes/bioconductor-prostatecancergrasso/meta.yaml index a12622be233ab..642718a61eedf 100644 --- a/recipes/bioconductor-prostatecancergrasso/meta.yaml +++ b/recipes/bioconductor-prostatecancergrasso/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "prostateCancerGrasso" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cc2f4713d5950c0fcd99dd320adbdb2d + md5: c331c996d943a14687439dfdf37b8029 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostatecancergrasso", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancergrasso/post-link.sh b/recipes/bioconductor-prostatecancergrasso/post-link.sh index b7bec21917d26..544c52ea34897 100644 --- a/recipes/bioconductor-prostatecancergrasso/post-link.sh +++ b/recipes/bioconductor-prostatecancergrasso/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancergrasso-1.28.0" +installBiocDataPackage.sh "prostatecancergrasso-1.30.0" diff --git a/recipes/bioconductor-prostatecancerstockholm/meta.yaml b/recipes/bioconductor-prostatecancerstockholm/meta.yaml index 09bd6e6c8db4f..483e6a2239ac4 100644 --- a/recipes/bioconductor-prostatecancerstockholm/meta.yaml +++ b/recipes/bioconductor-prostatecancerstockholm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "prostateCancerStockholm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2ec2d712681d173c561a57451acae94 + md5: 49326bf3b6f66be78fa1e6d6768b5538 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostatecancerstockholm", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancerstockholm/post-link.sh b/recipes/bioconductor-prostatecancerstockholm/post-link.sh index 09ddf03cf328d..b347e68cf857d 100644 --- a/recipes/bioconductor-prostatecancerstockholm/post-link.sh +++ b/recipes/bioconductor-prostatecancerstockholm/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancerstockholm-1.28.0" +installBiocDataPackage.sh "prostatecancerstockholm-1.30.0" diff --git a/recipes/bioconductor-prostatecancertaylor/meta.yaml b/recipes/bioconductor-prostatecancertaylor/meta.yaml index 5babe7d413b01..00ac0962d4074 100644 --- a/recipes/bioconductor-prostatecancertaylor/meta.yaml +++ b/recipes/bioconductor-prostatecancertaylor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "prostateCancerTaylor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d41f91c630547581ccabf8159a79d889 + md5: c90ff79776e9a658d4cf05e9a29706a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostatecancertaylor", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery, org.Hs.eg.db requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancertaylor/post-link.sh b/recipes/bioconductor-prostatecancertaylor/post-link.sh index f127abf7081f2..814031af6bc79 100644 --- a/recipes/bioconductor-prostatecancertaylor/post-link.sh +++ b/recipes/bioconductor-prostatecancertaylor/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancertaylor-1.28.0" +installBiocDataPackage.sh "prostatecancertaylor-1.30.0" diff --git a/recipes/bioconductor-prostatecancervarambally/meta.yaml b/recipes/bioconductor-prostatecancervarambally/meta.yaml index b88d542ce7ef5..65f3a1df66b5c 100644 --- a/recipes/bioconductor-prostatecancervarambally/meta.yaml +++ b/recipes/bioconductor-prostatecancervarambally/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "prostateCancerVarambally" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8008e839c2e72aee55433f2361efb0cb + md5: cf8fc1872af8c5c2b47372ce94ed4c5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prostatecancervarambally", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-prostatecancervarambally/post-link.sh b/recipes/bioconductor-prostatecancervarambally/post-link.sh index f89b0acc823e7..6a6d1ca836881 100644 --- a/recipes/bioconductor-prostatecancervarambally/post-link.sh +++ b/recipes/bioconductor-prostatecancervarambally/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancervarambally-1.28.0" +installBiocDataPackage.sh "prostatecancervarambally-1.30.0" diff --git a/recipes/bioconductor-proteinprofiles/meta.yaml b/recipes/bioconductor-proteinprofiles/meta.yaml index 45df829cdd2d0..ac403d2f66889 100644 --- a/recipes/bioconductor-proteinprofiles/meta.yaml +++ b/recipes/bioconductor-proteinprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "proteinProfiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ffcc07e3926008e6f478089073aa6443 + md5: 491483ff7b360413ae0eafa5ac07de14 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proteinprofiles", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: diff --git a/recipes/bioconductor-proteodisco/meta.yaml b/recipes/bioconductor-proteodisco/meta.yaml index 0a74dbf806d1b..6e6ba09dfda9e 100644 --- a/recipes/bioconductor-proteodisco/meta.yaml +++ b/recipes/bioconductor-proteodisco/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ProteoDisco" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3f18bfe0ae324151bd6a6ff32f1ea99 + md5: f69597248b6cbbdb2c1029a1dd3b39cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proteodisco", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi (>= 1.54.1), BSgenome (>= 1.60.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3), BiocStyle (>= 2.20.1), DelayedArray (>= 0.18.0), devtools (>= 2.4.2), knitr (>= 1.33), matrixStats (>= 0.59.0), markdown (>= 1.1), org.Hs.eg.db (>= 3.13.0), purrr (>= 0.3.4), RCurl (>= 1.98.1.3), readr (>= 1.4.0), ggplot2 (>= 3.3.5), rmarkdown (>= 2.9), rtracklayer (>= 1.52.0), seqinr (>= 4.2.8), stringr (>= 1.4.0), reshape2 (>= 1.4.4), scales (>= 1.1.1), testthat (>= 3.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-cleaver >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-cleaver >=1.40.0,<1.41.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-checkmate >=2.0.0' - 'r-dplyr >=1.0.6' @@ -41,17 +42,17 @@ requirements: - 'r-tibble >=3.1.2' - 'r-tidyr >=1.1.3' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-cleaver >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-cleaver >=1.40.0,<1.41.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-checkmate >=2.0.0' - 'r-dplyr >=1.0.6' diff --git a/recipes/bioconductor-proteomm/meta.yaml b/recipes/bioconductor-proteomm/meta.yaml index 5207b937a4d19..18d262626a71c 100644 --- a/recipes/bioconductor-proteomm/meta.yaml +++ b/recipes/bioconductor-proteomm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ProteoMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9f13f6998275db7f5a4374f3ae69883 + md5: 6497729c8cc0221c898927dcddeb00e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proteomm", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-gdata - r-ggplot2 @@ -29,7 +30,7 @@ requirements: - r-gtools - r-matrixstats run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-gdata - r-ggplot2 diff --git a/recipes/bioconductor-protgear/meta.yaml b/recipes/bioconductor-protgear/meta.yaml index 97862f28cf361..6d3a0b7331dc4 100644 --- a/recipes/bioconductor-protgear/meta.yaml +++ b/recipes/bioconductor-protgear/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "protGear" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d7b1ec8bb2be4491137f53da1b9f5f7 + md5: db63dca71894a3ebbf3b8b78512bccb4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-protgear", max_pin="x.x") }}' noarch: generic # Suggests: gridExtra (>= 2.3), png (>= 0.1-7) , magick (>= 2.7.3) , ggplotify (>= 0.1.0) , scales (>= 1.1.1) , shinythemes (>= 1.2.0) , shinyjs (>= 2.0.0) , shinyWidgets (>= 0.6.2) , shinycssloaders (>= 1.0.0) , shinyalert (>= 3.0.0) , shinyFiles (>= 0.9.1) , shinyFeedback (>= 0.3.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-data.table >=1.14.0' - 'r-dplyr >=0.8.0' @@ -54,10 +55,10 @@ requirements: - 'r-tibble >=3.1.0' - 'r-tidyr >=1.1.3' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - 'r-data.table >=1.14.0' - 'r-dplyr >=0.8.0' diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml index 15ba078511ed3..99dbefecd9faf 100644 --- a/recipes/bioconductor-protgenerics/meta.yaml +++ b/recipes/bioconductor-protgenerics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "ProtGenerics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7848b0ce11174fd3e995eb39dc57766a + md5: 5d55c00588169aa089bb457e2d94669a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-protgenerics", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: diff --git a/recipes/bioconductor-psea/meta.yaml b/recipes/bioconductor-psea/meta.yaml index d3bcfe4d2b3da..2460bda29bef8 100644 --- a/recipes/bioconductor-psea/meta.yaml +++ b/recipes/bioconductor-psea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "PSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dfe8429c4952bb970f612fb15cfe8545 + md5: c8f9f8210c265d722d76668e19a6fd7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-psea", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-psichomics/meta.yaml b/recipes/bioconductor-psichomics/meta.yaml index cf57efd937530..34f50e50ef81c 100644 --- a/recipes/bioconductor-psichomics/meta.yaml +++ b/recipes/bioconductor-psichomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "psichomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5a9ad76e280bfbe775fda70657d72adc + md5: 8d6d1c34972e5d4b389d9263ab2077db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-psichomics", max_pin="x.x") }}' # Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-colourpicker @@ -59,13 +60,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-colourpicker diff --git a/recipes/bioconductor-psmatch/meta.yaml b/recipes/bioconductor-psmatch/meta.yaml index 2946b78c9dfa2..86c4f75515374 100644 --- a/recipes/bioconductor-psmatch/meta.yaml +++ b/recipes/bioconductor-psmatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "PSMatch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17a718dd3fa26d78a2584f90bc5b0631 + md5: 4c63ca3d541af4e5925bcc2bde7d67ea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-psmatch", max_pin="x.x") }}' noarch: generic # Suggests: msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-igraph - r-matrix run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-igraph - r-matrix diff --git a/recipes/bioconductor-psygenet2r/meta.yaml b/recipes/bioconductor-psygenet2r/meta.yaml index d8785e016a310..4550ccfe6407e 100644 --- a/recipes/bioconductor-psygenet2r/meta.yaml +++ b/recipes/bioconductor-psygenet2r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.2" %} +{% set version = "1.34.0" %} {% set name = "psygenet2r" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ce5ce92ebd24818a539a905621b0f4e2 + md5: 69234da568b765050beb79aa46205114 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-psygenet2r", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-bgeedb >=2.26.0,<2.27.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-bgeedb >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-ggplot2 - r-igraph @@ -34,11 +35,11 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-bgeedb >=2.26.0,<2.27.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-bgeedb >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-ggplot2 - r-igraph diff --git a/recipes/bioconductor-ptairdata/meta.yaml b/recipes/bioconductor-ptairdata/meta.yaml index 65052ec0ce765..47412396819e7 100644 --- a/recipes/bioconductor-ptairdata/meta.yaml +++ b/recipes/bioconductor-ptairdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ptairData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ede739875473864ed372a4fb877b1852 + md5: eea0fcfdd0047d72092a3b6beb326129 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ptairdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-signal run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-signal - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ptairdata/post-link.sh b/recipes/bioconductor-ptairdata/post-link.sh index 1f8d934053b1f..8d2982bffafe3 100644 --- a/recipes/bioconductor-ptairdata/post-link.sh +++ b/recipes/bioconductor-ptairdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ptairdata-1.8.0" +installBiocDataPackage.sh "ptairdata-1.10.0" diff --git a/recipes/bioconductor-ptairms/meta.yaml b/recipes/bioconductor-ptairms/meta.yaml index f69b15f2e94b9..dbf733b5430bc 100644 --- a/recipes/bioconductor-ptairms/meta.yaml +++ b/recipes/bioconductor-ptairms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ptairMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d7e194913f9006f5782be7aa4944714 + md5: 771ce745db55fad5684a47026df33abe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ptairms", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData, ropls requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-bit64 - r-chron @@ -46,9 +47,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-bit64 - r-chron @@ -80,6 +81,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Pre-processing PTR-TOF-MS Data' - description: 'This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the ''sample by features'' table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and quantification, feature alignment, missing value imputation and feature annotation. Applications to exhaled air and cell culture in headspace are described in the vignettes and examples. This package was used for data analysis of Gassin Delyle study on adults undergoing invasive mechanical ventilation in the intensive care unit due to severe COVID-19 or non-COVID-19 acute respiratory distress syndrome (ARDS), and permit to identfy four potentiel biomarquers of the infection.' + description: 'This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the ''sample by features'' table of peak intensities in addition to the sample and feature metadata (as a singl=1.56.0,<1.57.0' - - 'bioconductor-lobstahs >=1.26.0,<1.27.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-lobstahs >=1.28.0,<1.29.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-camera >=1.56.0,<1.57.0' - - 'bioconductor-lobstahs >=1.26.0,<1.27.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-camera >=1.58.0,<1.59.0' + - 'bioconductor-lobstahs >=1.28.0,<1.29.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pth2o2lipids/post-link.sh b/recipes/bioconductor-pth2o2lipids/post-link.sh index 1a5c3167d93b6..db6d6c3fc4d12 100644 --- a/recipes/bioconductor-pth2o2lipids/post-link.sh +++ b/recipes/bioconductor-pth2o2lipids/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pth2o2lipids-1.26.0" +installBiocDataPackage.sh "pth2o2lipids-1.28.0" diff --git a/recipes/bioconductor-puma/meta.yaml b/recipes/bioconductor-puma/meta.yaml index c7823e3ecf680..991e8eb47bf36 100644 --- a/recipes/bioconductor-puma/meta.yaml +++ b/recipes/bioconductor-puma/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.42.0" %} +{% set version = "3.44.0" %} {% set name = "puma" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ec485bb2cd3bc9d97a2badb8b1c0be2d + md5: ed1d90c9c9b7751611b0f32edf0a1ffb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-puma", max_pin="x.x") }}' # Suggests: pumadata, affydata, snow, limma, ROCR,annotate requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-mclust - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - r-base - r-mclust build: diff --git a/recipes/bioconductor-pumadata/meta.yaml b/recipes/bioconductor-pumadata/meta.yaml index b67c027c521de..a621ddfcce813 100644 --- a/recipes/bioconductor-pumadata/meta.yaml +++ b/recipes/bioconductor-pumadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "pumadata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8201e94e0c66444c72b8f45bd3ca7020 + md5: 811d6234d1d4e310beb7111601b157b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pumadata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-puma >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-puma >=3.44.0,<3.45.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-puma >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-puma >=3.44.0,<3.45.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pumadata/post-link.sh b/recipes/bioconductor-pumadata/post-link.sh index a66648cc03439..1b94fc5e7a3cf 100644 --- a/recipes/bioconductor-pumadata/post-link.sh +++ b/recipes/bioconductor-pumadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pumadata-2.36.0" +installBiocDataPackage.sh "pumadata-2.38.0" diff --git a/recipes/bioconductor-purecn/meta.yaml b/recipes/bioconductor-purecn/meta.yaml index 2c5bcc9a97740..a34ed6b085135 100644 --- a/recipes/bioconductor-purecn/meta.yaml +++ b/recipes/bioconductor-purecn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.4" %} +{% set version = "2.8.1" %} {% set name = "PureCN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ec5551dfa20ade4fa9d0bbb6767709c + md5: d668ed7c332244073d26762dd291004f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-purecn", max_pin="x.x") }}' noarch: generic # Suggests: BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-futile.logger @@ -45,20 +46,20 @@ requirements: - r-rcolorbrewer - r-vgam run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-futile.logger diff --git a/recipes/bioconductor-pvac/meta.yaml b/recipes/bioconductor-pvac/meta.yaml index 66f2c8112a2a8..904378bd67a73 100644 --- a/recipes/bioconductor-pvac/meta.yaml +++ b/recipes/bioconductor-pvac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "pvac" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: abfcf7faff5f1bc03741c07c72eb6c29 + md5: ae148a3c65e5b6efc44cfea7d208d918 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pvac", max_pin="x.x") }}' noarch: generic # Suggests: pbapply, affydata, ALLMLL, genefilter requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-pvca/meta.yaml b/recipes/bioconductor-pvca/meta.yaml index d0aad607a7176..c02a34e9d4f84 100644 --- a/recipes/bioconductor-pvca/meta.yaml +++ b/recipes/bioconductor-pvca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "pvca" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e0f8e4f5b7de7c8a1eac5199675c140c + md5: dcc72a578e6ec7d738fab213c4d27e20 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pvca", max_pin="x.x") }}' noarch: generic # Suggests: golubEsets requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-lme4 - r-matrix run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-lme4 - r-matrix diff --git a/recipes/bioconductor-pviz/meta.yaml b/recipes/bioconductor-pviz/meta.yaml index 9e8a823fee0fd..83a82e5290e48 100644 --- a/recipes/bioconductor-pviz/meta.yaml +++ b/recipes/bioconductor-pviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "Pviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a6f2ef898de7e8a4fb115b42f651872 + md5: 1a1513067c6a873f9523f20eb85f2878 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pviz", max_pin="x.x") }}' noarch: generic # Suggests: knitr, pepDat requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table test: diff --git a/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml b/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml index 6fb8ca4fd431f..0fc2d9e14d907 100644 --- a/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.34.0" %} +{% set version = "4.36.0" %} {% set name = "PWMEnrich.Dmelanogaster.background" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 907d3ff8c0fb527c01dbf099a075f732 + md5: b671ba0cff5c0c6017fd3f72d0afc547 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pwmenrich.dmelanogaster.background", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base run: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh b/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh index 46d30a6d9777d..f9aedbea31b16 100644 --- a/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pwmenrich.dmelanogaster.background-4.34.0" +installBiocDataPackage.sh "pwmenrich.dmelanogaster.background-4.36.0" diff --git a/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml b/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml index f89270babbb6d..2cc73594c1eb4 100644 --- a/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.34.0" %} +{% set version = "4.36.0" %} {% set name = "PWMEnrich.Hsapiens.background" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02021cd798df13ad0f124fdc481ebe33 + md5: 7c7b177c29fc31c7546d4e7160a9b977 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pwmenrich.hsapiens.background", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base run: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh b/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh index 00e6fb83781aa..5fd33b45910e0 100644 --- a/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pwmenrich.hsapiens.background-4.34.0" +installBiocDataPackage.sh "pwmenrich.hsapiens.background-4.36.0" diff --git a/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml b/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml index 9a674ea664f6b..14f7a80059072 100644 --- a/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.34.0" %} +{% set version = "4.36.0" %} {% set name = "PWMEnrich.Mmusculus.background" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e81cb70d4a4850829fa5a83003c75404 + md5: 5d54401a941d1efe7148da2ddc714d65 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pwmenrich.mmusculus.background", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base run: - - 'bioconductor-pwmenrich >=4.36.0,<4.37.0' + - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh b/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh index cf21e15375be7..b583b5d163e55 100644 --- a/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pwmenrich.mmusculus.background-4.34.0" +installBiocDataPackage.sh "pwmenrich.mmusculus.background-4.36.0" diff --git a/recipes/bioconductor-pwmenrich/meta.yaml b/recipes/bioconductor-pwmenrich/meta.yaml index 4b8dbaf802a26..e3e4139a4902f 100644 --- a/recipes/bioconductor-pwmenrich/meta.yaml +++ b/recipes/bioconductor-pwmenrich/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.36.0" %} +{% set version = "4.38.0" %} {% set name = "PWMEnrich" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d26185e888435e846dec08f4f6b566d + md5: ced56cbfbab381f5736f4f58fe26b9f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pwmenrich", max_pin="x.x") }}' noarch: generic # Suggests: MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base - r-evd - r-gdata run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base - r-evd - r-gdata diff --git a/recipes/bioconductor-pwomics/meta.yaml b/recipes/bioconductor-pwomics/meta.yaml index dfd46023a8190..9ad50be8600cb 100644 --- a/recipes/bioconductor-pwomics/meta.yaml +++ b/recipes/bioconductor-pwomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "pwOmics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f2c44535d54b08ef853fd4d7fea7092 + md5: fcb2cc2e104a970552cc4f45ce4a1197 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pwomics", max_pin="x.x") }}' noarch: generic -# Suggests: ebdbNet, longitudinal, Mfuzz +# Suggests: ebdbNet, longitudinal, Mfuzz, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbiopaxparser >=2.40.0,<2.41.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbiopaxparser >=2.42.0,<2.43.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-data.table - r-gplots - r-igraph run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbiopaxparser >=2.40.0,<2.41.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbiopaxparser >=2.42.0,<2.43.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-data.table - r-gplots diff --git a/recipes/bioconductor-pwrewas.data/meta.yaml b/recipes/bioconductor-pwrewas.data/meta.yaml index c7be770b6480c..3c654ffcdf181 100644 --- a/recipes/bioconductor-pwrewas.data/meta.yaml +++ b/recipes/bioconductor-pwrewas.data/meta.yaml @@ -27,7 +27,7 @@ requirements: - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qckitfastq/meta.yaml b/recipes/bioconductor-qckitfastq/meta.yaml index 459c1c90d6de9..ecb59cbec82ca 100644 --- a/recipes/bioconductor-qckitfastq/meta.yaml +++ b/recipes/bioconductor-qckitfastq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "qckitfastq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,7 +11,7 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3c41af38fcd03a1f5e2bf17aa58969c0 + md5: 60955b37d9eb0868da1c5ecd262334e8 patches: - shared_timed_mutex.patch build: @@ -19,13 +19,14 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qckitfastq", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, kableExtra, testthat # SystemRequirements: GNU make requirements: host: - - 'bioconductor-rseqan >=1.20.0,<1.21.0' - - 'bioconductor-seqtools >=1.34.0,<1.35.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-rseqan >=1.22.0,<1.23.0' + - 'bioconductor-seqtools >=1.36.0,<1.37.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr @@ -37,9 +38,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-rseqan >=1.20.0,<1.21.0' - - 'bioconductor-seqtools >=1.34.0,<1.35.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-rseqan >=1.22.0,<1.23.0' + - 'bioconductor-seqtools >=1.36.0,<1.37.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-qcmetrics/meta.yaml b/recipes/bioconductor-qcmetrics/meta.yaml index 9a0b45ade18c7..2cdd85a42a547 100644 --- a/recipes/bioconductor-qcmetrics/meta.yaml +++ b/recipes/bioconductor-qcmetrics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "qcmetrics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6285c583fa47f8be686d506160602efc + md5: 68f2a395be6986c02f8473dbe25ed621 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qcmetrics", max_pin="x.x") }}' noarch: generic # Suggests: affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-knitr - r-pander - r-xtable run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-knitr - r-pander diff --git a/recipes/bioconductor-qdnaseq.hg19/meta.yaml b/recipes/bioconductor-qdnaseq.hg19/meta.yaml index c3c0694654834..bd3148547dbbb 100644 --- a/recipes/bioconductor-qdnaseq.hg19/meta.yaml +++ b/recipes/bioconductor-qdnaseq.hg19/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "QDNAseq.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b81f056006151fd4a2f55935ee57f67 + md5: 2b663d8771f16d55db88ec3321942ead build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qdnaseq.hg19", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qdnaseq.hg19/post-link.sh b/recipes/bioconductor-qdnaseq.hg19/post-link.sh index 900524cd9f150..f95428a20b4fd 100644 --- a/recipes/bioconductor-qdnaseq.hg19/post-link.sh +++ b/recipes/bioconductor-qdnaseq.hg19/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qdnaseq.hg19-1.30.0" +installBiocDataPackage.sh "qdnaseq.hg19-1.32.0" diff --git a/recipes/bioconductor-qdnaseq.mm10/meta.yaml b/recipes/bioconductor-qdnaseq.mm10/meta.yaml index a39e1bbf1d1de..a14c48bb16146 100644 --- a/recipes/bioconductor-qdnaseq.mm10/meta.yaml +++ b/recipes/bioconductor-qdnaseq.mm10/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "QDNAseq.mm10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7c1a5cec6ee30213a4389b40979b9ef + md5: 2d7b80c2bec7146aec28384b7875acca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qdnaseq.mm10", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-qdnaseq >=1.36.0,<1.37.0' + - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qdnaseq.mm10/post-link.sh b/recipes/bioconductor-qdnaseq.mm10/post-link.sh index 6f9e4ae2877cd..05c6fcc404271 100644 --- a/recipes/bioconductor-qdnaseq.mm10/post-link.sh +++ b/recipes/bioconductor-qdnaseq.mm10/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qdnaseq.mm10-1.30.0" +installBiocDataPackage.sh "qdnaseq.mm10-1.32.0" diff --git a/recipes/bioconductor-qdnaseq/meta.yaml b/recipes/bioconductor-qdnaseq/meta.yaml index adfb87e341164..aae4b1e35a592 100644 --- a/recipes/bioconductor-qdnaseq/meta.yaml +++ b/recipes/bioconductor-qdnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "QDNAseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d44cd046b4d2157547009cb1fdfa442 + md5: 589b066b44091955991b4f66ac86b9ee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qdnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb (>= 1.6.0), future (>= 1.22.1), parallelly (>= 1.28.1), R.cache (>= 0.13.0), QDNAseq.hg19, QDNAseq.mm10 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-future.apply >=1.8.1' - 'r-matrixstats >=0.60.0' - 'r-r.utils >=2.9.0' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cghbase >=1.60.0,<1.61.0' - - 'bioconductor-cghcall >=2.62.0,<2.63.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cghbase >=1.62.0,<1.63.0' + - 'bioconductor-cghcall >=2.64.0,<2.65.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-future.apply >=1.8.1' - 'r-matrixstats >=0.60.0' diff --git a/recipes/bioconductor-qfeatures/meta.yaml b/recipes/bioconductor-qfeatures/meta.yaml index 720858efa736e..f071f392d180f 100644 --- a/recipes/bioconductor-qfeatures/meta.yaml +++ b/recipes/bioconductor-qfeatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "QFeatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7b1b85fe9194b0d05f0049c1a43ebb8 + md5: 6833061a024bb9783b7d9a85bc282a88 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qfeatures", max_pin="x.x") }}' noarch: generic # Suggests: SingleCellExperiment, Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-lazyeval - r-plotly run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-lazyeval diff --git a/recipes/bioconductor-qmtools/meta.yaml b/recipes/bioconductor-qmtools/meta.yaml index 2e6747f0bf6f8..8ec0b0553e167 100644 --- a/recipes/bioconductor-qmtools/meta.yaml +++ b/recipes/bioconductor-qmtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "qmtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3dd6957b8b5e757e4acaa92338fc289e + md5: 941d7cbf1dc8c2622fe97bda18a2bf49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qmtools", max_pin="x.x") }}' noarch: generic # Suggests: Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-heatmaply @@ -33,9 +34,9 @@ requirements: - r-scales - r-vim run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-heatmaply diff --git a/recipes/bioconductor-qpcrnorm/meta.yaml b/recipes/bioconductor-qpcrnorm/meta.yaml index 11bb25b31ea50..72c295aba9034 100644 --- a/recipes/bioconductor-qpcrnorm/meta.yaml +++ b/recipes/bioconductor-qpcrnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "qpcrNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 27b2a54f8a20b56b34273c690e85ca16 + md5: 43fa513309301e6d8e89fcef668c7b28 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qpcrnorm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-qpgraph/meta.yaml b/recipes/bioconductor-qpgraph/meta.yaml index ea0a0c777fd9d..4287b9ed5aeb4 100644 --- a/recipes/bioconductor-qpgraph/meta.yaml +++ b/recipes/bioconductor-qpgraph/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.2" %} +{% set version = "2.36.0" %} {% set name = "qpgraph" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c8599307a26a9048d0094ea30862da09 + md5: 10be7ba90f9349fb4de4aa84e6fecaa4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qpgraph", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-matrix >=1.5-0' - r-mvtnorm @@ -38,17 +39,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-matrix >=1.5-0' - r-mvtnorm diff --git a/recipes/bioconductor-qplexanalyzer/meta.yaml b/recipes/bioconductor-qplexanalyzer/meta.yaml index 10626e9250bcc..6b01c08b890cd 100644 --- a/recipes/bioconductor-qplexanalyzer/meta.yaml +++ b/recipes/bioconductor-qplexanalyzer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "qPLEXanalyzer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a45ddc801efbbb143d4bceb0edb67a7 + md5: d30edcfbf4e355e0c40bd7cf16d396fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qplexanalyzer", max_pin="x.x") }}' noarch: generic # Suggests: gridExtra, knitr, qPLEXdata, rmarkdown, statmod, testthat, UniProt.ws, vdiffr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-assertthat - r-base - 'r-dplyr >=1.0.0' @@ -44,13 +45,13 @@ requirements: - r-tidyr - r-tidyselect run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-assertthat - r-base - 'r-dplyr >=1.0.0' diff --git a/recipes/bioconductor-qplexdata/meta.yaml b/recipes/bioconductor-qplexdata/meta.yaml index 02aab7e2337f6..d72d4ac30f891 100644 --- a/recipes/bioconductor-qplexdata/meta.yaml +++ b/recipes/bioconductor-qplexdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "qPLEXdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ea69c2e1a071fd94fcb169af5c61422 + md5: af947f54391fc79c81308890b1e95d96 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qplexdata", max_pin="x.x") }}' noarch: generic +# Suggests: statmod requirements: host: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qplexanalyzer >=1.18.0,<1.19.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qplexanalyzer >=1.20.0,<1.21.0' - r-base - r-dplyr - r-knitr run: - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-qplexanalyzer >=1.18.0,<1.19.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-qplexanalyzer >=1.20.0,<1.21.0' - r-base - r-dplyr - r-knitr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qplexdata/post-link.sh b/recipes/bioconductor-qplexdata/post-link.sh index b3776da8b113c..5bfe1edb7e282 100644 --- a/recipes/bioconductor-qplexdata/post-link.sh +++ b/recipes/bioconductor-qplexdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qplexdata-1.18.0" +installBiocDataPackage.sh "qplexdata-1.20.0" diff --git a/recipes/bioconductor-qsea/meta.yaml b/recipes/bioconductor-qsea/meta.yaml index 25e311d360427..9bafebacc6db4 100644 --- a/recipes/bioconductor-qsea/meta.yaml +++ b/recipes/bioconductor-qsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "qsea" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8717b734a71f34dbf8b231134752afde + md5: 2891ba342f17500cee6391d1f388c3c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qsea", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hmmcopy >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hmmcopy >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-gtools - r-zoo - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hmmcopy >=1.42.0,<1.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hmmcopy >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-gtools - r-zoo diff --git a/recipes/bioconductor-qsmooth/meta.yaml b/recipes/bioconductor-qsmooth/meta.yaml index 6ed95bf40b208..659687e2f8c11 100644 --- a/recipes/bioconductor-qsmooth/meta.yaml +++ b/recipes/bioconductor-qsmooth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "qsmooth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 24fdc20a48b8eb73da6122e29420738e + md5: 471983d71a4b056b71b10fe15c3f7b1c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qsmooth", max_pin="x.x") }}' noarch: generic # Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-hmisc run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-hmisc test: diff --git a/recipes/bioconductor-qsutils/meta.yaml b/recipes/bioconductor-qsutils/meta.yaml index 9524de10c95a7..67ebd30438806 100644 --- a/recipes/bioconductor-qsutils/meta.yaml +++ b/recipes/bioconductor-qsutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "QSutils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9ad7bfbc8487c40238707a43d8607d3 + md5: 3a1816762d5d0d26145c352281211f80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qsutils", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, ggplot2 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-ape - r-base - r-psych run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-ape - r-base - r-psych diff --git a/recipes/bioconductor-qsvar/meta.yaml b/recipes/bioconductor-qsvar/meta.yaml index 95ef83f52c2b6..1da9a23ce0762 100644 --- a/recipes/bioconductor-qsvar/meta.yaml +++ b/recipes/bioconductor-qsvar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "qsvaR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fda6f9c474c90089486be809da7b2955 + md5: e9531cc164f93967a5d5d0469d47f7c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qsvar", max_pin="x.x") }}' noarch: generic # Suggests: BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-qtlexperiment/build.sh b/recipes/bioconductor-qtlexperiment/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-qtlexperiment/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qtlexperiment/meta.yaml b/recipes/bioconductor-qtlexperiment/meta.yaml new file mode 100644 index 0000000000000..d7d4285a69261 --- /dev/null +++ b/recipes/bioconductor-qtlexperiment/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "QTLExperiment" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fe7642e0952c4c68e5417906dfb66fb3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qtlexperiment", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown, covr +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-ashr + - r-base + - r-checkmate + - r-collapse + - r-dplyr + - r-rlang + - r-tibble + - r-tidyr + - r-vroom + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-ashr + - r-base + - r-checkmate + - r-collapse + - r-dplyr + - r-rlang + - r-tibble + - r-tidyr + - r-vroom +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'S4 classes for QTL summary statistics and metadata' + description: 'QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It is based on the ''SummarizedExperiment'' class and contains functions for creating, merging, and subsetting objects. ''QTLExperiment'' also stores experiment metadata and has checks in place to ensure that transformations apply correctly.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-qtlizer/meta.yaml b/recipes/bioconductor-qtlizer/meta.yaml index eabb7717c1a6e..e151c4ba3c0fc 100644 --- a/recipes/bioconductor-qtlizer/meta.yaml +++ b/recipes/bioconductor-qtlizer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Qtlizer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f1b7e4abafbf2a5ad5516d174fe1605 + md5: ea7e6227ebf6708e465681021fb77b19 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qtlizer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-curl - r-httr - r-stringi run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-curl - r-httr diff --git a/recipes/bioconductor-quantiseqr/meta.yaml b/recipes/bioconductor-quantiseqr/meta.yaml index ecf946508bbe4..92068f91ebef4 100644 --- a/recipes/bioconductor-quantiseqr/meta.yaml +++ b/recipes/bioconductor-quantiseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "quantiseqr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5917b18de8ecdfc1d3ad9683c14b0d4c + md5: 34cd21d2e59e1f8f58001fdcc49eaf44 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quantiseqr", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-limsolve @@ -31,9 +32,9 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-limsolve diff --git a/recipes/bioconductor-quantro/meta.yaml b/recipes/bioconductor-quantro/meta.yaml index 40605f161c433..78285b4ad918e 100644 --- a/recipes/bioconductor-quantro/meta.yaml +++ b/recipes/bioconductor-quantro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "quantro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 24fc384ea9ede169587bac30b26ba294 + md5: 3e7912df8d9bc50c461074539540f289 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quantro", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-doparallel - r-foreach @@ -30,8 +31,8 @@ requirements: - r-iterators - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-quantsmooth/meta.yaml b/recipes/bioconductor-quantsmooth/meta.yaml index 601aeceed6b4a..3145b221ce689 100644 --- a/recipes/bioconductor-quantsmooth/meta.yaml +++ b/recipes/bioconductor-quantsmooth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "quantsmooth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 02f6e69a0d90b985b5ea59123514d22f + md5: cb47e0040fd219ad15aebf094dd379cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quantsmooth", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-quartpac/meta.yaml b/recipes/bioconductor-quartpac/meta.yaml index 41719f9389dda..ccaac8ad09882 100644 --- a/recipes/bioconductor-quartpac/meta.yaml +++ b/recipes/bioconductor-quartpac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "QuartPAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcfa63b6c83c62a6a6ceabd014aae563 + md5: 91af5166d133016b9beaa8539f0fcef7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quartpac", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, rgl requirements: host: - - 'bioconductor-graphpac >=1.42.0,<1.43.0' - - 'bioconductor-ipac >=1.44.0,<1.45.0' - - 'bioconductor-spacepac >=1.38.0,<1.39.0' + - 'bioconductor-graphpac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' + - 'bioconductor-spacepac >=1.40.0,<1.41.0' - r-base - r-data.table run: - - 'bioconductor-graphpac >=1.42.0,<1.43.0' - - 'bioconductor-ipac >=1.44.0,<1.45.0' - - 'bioconductor-spacepac >=1.38.0,<1.39.0' + - 'bioconductor-graphpac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' + - 'bioconductor-spacepac >=1.40.0,<1.41.0' - r-base - r-data.table test: diff --git a/recipes/bioconductor-quasr/meta.yaml b/recipes/bioconductor-quasr/meta.yaml index ef705eccba5a3..c95104f9a8972 100644 --- a/recipes/bioconductor-quasr/meta.yaml +++ b/recipes/bioconductor-quasr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.1" %} +{% set version = "1.42.1" %} {% set name = "QuasR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,54 +11,55 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 08e936fb92d8ccfc031fb6ffeea50747 + md5: ace4fd8823c92add78b78c8e05b366aa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quasr", max_pin="x.x") }}' # Suggests: Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat # SystemRequirements: GNU make requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbowtie >=1.40.0,<1.41.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbowtie >=1.42.0,<1.43.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-quaternaryprod/meta.yaml b/recipes/bioconductor-quaternaryprod/meta.yaml index c9c986003df15..335557456ba9f 100644 --- a/recipes/bioconductor-quaternaryprod/meta.yaml +++ b/recipes/bioconductor-quaternaryprod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "QuaternaryProd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad10afde46e2b65c39b96ba7333cf930 + md5: 73dfc14934979c18429472a3d6870ece build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-quaternaryprod", max_pin="x.x") }}' # Suggests: knitr requirements: host: diff --git a/recipes/bioconductor-qubic/meta.yaml b/recipes/bioconductor-qubic/meta.yaml index 10045a4ed6915..dfff731e76d06 100644 --- a/recipes/bioconductor-qubic/meta.yaml +++ b/recipes/bioconductor-qubic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "QUBIC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef7e2f43d1b1bf14a659a8643a0f5379 + md5: 728f7aca6c2d2913d424694e9b31c41c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qubic", max_pin="x.x") }}' # Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown # SystemRequirements: C++11, Rtools (>= 3.1) requirements: diff --git a/recipes/bioconductor-qubicdata/meta.yaml b/recipes/bioconductor-qubicdata/meta.yaml index 9e299269570fc..349cf66d0a19b 100644 --- a/recipes/bioconductor-qubicdata/meta.yaml +++ b/recipes/bioconductor-qubicdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "QUBICdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47be84c681eabf3ba1851a935762e23a + md5: 0670dfaee6f8d532cf3506428a5932c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qubicdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-qubicdata/post-link.sh b/recipes/bioconductor-qubicdata/post-link.sh index 3d91df27a6fab..e44c7a49f8d46 100644 --- a/recipes/bioconductor-qubicdata/post-link.sh +++ b/recipes/bioconductor-qubicdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qubicdata-1.28.0" +installBiocDataPackage.sh "qubicdata-1.30.0" diff --git a/recipes/bioconductor-qusage/meta.yaml b/recipes/bioconductor-qusage/meta.yaml index 5d2be31ad1f00..b458324664fca 100644 --- a/recipes/bioconductor-qusage/meta.yaml +++ b/recipes/bioconductor-qusage/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "qusage" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d98b2598bdae73d4c17fe40586dd3afb + md5: f4675daa1494bbf070a084d05a2e672b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qusage", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-emmeans - r-fftw - r-nlme run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-emmeans - r-fftw diff --git a/recipes/bioconductor-qvalue/meta.yaml b/recipes/bioconductor-qvalue/meta.yaml index 2425f0321e6ae..255657b20155b 100644 --- a/recipes/bioconductor-qvalue/meta.yaml +++ b/recipes/bioconductor-qvalue/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "qvalue" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 380fe077649cd719ccc6abdf683f2be7 + md5: d6d57a60a814587681cf438b4e6ee9bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-qvalue", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: diff --git a/recipes/bioconductor-r10kcod.db/meta.yaml b/recipes/bioconductor-r10kcod.db/meta.yaml index 4a52c7c605332..fe56f9587a20a 100644 --- a/recipes/bioconductor-r10kcod.db/meta.yaml +++ b/recipes/bioconductor-r10kcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "r10kcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4a7a25fee64294cfb5adccaa6cf28772 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-r10kcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-r3cpet/meta.yaml b/recipes/bioconductor-r3cpet/meta.yaml index 4dbb3f662a152..8e04b83625ff9 100644 --- a/recipes/bioconductor-r3cpet/meta.yaml +++ b/recipes/bioconductor-r3cpet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "R3CPET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7010509ac5d68785413f584462b19cd5 + md5: 4eaced963afa114068f2c36982e1add3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-r3cpet", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clvalid - r-data.table @@ -39,12 +40,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-clvalid - r-data.table diff --git a/recipes/bioconductor-r3cseq/meta.yaml b/recipes/bioconductor-r3cseq/meta.yaml index b84ee7f76b7b4..cf83b123ff451 100644 --- a/recipes/bioconductor-r3cseq/meta.yaml +++ b/recipes/bioconductor-r3cseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "r3Cseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7106a2893f7db6ba10481edcfc36186d + md5: 548b2dc3319fc848c932bcb142edbd61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-r3cseq", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-rcolorbrewer - r-sqldf - r-vgam run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-data.table - r-rcolorbrewer diff --git a/recipes/bioconductor-r453plus1toolbox/meta.yaml b/recipes/bioconductor-r453plus1toolbox/meta.yaml index 8df159384666f..8870d430d6725 100644 --- a/recipes/bioconductor-r453plus1toolbox/meta.yaml +++ b/recipes/bioconductor-r453plus1toolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "R453Plus1Toolbox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2e33a0e2ede03b423ce99fda54bcc54b + md5: 2d7ad69c3b68b4a635129d296599c210 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-r453plus1toolbox", max_pin="x.x") }}' # Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-r2html - r-teachingdemos @@ -40,19 +41,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-r2html - r-teachingdemos diff --git a/recipes/bioconductor-r4rna/meta.yaml b/recipes/bioconductor-r4rna/meta.yaml index 4b298c5b3f270..5cb61ea244f9a 100644 --- a/recipes/bioconductor-r4rna/meta.yaml +++ b/recipes/bioconductor-r4rna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "R4RNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29316712c46983e36ff86e8bd0ebd2a4 + md5: a77903559307ab481671650646dd85e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-r4rna", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base test: commands: diff --git a/recipes/bioconductor-radiogx/meta.yaml b/recipes/bioconductor-radiogx/meta.yaml index 0547a675591b5..6aa2d3edaaaa0 100644 --- a/recipes/bioconductor-radiogx/meta.yaml +++ b/recipes/bioconductor-radiogx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "RadioGx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07e2cfb998c9754ffec01a7ca0dae866 + md5: a7e06ef2f71341c5252a5e2b874fdf17 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-radiogx", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, BiocStyle, knitr, pander, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-catools @@ -38,12 +39,12 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-catools diff --git a/recipes/bioconductor-rae230a.db/meta.yaml b/recipes/bioconductor-rae230a.db/meta.yaml index 1c69dfc10cf40..afeee8e0950b8 100644 --- a/recipes/bioconductor-rae230a.db/meta.yaml +++ b/recipes/bioconductor-rae230a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rae230a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a2a80af1669fc038a64effbf5a4b246d build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230acdf/meta.yaml b/recipes/bioconductor-rae230acdf/meta.yaml index 912b6a851adcc..650f0d564ab13 100644 --- a/recipes/bioconductor-rae230acdf/meta.yaml +++ b/recipes/bioconductor-rae230acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6f2281124e1be164d5fd599e84f6adbc build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230aprobe/meta.yaml b/recipes/bioconductor-rae230aprobe/meta.yaml index 63b5b3e81ddd0..b7441cbf4679b 100644 --- a/recipes/bioconductor-rae230aprobe/meta.yaml +++ b/recipes/bioconductor-rae230aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6f2d77e1d9c1e3afb96ef78b3202bb0b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230b.db/meta.yaml b/recipes/bioconductor-rae230b.db/meta.yaml index 82efc0b4d7aea..0273888d9117e 100644 --- a/recipes/bioconductor-rae230b.db/meta.yaml +++ b/recipes/bioconductor-rae230b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rae230b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4f0474ed22bf5ebd932dd6a4d9573551 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230bcdf/meta.yaml b/recipes/bioconductor-rae230bcdf/meta.yaml index 6f52923f1d90e..38c382de21f3c 100644 --- a/recipes/bioconductor-rae230bcdf/meta.yaml +++ b/recipes/bioconductor-rae230bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bd61c17402e9c04be1000c16e0356618 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rae230bprobe/meta.yaml b/recipes/bioconductor-rae230bprobe/meta.yaml index acd25efbdb3a0..242c7cdb4229c 100644 --- a/recipes/bioconductor-rae230bprobe/meta.yaml +++ b/recipes/bioconductor-rae230bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rae230bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7bdb3a07e1f00de8ff510a69bdac4c53 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rae230bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-raer/build.sh b/recipes/bioconductor-raer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-raer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-raer/meta.yaml b/recipes/bioconductor-raer/meta.yaml new file mode 100644 index 0000000000000..61beb51eb00aa --- /dev/null +++ b/recipes/bioconductor-raer/meta.yaml @@ -0,0 +1,80 @@ +{% set version = "1.0.0" %} +{% set name = "raer" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0b5c050626ce21756f90b4f9c967465b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raer", max_pin="x.x") }}' +# Suggests: testthat (>= 3.0.0), knitr, DESeq2, edgeR, limma, rmarkdown, BiocStyle, ComplexHeatmap, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle, AnnotationHub, covr, raerdata +# SystemRequirements: GNU make +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cli + - r-data.table + - r-matrix + - r-r.utils + - libblas + - liblapack + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-cli + - r-data.table + - r-matrix + - r-r.utils + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'RNA editing tools in R' + description: 'Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.' + license_file: LICENSE + diff --git a/recipes/bioconductor-raerdata/meta.yaml b/recipes/bioconductor-raerdata/meta.yaml new file mode 100644 index 0000000000000..a93eb084ad4ba --- /dev/null +++ b/recipes/bioconductor-raerdata/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "raerdata" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8f250d12f89396f8d4351da5045cf22c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raerdata", max_pin="x.x") }}' + noarch: generic +# Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'A collection of datasets for use with raer package' + description: 'raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided.' + license_file: LICENSE + diff --git a/recipes/bioconductor-raerdata/post-link.sh b/recipes/bioconductor-raerdata/post-link.sh new file mode 100644 index 0000000000000..f8c5dd141a4fe --- /dev/null +++ b/recipes/bioconductor-raerdata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "raerdata-1.0.0" diff --git a/recipes/bioconductor-raerdata/pre-unlink.sh b/recipes/bioconductor-raerdata/pre-unlink.sh new file mode 100644 index 0000000000000..fe52b6b760486 --- /dev/null +++ b/recipes/bioconductor-raerdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ raerdata diff --git a/recipes/bioconductor-raex10stprobeset.db/meta.yaml b/recipes/bioconductor-raex10stprobeset.db/meta.yaml index 5a0fae703d91b..27cc03aa38783 100644 --- a/recipes/bioconductor-raex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-raex10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "raex10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a386809ea8da340f315e378fa329b3ac build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raex10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml index e131376b0b124..98b38f78e2267 100644 --- a/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "raex10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3a0c511a1073c67172770bc3e4b842b5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raex10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-raexexonprobesetlocation/meta.yaml b/recipes/bioconductor-raexexonprobesetlocation/meta.yaml index e536a6c1c1889..370160c4212b6 100644 --- a/recipes/bioconductor-raexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-raexexonprobesetlocation/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.15.0" %} {% set name = "RaExExonProbesetLocation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d547bcd30685495283b32f0f86ecc79b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raexexonprobesetlocation", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10stprobeset.db/meta.yaml b/recipes/bioconductor-ragene10stprobeset.db/meta.yaml index a84b92471aa9b..d5ca4b4037b08 100644 --- a/recipes/bioconductor-ragene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene10stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene10stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 358685c380b37027a064924069b9ee40 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene10stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml index b491aacb14471..4169739b0d7d0 100644 --- a/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene10sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5ff95454493a72bfa2546d82d32fbec1 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene10sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10stv1cdf/meta.yaml b/recipes/bioconductor-ragene10stv1cdf/meta.yaml index 1797ced105faf..f9095368dcbb5 100644 --- a/recipes/bioconductor-ragene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-ragene10stv1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ragene10stv1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: df696e9dbf5b3f2761b6a0a5914be058 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene10stv1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene10stv1probe/meta.yaml b/recipes/bioconductor-ragene10stv1probe/meta.yaml index 163ed6d32bf18..36db272a8a25c 100644 --- a/recipes/bioconductor-ragene10stv1probe/meta.yaml +++ b/recipes/bioconductor-ragene10stv1probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ragene10stv1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 94978b6efb075aacf31ccdc8000e40fa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene10stv1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene11stprobeset.db/meta.yaml b/recipes/bioconductor-ragene11stprobeset.db/meta.yaml index 945be5c32fcb5..9605b8d84ad9a 100644 --- a/recipes/bioconductor-ragene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene11stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene11stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 86f7704c4852c514b3bc3221f7692ba3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene11stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml index e90c54b294548..a4a85cda35e82 100644 --- a/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene11sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f7fbe318547f911b520415a90b3440e9 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene11sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene20stprobeset.db/meta.yaml b/recipes/bioconductor-ragene20stprobeset.db/meta.yaml index 1fbbb3c6d6e9e..67108c15a1dd4 100644 --- a/recipes/bioconductor-ragene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene20stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene20stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 23a43899a22078f4c13b7b1d45176319 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene20stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml index 6a38b64f3ce7c..28fc801a28399 100644 --- a/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene20sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b44c5f6ac2b2e3eb4d820d08f7a38644 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene20sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene21stprobeset.db/meta.yaml b/recipes/bioconductor-ragene21stprobeset.db/meta.yaml index 8739c96546c4c..0b4be17e863db 100644 --- a/recipes/bioconductor-ragene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene21stprobeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene21stprobeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6451885f99ce3873d5d4dbacdf968181 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene21stprobeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml index 0aae6a57270bb..06c45bcb7dee6 100644 --- a/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "ragene21sttranscriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6ffe13e1594add0a5169b2083b608336 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ragene21sttranscriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-raggedexperiment/meta.yaml b/recipes/bioconductor-raggedexperiment/meta.yaml index b27b8f891f221..5caad78ba3f76 100644 --- a/recipes/bioconductor-raggedexperiment/meta.yaml +++ b/recipes/bioconductor-raggedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RaggedExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05b6897d69250f287a753601e550080f + md5: 5704ce0834ff2770c489c3882ef4acec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raggedexperiment", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-raids/build.sh b/recipes/bioconductor-raids/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-raids/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-raids/meta.yaml b/recipes/bioconductor-raids/meta.yaml new file mode 100644 index 0000000000000..507252a73a248 --- /dev/null +++ b/recipes/bioconductor-raids/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.0.0" %} +{% set name = "RAIDS" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 768d047b002bb44e1178d69233878818 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raids", max_pin="x.x") }}' + noarch: generic +# Suggests: testthat, knitr, rmarkdown, BiocStyle, withr, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genesis >=2.32.0,<2.33.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-class + - r-proc + - r-rlang + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genesis >=2.32.0,<2.33.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-class + - r-proc + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Apache License (>= 2)' + summary: 'Accurate Inference of Genetic Ancestry from Cancer Sequences' + description: 'This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.' + diff --git a/recipes/bioconductor-rain/meta.yaml b/recipes/bioconductor-rain/meta.yaml index 7d79f13920b07..f06f49eb3f548 100644 --- a/recipes/bioconductor-rain/meta.yaml +++ b/recipes/bioconductor-rain/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "rain" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9749ba6b883017a62470ef1ba33a5148 + md5: e523c08337422230710fd1f2a5a392cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rain", max_pin="x.x") }}' noarch: generic # Suggests: lattice, BiocStyle requirements: host: - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-gmp run: - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - r-gmp test: diff --git a/recipes/bioconductor-ramr/meta.yaml b/recipes/bioconductor-ramr/meta.yaml index 12bb7b578b6a0..196dcea668264 100644 --- a/recipes/bioconductor-ramr/meta.yaml +++ b/recipes/bioconductor-ramr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ramr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d61b7ccd6f2bf988a00a4e95d9307653 + md5: 6a6278f2ad74018661b9985eb978e90c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ramr", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-dorng @@ -35,10 +36,10 @@ requirements: - r-matrixstats - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-doparallel - r-dorng diff --git a/recipes/bioconductor-ramwas/meta.yaml b/recipes/bioconductor-ramwas/meta.yaml index 045ea8fdde6ff..233f285fb2a8e 100644 --- a/recipes/bioconductor-ramwas/meta.yaml +++ b/recipes/bioconductor-ramwas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ramwas" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: be4fe215633bd48a9802b7ad6a22a39f + md5: ccbff0a1c4bd31c8ceb9d2641d6608d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ramwas", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-digest - r-filematrix @@ -33,11 +34,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-digest - r-filematrix diff --git a/recipes/bioconductor-randomwalkrestartmh/meta.yaml b/recipes/bioconductor-randomwalkrestartmh/meta.yaml index c96acc8e7ac67..aad822b818c73 100644 --- a/recipes/bioconductor-randomwalkrestartmh/meta.yaml +++ b/recipes/bioconductor-randomwalkrestartmh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RandomWalkRestartMH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 334449d593d86853a0203fcb7ccb4d6d + md5: ace5e6d73a365094a41a864a47deb893 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-randomwalkrestartmh", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-randpack/meta.yaml b/recipes/bioconductor-randpack/meta.yaml index a62a77797a627..626ee120a1935 100644 --- a/recipes/bioconductor-randpack/meta.yaml +++ b/recipes/bioconductor-randpack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "randPack" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 074bd51f6b64411a009463888a08ffe4 + md5: 71791ade28f58d981a510c8b660ae1e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-randpack", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-randrotation/meta.yaml b/recipes/bioconductor-randrotation/meta.yaml index d05d67a6aa7d8..5d4447925d490 100644 --- a/recipes/bioconductor-randrotation/meta.yaml +++ b/recipes/bioconductor-randrotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "randRotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af48011b48390b6567ccda6141ee4f12 + md5: a05faf1fe582450a789fc2d58960fa97 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-randrotation", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle, testthat (>= 2.1.0), limma, sva requirements: diff --git a/recipes/bioconductor-rankprod/meta.yaml b/recipes/bioconductor-rankprod/meta.yaml index 159db0a61e95b..2ebbe68585c00 100644 --- a/recipes/bioconductor-rankprod/meta.yaml +++ b/recipes/bioconductor-rankprod/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.26.0" %} +{% set version = "3.28.0" %} {% set name = "RankProd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6fa483ed8d64249e1280088bc1fd78a4 + md5: 39f3eba64601984ad265d91f3a150180 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rankprod", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-raresim/meta.yaml b/recipes/bioconductor-raresim/meta.yaml index edae4c455e23d..fdd6a7e5a167e 100644 --- a/recipes/bioconductor-raresim/meta.yaml +++ b/recipes/bioconductor-raresim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "RAREsim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a227aacb1583b3ea793e127a30e6796f + md5: 6ec5b86f348e2d4ffb365da80651041e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-raresim", max_pin="x.x") }}' noarch: generic # Suggests: markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) requirements: diff --git a/recipes/bioconductor-rarevariantvis/meta.yaml b/recipes/bioconductor-rarevariantvis/meta.yaml index e41ef7739083e..a55ff5d23bcd9 100644 --- a/recipes/bioconductor-rarevariantvis/meta.yaml +++ b/recipes/bioconductor-rarevariantvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "RareVariantVis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,46 +11,47 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 679826e7c9df1bbb563a740f197fa2c2 + md5: 2157172a825bbc826d5c2f3d17a41987 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rarevariantvis", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-googlevis - r-gtools run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-googlevis - r-gtools diff --git a/recipes/bioconductor-rarr/meta.yaml b/recipes/bioconductor-rarr/meta.yaml index 46ecddaef2c4d..5f28e2f9eb0be 100644 --- a/recipes/bioconductor-rarr/meta.yaml +++ b/recipes/bioconductor-rarr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "Rarr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,13 +11,14 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d1368ed8413be31e3d59401f1642991 + md5: 94af864ae3de3557840993a429944ea2 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, covr, knitr, tinytest + run_exports: '{{ pin_subpackage("bioconductor-rarr", max_pin="x.x") }}' +# Suggests: BiocStyle, covr, knitr, tinytest, mockery # SystemRequirements: GNU make requirements: host: diff --git a/recipes/bioconductor-rat.db0/meta.yaml b/recipes/bioconductor-rat.db0/meta.yaml index 9664ceae6fa59..97008b6343456 100644 --- a/recipes/bioconductor-rat.db0/meta.yaml +++ b/recipes/bioconductor-rat.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "rat.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 86993da680822a050e85f1208713f3c8 + md5: cde666f86ec7b61beb8cf1037511f977 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rat.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat.db0/post-link.sh b/recipes/bioconductor-rat.db0/post-link.sh index c3e3d4f5e5bbb..b40a101d33dc3 100644 --- a/recipes/bioconductor-rat.db0/post-link.sh +++ b/recipes/bioconductor-rat.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rat.db0-3.17.0" +installBiocDataPackage.sh "rat.db0-3.18.0" diff --git a/recipes/bioconductor-rat2302.db/meta.yaml b/recipes/bioconductor-rat2302.db/meta.yaml index 3837f56dc958d..2a342615aa394 100644 --- a/recipes/bioconductor-rat2302.db/meta.yaml +++ b/recipes/bioconductor-rat2302.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rat2302.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b1404d8a16fec681f0fd682589a685ea build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rat2302.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat2302cdf/meta.yaml b/recipes/bioconductor-rat2302cdf/meta.yaml index 4aaf5fcb18bd5..043a6a2d81dd8 100644 --- a/recipes/bioconductor-rat2302cdf/meta.yaml +++ b/recipes/bioconductor-rat2302cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rat2302cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a033730f79a11d45b4cd7e7c520f8052 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rat2302cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat2302frmavecs/meta.yaml b/recipes/bioconductor-rat2302frmavecs/meta.yaml index 24f0971b2d763..5eb5dfee57f4f 100644 --- a/recipes/bioconductor-rat2302frmavecs/meta.yaml +++ b/recipes/bioconductor-rat2302frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.11" %} {% set name = "rat2302frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 44d9f00c2f3806899c6605d1ba274066 build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rat2302frmavecs", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-frma >=1.52.0,<1.53.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-frma >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rat2302probe/meta.yaml b/recipes/bioconductor-rat2302probe/meta.yaml index 531f316a7171b..e2c76e6e9f797 100644 --- a/recipes/bioconductor-rat2302probe/meta.yaml +++ b/recipes/bioconductor-rat2302probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rat2302probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d1d9215e52b9e845cc4d7c902536e0d6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rat2302probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ratchrloc/meta.yaml b/recipes/bioconductor-ratchrloc/meta.yaml index c07eec45d96dc..d3fe6a6509e9a 100644 --- a/recipes/bioconductor-ratchrloc/meta.yaml +++ b/recipes/bioconductor-ratchrloc/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.1.6" %} {% set name = "ratCHRLOC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6fecff4821a5a47e3bd38a2ff78173d5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ratchrloc", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rattoxfxcdf/meta.yaml b/recipes/bioconductor-rattoxfxcdf/meta.yaml index d529581444b92..73dd35e04127f 100644 --- a/recipes/bioconductor-rattoxfxcdf/meta.yaml +++ b/recipes/bioconductor-rattoxfxcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rattoxfxcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 912d0fa424615fcd92773ed174d5efdd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rattoxfxcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rattoxfxprobe/meta.yaml b/recipes/bioconductor-rattoxfxprobe/meta.yaml index 525a470b0ffa1..f32aeb6966e55 100644 --- a/recipes/bioconductor-rattoxfxprobe/meta.yaml +++ b/recipes/bioconductor-rattoxfxprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rattoxfxprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 202791c72e8c956b9854fa4d9ba67a24 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rattoxfxprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rattus.norvegicus/meta.yaml b/recipes/bioconductor-rattus.norvegicus/meta.yaml index 5902d0a0bb074..3d57f0f02545d 100644 --- a/recipes/bioconductor-rattus.norvegicus/meta.yaml +++ b/recipes/bioconductor-rattus.norvegicus/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.1" %} {% set name = "Rattus.norvegicus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,30 +13,31 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5692fdeb0bc7f94e1db35f097cad99a9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rattus.norvegicus", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.12.0,<3.13.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - 'bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.12.0,<3.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rawrr/meta.yaml b/recipes/bioconductor-rawrr/meta.yaml index 1bfc3b3af36a5..08f497e744570 100644 --- a/recipes/bioconductor-rawrr/meta.yaml +++ b/recipes/bioconductor-rawrr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.2" %} {% set name = "rawrr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: def45f50cec22561ffbc1022eed93032 + md5: 42213a8a733115af719162fc1a72d6a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rawrr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat # SystemRequirements: mono-runtime 4.x or higher (including System.Data library) on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft Windows. diff --git a/recipes/bioconductor-rbcbook1/meta.yaml b/recipes/bioconductor-rbcbook1/meta.yaml index cfead0d6598f5..59907071a6fca 100644 --- a/recipes/bioconductor-rbcbook1/meta.yaml +++ b/recipes/bioconductor-rbcbook1/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "RbcBook1" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 849ecc7e9f264ce9bacce3f8a6d64c3f + md5: 16f681613c1c4d309b032c64cfe18c4a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbcbook1", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-rpart run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-rpart test: diff --git a/recipes/bioconductor-rbec/meta.yaml b/recipes/bioconductor-rbec/meta.yaml index f657f26389496..92930222940ff 100644 --- a/recipes/bioconductor-rbec/meta.yaml +++ b/recipes/bioconductor-rbec/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "Rbec" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a954c964eccec52381d10c1344b4796c + md5: f295d8ade5faf2c0b770f2b075262116 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbec", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-dada2 >=1.28.0,<1.29.0' + - 'bioconductor-dada2 >=1.30.0,<1.31.0' - r-base - r-doparallel - r-foreach @@ -30,7 +31,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-dada2 >=1.28.0,<1.29.0' + - 'bioconductor-dada2 >=1.30.0,<1.31.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-rbgl/meta.yaml b/recipes/bioconductor-rbgl/meta.yaml index 02005957b371d..f201a7627ea36 100644 --- a/recipes/bioconductor-rbgl/meta.yaml +++ b/recipes/bioconductor-rbgl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "RBGL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f8bf9943c7d1fbf6ce2e027109a8b4f + md5: a18b5ad5c49f058b6f65a2bd0a4274d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbgl", max_pin="x.x") }}' # Suggests: Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-bh - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-bh build: diff --git a/recipes/bioconductor-rbioformats/meta.yaml b/recipes/bioconductor-rbioformats/meta.yaml index c75d3f2a6b06c..0b180c33b55f5 100644 --- a/recipes/bioconductor-rbioformats/meta.yaml +++ b/recipes/bioconductor-rbioformats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "RBioFormats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2078329911e3b0b5979225dd524f28f + md5: cd83827dd164a9b44ba3d0d08fd77b38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbioformats", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat, xml2 # SystemRequirements: Java (>= 1.7) requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rjava >=0.9-6' - openjdk run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rjava >=0.9-6' - openjdk diff --git a/recipes/bioconductor-rbioinf/meta.yaml b/recipes/bioconductor-rbioinf/meta.yaml index 0e6032254ba56..9cf94f1be6a6b 100644 --- a/recipes/bioconductor-rbioinf/meta.yaml +++ b/recipes/bioconductor-rbioinf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "RBioinf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a706a1b48cbed097dcb5ab1266fe0e90 + md5: ec036823fe8f50106f37436eec716add build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbioinf", max_pin="x.x") }}' # Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rbiopaxparser/meta.yaml b/recipes/bioconductor-rbiopaxparser/meta.yaml index 104a20d71ef31..b48a0a08c3e8a 100644 --- a/recipes/bioconductor-rbiopaxparser/meta.yaml +++ b/recipes/bioconductor-rbiopaxparser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "rBiopaxParser" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee84f721ce8bafac32c3c847500b9481 + md5: 53e24a8896bf17bd56fe48d62427eb33 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbiopaxparser", max_pin="x.x") }}' noarch: generic # Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph requirements: diff --git a/recipes/bioconductor-rbm/meta.yaml b/recipes/bioconductor-rbm/meta.yaml index 6d455e14c5162..216f62b73d664 100644 --- a/recipes/bioconductor-rbm/meta.yaml +++ b/recipes/bioconductor-rbm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RBM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 836597b482a58256a1e2021fd9b411ff + md5: 4ae63966d6e9cfd1d3ce001f65a02abe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-rbowtie/meta.yaml b/recipes/bioconductor-rbowtie/meta.yaml index 207599443dbf9..9263ed9e3b853 100644 --- a/recipes/bioconductor-rbowtie/meta.yaml +++ b/recipes/bioconductor-rbowtie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "Rbowtie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5421ecbf4cfa6eb177dc24e71ab9360c + md5: 409fc50371b1eaf9be2af500aff05249 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbowtie", max_pin="x.x") }}' # Suggests: testthat, parallel, BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-rbowtie2/meta.yaml b/recipes/bioconductor-rbowtie2/meta.yaml index 70f57c0c2e4ab..cf394a23f4368 100644 --- a/recipes/bioconductor-rbowtie2/meta.yaml +++ b/recipes/bioconductor-rbowtie2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "Rbowtie2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4410870693059284f2d83f0e66f0c343 + md5: dbba503f3134fdb9c6521c060ec2d5fc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbowtie2", max_pin="x.x") }}' # Suggests: knitr, testthat (>= 3.0.0), rmarkdown # SystemRequirements: C++11, GNU make, samtools requirements: host: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-magrittr - libblas - liblapack - - zlib run: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-magrittr - - zlib build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-rbsurv/meta.yaml b/recipes/bioconductor-rbsurv/meta.yaml index c4316931efc32..399aaa8374e09 100644 --- a/recipes/bioconductor-rbsurv/meta.yaml +++ b/recipes/bioconductor-rbsurv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.58.0" %} +{% set version = "2.60.0" %} {% set name = "rbsurv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 77140e1902a32fa5df323496a5cbc7fb + md5: e2791c7a40004e031fd88e0995f4dc13 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbsurv", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival test: diff --git a/recipes/bioconductor-rbwa/build.sh b/recipes/bioconductor-rbwa/build.sh index 9a888f987910c..578c85ee502d7 100644 --- a/recipes/bioconductor-rbwa/build.sh +++ b/recipes/bioconductor-rbwa/build.sh @@ -8,4 +8,4 @@ CXX=$CXX -I${PREFIX}/include -L${PREFIX}/lib CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rbwa/meta.yaml b/recipes/bioconductor-rbwa/meta.yaml index 374d5fce73c70..b777c8844fbd4 100644 --- a/recipes/bioconductor-rbwa/meta.yaml +++ b/recipes/bioconductor-rbwa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "Rbwa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fae3f23359b0d79625367cfb21ae2757 + md5: 036e0acc237e1249e5509df62d6c9968 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rbwa", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: @@ -40,4 +41,3 @@ about: summary: 'R wrapper for BWA-backtrack and BWA-MEM aligners' description: 'Provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.' license_file: LICENSE - diff --git a/recipes/bioconductor-rcas/meta.yaml b/recipes/bioconductor-rcas/meta.yaml index 007c19da31eb7..bfcfb29ffe1ef 100644 --- a/recipes/bioconductor-rcas/meta.yaml +++ b/recipes/bioconductor-rcas/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.2" %} {% set name = "RCAS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af0a35923e6cd6eb176f8498cdf75951 + md5: 379c5b756cc12ca37913f7b51d8d29eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcas", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, covr +# Suggests: testthat, covr, BiocManager # SystemRequirements: pandoc (>= 1.12.3) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table @@ -51,17 +52,17 @@ requirements: - r-rsqlite - 'pandoc >=1.12.3' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomation >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table diff --git a/recipes/bioconductor-rcaspar/meta.yaml b/recipes/bioconductor-rcaspar/meta.yaml index d6b239689a705..8d9c57743bd22 100644 --- a/recipes/bioconductor-rcaspar/meta.yaml +++ b/recipes/bioconductor-rcaspar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "RCASPAR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3df5d1c22c9b55868fd054e5e07e516 + md5: 54a7734c80b26a4b0080fbdeb583af02 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcaspar", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-rcellminer/meta.yaml b/recipes/bioconductor-rcellminer/meta.yaml index ee2ba8cad5219..9ae4c09d89d57 100644 --- a/recipes/bioconductor-rcellminer/meta.yaml +++ b/recipes/bioconductor-rcellminer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "rcellminer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c97d997df69e2442dfddc352db63d6e + md5: e74fd74daff68802d805b6bc0336499d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcellminer", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW, parallel, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-rcellminerdata >=2.22.0,<2.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-rcellminerdata >=2.24.0,<2.25.0' - r-base - r-ggplot2 - r-gplots - r-shiny - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-rcellminerdata >=2.22.0,<2.23.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-rcellminerdata >=2.24.0,<2.25.0' - r-base - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-rcellminerdata/meta.yaml b/recipes/bioconductor-rcellminerdata/meta.yaml index 45c41b13a4544..6d0d65c26be67 100644 --- a/recipes/bioconductor-rcellminerdata/meta.yaml +++ b/recipes/bioconductor-rcellminerdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "rcellminerData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45f581dfcac9cd66a5cb2ca6f0706d7a + md5: 2f45852d4eeb438b6a1feb156200b2bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcellminerdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, BiocStyle, rcellminer, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rcellminerdata/post-link.sh b/recipes/bioconductor-rcellminerdata/post-link.sh index db2270d4a5fbd..c6a6cbff8fe34 100644 --- a/recipes/bioconductor-rcellminerdata/post-link.sh +++ b/recipes/bioconductor-rcellminerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rcellminerdata-2.22.0" +installBiocDataPackage.sh "rcellminerdata-2.24.0" diff --git a/recipes/bioconductor-rcgh/meta.yaml b/recipes/bioconductor-rcgh/meta.yaml index c94462cecac67..add2e2dfda8d6 100644 --- a/recipes/bioconductor-rcgh/meta.yaml +++ b/recipes/bioconductor-rcgh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "rCGH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 517f6a662b4aa90862de3f26c5b48e10 + md5: 80510d5207fb0ad5d517a99b35734621 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcgh", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, BiocGenerics, RUnit requirements: host: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-lattice @@ -41,19 +42,19 @@ requirements: - r-plyr - 'r-shiny >=0.11.1' run: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-lattice diff --git a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml index b4de3e01687bd..b884d5531ab95 100644 --- a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml +++ b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RcisTarget.hg19.motifDBs.cisbpOnly.500bp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 74b4a09e41b8af5f638848ca86f3ec53 + md5: b8cdbfafeb9966332876fdf9be8dbb5a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp", max_pin="x.x") }}' noarch: generic requirements: host: @@ -26,7 +27,7 @@ requirements: - r-base - r-data.table - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh index 07379bec0ec86..6674b4221ffd9 100644 --- a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh +++ b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rcistarget.hg19.motifdbs.cisbponly.500bp-1.20.0" +installBiocDataPackage.sh "rcistarget.hg19.motifdbs.cisbponly.500bp-1.22.0" diff --git a/recipes/bioconductor-rcm/meta.yaml b/recipes/bioconductor-rcm/meta.yaml index 0bcfbcce34ece..78a7ec4e17ce7 100644 --- a/recipes/bioconductor-rcm/meta.yaml +++ b/recipes/bioconductor-rcm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "RCM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9be63e477e29d2fd363285ec9e89ea0b + md5: 2512426fe72a0dfede77816e98935ca1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcm", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-alabama - r-base - r-dbi @@ -35,8 +36,8 @@ requirements: - r-tseries - r-vgam run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-alabama - r-base - r-dbi diff --git a/recipes/bioconductor-rcollectl/meta.yaml b/recipes/bioconductor-rcollectl/meta.yaml index 3d0b3933b0e20..da65e37613492 100644 --- a/recipes/bioconductor-rcollectl/meta.yaml +++ b/recipes/bioconductor-rcollectl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "Rcollectl" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4eb21452f5d214449462f4a7d81b0b6 + md5: 855c39cf9aece9c63b3febc0c0d5654b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcollectl", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, knitcitations, sessioninfo, rmarkdown, testthat, covr # SystemRequirements: collectl diff --git a/recipes/bioconductor-rcpi/meta.yaml b/recipes/bioconductor-rcpi/meta.yaml index 2452d1d26bab5..5da588cf6c1df 100644 --- a/recipes/bioconductor-rcpi/meta.yaml +++ b/recipes/bioconductor-rcpi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "Rcpi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1837722429b7d18ab4594197a3aeb350 + md5: 2f3697ca19200881f65d7d37f3d34e33 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcpi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - r-base - r-doparallel - r-foreach @@ -30,8 +31,8 @@ requirements: - r-rjson - r-rlang run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-rcwl/meta.yaml b/recipes/bioconductor-rcwl/meta.yaml index 5d55d43dac0a0..fbd644f83afd4 100644 --- a/recipes/bioconductor-rcwl/meta.yaml +++ b/recipes/bioconductor-rcwl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Rcwl" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09262e7d3dc5c04ce919d8cebe9418a8 + md5: f427ee3f7f5ba2458f8f97b694b48a85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcwl", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-batchtools - r-codetools @@ -32,9 +33,9 @@ requirements: - r-shiny - r-yaml run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-batchtools - r-codetools diff --git a/recipes/bioconductor-rcwlpipelines/build_failure.linux-64.yaml b/recipes/bioconductor-rcwlpipelines/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6ae0fde6d9352 --- /dev/null +++ b/recipes/bioconductor-rcwlpipelines/build_failure.linux-64.yaml @@ -0,0 +1,61 @@ +recipe_sha: af004261d70c636e2d08ed30d7cbe6563df507346a88a94d377d6a64ee5d934a # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + package r-base-4.3.0-h0fc540b_0 requires icu >=72.1,<73.0a0, but none of the providers can be installed +category: |- + dependency issue +log: |- + 02:31:45 BIOCONDA INFO (OUT) RuntimeError: Solver could not find solution.Mamba failed to solve: + 02:31:45 BIOCONDA INFO (OUT) - r-base 4.3.* + 02:31:45 BIOCONDA INFO (OUT) - r-httr + 02:31:45 BIOCONDA INFO (OUT) - nodejs 14.* + 02:31:45 BIOCONDA INFO (OUT) - r-git2r + 02:31:45 BIOCONDA INFO (OUT) - bioconductor-s4vectors >=0.40.0,<0.41.0 + 02:31:45 BIOCONDA INFO (OUT) - r-rappdirs + 02:31:45 BIOCONDA INFO (OUT) - bioconductor-rcwl >=1.18.0,<1.19.0 + 02:31:45 BIOCONDA INFO (OUT) - bioconductor-biocfilecache >=2.10.0,<2.11.0 + 02:31:45 BIOCONDA INFO (OUT) + 02:31:45 BIOCONDA INFO (OUT) with channels: + 02:31:45 BIOCONDA INFO (OUT) - file:///opt/host-conda-bld + 02:31:45 BIOCONDA INFO (OUT) - conda-forge + 02:31:45 BIOCONDA INFO (OUT) - bioconda + 02:31:45 BIOCONDA INFO (OUT) - defaults + 02:31:45 BIOCONDA INFO (OUT) + 02:31:45 BIOCONDA INFO (OUT) The reported errors are: + 02:31:45 BIOCONDA INFO (OUT) - Encountered problems while solving: + 02:31:45 BIOCONDA INFO (OUT) - - package r-base-4.3.0-h0fc540b_0 requires icu >=72.1,<73.0a0, but none of the providers can be installed + 02:31:45 BIOCONDA INFO (OUT) - + 02:31:45 BIOCONDA INFO (OUT) + 02:31:45 BIOCONDA INFO (OUT) During handling of the above exception, another exception occurred: + 02:31:45 BIOCONDA INFO (OUT) + 02:31:45 BIOCONDA INFO (OUT) Traceback (most recent call last): + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in + 02:31:45 BIOCONDA INFO (OUT) sys.exit(main()) + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 02:31:45 BIOCONDA INFO (OUT) call_conda_build(action, config) + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 02:31:45 BIOCONDA INFO (OUT) result = api.build( + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 02:31:45 BIOCONDA INFO (OUT) return build_tree( + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + 02:31:45 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + 02:31:45 BIOCONDA INFO (OUT) output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + 02:31:45 BIOCONDA INFO (OUT) for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + 02:31:45 BIOCONDA INFO (OUT) conda_packages = finalize_outputs_pass( + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + 02:31:45 BIOCONDA INFO (OUT) fm = finalize_metadata( + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + 02:31:45 BIOCONDA INFO (OUT) build_unsat, host_unsat = add_upstream_pins(m, + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + 02:31:45 BIOCONDA INFO (OUT) host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + 02:31:45 BIOCONDA INFO (OUT) deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + 02:31:45 BIOCONDA INFO (OUT) actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + 02:31:45 BIOCONDA INFO (OUT) raise err + 02:31:45 BIOCONDA INFO (OUT) conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base==4.3.0=h0fc540b_0"), MatchSpec("icu[version='>=72.1,<73.0a0']")} + diff --git a/recipes/bioconductor-rcwlpipelines/meta.yaml b/recipes/bioconductor-rcwlpipelines/meta.yaml index daa823b3014ed..f933217359628 100644 --- a/recipes/bioconductor-rcwlpipelines/meta.yaml +++ b/recipes/bioconductor-rcwlpipelines/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "RcwlPipelines" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c4531dad2b967b01fc7520ec5ad5e5d + md5: 5ff1c2848694b09cc639a56009392cf3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcwlpipelines", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: nodejs requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-rcwl >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-rcwl >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-git2r - r-httr - r-rappdirs - - nodejs >=18 + - nodejs run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-rcwl >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-rcwl >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-git2r - r-httr - r-rappdirs - - nodejs >=18 + - nodejs test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rcx/meta.yaml b/recipes/bioconductor-rcx/meta.yaml index 50e3dbc1a19f1..63f9f80394e5d 100644 --- a/recipes/bioconductor-rcx/meta.yaml +++ b/recipes/bioconductor-rcx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "RCX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04d1a91c0621fd0704b6653244ebc5e9 + md5: 4fdd9c350200e6854c3ed1db44572826 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcx", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown, base64enc, graph requirements: diff --git a/recipes/bioconductor-rcy3/meta.yaml b/recipes/bioconductor-rcy3/meta.yaml index ba7877a398d7a..e0c575aaae226 100644 --- a/recipes/bioconductor-rcy3/meta.yaml +++ b/recipes/bioconductor-rcy3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.1" %} {% set name = "RCy3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a92632aee8b33ce6fb02007d5185e9d + md5: d4f51eaf382ede111f69aefd2660e383 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcy3", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, igraph, grDevices # SystemRequirements: Cytoscape (>= 3.7.1), CyREST (>= 3.8.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-base64enc - r-base64url @@ -36,13 +37,13 @@ requirements: - r-rcolorbrewer - r-rcurl - r-rjsonio - - r-uchardet + - r-stringi - r-uuid - r-xml - 'cytoscape >=3.7.1' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-base64enc - r-base64url @@ -55,7 +56,7 @@ requirements: - r-rcolorbrewer - r-rcurl - r-rjsonio - - r-uchardet + - r-stringi - r-uuid - r-xml - 'cytoscape >=3.7.1' diff --git a/recipes/bioconductor-rcyjs/meta.yaml b/recipes/bioconductor-rcyjs/meta.yaml index f6398c9c572c1..d1b93b6a7c224 100644 --- a/recipes/bioconductor-rcyjs/meta.yaml +++ b/recipes/bioconductor-rcyjs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "RCyjs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17cff1b9dd82ea88c53dab0026483a8b + md5: b02526ea0ff36d61fdac395633bc4a4d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rcyjs", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-browserviz >=2.22.0,<2.23.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-browserviz >=2.24.0,<2.25.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-base64enc - 'r-httpuv >=1.5.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-browserviz >=2.22.0,<2.23.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-browserviz >=2.24.0,<2.25.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-base64enc - 'r-httpuv >=1.5.0' diff --git a/recipes/bioconductor-rdgidb/meta.yaml b/recipes/bioconductor-rdgidb/meta.yaml index 8a80f191c2fba..60e0aeffac71e 100644 --- a/recipes/bioconductor-rdgidb/meta.yaml +++ b/recipes/bioconductor-rdgidb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "rDGIdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c908760f3b9a2722fc61aa3e3f02085 + md5: 5f3f78a4035bbb5597811f38c68b8e4f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rdgidb", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitr,testthat requirements: diff --git a/recipes/bioconductor-rdisop/meta.yaml b/recipes/bioconductor-rdisop/meta.yaml index b513069f63ddb..a2c7a9d73dcd3 100644 --- a/recipes/bioconductor-rdisop/meta.yaml +++ b/recipes/bioconductor-rdisop/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "Rdisop" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 601cefd4030ddf03d7160eafbd882d58 + md5: 508c96aaea70daa872ec75712570f6da build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rdisop", max_pin="x.x") }}' # Suggests: RUnit # SystemRequirements: None requirements: diff --git a/recipes/bioconductor-rdrtoolbox/meta.yaml b/recipes/bioconductor-rdrtoolbox/meta.yaml index 985fed010963b..8cf36b1c8d51c 100644 --- a/recipes/bioconductor-rdrtoolbox/meta.yaml +++ b/recipes/bioconductor-rdrtoolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "RDRToolbox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa5250922a670612beb7076f719c5eec + md5: 4b0e59a1ea48dd51e11d8d18666cf2d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rdrtoolbox", max_pin="x.x") }}' noarch: generic # Suggests: golubEsets requirements: diff --git a/recipes/bioconductor-reactome.db/meta.yaml b/recipes/bioconductor-reactome.db/meta.yaml index 298a51b995f7e..242822e8bae25 100644 --- a/recipes/bioconductor-reactome.db/meta.yaml +++ b/recipes/bioconductor-reactome.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.84.0" %} +{% set version = "1.86.2" %} {% set name = "reactome.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ce62dbac370a30e260d8e45891939693 + md5: ff56f3908b347cb18e3e4ccedf7f584e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactome.db", max_pin="x.x") }}' noarch: generic # Suggests: RSQLite requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' @@ -35,7 +36,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: 'CC BY 4.0' summary: 'A set of annotation maps for reactome' - description: 'A set of annotation maps for reactome assembled using data from reactome' + description: 'A set of annotation maps for reactome assembled using data from reactome. This package has been created by a third-party developer, and is not affiliated with the Reactome team.' extra: parent_recipe: name: bioconductor-reactome.db diff --git a/recipes/bioconductor-reactome.db/post-link.sh b/recipes/bioconductor-reactome.db/post-link.sh index 876c20ee8f1c5..505cfbf3b984f 100644 --- a/recipes/bioconductor-reactome.db/post-link.sh +++ b/recipes/bioconductor-reactome.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "reactome.db-1.84.0" +installBiocDataPackage.sh "reactome.db-1.86.2" diff --git a/recipes/bioconductor-reactomecontentservice4r/meta.yaml b/recipes/bioconductor-reactomecontentservice4r/meta.yaml index 79c1cafcbf884..6e385b59f6091 100644 --- a/recipes/bioconductor-reactomecontentservice4r/meta.yaml +++ b/recipes/bioconductor-reactomecontentservice4r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ReactomeContentService4R" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50dd55d0d0765fb797dac403502775cf + md5: 3ec9de10a86259a6aae5308f6dfc0fa4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactomecontentservice4r", max_pin="x.x") }}' noarch: generic # Suggests: pdftools, testthat, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-reactomegraph4r/meta.yaml b/recipes/bioconductor-reactomegraph4r/meta.yaml index 082f8e215f520..3ae2c6b087f58 100644 --- a/recipes/bioconductor-reactomegraph4r/meta.yaml +++ b/recipes/bioconductor-reactomegraph4r/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ReactomeGraph4R" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4501886646fb5b54869a77a3456db1a5 + md5: 47a818d1c6d25db90a547d315d1189e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactomegraph4r", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, stringr, networkD3, visNetwork, wesanderson requirements: host: - - 'bioconductor-reactomecontentservice4r >=1.8.0,<1.9.0' + - 'bioconductor-reactomecontentservice4r >=1.10.0,<1.11.0' - r-base - r-data.table - r-doparallel @@ -33,7 +34,7 @@ requirements: - r-purrr - r-rlang run: - - 'bioconductor-reactomecontentservice4r >=1.8.0,<1.9.0' + - 'bioconductor-reactomecontentservice4r >=1.10.0,<1.11.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-reactomegsa.data/meta.yaml b/recipes/bioconductor-reactomegsa.data/meta.yaml index 33d4444292b5a..bec7f216b21da 100644 --- a/recipes/bioconductor-reactomegsa.data/meta.yaml +++ b/recipes/bioconductor-reactomegsa.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.1" %} {% set name = "ReactomeGSA.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c6b8b4eeacfc2f316c8c0aa021938f1 + md5: bd236d4d4078f99ea5d473fde1ff065f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactomegsa.data", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-reactomegsa >=1.14.0,<1.15.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-reactomegsa >=1.16.0,<1.17.0' - r-base - r-seurat run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-reactomegsa >=1.14.0,<1.15.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-reactomegsa >=1.16.0,<1.17.0' - r-base - r-seurat - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-reactomegsa.data/post-link.sh b/recipes/bioconductor-reactomegsa.data/post-link.sh index 8712bc92d4982..7105dd31e819c 100644 --- a/recipes/bioconductor-reactomegsa.data/post-link.sh +++ b/recipes/bioconductor-reactomegsa.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "reactomegsa.data-1.14.0" +installBiocDataPackage.sh "reactomegsa.data-1.16.1" diff --git a/recipes/bioconductor-reactomegsa/meta.yaml b/recipes/bioconductor-reactomegsa/meta.yaml index 3e7ec0c8fb08d..eca696e84304c 100644 --- a/recipes/bioconductor-reactomegsa/meta.yaml +++ b/recipes/bioconductor-reactomegsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.1" %} {% set name = "ReactomeGSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ceb80478cd55d9675e6d0a6093023cab + md5: c4ef9b68baf6957b7a3abf38bd4ffb39 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactomegsa", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase, devtools requirements: diff --git a/recipes/bioconductor-reactomepa/meta.yaml b/recipes/bioconductor-reactomepa/meta.yaml index 22181302d424b..7157cb19579aa 100644 --- a/recipes/bioconductor-reactomepa/meta.yaml +++ b/recipes/bioconductor-reactomepa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "ReactomePA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f827baf24cebacfc6d5960d8639ada5 + md5: c31f563d1848fd0bafdbedb6b7f9bb66 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reactomepa", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - 'r-ggplot2 >=3.3.5' - r-ggraph - r-gson - r-igraph run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - r-base - 'r-ggplot2 >=3.3.5' - r-ggraph diff --git a/recipes/bioconductor-readqpcr/meta.yaml b/recipes/bioconductor-readqpcr/meta.yaml index 90b685245eff9..999355ab15670 100644 --- a/recipes/bioconductor-readqpcr/meta.yaml +++ b/recipes/bioconductor-readqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "ReadqPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8b34a2498b00f76095ad92c8ccc11eb + md5: b92a0fe88b39abffbc0c46c36a76a8de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-readqpcr", max_pin="x.x") }}' noarch: generic # Suggests: qpcR requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-rebet/meta.yaml b/recipes/bioconductor-rebet/meta.yaml index ab5de905c1863..8771d5bd544a0 100644 --- a/recipes/bioconductor-rebet/meta.yaml +++ b/recipes/bioconductor-rebet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "REBET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7dc401e0d069b5ab67336904d617402 + md5: fc1e4bc02e112473630da74fce831189 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rebet", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-asset >=2.18.0,<2.19.0' + - 'bioconductor-asset >=2.20.0,<2.21.0' - r-base - libblas - liblapack run: - - 'bioconductor-asset >=2.18.0,<2.19.0' + - 'bioconductor-asset >=2.20.0,<2.21.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rebook/meta.yaml b/recipes/bioconductor-rebook/meta.yaml index 189c783a94af4..8ea103b7b63c5 100644 --- a/recipes/bioconductor-rebook/meta.yaml +++ b/recipes/bioconductor-rebook/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "rebook" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b71e3b95cce07920b7ce27a330f581ff + md5: 05a8502e7f25563382e9e277b3199339 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rebook", max_pin="x.x") }}' noarch: generic # Suggests: testthat, igraph, XML, BiocManager, RCurl, bookdown, rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base - r-codedepends - r-filelock - 'r-knitr >=1.32' - r-rmarkdown run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-dir.expiry >=1.8.0,<1.9.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' - r-base - r-codedepends - r-filelock diff --git a/recipes/bioconductor-receptloss/meta.yaml b/recipes/bioconductor-receptloss/meta.yaml index 55a5cd3f1fc37..1dd994f66fc91 100644 --- a/recipes/bioconductor-receptloss/meta.yaml +++ b/recipes/bioconductor-receptloss/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "receptLoss" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45eb200329852f199e2ccd81408799c5 + md5: 3ccddd0181e8b78b843807d1378f86ef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-receptloss", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 2.1.0), here requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 - r-magrittr - r-tidyr run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-reconsi/meta.yaml b/recipes/bioconductor-reconsi/meta.yaml index c85ae3b34f3a1..7157b2fd15860 100644 --- a/recipes/bioconductor-reconsi/meta.yaml +++ b/recipes/bioconductor-reconsi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "reconsi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf6ff0103385ff01c60c0a0267fc24c1 + md5: 884019da85885289094a2aed95d18314 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reconsi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-ggplot2 - r-ks @@ -29,7 +30,7 @@ requirements: - r-matrixstats - r-reshape2 run: - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-ggplot2 - r-ks diff --git a/recipes/bioconductor-recount/meta.yaml b/recipes/bioconductor-recount/meta.yaml index 020e059f3a9ae..d016fb257b38b 100644 --- a/recipes/bioconductor-recount/meta.yaml +++ b/recipes/bioconductor-recount/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "recount" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7dd19c0ea4ada1a5389c83cd7ad24641 + md5: 80d2f08ec7c30f139b1967db7cd07f7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-recount", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-downloader - r-rcurl - r-rentrez run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-downloader - r-rcurl diff --git a/recipes/bioconductor-recount3/meta.yaml b/recipes/bioconductor-recount3/meta.yaml index f8614bbd6239a..4acc5addbf239 100644 --- a/recipes/bioconductor-recount3/meta.yaml +++ b/recipes/bioconductor-recount3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.2" %} +{% set version = "1.12.0" %} {% set name = "recount3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e914f149ed1771b7e03d34b66d9379c7 + md5: 0e3b0229faa614fbbc49547e44b342d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-recount3", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown, testthat, pryr, interactiveDisplayBase, recount requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-httr @@ -33,11 +34,11 @@ requirements: - r-r.utils - r-sessioninfo run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-httr diff --git a/recipes/bioconductor-recountmethylation/meta.yaml b/recipes/bioconductor-recountmethylation/meta.yaml index 190a95ddd4d17..8270e20eb93ab 100644 --- a/recipes/bioconductor-recountmethylation/meta.yaml +++ b/recipes/bioconductor-recountmethylation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "recountmethylation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7d8ce3ec6caee2a883704ba14921a753 + md5: 56d6b1dcb581c96c3ee93c4def178a1c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-recountmethylation", max_pin="x.x") }}' noarch: generic -# Suggests: minfiData, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub +# Suggests: minfiData, minfiDataEPIC, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-r.utils - r-rcurl - r-reticulate run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-r.utils - r-rcurl diff --git a/recipes/bioconductor-recoup/meta.yaml b/recipes/bioconductor-recoup/meta.yaml index 7afbda57cf0b1..3d9060186612c 100644 --- a/recipes/bioconductor-recoup/meta.yaml +++ b/recipes/bioconductor-recoup/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "recoup" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43f3f62872c4b637d75c9ebeb37831b9 + md5: 021e00a6ca090381be16bf88e12eef05 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-recoup", max_pin="x.x") }}' noarch: generic # Suggests: grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-ggplot2 @@ -40,18 +41,18 @@ requirements: - r-rsqlite - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-ggplot2 diff --git a/recipes/bioconductor-reder/meta.yaml b/recipes/bioconductor-reder/meta.yaml index 6b1d9b412d1a2..f41f96e824ee1 100644 --- a/recipes/bioconductor-reder/meta.yaml +++ b/recipes/bioconductor-reder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.1" %} +{% set version = "2.6.0" %} {% set name = "RedeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 456d8535d228fd0767c9bcae10dea8c5 + md5: 033b5763d95dc222256a4ef85b7e3a99 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reder", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, markdown, TreeAndLeaf # SystemRequirements: Java Runtime Environment (Java>= 11) diff --git a/recipes/bioconductor-redisparam/meta.yaml b/recipes/bioconductor-redisparam/meta.yaml index e27ff9b17ddc6..1ae122c83be0f 100644 --- a/recipes/bioconductor-redisparam/meta.yaml +++ b/recipes/bioconductor-redisparam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RedisParam" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5149581ff1eb737d62129ff61417385c + md5: cf24018f96bc9de6286d2806dfd7bfaa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-redisparam", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat, BiocStyle # SystemRequirements: hiredis requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-futile.logger - r-redux - r-withr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-futile.logger - r-redux diff --git a/recipes/bioconductor-redseq/meta.yaml b/recipes/bioconductor-redseq/meta.yaml index aeb8f861a45bb..452649f180224 100644 --- a/recipes/bioconductor-redseq/meta.yaml +++ b/recipes/bioconductor-redseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "REDseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9534df4cbe43b5e8681406ff2b3e163 + md5: f20e437ad9c48683bdaeda1825f87f85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-redseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-regionalpcs/build.sh b/recipes/bioconductor-regionalpcs/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-regionalpcs/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-regionalpcs/meta.yaml b/recipes/bioconductor-regionalpcs/meta.yaml new file mode 100644 index 0000000000000..dfc7d8dcc70b5 --- /dev/null +++ b/recipes/bioconductor-regionalpcs/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.0" %} +{% set name = "regionalpcs" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 37f0fc1370efacc719f72b419455096a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regionalpcs", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, RMTstat, testthat (>= 3.0.0), BiocStyle, tidyr, minfiData, TxDb.Hsapiens.UCSC.hg19.knownGene, IRanges +requirements: + host: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-pcatools >=2.14.0,<2.15.0' + - r-base + - r-dplyr + - r-tibble + run: + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-pcatools >=2.14.0,<2.15.0' + - r-base + - r-dplyr + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Summarizing Regional Methylation with Regional Principal Components Analysis' + description: 'Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic regions to summarize the variability in methylation levels across CpGs. The number of principal components is chosen using either the Marcenko-Pasteur or Gavish-Donoho method to identify relevant signal in the data.' + license_file: LICENSE + diff --git a/recipes/bioconductor-regionalst/build.sh b/recipes/bioconductor-regionalst/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-regionalst/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-regionalst/meta.yaml b/recipes/bioconductor-regionalst/meta.yaml new file mode 100644 index 0000000000000..014618ed68bf1 --- /dev/null +++ b/recipes/bioconductor-regionalst/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.1" %} +{% set name = "RegionalST" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d9589bef7f1408c77dee510baa14b4ad +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regionalst", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, gplots, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-bayesspace >=1.12.0,<1.13.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-toast >=1.16.0,<1.17.0' + - r-assertthat + - r-base + - r-colorspace + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-magrittr + - r-rcolorbrewer + - r-seurat + - r-shiny + - r-tibble + run: + - 'bioconductor-bayesspace >=1.12.0,<1.13.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-toast >=1.16.0,<1.17.0' + - r-assertthat + - r-base + - r-colorspace + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-magrittr + - r-rcolorbrewer + - r-seurat + - r-shiny + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data' + description: 'This package analyze spatial transcriptomics data through cross-regional analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-regioner/meta.yaml b/recipes/bioconductor-regioner/meta.yaml index 266bf8254d054..0b0d546a5ab73 100644 --- a/recipes/bioconductor-regioner/meta.yaml +++ b/recipes/bioconductor-regioner/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "regioneR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f7f3f5515755c14cc156c8c3b1e0789 + md5: c2a9b6e46aa1aded948991c482cbf8a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regioner", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19.masked, testthat requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-memoise run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-memoise test: diff --git a/recipes/bioconductor-regionereloaded/meta.yaml b/recipes/bioconductor-regionereloaded/meta.yaml index c4e42ad969a11..c7131511ca7c5 100644 --- a/recipes/bioconductor-regionereloaded/meta.yaml +++ b/recipes/bioconductor-regionereloaded/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "regioneReloaded" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2357349974289f47a26a0d3c30dabb5 + md5: 38175e4bcc9ccb951f79fca8238897b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regionereloaded", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-regioner >=1.32.0,<1.33.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' - r-base - r-cluster - r-ggplot2 @@ -32,7 +33,7 @@ requirements: - r-scales - r-umap run: - - 'bioconductor-regioner >=1.32.0,<1.33.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' - r-base - r-cluster - r-ggplot2 diff --git a/recipes/bioconductor-regionreport/meta.yaml b/recipes/bioconductor-regionreport/meta.yaml index 2a041519f0dd4..2b14e31961044 100644 --- a/recipes/bioconductor-regionreport/meta.yaml +++ b/recipes/bioconductor-regionreport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "regionReport" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3bbf529af46b5340193184f866cb4721 + md5: 8ec5fb1e7db2235d543b2a9a6660a3b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regionreport", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.29.1), sessioninfo, DT, edgeR, ggbio (>= 1.35.2), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deformats >=1.28.0,<1.29.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deformats >=1.30.0,<1.31.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-knitr >=1.6' - 'r-knitrbootstrap >=0.9.0' - r-refmanager - 'r-rmarkdown >=0.9.5' run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deformats >=1.28.0,<1.29.0' - - 'bioconductor-derfinder >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deformats >=1.30.0,<1.31.0' + - 'bioconductor-derfinder >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-knitr >=1.6' - 'r-knitrbootstrap >=0.9.0' diff --git a/recipes/bioconductor-regparallel/meta.yaml b/recipes/bioconductor-regparallel/meta.yaml index 64ec9f3fe8745..c057ce329d0b4 100644 --- a/recipes/bioconductor-regparallel/meta.yaml +++ b/recipes/bioconductor-regparallel/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "RegParallel" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac6ed5e19a8dcfe359e97ccf89949dd1 + md5: 68533561edc82ac22088ffdd6e988aad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regparallel", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr, Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown requirements: @@ -39,7 +40,7 @@ requirements: - r-stringr - r-survival - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-regparallel/post-link.sh b/recipes/bioconductor-regparallel/post-link.sh index 647e5431ffe5e..72bade8afac71 100644 --- a/recipes/bioconductor-regparallel/post-link.sh +++ b/recipes/bioconductor-regparallel/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "regparallel-1.18.0" +installBiocDataPackage.sh "regparallel-1.20.0" diff --git a/recipes/bioconductor-regsplice/meta.yaml b/recipes/bioconductor-regsplice/meta.yaml index 5b0e0e6806a81..4c0ad8ce56a86 100644 --- a/recipes/bioconductor-regsplice/meta.yaml +++ b/recipes/bioconductor-regsplice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "regsplice" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 710fabf735b71d3a00303d4e53d57ce0 + md5: 3f63d2e93b02aec3ed044e2c56938d12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regsplice", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-glmnet - r-pbapply run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-glmnet - r-pbapply diff --git a/recipes/bioconductor-regutools/meta.yaml b/recipes/bioconductor-regutools/meta.yaml index a341f9c3a2139..84af8fe9dc688 100644 --- a/recipes/bioconductor-regutools/meta.yaml +++ b/recipes/bioconductor-regutools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "regutools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0f21e48a748b216be4eb31d3d6646185 + md5: f8b22dfa98af4304de7be1654159626a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-regutools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - r-rsqlite diff --git a/recipes/bioconductor-remp/meta.yaml b/recipes/bioconductor-remp/meta.yaml index 527302ae3737b..d8706ceaf727c 100644 --- a/recipes/bioconductor-remp/meta.yaml +++ b/recipes/bioconductor-remp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "REMP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f922355791b56e6db96c5fc289f60e76 + md5: ee8e5abfbef5fc5798de790cacbe2cfe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-remp", max_pin="x.x") }}' noarch: generic # Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-doparallel @@ -45,20 +46,20 @@ requirements: - r-readr - r-settings run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-doparallel diff --git a/recipes/bioconductor-repitools/meta.yaml b/recipes/bioconductor-repitools/meta.yaml index 90256ba30f818..c78c6b1bf1018 100644 --- a/recipes/bioconductor-repitools/meta.yaml +++ b/recipes/bioconductor-repitools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "Repitools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 614a2e515290ab172e482b38aefcf07c + md5: 3388cac60efdea157e1975abc5dcccd2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-repitools", max_pin="x.x") }}' # Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-gplots @@ -42,19 +43,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-gplots diff --git a/recipes/bioconductor-reportingtools/meta.yaml b/recipes/bioconductor-reportingtools/meta.yaml index cd3ada7e1ae4b..c00a0944d468c 100644 --- a/recipes/bioconductor-reportingtools/meta.yaml +++ b/recipes/bioconductor-reportingtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.39.0" %} +{% set version = "2.42.2" %} {% set name = "ReportingTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d17684737cbd651051b60339872967f + md5: 5f5adbf6b8570e232b9f3e98f75eab59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reportingtools", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pfam.db >=3.17.0,<3.18.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pfam.db >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-hwriter @@ -42,19 +43,19 @@ requirements: - r-r.utils - r-xml run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-pfam.db >=3.17.0,<3.18.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-pfam.db >=3.18.0,<3.19.0' - r-base - r-ggplot2 - r-hwriter diff --git a/recipes/bioconductor-repviz/meta.yaml b/recipes/bioconductor-repviz/meta.yaml index 284380aa6d46a..eb6ecad3257e6 100644 --- a/recipes/bioconductor-repviz/meta.yaml +++ b/recipes/bioconductor-repviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "RepViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 299815c83d5eeba7e716951e52b4f767 + md5: a740655d18448d4fb24e37ff1c60820d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-repviz", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-reqon/meta.yaml b/recipes/bioconductor-reqon/meta.yaml index 0c703203847d4..b0abd687e3d96 100644 --- a/recipes/bioconductor-reqon/meta.yaml +++ b/recipes/bioconductor-reqon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "ReQON" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa89144c5794fee3c455972783956d63 + md5: 3940db44a4b48a5b04d87c9466df72c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reqon", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle # SystemRequirements: Java version >= 1.6 requirements: host: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-seqbias >=1.48.0,<1.49.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-seqbias >=1.50.0,<1.51.0' - r-base - r-rjava - openjdk run: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-seqbias >=1.48.0,<1.49.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-seqbias >=1.50.0,<1.51.0' - r-base - r-rjava - openjdk diff --git a/recipes/bioconductor-residualmatrix/meta.yaml b/recipes/bioconductor-residualmatrix/meta.yaml index 9dd8341117bf8..aa7ea294a226e 100644 --- a/recipes/bioconductor-residualmatrix/meta.yaml +++ b/recipes/bioconductor-residualmatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ResidualMatrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d4291731f44ec7111ac14306ce53f18 + md5: 76eaee4311380f83265d9b5ecacd7e49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-residualmatrix", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-resolve/meta.yaml b/recipes/bioconductor-resolve/meta.yaml index 353621ed4826b..3f516a9501e1f 100644 --- a/recipes/bioconductor-resolve/meta.yaml +++ b/recipes/bioconductor-resolve/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RESOLVE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 090d75906aa025a56311fe6092ad8356 + md5: 3dd3a656ed19f5faa759f4b37c459f53 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-resolve", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, testthat, knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mutationalpatterns >=3.10.0,<3.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mutationalpatterns >=3.12.0,<3.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 @@ -38,14 +39,14 @@ requirements: - r-nnls - r-reshape2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mutationalpatterns >=3.10.0,<3.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-mutationalpatterns >=3.12.0,<3.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-restfulse/meta.yaml b/recipes/bioconductor-restfulse/meta.yaml index 7ce223f2c7b79..952a18777ff3c 100644 --- a/recipes/bioconductor-restfulse/meta.yaml +++ b/recipes/bioconductor-restfulse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "restfulSE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b746d7b3033fbb1c539462dfb1a5981a + md5: 80c91d615f5ff4997fce69087d3ea106 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-restfulse", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, Rtsne, org.Mm.eg.db, org.Hs.eg.db, BiocStyle, restfulSEData, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-rhdf5client >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-rhdf5client >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bigrquery - r-dbi @@ -38,15 +39,15 @@ requirements: - r-reshape2 - r-rlang run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-rhdf5client >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-rhdf5client >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bigrquery - r-dbi diff --git a/recipes/bioconductor-restfulsedata/meta.yaml b/recipes/bioconductor-restfulsedata/meta.yaml index ea8b5003020a0..8e3b21dac9c8d 100644 --- a/recipes/bioconductor-restfulsedata/meta.yaml +++ b/recipes/bioconductor-restfulsedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "restfulSEData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e92deb8a55a329887e87c9d4520e4b9e + md5: c69fe04b8675edd0faa593fb5ffc72c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-restfulsedata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, rhdf5client requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-restfulsedata/post-link.sh b/recipes/bioconductor-restfulsedata/post-link.sh index 4242d77395d84..08150a2be497b 100644 --- a/recipes/bioconductor-restfulsedata/post-link.sh +++ b/recipes/bioconductor-restfulsedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "restfulsedata-1.22.1" +installBiocDataPackage.sh "restfulsedata-1.24.0" diff --git a/recipes/bioconductor-retrofit/meta.yaml b/recipes/bioconductor-retrofit/meta.yaml index ea56377150869..82688026bb8d0 100644 --- a/recipes/bioconductor-retrofit/meta.yaml +++ b/recipes/bioconductor-retrofit/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "retrofit" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5634b1f69b84d0477586d9cda2223903 + md5: 2b804a752a293f14495e94adb39df466 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-retrofit", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl requirements: host: diff --git a/recipes/bioconductor-reusedata/build_failure.linux-64.yaml b/recipes/bioconductor-reusedata/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ecc86f7cff23e --- /dev/null +++ b/recipes/bioconductor-reusedata/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1370555a597842bfc527b0664421636a289d7b039c85298dda7098e9b36ad0b9 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.0MB/s 0.0s + [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m + [?25l[2K[0G[] 0.0s + [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s + opt/conda/conda-bld/noarch 127.0 B @ 2.0MB/s 0.0s + [?25hMamba failed to solve: + - bioconductor-basilisk >=1.14.0,<1.15.0 + - bioconductor-biocfilecache >=2.10.0,<2.11.0 + - bioconductor-rcwl >=1.18.0,<1.19.0 + - r-yaml + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-base 4.3.* + - bioconductor-rcwlpipelines >=1.18.0,<1.19.0 + - r-jsonlite + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-rcwlpipelines >=1.18.0,<1.19.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-basilisk >=1.14.0,<1.15.0 + - bioconductor-biocfilecache >=2.10.0,<2.11.0 + - bioconductor-rcwl >=1.18.0,<1.19.0 + - r-yaml + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-base 4.3.* + - bioconductor-rcwlpipelines >=1.18.0,<1.19.0 + - r-jsonlite + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-rcwlpipelines >=1.18.0,<1.19.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rcwlpipelines[version='>=1.18.0,<1.19.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-reusedata/meta.yaml b/recipes/bioconductor-reusedata/meta.yaml index f45c8f9250f15..3e52defa7ad81 100644 --- a/recipes/bioconductor-reusedata/meta.yaml +++ b/recipes/bioconductor-reusedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.2" %} {% set name = "ReUseData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 93524bd7dc0a684ac5e2413f414197bd + md5: c0041ec5d810d0d043c7375e04e78c06 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-reusedata", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat (>= 3.0.0) +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-rcwl >=1.16.0,<1.17.0' - - 'bioconductor-rcwlpipelines >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-rcwl >=1.18.0,<1.19.0' + - 'bioconductor-rcwlpipelines >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-jsonlite - r-yaml run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-rcwl >=1.16.0,<1.17.0' - - 'bioconductor-rcwlpipelines >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-rcwl >=1.18.0,<1.19.0' + - 'bioconductor-rcwlpipelines >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-jsonlite - r-yaml diff --git a/recipes/bioconductor-rexposome/meta.yaml b/recipes/bioconductor-rexposome/meta.yaml index dbe866c47fb93..83b17e2db684f 100644 --- a/recipes/bioconductor-rexposome/meta.yaml +++ b/recipes/bioconductor-rexposome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.1" %} {% set name = "rexposome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46e7c4f67ccb5a1e7fc583d4eb36bb0f + md5: 5dec247e3db216fed87e97cbfbf254cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rexposome", max_pin="x.x") }}' noarch: generic -# Suggests: mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown +# Suggests: mclust, flexmix, testthat, BiocStyle, knitr, formatR, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-corrplot - r-factominer - r-ggplot2 - r-ggrepel + - r-ggridges - r-glmnet - r-gplots - r-gridextra @@ -44,14 +46,15 @@ requirements: - r-scatterplot3d - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-circlize - r-corrplot - r-factominer - r-ggplot2 - r-ggrepel + - r-ggridges - r-glmnet - r-gplots - r-gridextra diff --git a/recipes/bioconductor-rfarm/meta.yaml b/recipes/bioconductor-rfarm/meta.yaml index 988866dc15b2d..0251337690723 100644 --- a/recipes/bioconductor-rfarm/meta.yaml +++ b/recipes/bioconductor-rfarm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.11.2" %} +{% set version = "1.14.0" %} {% set name = "rfaRm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f9f5b86baf2759fb096e5236b4ecacbd + md5: c12fb6805f6eecba196474a4527f241a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rfarm", max_pin="x.x") }}' noarch: generic -# Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics +# Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics, RUnit requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-httr + - r-jsonlite - r-magick - r-rsvg - r-rvest - r-stringi - r-xml2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-httr + - r-jsonlite - r-magick - r-rsvg - r-rvest diff --git a/recipes/bioconductor-rfastp/meta.yaml b/recipes/bioconductor-rfastp/meta.yaml index 6cd2d96a5df41..8acaaa9125710 100644 --- a/recipes/bioconductor-rfastp/meta.yaml +++ b/recipes/bioconductor-rfastp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Rfastp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9dfcaf1b205d287c9af287d0b6e86f1b + md5: 9f6903cb485151c4d3c368abf5193309 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rfastp", max_pin="x.x") }}' # Suggests: BiocStyle, testthat, knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-rcpp @@ -31,8 +32,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-rcpp diff --git a/recipes/bioconductor-rforproteomics/meta.yaml b/recipes/bioconductor-rforproteomics/meta.yaml index 258d0fdab9cb3..4a0c7b03f4d54 100644 --- a/recipes/bioconductor-rforproteomics/meta.yaml +++ b/recipes/bioconductor-rforproteomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.1" %} +{% set version = "1.40.0" %} {% set name = "RforProteomics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2dbad7c535bf6a39299cad51ede9aafd + md5: 6d75aedb5902ea26a18e39da6848db4c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rforproteomics", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, rpx (>= 2.0.3), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSnID, msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate, magick, cleaver requirements: host: - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-biocmanager - r-r.utils run: - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' - r-base - r-biocmanager - r-r.utils - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rforproteomics/post-link.sh b/recipes/bioconductor-rforproteomics/post-link.sh index a5c4558d939da..8efbae4b8ad53 100644 --- a/recipes/bioconductor-rforproteomics/post-link.sh +++ b/recipes/bioconductor-rforproteomics/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rforproteomics-1.38.1" +installBiocDataPackage.sh "rforproteomics-1.40.0" diff --git a/recipes/bioconductor-rfpred/meta.yaml b/recipes/bioconductor-rfpred/meta.yaml index 465baae9b458d..3c6bb3e73f786 100644 --- a/recipes/bioconductor-rfpred/meta.yaml +++ b/recipes/bioconductor-rfpred/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "rfPred" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 579bec97ce1052f870abdf8255c098b8 + md5: 125e88d593749d17979dfd08a67ea330 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rfpred", max_pin="x.x") }}' # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-data.table - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-data.table build: diff --git a/recipes/bioconductor-rgadem/meta.yaml b/recipes/bioconductor-rgadem/meta.yaml index 0a01ce8e67e15..9ea5c84cd97c1 100644 --- a/recipes/bioconductor-rgadem/meta.yaml +++ b/recipes/bioconductor-rgadem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.48.0" %} +{% set version = "2.50.0" %} {% set name = "rGADEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2cdce4776f91cfd938ce4930774c4b8a + md5: 17a121fa91f30cba09ed9dbb6b318555 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgadem", max_pin="x.x") }}' # Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rgenometracks/meta.yaml b/recipes/bioconductor-rgenometracks/meta.yaml index bfd570946be6d..56ab97b269241 100644 --- a/recipes/bioconductor-rgenometracks/meta.yaml +++ b/recipes/bioconductor-rgenometracks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "rGenomeTracks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfd465d74676896a9198011488d2f167 + md5: 860c81f62e3abf51de44d4dcdcdbfeef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgenometracks", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat (>= 3.0.0) # SystemRequirements: pyGenomeTracks (prefered to use install_pyGenomeTracks()) diff --git a/recipes/bioconductor-rgenometracksdata/meta.yaml b/recipes/bioconductor-rgenometracksdata/meta.yaml index a2e79700c4baa..f99c1c756acc0 100644 --- a/recipes/bioconductor-rgenometracksdata/meta.yaml +++ b/recipes/bioconductor-rgenometracksdata/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.0" %} {% set name = "rGenomeTracksData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 713103a8b4b4e48fa762ef589a43ffb8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgenometracksdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocManager, devtools requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgmql/meta.yaml b/recipes/bioconductor-rgmql/meta.yaml index 94c7ab649c2b7..661ae8f96255e 100644 --- a/recipes/bioconductor-rgmql/meta.yaml +++ b/recipes/bioconductor-rgmql/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RGMQL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8c068a6ec053a10f5651e97f405dd41 + md5: 78de1ecefadf0a7729bf7b62b50a2c1b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgmql", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rgmqllib >=1.20.0,<1.21.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rgmqllib >=1.22.0,<1.23.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr @@ -35,11 +36,11 @@ requirements: - r-rjava - r-xml2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rgmqllib >=1.20.0,<1.21.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rgmqllib >=1.22.0,<1.23.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-rgmqllib/meta.yaml b/recipes/bioconductor-rgmqllib/meta.yaml index d9b7f55fe7321..8807cc1353fdd 100644 --- a/recipes/bioconductor-rgmqllib/meta.yaml +++ b/recipes/bioconductor-rgmqllib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RGMQLlib" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9153c4ade0f2149a136bdaefb123f6d + md5: d8ad27b1fe0c5eff6135285db972cab2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgmqllib", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgmqllib/post-link.sh b/recipes/bioconductor-rgmqllib/post-link.sh index d86d102653d10..1b73edc0605c1 100644 --- a/recipes/bioconductor-rgmqllib/post-link.sh +++ b/recipes/bioconductor-rgmqllib/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rgmqllib-1.20.0" +installBiocDataPackage.sh "rgmqllib-1.22.0" diff --git a/recipes/bioconductor-rgntx/meta.yaml b/recipes/bioconductor-rgntx/meta.yaml index db65eb48352f6..265575b96ae87 100644 --- a/recipes/bioconductor-rgntx/meta.yaml +++ b/recipes/bioconductor-rgntx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RgnTX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a49f7294a76c9678e892b9f575c9efd + md5: 4ce438a2822a6541467c9781a3c48b26 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgntx", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-ggplot2 run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-ggplot2 diff --git a/recipes/bioconductor-rgoslin/meta.yaml b/recipes/bioconductor-rgoslin/meta.yaml index 861b06ce8fdb8..ed8b1ed6bb203 100644 --- a/recipes/bioconductor-rgoslin/meta.yaml +++ b/recipes/bioconductor-rgoslin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "rgoslin" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5835d13bddd6f4b07f4f41da411bec20 + md5: 211ef77e63cc8394ebc5eee33328cd08 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgoslin", max_pin="x.x") }}' # Suggests: testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra, BiocManager, stringr, stringi, ggplot2, tibble, lipidr requirements: host: diff --git a/recipes/bioconductor-rgraph2js/meta.yaml b/recipes/bioconductor-rgraph2js/meta.yaml index 6f0f850f1a585..0212b86e5dd86 100644 --- a/recipes/bioconductor-rgraph2js/meta.yaml +++ b/recipes/bioconductor-rgraph2js/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RGraph2js" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54578f3d4a51613dbc158bd4fafc3377 + md5: ccb2f26623270911ba855aa97e1269e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgraph2js", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna # SystemRequirements: jQuery, jQueryUI, qTip2, D3js and Raphael are required Javascript libraries made available via the online CDNJS service (http://cdnjs.cloudflare.com). requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-digest - r-rjson - r-whisker - jquery run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-digest - r-rjson diff --git a/recipes/bioconductor-rgraphviz/meta.yaml b/recipes/bioconductor-rgraphviz/meta.yaml index b9045b863c929..d28bc09c5210b 100644 --- a/recipes/bioconductor-rgraphviz/meta.yaml +++ b/recipes/bioconductor-rgraphviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "Rgraphviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d75a9db059a381ad08e88bf396be9e0 + md5: b93e5d1c383b1e5cd06e4dec89a43ce8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgraphviz", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics, XML # SystemRequirements: optionally Graphviz (>= 2.16) requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - libblas - liblapack run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rgreat/meta.yaml b/recipes/bioconductor-rgreat/meta.yaml index 97c18c4b4c2a8..607172e832e2e 100644 --- a/recipes/bioconductor-rgreat/meta.yaml +++ b/recipes/bioconductor-rgreat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "rGREAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4dba74b97e8ebb8e34ba72ae35e48dc + md5: 89ee57f3429887678846bba965ce84dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgreat", max_pin="x.x") }}' # Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-circlize - r-digest @@ -47,16 +48,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-circlize - r-digest diff --git a/recipes/bioconductor-rgsea/meta.yaml b/recipes/bioconductor-rgsea/meta.yaml index f31a86d27a77d..9042f59b32251 100644 --- a/recipes/bioconductor-rgsea/meta.yaml +++ b/recipes/bioconductor-rgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "RGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3038e7d2181e5ece758f5f98a877c15 + md5: 426ab6d4dc463399d014c6e76c3f8c75 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgsea", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, GEOquery, knitr, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-rgsepd/meta.yaml b/recipes/bioconductor-rgsepd/meta.yaml index 3ede6367c46d0..c3b4954bb93cf 100644 --- a/recipes/bioconductor-rgsepd/meta.yaml +++ b/recipes/bioconductor-rgsepd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "rgsepd" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8ccc8627b86ca25b735319429fd56c2c + md5: 0ca30d2f68c98bcc24cc5c5fbc5951b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgsepd", max_pin="x.x") }}' noarch: generic # Suggests: boot, tools, BiocGenerics, knitr, xtable requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gplots test: diff --git a/recipes/bioconductor-rgu34a.db/meta.yaml b/recipes/bioconductor-rgu34a.db/meta.yaml index eeb53355f2cb0..460be188747cf 100644 --- a/recipes/bioconductor-rgu34a.db/meta.yaml +++ b/recipes/bioconductor-rgu34a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rgu34a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e99dc4c05360b49a2249cb5de0b1dd4e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34acdf/meta.yaml b/recipes/bioconductor-rgu34acdf/meta.yaml index 28cf17672e23e..195b7856cd031 100644 --- a/recipes/bioconductor-rgu34acdf/meta.yaml +++ b/recipes/bioconductor-rgu34acdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34acdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: dcfa7ecce00e529f93809759ed837b8d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34acdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34aprobe/meta.yaml b/recipes/bioconductor-rgu34aprobe/meta.yaml index 7e74747aa85c4..2e3ca3c13f057 100644 --- a/recipes/bioconductor-rgu34aprobe/meta.yaml +++ b/recipes/bioconductor-rgu34aprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34aprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 902aee259a2894fa8713c4bf9266c0e2 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34aprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34b.db/meta.yaml b/recipes/bioconductor-rgu34b.db/meta.yaml index dfa15c3c3da20..2be3c456f72de 100644 --- a/recipes/bioconductor-rgu34b.db/meta.yaml +++ b/recipes/bioconductor-rgu34b.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rgu34b.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 5aeb80d5190bf2dcffa6b9264d3db33f build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34b.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34bcdf/meta.yaml b/recipes/bioconductor-rgu34bcdf/meta.yaml index 8b4984130ab18..c49a72cd0134b 100644 --- a/recipes/bioconductor-rgu34bcdf/meta.yaml +++ b/recipes/bioconductor-rgu34bcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34bcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 428b3a39f0d8addd7d863539b8cda6ea build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34bcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34bprobe/meta.yaml b/recipes/bioconductor-rgu34bprobe/meta.yaml index f4e8278899c40..01e2a8f025744 100644 --- a/recipes/bioconductor-rgu34bprobe/meta.yaml +++ b/recipes/bioconductor-rgu34bprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34bprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2d6488309c5e54231a18e2ecf5608bb1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34bprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34c.db/meta.yaml b/recipes/bioconductor-rgu34c.db/meta.yaml index e558c4807edf5..61199d1900ac5 100644 --- a/recipes/bioconductor-rgu34c.db/meta.yaml +++ b/recipes/bioconductor-rgu34c.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rgu34c.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e19f250869a9894bc9d069a4baf39a3c build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34c.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34ccdf/meta.yaml b/recipes/bioconductor-rgu34ccdf/meta.yaml index ba71a4c1c16f8..8360de7865875 100644 --- a/recipes/bioconductor-rgu34ccdf/meta.yaml +++ b/recipes/bioconductor-rgu34ccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34ccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 556a7130086004d26095594da31c6410 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34ccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgu34cprobe/meta.yaml b/recipes/bioconductor-rgu34cprobe/meta.yaml index 32165588998fb..1d514934bc4ab 100644 --- a/recipes/bioconductor-rgu34cprobe/meta.yaml +++ b/recipes/bioconductor-rgu34cprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rgu34cprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d1a6c433acd30b95fa7be89147105b74 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgu34cprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rguatlas4k.db/meta.yaml b/recipes/bioconductor-rguatlas4k.db/meta.yaml index 620f460bdb39c..e8a0ab33ef629 100644 --- a/recipes/bioconductor-rguatlas4k.db/meta.yaml +++ b/recipes/bioconductor-rguatlas4k.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rguatlas4k.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 6a360676e08319ec5465c47c758110bd build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rguatlas4k.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgug4105a.db/meta.yaml b/recipes/bioconductor-rgug4105a.db/meta.yaml index 3348d296af03d..856bf606c03aa 100644 --- a/recipes/bioconductor-rgug4105a.db/meta.yaml +++ b/recipes/bioconductor-rgug4105a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgug4105a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3ccf354083ae36a7ae687fb8209c4e5b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgug4105a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgug4130a.db/meta.yaml b/recipes/bioconductor-rgug4130a.db/meta.yaml index 6440322352513..29321c986ab3a 100644 --- a/recipes/bioconductor-rgug4130a.db/meta.yaml +++ b/recipes/bioconductor-rgug4130a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgug4130a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 13643ac109aaf12590a5b6e379609b79 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgug4130a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rgug4131a.db/meta.yaml b/recipes/bioconductor-rgug4131a.db/meta.yaml index 22167eb35715e..1c64418da6bcc 100644 --- a/recipes/bioconductor-rgug4131a.db/meta.yaml +++ b/recipes/bioconductor-rgug4131a.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "rgug4131a.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1168d4906fb8ce60cbc0fa6cfa3b8ec6 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rgug4131a.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 22e76300066cf..7e644a64ce038 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -1,49 +1,43 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.1" %} {% set name = "rhdf5" %} -{% set full_name = "bioconductor-" ~ name|lower %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: - name: '{{ full_name }}' + name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ full_name }}/{{ full_name }}_{{ version }}_src_all.tar.gz' - md5: 19c8340a70f1ce28043ba56bb9da1238 + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 947e662fe5f427ed0cc839e8049b431e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - run_exports: - # This pinning is preliminary. It should be changed if either: - # * a general policy for pinning bioconductor packages is decided and differs: - # https://github.com/bioconda/bioconda-recipes/issues/43905 - # * the author of this package assures us that he adheres to semantic - # versioning, in which case we can unpin the minor version, see: - # https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782567153 - - {{ pin_subpackage(full_name, max_pin="x.x") }} + run_exports: '{{ pin_subpackage("bioconductor-rhdf5", max_pin="x.x") }}' # Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel # SystemRequirements: GNU make requirements: - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make host: - - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-rhdf5filters >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -56,7 +50,7 @@ extra: identifiers: - biotools:rhdf5 parent_recipe: - name: '{{ full_name }}' - path: 'recipes/{{ full_name }}' + name: bioconductor-rhdf5 + path: recipes/bioconductor-rhdf5 version: 2.24.0 diff --git a/recipes/bioconductor-rhdf5client/meta.yaml b/recipes/bioconductor-rhdf5client/meta.yaml index 986ec5a995fa4..e9c92f1d8f081 100644 --- a/recipes/bioconductor-rhdf5client/meta.yaml +++ b/recipes/bioconductor-rhdf5client/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "rhdf5client" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fa6adb48f0ca8e63d458da7f96ae3a97 + md5: 9205b30177d59d75b7e544f795a90de5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhdf5client", max_pin="x.x") }}' # Suggests: knitr, testthat, BiocStyle, DT, rmarkdown requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-data.table - r-httr @@ -28,7 +29,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - r-base - r-data.table - r-httr diff --git a/recipes/bioconductor-rhdf5filters/meta.yaml b/recipes/bioconductor-rhdf5filters/meta.yaml index 5b9f894ca93e7..8d776ef525662 100644 --- a/recipes/bioconductor-rhdf5filters/meta.yaml +++ b/recipes/bioconductor-rhdf5filters/meta.yaml @@ -1,47 +1,39 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.1" %} {% set name = "rhdf5filters" %} -{% set full_name = "bioconductor-" ~ name|lower %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: - name: '{{ full_name }}' + name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ full_name }}/{{ full_name }}_{{ version }}_src_all.tar.gz' - md5: 8cef74eea9c788b536c4561603f265b4 + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3ecb2d30759fee6bde37bbb1f90fbf79 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ - run_exports: - # This pinning is preliminary. It should be changed if either: - # * a general policy for pinning bioconductor packages is decided and differs: - # https://github.com/bioconda/bioconda-recipes/issues/43905 - # * the author of this package assures us that he adheres to semantic - # versioning, in which case we can unpin the minor version, see: - # https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782567153 - - {{ pin_subpackage(full_name, max_pin="x.x") }} + run_exports: '{{ pin_subpackage("bioconductor-rhdf5filters", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.34.0) # SystemRequirements: GNU make requirements: - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make host: - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base - libblas - liblapack run: - - 'bioconductor-rhdf5lib >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rhdf5lib/meta.yaml b/recipes/bioconductor-rhdf5lib/meta.yaml index 16d7c44733a9d..0909d78d3986e 100644 --- a/recipes/bioconductor-rhdf5lib/meta.yaml +++ b/recipes/bioconductor-rhdf5lib/meta.yaml @@ -1,45 +1,36 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "Rhdf5lib" %} -{% set full_name = "bioconductor-" ~ name|lower %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: - name: '{{ full_name }}' + name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ full_name }}/{{ full_name }}_{{ version }}_src_all.tar.gz' - md5: 27c19bd24858ba26ff4762d41f3b2a16 + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 722160d55897324217ba8dc2cb60f3cd build: number: 1 rpaths: - lib/R/lib/ - lib/ - run_exports: - # This pinning is preliminary. It should be changed if either: - # * a general policy for pinning bioconductor packages is decided and differs: - # https://github.com/bioconda/bioconda-recipes/issues/43905 - # * the author of this package assures us that he adheres to semantic - # versioning, in which case we can unpin the minor version, see: - # https://github.com/grimbough/rhdf5/issues/131#issuecomment-1782567153 - - {{ pin_subpackage(full_name, max_pin="x.x") }} + run_exports: '{{ pin_subpackage("bioconductor-rhdf5lib", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery # SystemRequirements: GNU make requirements: - build: - - {{ compiler('c') }} - - automake - - make host: - r-base - libblas - liblapack - - libcurl run: - r-base + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' @@ -50,7 +41,7 @@ about: description: 'Provides C and C++ hdf5 libraries.' extra: parent_recipe: - name: '{{ full_name }}' - path: 'recipes/{{ full_name }}' + name: bioconductor-rhdf5lib + path: recipes/bioconductor-rhdf5lib version: 1.2.1 diff --git a/recipes/bioconductor-rhesus.db0/meta.yaml b/recipes/bioconductor-rhesus.db0/meta.yaml index c44f1b4b386d8..72604a3cbf18b 100644 --- a/recipes/bioconductor-rhesus.db0/meta.yaml +++ b/recipes/bioconductor-rhesus.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "rhesus.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16b4999171a6b36e72c19b3f15b46354 + md5: 26d7aa426d23f0c64cb0918f90c32314 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhesus.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rhesus.db0/post-link.sh b/recipes/bioconductor-rhesus.db0/post-link.sh index 4d13d03af1f40..ff96f3afab411 100644 --- a/recipes/bioconductor-rhesus.db0/post-link.sh +++ b/recipes/bioconductor-rhesus.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rhesus.db0-3.17.0" +installBiocDataPackage.sh "rhesus.db0-3.18.0" diff --git a/recipes/bioconductor-rhesuscdf/meta.yaml b/recipes/bioconductor-rhesuscdf/meta.yaml index cc7dff4a990b5..5551420081edf 100644 --- a/recipes/bioconductor-rhesuscdf/meta.yaml +++ b/recipes/bioconductor-rhesuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rhesuscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 994e16da5dd31bc2796d0da40aa2634f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhesuscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rhesusprobe/meta.yaml b/recipes/bioconductor-rhesusprobe/meta.yaml index 4410c54c821e3..f06026d876a7c 100644 --- a/recipes/bioconductor-rhesusprobe/meta.yaml +++ b/recipes/bioconductor-rhesusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rhesusprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4169c1c997c4c08b027bc7489533e11e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhesusprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml b/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml index 27e070df145eb..52618980dd6d5 100644 --- a/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml +++ b/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "rheumaticConditionWOLLBOLD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58d7b58e54ba5cbd75fafa85aa09f476 + md5: 8c8a5f56b923fe79c4a4902028d6fc5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rheumaticconditionwollbold", max_pin="x.x") }}' noarch: generic # Suggests: genefilter, Biobase, hgu133plus2.db requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh b/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh index 658d350311901..72f477eba6f72 100644 --- a/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh +++ b/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rheumaticconditionwollbold-1.38.0" +installBiocDataPackage.sh "rheumaticconditionwollbold-1.40.0" diff --git a/recipes/bioconductor-rhisat2/meta.yaml b/recipes/bioconductor-rhisat2/meta.yaml index eea04e8b05160..9bb4b0181af5c 100644 --- a/recipes/bioconductor-rhisat2/meta.yaml +++ b/recipes/bioconductor-rhisat2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Rhisat2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7075cf678dc031a22f157fcf950a7e64 + md5: bcfb03ad1e10fa471b46f2b214ddbb2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhisat2", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: GNU make requirements: host: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-sgseq >=1.34.0,<1.35.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-sgseq >=1.36.0,<1.37.0' - r-base - libblas - liblapack run: - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-sgseq >=1.34.0,<1.35.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-sgseq >=1.36.0,<1.37.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-rhtslib/meta.yaml b/recipes/bioconductor-rhtslib/meta.yaml index 061b2f2176c4e..52867f4d7faa2 100644 --- a/recipes/bioconductor-rhtslib/meta.yaml +++ b/recipes/bioconductor-rhtslib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "Rhtslib" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 862d4cd4c10064f45fc69c63969a4881 + md5: 8aa7fa3050a484702c3065c797948ba8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhtslib", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle # SystemRequirements: libbz2 & liblzma & libcurl (with header files), GNU make requirements: host: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-ri16cod.db/meta.yaml b/recipes/bioconductor-ri16cod.db/meta.yaml index 809b448fabd35..8bd8e75824883 100644 --- a/recipes/bioconductor-ri16cod.db/meta.yaml +++ b/recipes/bioconductor-ri16cod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "ri16cod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: cd01b429295fdbba21dbe566effacbdd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ri16cod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ribocrypt/meta.yaml b/recipes/bioconductor-ribocrypt/meta.yaml index 397596bcce7f1..88ff4d20e3b05 100644 --- a/recipes/bioconductor-ribocrypt/meta.yaml +++ b/recipes/bioconductor-ribocrypt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RiboCrypt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77955ef06f1325b0e0b63971e7ae2aee + md5: b5551bc35ad9798b4b1b401f7a08b280 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ribocrypt", max_pin="x.x") }}' noarch: generic # Suggests: testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-orfik >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-orfik >=1.22.0,<1.23.0' - r-base - r-bslib - r-data.table @@ -49,14 +50,14 @@ requirements: - r-shinyjqui - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-orfik >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-orfik >=1.22.0,<1.23.0' - r-base - r-bslib - r-data.table diff --git a/recipes/bioconductor-ribodipa/meta.yaml b/recipes/bioconductor-ribodipa/meta.yaml index bc9d90f73db21..e581d9847010c 100644 --- a/recipes/bioconductor-ribodipa/meta.yaml +++ b/recipes/bioconductor-ribodipa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "RiboDiPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05d7eabe7434b8191f138d0bea0bef29 + md5: 0aab649d27962694300a1e3b42b9417d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ribodipa", max_pin="x.x") }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel @@ -42,16 +43,16 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-riboprofiling/meta.yaml b/recipes/bioconductor-riboprofiling/meta.yaml index a9d839aa7db0a..51945ec4291e6 100644 --- a/recipes/bioconductor-riboprofiling/meta.yaml +++ b/recipes/bioconductor-riboprofiling/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "RiboProfiling" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf30f41d5ac40e786a37ea0becb370d7 + md5: ec32fb1993efa63a677422612e03ded7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-riboprofiling", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 @@ -39,17 +40,17 @@ requirements: - r-reshape2 - r-sqldf run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-ribor/meta.yaml b/recipes/bioconductor-ribor/meta.yaml index fc43ff4e568ce..d88e8a7571a55 100644 --- a/recipes/bioconductor-ribor/meta.yaml +++ b/recipes/bioconductor-ribor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ribor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 62847bbc0483e71852fda8fd089729d0 + md5: 6d86ac039324d8fa1b6c708f42da44e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ribor", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 @@ -31,8 +32,8 @@ requirements: - r-tidyr - r-yaml run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-riboseqr/build.sh b/recipes/bioconductor-riboseqr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-riboseqr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-riboseqr/meta.yaml b/recipes/bioconductor-riboseqr/meta.yaml new file mode 100644 index 0000000000000..548f9398d22d6 --- /dev/null +++ b/recipes/bioconductor-riboseqr/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.36.0" %} +{% set name = "riboSeqR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: eb9c84e564128ad11960fac5955c4d2f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-riboseqr", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - r-abind + - r-base + run: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - r-abind + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Analysis of sequencing data from ribosome profiling experiments' + description: 'Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-ribosomeprofilingqc/meta.yaml b/recipes/bioconductor-ribosomeprofilingqc/meta.yaml index df277d3caf594..a96b273f005a2 100644 --- a/recipes/bioconductor-ribosomeprofilingqc/meta.yaml +++ b/recipes/bioconductor-ribosomeprofilingqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ribosomeProfilingQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c9cafb9bd9b9816cc073d7da37b1b4c + md5: f26a7222a62ed0c3462336d1c945cea6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ribosomeprofilingqc", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, limma, testthat, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-cluster - r-ggfittext @@ -45,23 +46,23 @@ requirements: - r-ggrepel - r-scales run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-motifstack >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-cluster - r-ggfittext diff --git a/recipes/bioconductor-ricecdf/meta.yaml b/recipes/bioconductor-ricecdf/meta.yaml index a93eb09926db1..f47b3ea6adb91 100644 --- a/recipes/bioconductor-ricecdf/meta.yaml +++ b/recipes/bioconductor-ricecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ricecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 51db6f51f4adcfb7f4940d07668db8b8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ricecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-riceprobe/meta.yaml b/recipes/bioconductor-riceprobe/meta.yaml index 63f1d8d7cf35c..297a6847aeceb 100644 --- a/recipes/bioconductor-riceprobe/meta.yaml +++ b/recipes/bioconductor-riceprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "riceprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 2fac7746c343546cf30e6d54bc1e2019 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-riceprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rifi/meta.yaml b/recipes/bioconductor-rifi/meta.yaml index 374b3a83ddb43..05ed25ea6941c 100644 --- a/recipes/bioconductor-rifi/meta.yaml +++ b/recipes/bioconductor-rifi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "rifi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 40bcaaa842e5f3d40b4da6e31ac73996 + md5: 5d070b26ca40e04e4e3f9851853caa48 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rifi", max_pin="x.x") }}' noarch: generic # Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-car - r-cowplot @@ -40,9 +41,9 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-car - r-cowplot diff --git a/recipes/bioconductor-rificomparative/meta.yaml b/recipes/bioconductor-rificomparative/meta.yaml index f4846e577662c..fd8f33a8cb823 100644 --- a/recipes/bioconductor-rificomparative/meta.yaml +++ b/recipes/bioconductor-rificomparative/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "rifiComparative" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e82d286dbce65abb273d2c7107d0ed87 + md5: d371dc0f2b156f4565b09b7cfa5406e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rificomparative", max_pin="x.x") }}' noarch: generic -# Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle +# Suggests: DescTools, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-dta >=2.46.0,<2.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dta >=2.48.0,<2.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-devtools @@ -43,10 +44,10 @@ requirements: - r-tibble - r-writexl run: - - 'bioconductor-dta >=2.46.0,<2.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dta >=2.48.0,<2.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-devtools @@ -70,7 +71,7 @@ test: about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENSE' - summary: '''rifiComparative'' compares the outputs of ''rifi'' under two different conditions.' - description: '''rifiComparative'' is an extension of the ''rifi'' package. It is designed to compare the outputs of ''rifi'' under two different conditions by utilizing the half-life and mRNA at time 0 segments. To perform the segmentation, it takes into account the difference in half-life between the two conditions and the log2FC (fold change) of the mRNA at time 0. This package offers various functionalities such as segmentation, statistical analysis, summary tables, visualization of fragments, and additional plots that can be helpful for further analysis.' + summary: '''rifiComparative'' compares the output of rifi from two different conditions.' + description: '''rifiComparative'' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.' license_file: LICENSE diff --git a/recipes/bioconductor-rimmport/meta.yaml b/recipes/bioconductor-rimmport/meta.yaml index 9c9a4be1b3071..b64ed9ed2061d 100644 --- a/recipes/bioconductor-rimmport/meta.yaml +++ b/recipes/bioconductor-rimmport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RImmPort" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4586b7b4e16bfbfe7437943b0f33b892 + md5: 9a35da0a38439eee55d04ff8321ff09d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rimmport", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: diff --git a/recipes/bioconductor-ringo/meta.yaml b/recipes/bioconductor-ringo/meta.yaml index 8120d86801dc5..a2308eca149c4 100644 --- a/recipes/bioconductor-ringo/meta.yaml +++ b/recipes/bioconductor-ringo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "Ringo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 091ac77889415d4c7f2a018c2aef8ffd + md5: 2aa9ffb65c3d24fed5141f139f8721ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ringo", max_pin="x.x") }}' # Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-lattice - r-matrix @@ -32,11 +33,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-lattice - r-matrix diff --git a/recipes/bioconductor-risa/meta.yaml b/recipes/bioconductor-risa/meta.yaml index f7c42e97b03be..f7e20d8c31a4e 100644 --- a/recipes/bioconductor-risa/meta.yaml +++ b/recipes/bioconductor-risa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "Risa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba3487e592132bda3e87cb245b057fb1 + md5: 3d0fb12044023bc34defac509b8b4ab6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-risa", max_pin="x.x") }}' # Suggests: faahKO (>= 1.2.11) requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - 'r-rcpp >=0.9.13' - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-xcms >=3.22.0,<3.23.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-xcms >=4.0.0,<4.1.0' - r-base - 'r-rcpp >=0.9.13' build: diff --git a/recipes/bioconductor-ritan/meta.yaml b/recipes/bioconductor-ritan/meta.yaml index e4ce931394e66..3b41d1b6ab646 100644 --- a/recipes/bioconductor-ritan/meta.yaml +++ b/recipes/bioconductor-ritan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RITAN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3aada1fd1d9ff040f43ff6fd6e8be55d + md5: d9b8cf771e70cd374ba72e63aa439865 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ritan", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, BgeeDB requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-bgeedb >=2.26.0,<2.27.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-bgeedb >=2.28.0,<2.29.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-ritandata >=1.24.0,<1.25.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-ritandata >=1.26.0,<1.27.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-dynamictreecut - r-ggplot2 @@ -45,13 +46,13 @@ requirements: - r-reshape2 - r-sqldf run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-bgeedb >=2.26.0,<2.27.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-bgeedb >=2.28.0,<2.29.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-ritandata >=1.24.0,<1.25.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-ritandata >=1.26.0,<1.27.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-base - r-dynamictreecut - r-ggplot2 diff --git a/recipes/bioconductor-ritandata/meta.yaml b/recipes/bioconductor-ritandata/meta.yaml index 1204ac1b5ac42..5ca38c3c23f92 100644 --- a/recipes/bioconductor-ritandata/meta.yaml +++ b/recipes/bioconductor-ritandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RITANdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee9657a5c821eb892c79ef6a1ee4c5e5 + md5: 12987879ef374ad399dd440a058b9a47 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ritandata", max_pin="x.x") }}' noarch: generic +# Suggests: knitr requirements: host: - r-base run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'file LICENSE' - summary: 'This package contains the annotation and network data sets' - description: 'Data such as is contained in these two R data files in this package are required for the RITAN package examples. Users may use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes for more information, such as gathering more up-to-date annotation data.' + summary: 'This package contains reference annotation and network data sets' + description: 'Data such as is contained in the two R data files in this package are required for the RITAN package examples. Users are highly encouraged to use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes and RITAN.md for more information, such as gathering more up-to-date annotation data.' license_file: LICENSE diff --git a/recipes/bioconductor-ritandata/post-link.sh b/recipes/bioconductor-ritandata/post-link.sh index 2f95569f41478..41e2751e05e13 100644 --- a/recipes/bioconductor-ritandata/post-link.sh +++ b/recipes/bioconductor-ritandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ritandata-1.24.0" +installBiocDataPackage.sh "ritandata-1.26.0" diff --git a/recipes/bioconductor-river/meta.yaml b/recipes/bioconductor-river/meta.yaml index 1f09b68b21b10..cf84189dac66b 100644 --- a/recipes/bioconductor-river/meta.yaml +++ b/recipes/bioconductor-river/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RIVER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea28b47a8fe878e4abf8e3cf1b673037 + md5: 7b8f82011a163ae4f4a31f2172d49124 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-river", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-ggplot2 - r-glmnet - r-proc run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-ggplot2 - r-glmnet diff --git a/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml index 8300621962a83..4c214aee9eaf1 100644 --- a/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml +++ b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RJMCMCNucleosomes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f88945884d72fdd6ee15d6008afc07a5 + md5: cec0a46571d187963e019f18fff144f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rjmcmcnucleosomes", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit -# SystemRequirements: Rcpp +# SystemRequirements: Rcpp, gsl requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusseeker >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusseeker >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rcpp >=0.12.5' - libblas - liblapack + - gsl run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-consensusseeker >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-consensusseeker >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-rcpp >=0.12.5' + - gsl build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -54,4 +57,3 @@ about: license: Artistic-2.0 summary: 'Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)' description: 'This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.' - diff --git a/recipes/bioconductor-rlassocox/meta.yaml b/recipes/bioconductor-rlassocox/meta.yaml index 7a9ab1a25b16f..18539199c38bb 100644 --- a/recipes/bioconductor-rlassocox/meta.yaml +++ b/recipes/bioconductor-rlassocox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "RLassoCox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8cc79742a37f2121756c4ac8897025a4 + md5: 3f92bc442df2edc28546415bc716123b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rlassocox", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: diff --git a/recipes/bioconductor-rlhub/meta.yaml b/recipes/bioconductor-rlhub/meta.yaml index d176101ac3623..9001fbc96cb20 100644 --- a/recipes/bioconductor-rlhub/meta.yaml +++ b/recipes/bioconductor-rlhub/meta.yaml @@ -29,7 +29,7 @@ requirements: - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rlmm/meta.yaml b/recipes/bioconductor-rlmm/meta.yaml index fc040d60e4170..f42b4445d98c7 100644 --- a/recipes/bioconductor-rlmm/meta.yaml +++ b/recipes/bioconductor-rlmm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "RLMM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f30cfdb4cb3043dc8dfd8018b7850ab + md5: 7c43c967fab2a5e90059b26e46de345b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rlmm", max_pin="x.x") }}' noarch: generic # SystemRequirements: Internal files Xba.CQV, Xba.regions (or other regions file) requirements: diff --git a/recipes/bioconductor-rlseq/build_failure.linux-64.yaml b/recipes/bioconductor-rlseq/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b874c0e162bfb --- /dev/null +++ b/recipes/bioconductor-rlseq/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: b7a51b994b018dcebdb6ac934d67a24cdfdf07103b98b0c4084cfbaab5d97155 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-rlhub is stuck at BioC 3.17 because of a build error on their side +category: |- + dependency issue +log: |2- + - bioconductor-regioner >=1.34.0,<1.35.0 + - bioconductor-annotationhub >=3.10.0,<3.11.0 + - bioconductor-genomeinfodb >=1.38.0,<1.39.0 + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-rlhub >=1.8.0,<1.9.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - r-callr + - bioconductor-complexheatmap >=2.18.0,<2.19.0 + - bioconductor-genomicfeatures >=1.54.0,<1.55.0 + - r-aws.s3 + - r-ggplotify + - r-rcolorbrewer + - r-valr + - r-caretensemble + - bioconductor-rtracklayer >=1.62.0,<1.63.0 + - r-venndiagram + - r-ggprism + - r-circlize + - bioconductor-rlhub >=1.8.0,<1.9.0 + - r-base 4.3.* + - r-ggplot2 + - r-dplyr + - bioconductor-genomicranges >=1.54.0,<1.55.0 + - r-pheatmap + - bioconductor-regioner >=1.34.0,<1.35.0 + - bioconductor-annotationhub >=3.10.0,<3.11.0 + - bioconductor-genomeinfodb >=1.38.0,<1.39.0 + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-rlhub >=1.8.0,<1.9.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rlhub[version='>=1.8.0,<1.9.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-rlseq/meta.yaml b/recipes/bioconductor-rlseq/meta.yaml index 539401a044180..3bdc73c481a19 100644 --- a/recipes/bioconductor-rlseq/meta.yaml +++ b/recipes/bioconductor-rlseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.5.2" %} {% set name = "RLSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11778a7b1e74c4332c8e5db472e3443d + md5: fefe852714378d866e0209fbe48fcf21 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rlseq", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiocStyle, covr, lintr, rcmdcheck, DT, httr, jsonlite, kableExtra, kernlab, knitr, magick, MASS, org.Hs.eg.db, R.utils, randomForest, readr, rmarkdown, rpart, testthat (>= 3.0.0), tibble, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, futile.logger requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rlhub >=1.6.0,<1.7.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rlhub >=1.8.0,<1.9.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-aws.s3 - r-base - r-callr @@ -43,14 +44,14 @@ requirements: - r-valr - r-venndiagram run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rlhub >=1.6.0,<1.7.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rlhub >=1.8.0,<1.9.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-aws.s3 - r-base - r-callr diff --git a/recipes/bioconductor-rmagpie/meta.yaml b/recipes/bioconductor-rmagpie/meta.yaml index e9c9eae1d81c7..dbd9d4ffce38e 100644 --- a/recipes/bioconductor-rmagpie/meta.yaml +++ b/recipes/bioconductor-rmagpie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "Rmagpie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 468886302bd604ea3fab549eebd6554a + md5: 939fbdcb38d890daf9880baea89c8685 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmagpie", max_pin="x.x") }}' noarch: generic # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-kernlab - r-pamr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-kernlab diff --git a/recipes/bioconductor-rmassbank/meta.yaml b/recipes/bioconductor-rmassbank/meta.yaml index b21127ce6a9f3..b45501cfdd4e3 100644 --- a/recipes/bioconductor-rmassbank/meta.yaml +++ b/recipes/bioconductor-rmassbank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.10.0" %} +{% set version = "3.12.0" %} {% set name = "RMassBank" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d1f67c8b225b67387d68ace4243102d + md5: 59330cd723448b79eb751c6864e3dfbf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmassbank", max_pin="x.x") }}' # Suggests: BiocStyle,gplots,RMassBankData (>= 1.33.1), xcms (>= 1.37.1), CAMERA, RUnit, knitr, rmarkdown # SystemRequirements: OpenBabel requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chemmineob >=1.38.0,<1.39.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chemmineob >=1.40.0,<1.41.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-data.table - r-digest - r-envipat + - r-glue - r-httr - r-logger - r-r.utils - r-rcdk - r-rcpp - - r-rcurl - r-readjdx - r-rjson - r-webchem @@ -47,23 +48,23 @@ requirements: - liblapack - openbabel run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chemmineob >=1.38.0,<1.39.0' - - 'bioconductor-chemminer >=3.52.0,<3.53.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chemmineob >=1.40.0,<1.41.0' + - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-data.table - r-digest - r-envipat + - r-glue - r-httr - r-logger - r-r.utils - r-rcdk - r-rcpp - - r-rcurl - r-readjdx - r-rjson - r-webchem diff --git a/recipes/bioconductor-rmassbankdata/meta.yaml b/recipes/bioconductor-rmassbankdata/meta.yaml index c0e415f6acd0f..add2a5313260a 100644 --- a/recipes/bioconductor-rmassbankdata/meta.yaml +++ b/recipes/bioconductor-rmassbankdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "RMassBankData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea11a54b5f2465431c43bb8edde6a112 + md5: ac6f883e962890eebb03c2368be8bcdc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmassbankdata", max_pin="x.x") }}' noarch: generic # Suggests: RMassBank requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rmassbankdata/post-link.sh b/recipes/bioconductor-rmassbankdata/post-link.sh index 3a9811ab26de7..fa1e79222fceb 100644 --- a/recipes/bioconductor-rmassbankdata/post-link.sh +++ b/recipes/bioconductor-rmassbankdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rmassbankdata-1.38.0" +installBiocDataPackage.sh "rmassbankdata-1.40.0" diff --git a/recipes/bioconductor-rmelting/meta.yaml b/recipes/bioconductor-rmelting/meta.yaml index 94265e7c9ff25..d3b27ada7ef61 100644 --- a/recipes/bioconductor-rmelting/meta.yaml +++ b/recipes/bioconductor-rmelting/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "rmelting" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 42f9700727064207960dab9d71653652 + md5: a73d7dd41b3d77dce067644b04412e9d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmelting", max_pin="x.x") }}' noarch: generic # Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat # SystemRequirements: Java diff --git a/recipes/bioconductor-rmir.hs.mirna/meta.yaml b/recipes/bioconductor-rmir.hs.mirna/meta.yaml index 12100652f5496..f38de5714e0ba 100644 --- a/recipes/bioconductor-rmir.hs.mirna/meta.yaml +++ b/recipes/bioconductor-rmir.hs.mirna/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.7" %} {% set name = "RmiR.Hs.miRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4aedac188382447d9907d2617aa2e8e6 build: - number: 14 + number: 15 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmir.hs.mirna", max_pin="x.x") }}' noarch: generic # Suggests: methods, hgug4112a.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rmir.hsa/meta.yaml b/recipes/bioconductor-rmir.hsa/meta.yaml index 09617d6a7c380..0f5eb625023cc 100644 --- a/recipes/bioconductor-rmir.hsa/meta.yaml +++ b/recipes/bioconductor-rmir.hsa/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.5" %} {% set name = "RmiR.hsa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f22a18d1a34d12f8fc4ba3daaf1379fd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmir.hsa", max_pin="x.x") }}' noarch: generic # Suggests: methods, hgug4112a.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rmmquant/meta.yaml b/recipes/bioconductor-rmmquant/meta.yaml index 938579ddf4d18..5091be475916f 100644 --- a/recipes/bioconductor-rmmquant/meta.yaml +++ b/recipes/bioconductor-rmmquant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Rmmquant" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e67a9d31d1acf84a37e1edc3c778d432 + md5: 8f12574d12fdfbb3ef7407666fb22a7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmmquant", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat # SystemRequirements: C++11 requirements: host: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tbx20bamsubset >=1.36.0,<1.37.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tbx20bamsubset >=1.38.0,<1.39.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-devtools @@ -36,14 +37,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tbx20bamsubset >=1.36.0,<1.37.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tbx20bamsubset >=1.38.0,<1.39.0' - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - r-base - r-devtools diff --git a/recipes/bioconductor-rmspc/meta.yaml b/recipes/bioconductor-rmspc/meta.yaml index 4709a931c1529..58eec5b7e1658 100644 --- a/recipes/bioconductor-rmspc/meta.yaml +++ b/recipes/bioconductor-rmspc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "rmspc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7f21760a50ad227a597419cc10c26f10 + md5: fd5ce900bcff0c0a4b4423a7cc261aec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rmspc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) # SystemRequirements: .NET 6.0 requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-biocmanager - r-processx - r-stringr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-biocmanager - r-processx diff --git a/recipes/bioconductor-rnaagecalc/meta.yaml b/recipes/bioconductor-rnaagecalc/meta.yaml index d0b26aa2751a5..dee8249e03b08 100644 --- a/recipes/bioconductor-rnaagecalc/meta.yaml +++ b/recipes/bioconductor-rnaagecalc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RNAAgeCalc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 467f0ca987822c00d042b03c1c7fe382 + md5: 8601edc9bd38ec2387cd9cd9a78b0da8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaagecalc", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 test: diff --git a/recipes/bioconductor-rnaeditr/meta.yaml b/recipes/bioconductor-rnaeditr/meta.yaml index a9c58c91a11ba..cbbbde1bbbebf 100644 --- a/recipes/bioconductor-rnaeditr/meta.yaml +++ b/recipes/bioconductor-rnaeditr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "rnaEditr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47abbe2ca055d268e3c5a03635549268 + md5: fb5365c7d12dcdc26838f4824e70a00d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaeditr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-corrplot - r-logistf - r-plyr - r-survival run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bumphunter >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-corrplot - r-logistf diff --git a/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml b/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml index 05f72360ba0f3..3fae561ac4294 100644 --- a/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml +++ b/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "RnAgilentDesign028282.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 72cafb0f7514a81f462acb3248e21aa9 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnagilentdesign028282.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnainteract/meta.yaml b/recipes/bioconductor-rnainteract/meta.yaml index 6a6592e48526e..a1bd4cfd25c05 100644 --- a/recipes/bioconductor-rnainteract/meta.yaml +++ b/recipes/bioconductor-rnainteract/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "RNAinteract" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b789fe4d04a6fba019a3aaf8ff61646b + md5: 571d13067f2afebde4247de5571e1086 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnainteract", max_pin="x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' - r-abind - r-base - r-gplots @@ -36,11 +37,11 @@ requirements: - r-locfit - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' - - 'bioconductor-geneplotter >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-splots >=1.66.0,<1.67.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' + - 'bioconductor-geneplotter >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-splots >=1.68.0,<1.69.0' - r-abind - r-base - r-gplots diff --git a/recipes/bioconductor-rnainteractmapk/meta.yaml b/recipes/bioconductor-rnainteractmapk/meta.yaml index e34bf3486e80c..47e1b53a2be90 100644 --- a/recipes/bioconductor-rnainteractmapk/meta.yaml +++ b/recipes/bioconductor-rnainteractmapk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "RNAinteractMAPK" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed5fd6239416fbacc80a8995c6e13fb7 + md5: c60bb748ed7dc37d409f5dde69354074 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnainteractmapk", max_pin="x.x") }}' noarch: generic # Suggests: qvalue requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-rnainteract >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-rnainteract >=1.50.0,<1.51.0' - r-base - r-fields - r-gdata @@ -31,9 +32,9 @@ requirements: - r-mass - r-sparselda run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-rnainteract >=1.48.0,<1.49.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-rnainteract >=1.50.0,<1.51.0' - r-base - r-fields - r-gdata @@ -41,7 +42,7 @@ requirements: - r-mass - r-sparselda - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnainteractmapk/post-link.sh b/recipes/bioconductor-rnainteractmapk/post-link.sh index 9e394a3288ff2..d87f516db77a0 100644 --- a/recipes/bioconductor-rnainteractmapk/post-link.sh +++ b/recipes/bioconductor-rnainteractmapk/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnainteractmapk-1.38.0" +installBiocDataPackage.sh "rnainteractmapk-1.40.0" diff --git a/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml b/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml index ab88f1c02fb0c..93407ca9b47f1 100644 --- a/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml +++ b/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAmodR.AlkAnilineSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de1fd6898807bda24c85bea3b82ba655 + md5: a8d93c4a0a55346a6d47edb5f4c4438e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnamodr.alkanilineseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Biostrings, RNAmodR.Data requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-rnamodr.data/meta.yaml b/recipes/bioconductor-rnamodr.data/meta.yaml index 772d4123cb9ef..beb72c08bfd72 100644 --- a/recipes/bioconductor-rnamodr.data/meta.yaml +++ b/recipes/bioconductor-rnamodr.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAmodR.Data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1299a93be9ed1090e5890741cebde152 + md5: cd4851e2f0c0a93c6d5a9163f542b07f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnamodr.data", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-experimenthubdata >=1.26.0,<1.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-experimenthubdata >=1.26.0,<1.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnamodr.data/post-link.sh b/recipes/bioconductor-rnamodr.data/post-link.sh index 35a51256142a0..7991a62b289cf 100644 --- a/recipes/bioconductor-rnamodr.data/post-link.sh +++ b/recipes/bioconductor-rnamodr.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnamodr.data-1.14.0" +installBiocDataPackage.sh "rnamodr.data-1.16.0" diff --git a/recipes/bioconductor-rnamodr.ml/meta.yaml b/recipes/bioconductor-rnamodr.ml/meta.yaml index 95059b708a6c3..1508ede453dec 100644 --- a/recipes/bioconductor-rnamodr.ml/meta.yaml +++ b/recipes/bioconductor-rnamodr.ml/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAmodR.ML" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef2e4335b21c319d46453cc8dd1dd2f4 + md5: b82e119e7d8c2387b22f4b38d0985970 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnamodr.ml", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ranger run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ranger test: diff --git a/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml b/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml index 1e051d06e76b0..a6f3883a418a5 100644 --- a/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml +++ b/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAmodR.RiboMethSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c10bb4524dada400d7e9e6fdb6fcafd + md5: fc22b6332a4e89e33ff8921d9e54aac7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnamodr.ribomethseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, RNAmodR.Data requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rnamodr >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rnamodr >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-rnamodr/meta.yaml b/recipes/bioconductor-rnamodr/meta.yaml index 9c834d67d273b..78ce0c695332d 100644 --- a/recipes/bioconductor-rnamodr/meta.yaml +++ b/recipes/bioconductor-rnamodr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAmodR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abd9121f4f35d864be10cac6bf1c0d9c + md5: ece4ec8fc16a95ec2ee8d9506283c57e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnamodr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-colorramps - r-ggplot2 @@ -43,20 +44,20 @@ requirements: - r-reshape2 - r-rocr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-colorramps - r-ggplot2 diff --git a/recipes/bioconductor-rnasense/meta.yaml b/recipes/bioconductor-rnasense/meta.yaml index fd03499b2d792..f75925da2198c 100644 --- a/recipes/bioconductor-rnasense/meta.yaml +++ b/recipes/bioconductor-rnasense/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RNAsense" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b29a1e11b8c90a33aa7ad1885a81b458 + md5: 514e6c09019b7f9116ddbedbdf514a5a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnasense", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-nbpseq run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-nbpseq diff --git a/recipes/bioconductor-rnaseqcomp/meta.yaml b/recipes/bioconductor-rnaseqcomp/meta.yaml index 1ae3f6bd5d654..874a5325d2799 100644 --- a/recipes/bioconductor-rnaseqcomp/meta.yaml +++ b/recipes/bioconductor-rnaseqcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "rnaseqcomp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 093b21b510a3c3dbe2652b8c97b10391 + md5: 2d0e9f4dd34f6746ff48994f8067f6f6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqcomp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-rnaseqcovarimpute/build.sh b/recipes/bioconductor-rnaseqcovarimpute/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rnaseqcovarimpute/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnaseqcovarimpute/meta.yaml b/recipes/bioconductor-rnaseqcovarimpute/meta.yaml new file mode 100644 index 0000000000000..21a2e0ab62a71 --- /dev/null +++ b/recipes/bioconductor-rnaseqcovarimpute/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.2" %} +{% set name = "RNAseqCovarImpute" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 17d14273ae359562d3f0cbf1c45b10a7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqcovarimpute", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, tidyr, stringr, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-dplyr + - r-foreach + - r-magrittr + - r-mice + - r-rlang + run: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-dplyr + - r-foreach + - r-magrittr + - r-mice + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Impute Covariate Data in RNA Sequencing Studies' + description: 'The RNAseqCovarImpute package implements multiple imputation of missing covariates and differential gene expression analysis by: 1) Randomly binning genes into smaller groups, 2) Creating M imputed datasets separately within each bin, where the imputation predictor matrix includes all covariates and the log counts per million (CPM) for the genes within each bin, 3) Estimating gene expression changes using voom followed by lmFit functions, separately on each M imputed dataset within each gene bin, 4) Un-binning the gene sets and stacking the M sets of model results before applying the squeezeVar function to apply a variance shrinking Bayesian procedure to each M set of model results, 5) Pooling the results with Rubins’ rules to produce combined coefficients, standard errors, and P-values, and 6) Adjusting P-values for multiplicity to account for false discovery rate (FDR).' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml index 8c3c00c1f2177..b3e826c19752f 100644 --- a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml +++ b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "RNAseqData.HNRNPC.bam.chr14" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c39f3f2306bb10cb47a97b1d2c893ad + md5: 9bfb7faf3c8770b15f3cf15bb670162d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqdata.hnrnpc.bam.chr14", max_pin="x.x") }}' noarch: generic # Suggests: GenomicAlignments, BiocManager requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh index 0e253883cfc15..02be065d14f92 100644 --- a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh +++ b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnaseqdata.hnrnpc.bam.chr14-0.38.0" +installBiocDataPackage.sh "rnaseqdata.hnrnpc.bam.chr14-0.40.0" diff --git a/recipes/bioconductor-rnaseqpower/meta.yaml b/recipes/bioconductor-rnaseqpower/meta.yaml index eb6b3310173ed..50beb5be190ca 100644 --- a/recipes/bioconductor-rnaseqpower/meta.yaml +++ b/recipes/bioconductor-rnaseqpower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "RNASeqPower" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ed9fb060724ab44d75be435f10eceeb + md5: 38da142eb3ee64f2e7684ead27e4520f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqpower", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-rnaseqsamplesize/meta.yaml b/recipes/bioconductor-rnaseqsamplesize/meta.yaml index 4fc692cb5bd46..470e4efabe95e 100644 --- a/recipes/bioconductor-rnaseqsamplesize/meta.yaml +++ b/recipes/bioconductor-rnaseqsamplesize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "RnaSeqSampleSize" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 99e670bb27777288f4c42bdb45964a89 + md5: faa40e62b53c345d9298c32310e6488c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqsamplesize", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-rnaseqsamplesizedata >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-rnaseqsamplesizedata >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -38,12 +39,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-recount >=1.26.0,<1.27.0' - - 'bioconductor-rnaseqsamplesizedata >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-recount >=1.28.0,<1.29.0' + - 'bioconductor-rnaseqsamplesizedata >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml b/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml index 8fd742f290e66..d6d8fc2ab7470 100644 --- a/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml +++ b/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RnaSeqSampleSizeData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 415e0dc4f463089c632c9106f6df7d89 + md5: a4edc47422b0be1d83521282c0599440 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnaseqsamplesizedata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base run: - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh b/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh index 538ec6640b572..0b665148a7ee6 100644 --- a/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh +++ b/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnaseqsamplesizedata-1.32.0" +installBiocDataPackage.sh "rnaseqsamplesizedata-1.34.0" diff --git a/recipes/bioconductor-rnbeads.hg19/meta.yaml b/recipes/bioconductor-rnbeads.hg19/meta.yaml index 0287d73aa353c..f712559b76362 100644 --- a/recipes/bioconductor-rnbeads.hg19/meta.yaml +++ b/recipes/bioconductor-rnbeads.hg19/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RnBeads.hg19" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 83a4f81f4c411d8139ba8673687a6a49 + md5: 92612251679ba9c6d2b88b90838edf1c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads.hg19", max_pin="x.x") }}' noarch: generic # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.hg19/post-link.sh b/recipes/bioconductor-rnbeads.hg19/post-link.sh index a2dd13d8a0453..b7529eae02133 100644 --- a/recipes/bioconductor-rnbeads.hg19/post-link.sh +++ b/recipes/bioconductor-rnbeads.hg19/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.hg19-1.32.0" +installBiocDataPackage.sh "rnbeads.hg19-1.34.0" diff --git a/recipes/bioconductor-rnbeads.hg38/meta.yaml b/recipes/bioconductor-rnbeads.hg38/meta.yaml index 33af85fcb32ac..8baae260b3c7f 100644 --- a/recipes/bioconductor-rnbeads.hg38/meta.yaml +++ b/recipes/bioconductor-rnbeads.hg38/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RnBeads.hg38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87b5a33c515443e05b5ab7cfeb7afa7a + md5: 44dd2d3ae3703e045016a34060a14b0a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads.hg38", max_pin="x.x") }}' noarch: generic # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.hg38/post-link.sh b/recipes/bioconductor-rnbeads.hg38/post-link.sh index 240286b0e5169..7752ddaad438f 100644 --- a/recipes/bioconductor-rnbeads.hg38/post-link.sh +++ b/recipes/bioconductor-rnbeads.hg38/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.hg38-1.32.0" +installBiocDataPackage.sh "rnbeads.hg38-1.34.0" diff --git a/recipes/bioconductor-rnbeads.mm10/meta.yaml b/recipes/bioconductor-rnbeads.mm10/meta.yaml index 32cb33a408c62..6b68058cd1575 100644 --- a/recipes/bioconductor-rnbeads.mm10/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm10/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "RnBeads.mm10" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b25dd4978d2d430192ae93b45945506 + md5: 0c935572ce46183bc5a7aaea31ea2519 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads.mm10", max_pin="x.x") }}' noarch: generic # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.mm10/post-link.sh b/recipes/bioconductor-rnbeads.mm10/post-link.sh index 8e68b5fa38fc2..f7a47eac3384f 100644 --- a/recipes/bioconductor-rnbeads.mm10/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm10/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.mm10-2.8.0" +installBiocDataPackage.sh "rnbeads.mm10-2.10.0" diff --git a/recipes/bioconductor-rnbeads.mm9/meta.yaml b/recipes/bioconductor-rnbeads.mm9/meta.yaml index c117153200f26..0788e300ed3ab 100644 --- a/recipes/bioconductor-rnbeads.mm9/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm9/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RnBeads.mm9" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 83951bafa8f84863f5cdd3e0128c1e0d + md5: 76f271051b1c542e5ac0da492777f933 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads.mm9", max_pin="x.x") }}' noarch: generic # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.mm9/post-link.sh b/recipes/bioconductor-rnbeads.mm9/post-link.sh index aea69f9cb33bb..6831e4e1b6ab5 100644 --- a/recipes/bioconductor-rnbeads.mm9/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm9/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.mm9-1.32.0" +installBiocDataPackage.sh "rnbeads.mm9-1.34.0" diff --git a/recipes/bioconductor-rnbeads.rn5/meta.yaml b/recipes/bioconductor-rnbeads.rn5/meta.yaml index 8dbb3257a3563..82d6777b5462e 100644 --- a/recipes/bioconductor-rnbeads.rn5/meta.yaml +++ b/recipes/bioconductor-rnbeads.rn5/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RnBeads.rn5" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 704db9c010242b63f68e02de58b77ee0 + md5: ed075717da62b68e7a9b47a14ac09a35 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads.rn5", max_pin="x.x") }}' noarch: generic # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnbeads.rn5/post-link.sh b/recipes/bioconductor-rnbeads.rn5/post-link.sh index e47bc2c56b22e..a47dfa0ed34b1 100644 --- a/recipes/bioconductor-rnbeads.rn5/post-link.sh +++ b/recipes/bioconductor-rnbeads.rn5/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.rn5-1.32.0" +installBiocDataPackage.sh "rnbeads.rn5-1.34.0" diff --git a/recipes/bioconductor-rnbeads/meta.yaml b/recipes/bioconductor-rnbeads/meta.yaml index 2f00032bce087..23bf5205b7e61 100644 --- a/recipes/bioconductor-rnbeads/meta.yaml +++ b/recipes/bioconductor-rnbeads/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "RnBeads" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 350ab4afb8a56dce1661f349388f7145 + md5: 40a269bbbddeb407ca5c4545cb6852ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnbeads", max_pin="x.x") }}' noarch: generic # Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-ff @@ -39,13 +40,13 @@ requirements: - r-matrixstats - r-plyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-ff diff --git a/recipes/bioconductor-rnits/meta.yaml b/recipes/bioconductor-rnits/meta.yaml index 4dd15afc090c0..64032849b40f0 100644 --- a/recipes/bioconductor-rnits/meta.yaml +++ b/recipes/bioconductor-rnits/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "Rnits" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9743b9d8fca7c4ae623a115779553815 + md5: 4b767809cee3875eb2f7f991fba83771 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnits", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, GEOquery, stringr requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-boot - r-ggplot2 - r-reshape2 run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-boot - r-ggplot2 diff --git a/recipes/bioconductor-rnu34.db/meta.yaml b/recipes/bioconductor-rnu34.db/meta.yaml index 326295a981604..bda66c2c787a1 100644 --- a/recipes/bioconductor-rnu34.db/meta.yaml +++ b/recipes/bioconductor-rnu34.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rnu34.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7345817f2f26270779d2409b8a17a5bd build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnu34.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnu34cdf/meta.yaml b/recipes/bioconductor-rnu34cdf/meta.yaml index d0398e2fadfb0..2611cd113cc77 100644 --- a/recipes/bioconductor-rnu34cdf/meta.yaml +++ b/recipes/bioconductor-rnu34cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rnu34cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0f2564fc6ac89de4d779faf253f23ce3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnu34cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rnu34probe/meta.yaml b/recipes/bioconductor-rnu34probe/meta.yaml index 6e71cfd8f8834..7c8368ad92536 100644 --- a/recipes/bioconductor-rnu34probe/meta.yaml +++ b/recipes/bioconductor-rnu34probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rnu34probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c5ef9793a437f2bf990f6e84d31da0de build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnu34probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-roar/meta.yaml b/recipes/bioconductor-roar/meta.yaml index c1e9fe04b60a1..3e8eae075f595 100644 --- a/recipes/bioconductor-roar/meta.yaml +++ b/recipes/bioconductor-roar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "roar" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1cbb5f5c6c86922f0f97a3c5318d9500 + md5: 563dcc245ffbc288c2e6ec9a9c138faa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-roar", max_pin="x.x") }}' noarch: generic # Suggests: RNAseqData.HNRNPC.bam.chr14, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-roastgsa/build.sh b/recipes/bioconductor-roastgsa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-roastgsa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-roastgsa/meta.yaml b/recipes/bioconductor-roastgsa/meta.yaml new file mode 100644 index 0000000000000..0f8d85c23ec25 --- /dev/null +++ b/recipes/bioconductor-roastgsa/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "roastgsa" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 83d20d90ed18c719222042ae3d9f46d3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-roastgsa", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2 +requirements: + host: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-ggplot2 + - r-gplots + - r-rcolorbrewer + run: + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - r-base + - r-ggplot2 + - r-gplots + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Rotation based gene set analysis' + description: 'This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-roberts2005annotation.db/meta.yaml b/recipes/bioconductor-roberts2005annotation.db/meta.yaml index 590ff86933c63..54bd6307c474c 100644 --- a/recipes/bioconductor-roberts2005annotation.db/meta.yaml +++ b/recipes/bioconductor-roberts2005annotation.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "Roberts2005Annotation.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fb28aaf1a1e0c81cf936badc674b754a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-roberts2005annotation.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-roc/meta.yaml b/recipes/bioconductor-roc/meta.yaml index cfe53ee311603..f03479e853006 100644 --- a/recipes/bioconductor-roc/meta.yaml +++ b/recipes/bioconductor-roc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "ROC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5df627cc8040f624fb107b972e9dc12 + md5: 2b84dc68639bbe6dbc5e4b9eeb429dbb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-roc", max_pin="x.x") }}' # Suggests: rmarkdown, Biobase, BiocStyle requirements: host: diff --git a/recipes/bioconductor-rocpai/meta.yaml b/recipes/bioconductor-rocpai/meta.yaml index 6519f055f9742..f3147e68cacfa 100644 --- a/recipes/bioconductor-rocpai/meta.yaml +++ b/recipes/bioconductor-rocpai/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ROCpAI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3672b1cf97ce197f0f992c5b8fc0d27e + md5: 8d2702c4029efeb23248e107384ffd27 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rocpai", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-fission >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fission >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-knitr run: - - 'bioconductor-fission >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-fission >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-knitr diff --git a/recipes/bioconductor-rolde/meta.yaml b/recipes/bioconductor-rolde/meta.yaml index 2144127e4bca7..839f45ba07b2e 100644 --- a/recipes/bioconductor-rolde/meta.yaml +++ b/recipes/bioconductor-rolde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "RolDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c372addd6ebd25bd625bc7c490b3b38d + md5: 12c19e976fa6e9be2e9fa9a433690355 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rolde", max_pin="x.x") }}' noarch: generic # Suggests: knitr, printr, rmarkdown, testthat requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rots >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rots >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dorng @@ -32,9 +33,9 @@ requirements: - r-nlme - r-rngtools run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-rots >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-rots >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dorng diff --git a/recipes/bioconductor-rols/meta.yaml b/recipes/bioconductor-rols/meta.yaml index 8ed0008c17f7d..caf228701c0ba 100644 --- a/recipes/bioconductor-rols/meta.yaml +++ b/recipes/bioconductor-rols/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "rols" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 20398c9ed6df71963c3f186cbb5007d2 + md5: ef7159fc8010e7a7a1c5ecf285b91fc8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rols", max_pin="x.x") }}' noarch: generic # Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httr - r-jsonlite - r-progress run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httr - r-jsonlite diff --git a/recipes/bioconductor-rontotools/meta.yaml b/recipes/bioconductor-rontotools/meta.yaml index c9696b3f8fe86..af20e2f7fb71a 100644 --- a/recipes/bioconductor-rontotools/meta.yaml +++ b/recipes/bioconductor-rontotools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "ROntoTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3c0b94ebd7487fcddaa27f914b3cd8c + md5: 11764a125b9411a5b2d2ba20f4c64024 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rontotools", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-boot run: - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-boot test: diff --git a/recipes/bioconductor-ropls/meta.yaml b/recipes/bioconductor-ropls/meta.yaml index fed107c32ab86..eda59d7bb9280 100644 --- a/recipes/bioconductor-ropls/meta.yaml +++ b/recipes/bioconductor-ropls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "ropls" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43cd3622aa3b6632a328590056d0b727 + md5: a1c4a1710eb179bb29f3831a5fe80849 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ropls", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-plotly run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-multidataset >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-multidataset >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-plotly diff --git a/recipes/bioconductor-roseq/meta.yaml b/recipes/bioconductor-roseq/meta.yaml index b7c8fd1c0f45c..487093f51cc24 100644 --- a/recipes/bioconductor-roseq/meta.yaml +++ b/recipes/bioconductor-roseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ROSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 825b4add5728a53d474403048dbbb8c4 + md5: 9af42531e92f5a535c6a139f0856e6e3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-roseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, RUnit, BiocGenerics requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-pbmcapply run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-pbmcapply test: diff --git a/recipes/bioconductor-rots/meta.yaml b/recipes/bioconductor-rots/meta.yaml index 94fa2835ce543..9ac10605af128 100644 --- a/recipes/bioconductor-rots/meta.yaml +++ b/recipes/bioconductor-rots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ROTS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fe2a766a69ca811fc88c2141b937e4f + md5: 02d51e24e501790ad3049c1bb5b3f90b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rots", max_pin="x.x") }}' # Suggests: testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-rpa/meta.yaml b/recipes/bioconductor-rpa/meta.yaml index 88699561f5d27..f6f0aaf7b94d8 100644 --- a/recipes/bioconductor-rpa/meta.yaml +++ b/recipes/bioconductor-rpa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "RPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7337a8f9784ebb75d6e058c977717f2 + md5: ea38f5a76b570c091b8f818c48c836cb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rpa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, parallel requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-rmarkdown run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-rmarkdown test: diff --git a/recipes/bioconductor-rprimer/meta.yaml b/recipes/bioconductor-rprimer/meta.yaml index b40f74abaaf73..cf4019c640733 100644 --- a/recipes/bioconductor-rprimer/meta.yaml +++ b/recipes/bioconductor-rprimer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "rprimer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e05e6e2bf6f84403840fa9654f99a7e + md5: f866266895669cd0e898d1ffb0df86fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rprimer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bslib - r-dt @@ -35,9 +36,9 @@ requirements: - r-shinycssloaders - r-shinyfeedback run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-bslib - r-dt diff --git a/recipes/bioconductor-rprotobuflib/meta.yaml b/recipes/bioconductor-rprotobuflib/meta.yaml index 887fd41d8f8d0..5b102fbec59c1 100644 --- a/recipes/bioconductor-rprotobuflib/meta.yaml +++ b/recipes/bioconductor-rprotobuflib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "RProtoBufLib" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73ac1a9dd31c1bc83d88a24008beb92b + md5: e7351127e6b19daaae94fcecc970292b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rprotobuflib", max_pin="x.x") }}' # Suggests: knitr, rmarkdown # SystemRequirements: GNU make requirements: diff --git a/recipes/bioconductor-rpx/meta.yaml b/recipes/bioconductor-rpx/meta.yaml index 99d8734560712..95d2c560c7b95 100644 --- a/recipes/bioconductor-rpx/meta.yaml +++ b/recipes/bioconductor-rpx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "rpx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 39f8bb2ca64ca8cde2630fb139038ea1 + md5: 7e3f2004892b6fb40746c0dcdd990a43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rpx", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BiocStyle, testthat, knitr, tibble, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-curl - r-jsonlite - r-rcurl - r-xml2 run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-base - r-curl - r-jsonlite diff --git a/recipes/bioconductor-rqc/meta.yaml b/recipes/bioconductor-rqc/meta.yaml index fbb30894aa710..c7e563d22e776 100644 --- a/recipes/bioconductor-rqc/meta.yaml +++ b/recipes/bioconductor-rqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "Rqc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64ea2b574c7fb886f19aade0f205d697 + md5: 425dbc839b22b6af4d19ca20174c24c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rqc", max_pin="x.x") }}' # Suggests: rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-ggplot2 - 'r-knitr >=1.7' @@ -42,17 +43,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-biovizbase >=1.48.0,<1.49.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-biovizbase >=1.50.0,<1.51.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base - r-ggplot2 - 'r-knitr >=1.7' diff --git a/recipes/bioconductor-rqt/meta.yaml b/recipes/bioconductor-rqt/meta.yaml index 4269eb2172ed2..b028572a28d95 100644 --- a/recipes/bioconductor-rqt/meta.yaml +++ b/recipes/bioconductor-rqt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "rqt" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b9f8ad7ad17223f2fb69df9879e33574 + md5: b6120899c4586c9dcfd093db762af1c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rqt", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-car - r-compquadform @@ -32,8 +33,8 @@ requirements: - r-pls - r-runit run: - - 'bioconductor-ropls >=1.32.0,<1.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ropls >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-car - r-compquadform diff --git a/recipes/bioconductor-rqubic/meta.yaml b/recipes/bioconductor-rqubic/meta.yaml index f7b64a6ae9e77..a7d84df176096 100644 --- a/recipes/bioconductor-rqubic/meta.yaml +++ b/recipes/bioconductor-rqubic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "rqubic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7cfb52fd500be860a103d30e22ede5e1 + md5: 018144d5ccfbe2df88a79212dedc2066 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rqubic", max_pin="x.x") }}' # Suggests: RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-biclust - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-biclust build: diff --git a/recipes/bioconductor-rrbsdata/meta.yaml b/recipes/bioconductor-rrbsdata/meta.yaml index 8659e51ec8464..eccd81fafefdc 100644 --- a/recipes/bioconductor-rrbsdata/meta.yaml +++ b/recipes/bioconductor-rrbsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RRBSdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a418c0df3db7d2285a1629bd473129ce + md5: 04bcf0f0348dc54984ca9506773820ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rrbsdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biseq >=1.40.0,<1.41.0' + - 'bioconductor-biseq >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-biseq >=1.40.0,<1.41.0' + - 'bioconductor-biseq >=1.42.0,<1.43.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rrbsdata/post-link.sh b/recipes/bioconductor-rrbsdata/post-link.sh index 92dd5a3f08424..9daeae9d07b91 100644 --- a/recipes/bioconductor-rrbsdata/post-link.sh +++ b/recipes/bioconductor-rrbsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rrbsdata-1.20.0" +installBiocDataPackage.sh "rrbsdata-1.22.0" diff --git a/recipes/bioconductor-rrdp/meta.yaml b/recipes/bioconductor-rrdp/meta.yaml index 3652e635a4bac..d4af9718a1b5b 100644 --- a/recipes/bioconductor-rrdp/meta.yaml +++ b/recipes/bioconductor-rrdp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "rRDP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73f762d80ae94c8d655ac6c07ec4c3c0 + md5: 1a6dbbc2c3e31aa382c312202e85ce62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rrdp", max_pin="x.x") }}' noarch: generic # Suggests: rRDPData -# SystemRequirements: Java +# SystemRequirements: Java JDK 1.4 or higher requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - - openjdk run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - - openjdk test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rrdpdata/meta.yaml b/recipes/bioconductor-rrdpdata/meta.yaml index 43018f4496c03..e76d77d70c8d6 100644 --- a/recipes/bioconductor-rrdpdata/meta.yaml +++ b/recipes/bioconductor-rrdpdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "rRDPData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81a8cf3a83812318bbacb9cc2503f8d1 + md5: 9ca56f1bf00bfaefb27c351ccc7346ae build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rrdpdata", max_pin="x.x") }}' noarch: generic # SystemRequirements: Java requirements: host: - - 'bioconductor-rrdp >=1.34.0,<1.35.0' + - 'bioconductor-rrdp >=1.36.0,<1.37.0' - r-base - openjdk run: - - 'bioconductor-rrdp >=1.34.0,<1.35.0' + - 'bioconductor-rrdp >=1.36.0,<1.37.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' - openjdk test: commands: diff --git a/recipes/bioconductor-rrdpdata/post-link.sh b/recipes/bioconductor-rrdpdata/post-link.sh index 257b850bd9bad..529c560bd8bc7 100644 --- a/recipes/bioconductor-rrdpdata/post-link.sh +++ b/recipes/bioconductor-rrdpdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rrdpdata-1.20.0" +installBiocDataPackage.sh "rrdpdata-1.22.0" diff --git a/recipes/bioconductor-rrho/meta.yaml b/recipes/bioconductor-rrho/meta.yaml index a588bc711b0b4..7873debb38070 100644 --- a/recipes/bioconductor-rrho/meta.yaml +++ b/recipes/bioconductor-rrho/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "RRHO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1715d1199550801cb72bb4d0077d6c7f + md5: 979e74a493ef06b25a98574facdd4c3f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rrho", max_pin="x.x") }}' noarch: generic # Suggests: lattice requirements: diff --git a/recipes/bioconductor-rrvgo/meta.yaml b/recipes/bioconductor-rrvgo/meta.yaml index 64076753029de..f22c0df7d085d 100644 --- a/recipes/bioconductor-rrvgo/meta.yaml +++ b/recipes/bioconductor-rrvgo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "rrvgo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b877ead2232a39f8df718f2a217968ac + md5: d84378ff00f99dfe761c41763a56315b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rrvgo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), shinydashboard, DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - r-base - r-ggplot2 - r-ggrepel @@ -34,9 +35,9 @@ requirements: - r-umap - r-wordcloud run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-rsamtools/meta.yaml b/recipes/bioconductor-rsamtools/meta.yaml index 74a81bf5f7acc..6f812efc1e88e 100644 --- a/recipes/bioconductor-rsamtools/meta.yaml +++ b/recipes/bioconductor-rsamtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "Rsamtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14fcdb18a7da2608dd3325bcd7cf1fc9 + md5: 63af2a7dd2513e992fd78b26ca2b3775 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rsamtools", max_pin="x.x") }}' # Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bitops - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-bitops build: diff --git a/recipes/bioconductor-rsbml/meta.yaml b/recipes/bioconductor-rsbml/meta.yaml index 94a4308dbd31c..d79175c91dce7 100644 --- a/recipes/bioconductor-rsbml/meta.yaml +++ b/recipes/bioconductor-rsbml/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.58.0" %} +{% set version = "2.60.0" %} {% set name = "rsbml" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5609d4db75e067a6ca2cead8e06e7d1d + md5: 9e3df3c47a3bbb5b92bf55b478078d1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rsbml", max_pin="x.x") }}' # SystemRequirements: libsbml (==5.10.2) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - libblas - liblapack - 'libsbml >=5.10.2' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - 'libsbml >=5.10.2' build: diff --git a/recipes/bioconductor-rscudo/meta.yaml b/recipes/bioconductor-rscudo/meta.yaml index 1bfe843a4066a..0709bb86099e6 100644 --- a/recipes/bioconductor-rscudo/meta.yaml +++ b/recipes/bioconductor-rscudo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "rScudo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a86ef401d20c50d959c82febca2329be + md5: 2ca44b84bbccb7ffdc9dc082d9a071ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rscudo", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-stringr diff --git a/recipes/bioconductor-rsemmed/meta.yaml b/recipes/bioconductor-rsemmed/meta.yaml index 580518cfebf91..1e8115b130485 100644 --- a/recipes/bioconductor-rsemmed/meta.yaml +++ b/recipes/bioconductor-rsemmed/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "rsemmed" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a7d28e150432339925902ebb48d4499e + md5: 379f918582942443c9823373180a9978 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rsemmed", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: diff --git a/recipes/bioconductor-rseqan/meta.yaml b/recipes/bioconductor-rseqan/meta.yaml index 6271ff68554e7..47423acccd913 100644 --- a/recipes/bioconductor-rseqan/meta.yaml +++ b/recipes/bioconductor-rseqan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RSeqAn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a456731aa836d8d5d813db5861eb6d31 + md5: 278ce2c8087516d02a4203bdcf9a6b9f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rseqan", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat requirements: host: diff --git a/recipes/bioconductor-rsubread/meta.yaml b/recipes/bioconductor-rsubread/meta.yaml index d59b0076ce4ba..65ccd28a75f2c 100644 --- a/recipes/bioconductor-rsubread/meta.yaml +++ b/recipes/bioconductor-rsubread/meta.yaml @@ -47,4 +47,3 @@ extra: name: bioconductor-rsubread path: recipes/bioconductor-rsubread version: 1.30.9 - diff --git a/recipes/bioconductor-rsvsim/meta.yaml b/recipes/bioconductor-rsvsim/meta.yaml index 0626335630506..8a08b4435d024 100644 --- a/recipes/bioconductor-rsvsim/meta.yaml +++ b/recipes/bioconductor-rsvsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "RSVSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58aa1505639580f74acc64c3f641b614 + md5: 0ce59bfd8791d8b1bf0b4fa48ea37e31 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rsvsim", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' - r-base test: commands: diff --git a/recipes/bioconductor-rsweep/meta.yaml b/recipes/bioconductor-rsweep/meta.yaml index 56cb2ae8fdb0d..62261663a3374 100644 --- a/recipes/bioconductor-rsweep/meta.yaml +++ b/recipes/bioconductor-rsweep/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "rSWeeP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3e60840b337a6d545b79f804ff0730c + md5: 42d80dcf3d267562e175115cdfd4c731 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rsweep", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, methods, knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-rta10probeset.db/meta.yaml b/recipes/bioconductor-rta10probeset.db/meta.yaml index c93a76873722d..02c8c7bd97fab 100644 --- a/recipes/bioconductor-rta10probeset.db/meta.yaml +++ b/recipes/bioconductor-rta10probeset.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "rta10probeset.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ce002623471eef89fb841f0bf3e7c9f8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rta10probeset.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml b/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml index 40b33d0356e54..2794ecc9761ab 100644 --- a/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "8.8.0" %} {% set name = "rta10transcriptcluster.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 14ade3f4fca2d1091ccb28e7a777f3e5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rta10transcriptcluster.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtca/meta.yaml b/recipes/bioconductor-rtca/meta.yaml index 976aa90b03b01..ab6f863af48a9 100644 --- a/recipes/bioconductor-rtca/meta.yaml +++ b/recipes/bioconductor-rtca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "RTCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03617e534844a5f3f0a7af4b9c810ca8 + md5: 8e1039d013ef1d5e08b48003ecffc25a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtca", max_pin="x.x") }}' noarch: generic # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gtools - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gtools - r-rcolorbrewer diff --git a/recipes/bioconductor-rtcga.clinical/meta.yaml b/recipes/bioconductor-rtcga.clinical/meta.yaml index fdaf2a4cc5641..0cbafa6e3191f 100644 --- a/recipes/bioconductor-rtcga.clinical/meta.yaml +++ b/recipes/bioconductor-rtcga.clinical/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "20151101.30.0" %} +{% set version = "20151101.32.0" %} {% set name = "RTCGA.clinical" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 772ed6b2aafe700536b01d9b4c55dfef + md5: 9c32b8aef86c9ad34ea8c3672575d724 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.clinical", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.clinical/post-link.sh b/recipes/bioconductor-rtcga.clinical/post-link.sh index 65dba96a8e66c..a682ce0470fa4 100644 --- a/recipes/bioconductor-rtcga.clinical/post-link.sh +++ b/recipes/bioconductor-rtcga.clinical/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.clinical-20151101.30.0" +installBiocDataPackage.sh "rtcga.clinical-20151101.32.0" diff --git a/recipes/bioconductor-rtcga.cnv/meta.yaml b/recipes/bioconductor-rtcga.cnv/meta.yaml index 4c5be8f8b8803..2b0f7466f8e32 100644 --- a/recipes/bioconductor-rtcga.cnv/meta.yaml +++ b/recipes/bioconductor-rtcga.cnv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.CNV" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c2f73f6edefa0ca82b7c6f9add37156 + md5: 15267c2322da59ccd344657a28d2ba6a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.cnv", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.cnv/post-link.sh b/recipes/bioconductor-rtcga.cnv/post-link.sh index 09dfafdfe1a37..046dd8d84df82 100644 --- a/recipes/bioconductor-rtcga.cnv/post-link.sh +++ b/recipes/bioconductor-rtcga.cnv/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.cnv-1.28.0" +installBiocDataPackage.sh "rtcga.cnv-1.30.0" diff --git a/recipes/bioconductor-rtcga.methylation/meta.yaml b/recipes/bioconductor-rtcga.methylation/meta.yaml index 4b33e944578bd..60cb29db9aef4 100644 --- a/recipes/bioconductor-rtcga.methylation/meta.yaml +++ b/recipes/bioconductor-rtcga.methylation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.methylation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1aff8900c676eb32d9655b0d4fbf834e + md5: 9d90704cb34a57878ef719348489c702 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.methylation", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.methylation/post-link.sh b/recipes/bioconductor-rtcga.methylation/post-link.sh index 4e1d367fc2b38..0149be259586a 100644 --- a/recipes/bioconductor-rtcga.methylation/post-link.sh +++ b/recipes/bioconductor-rtcga.methylation/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.methylation-1.28.0" +installBiocDataPackage.sh "rtcga.methylation-1.30.0" diff --git a/recipes/bioconductor-rtcga.mirnaseq/meta.yaml b/recipes/bioconductor-rtcga.mirnaseq/meta.yaml index 5060dc87de4be..b3bc9acfe4918 100644 --- a/recipes/bioconductor-rtcga.mirnaseq/meta.yaml +++ b/recipes/bioconductor-rtcga.mirnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.miRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61a11184082b390c05d74b660d06635d + md5: 744062c2f0db68a88e27db9d61929a79 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.mirnaseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.mirnaseq/post-link.sh b/recipes/bioconductor-rtcga.mirnaseq/post-link.sh index eca1a892dd0ca..4553a7939d834 100644 --- a/recipes/bioconductor-rtcga.mirnaseq/post-link.sh +++ b/recipes/bioconductor-rtcga.mirnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.mirnaseq-1.28.0" +installBiocDataPackage.sh "rtcga.mirnaseq-1.30.0" diff --git a/recipes/bioconductor-rtcga.mrna/meta.yaml b/recipes/bioconductor-rtcga.mrna/meta.yaml index f9aa8092374df..0fd9e1c2bc703 100644 --- a/recipes/bioconductor-rtcga.mrna/meta.yaml +++ b/recipes/bioconductor-rtcga.mrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.mRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63adca06a76cfc761b88b853a34580d1 + md5: c9774207df355ef5945677d36e915103 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.mrna", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.mrna/post-link.sh b/recipes/bioconductor-rtcga.mrna/post-link.sh index f0495038ac542..75fe3ba6ceb43 100644 --- a/recipes/bioconductor-rtcga.mrna/post-link.sh +++ b/recipes/bioconductor-rtcga.mrna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.mrna-1.28.0" +installBiocDataPackage.sh "rtcga.mrna-1.30.0" diff --git a/recipes/bioconductor-rtcga.mutations/meta.yaml b/recipes/bioconductor-rtcga.mutations/meta.yaml index bfa83041ff12b..dc0d506bc3755 100644 --- a/recipes/bioconductor-rtcga.mutations/meta.yaml +++ b/recipes/bioconductor-rtcga.mutations/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "20151101.30.0" %} +{% set version = "20151101.32.0" %} {% set name = "RTCGA.mutations" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d1f7686f0203ccdffd3c0d903947ffbb + md5: 0740acb5a6a47fd9d1281ccaf80bafed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.mutations", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.mutations/post-link.sh b/recipes/bioconductor-rtcga.mutations/post-link.sh index 7c0a1251f3c7f..82133986d47de 100644 --- a/recipes/bioconductor-rtcga.mutations/post-link.sh +++ b/recipes/bioconductor-rtcga.mutations/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.mutations-20151101.30.0" +installBiocDataPackage.sh "rtcga.mutations-20151101.32.0" diff --git a/recipes/bioconductor-rtcga.pancan12/meta.yaml b/recipes/bioconductor-rtcga.pancan12/meta.yaml index 196c2545fba7a..fed3714cbbb38 100644 --- a/recipes/bioconductor-rtcga.pancan12/meta.yaml +++ b/recipes/bioconductor-rtcga.pancan12/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.PANCAN12" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c4fcdde44501b93a022b8b1fe3abf96 + md5: 8b0742d189afe05f47a2656556d85d0b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.pancan12", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.pancan12/post-link.sh b/recipes/bioconductor-rtcga.pancan12/post-link.sh index 60c525c0a3a63..a5698c90619ab 100644 --- a/recipes/bioconductor-rtcga.pancan12/post-link.sh +++ b/recipes/bioconductor-rtcga.pancan12/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.pancan12-1.28.0" +installBiocDataPackage.sh "rtcga.pancan12-1.30.0" diff --git a/recipes/bioconductor-rtcga.rnaseq/meta.yaml b/recipes/bioconductor-rtcga.rnaseq/meta.yaml index 1fab0e5b25a53..8d5fa4f1313d2 100644 --- a/recipes/bioconductor-rtcga.rnaseq/meta.yaml +++ b/recipes/bioconductor-rtcga.rnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "20151101.30.0" %} +{% set version = "20151101.32.0" %} {% set name = "RTCGA.rnaseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df65c9add93e3fa3f2f321442057c807 + md5: 47bee14c68ff4d1014677eca0ed969a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.rnaseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.rnaseq/post-link.sh b/recipes/bioconductor-rtcga.rnaseq/post-link.sh index 55c6465239030..50935322d590a 100644 --- a/recipes/bioconductor-rtcga.rnaseq/post-link.sh +++ b/recipes/bioconductor-rtcga.rnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.rnaseq-20151101.30.0" +installBiocDataPackage.sh "rtcga.rnaseq-20151101.32.0" diff --git a/recipes/bioconductor-rtcga.rppa/meta.yaml b/recipes/bioconductor-rtcga.rppa/meta.yaml index e84e52e6ee075..62d36b44246ca 100644 --- a/recipes/bioconductor-rtcga.rppa/meta.yaml +++ b/recipes/bioconductor-rtcga.rppa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RTCGA.RPPA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: caff1ad6b62dbd868be8cf6452cc4312 + md5: 5eccece412039d43cdf74aec284fa0d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga.rppa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rtcga >=1.30.0,<1.31.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtcga.rppa/post-link.sh b/recipes/bioconductor-rtcga.rppa/post-link.sh index 529c9967d90f1..382ca3c6abed1 100644 --- a/recipes/bioconductor-rtcga.rppa/post-link.sh +++ b/recipes/bioconductor-rtcga.rppa/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.rppa-1.28.0" +installBiocDataPackage.sh "rtcga.rppa-1.30.0" diff --git a/recipes/bioconductor-rtcga/meta.yaml b/recipes/bioconductor-rtcga/meta.yaml index 988503b8e726c..84fabac1dc0ff 100644 --- a/recipes/bioconductor-rtcga/meta.yaml +++ b/recipes/bioconductor-rtcga/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "RTCGA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3e0d94c8945799da632011ed8db9c34 + md5: 97f413704d77f40ecbe00a1e0d25602d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcga", max_pin="x.x") }}' noarch: generic # Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr requirements: diff --git a/recipes/bioconductor-rtcgatoolbox/meta.yaml b/recipes/bioconductor-rtcgatoolbox/meta.yaml index 6300eefa7e782..22e51db05ee47 100644 --- a/recipes/bioconductor-rtcgatoolbox/meta.yaml +++ b/recipes/bioconductor-rtcgatoolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.1" %} {% set name = "RTCGAToolbox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a4dce01f2ceec3f3881c02b9bd0b5f7 + md5: 002662ddf44b6ca3e771db3adcbda6d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtcgatoolbox", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-data.table - r-httr - - r-rcircos - r-rcurl - r-rjsonio - r-rvest - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-data.table - r-httr - - r-rcircos - r-rcurl - r-rjsonio - r-rvest diff --git a/recipes/bioconductor-rtn/meta.yaml b/recipes/bioconductor-rtn/meta.yaml index e222318b7961b..31510ebec49e0 100644 --- a/recipes/bioconductor-rtn/meta.yaml +++ b/recipes/bioconductor-rtn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "RTN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 486eee6f562b159c0d54c65a4bd957d4 + md5: 3e79f58bcc4f0ac95a48819a0027028e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtn", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-car - r-data.table @@ -37,13 +38,13 @@ requirements: - r-pwr - r-snow run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minet >=3.58.0,<3.59.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minet >=3.60.0,<3.61.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-car - r-data.table diff --git a/recipes/bioconductor-rtnduals/meta.yaml b/recipes/bioconductor-rtnduals/meta.yaml index 1596d9b351656..b9f3b2044cd8e 100644 --- a/recipes/bioconductor-rtnduals/meta.yaml +++ b/recipes/bioconductor-rtnduals/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RTNduals" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95497f3821f66f3cd274745614587884 + md5: 5a4f986eb1a34493a1a577ea3546fe92 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtnduals", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics requirements: host: - - 'bioconductor-rtn >=2.24.0,<2.25.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-rtn >=2.24.0,<2.25.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' - r-base test: commands: diff --git a/recipes/bioconductor-rtnsurvival/meta.yaml b/recipes/bioconductor-rtnsurvival/meta.yaml index 71d2686f5b910..42c05a101eef4 100644 --- a/recipes/bioconductor-rtnsurvival/meta.yaml +++ b/recipes/bioconductor-rtnsurvival/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RTNsurvival" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f61ac2a0851b96b39fef5a9b4299e20 + md5: db9d03eee81fed17fae3acb66a07893f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtnsurvival", max_pin="x.x") }}' noarch: generic # Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics requirements: host: - - 'bioconductor-rtn >=2.24.0,<2.25.0' - - 'bioconductor-rtnduals >=1.24.0,<1.25.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' + - 'bioconductor-rtnduals >=1.26.0,<1.27.0' - r-base - r-data.table - r-dunn.test @@ -33,8 +34,8 @@ requirements: - r-scales - r-survival run: - - 'bioconductor-rtn >=2.24.0,<2.25.0' - - 'bioconductor-rtnduals >=1.24.0,<1.25.0' + - 'bioconductor-rtn >=2.26.0,<2.27.0' + - 'bioconductor-rtnduals >=1.26.0,<1.27.0' - r-base - r-data.table - r-dunn.test diff --git a/recipes/bioconductor-rtopper/meta.yaml b/recipes/bioconductor-rtopper/meta.yaml index f3de0abc3850e..70748cb77078b 100644 --- a/recipes/bioconductor-rtopper/meta.yaml +++ b/recipes/bioconductor-rtopper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "RTopper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05f914a8fec4de3ad0769d298e50719e + md5: e551ec836b4c0743feabbd2deff66cb8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtopper", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db, KEGGREST, GO.db requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base test: commands: diff --git a/recipes/bioconductor-rtpca/meta.yaml b/recipes/bioconductor-rtpca/meta.yaml index 6ca2b8c374d97..dc314446feed5 100644 --- a/recipes/bioconductor-rtpca/meta.yaml +++ b/recipes/bioconductor-rtpca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Rtpca" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92e3001dc980973d8a33bc0a8310d99c + md5: 671f34f1c510812fc37d66ed50378d75 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtpca", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-dplyr - r-fdrtool @@ -30,7 +31,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-dplyr - r-fdrtool diff --git a/recipes/bioconductor-rtracklayer/meta.yaml b/recipes/bioconductor-rtracklayer/meta.yaml index 967607fc68109..e278e9ce8f4ea 100644 --- a/recipes/bioconductor-rtracklayer/meta.yaml +++ b/recipes/bioconductor-rtracklayer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.60.0" %} +{% set version = "1.62.0" %} {% set name = "rtracklayer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ea85a15c469bbc3b7c909fee857b02bc + md5: a16a9ca02e49808b38823899860abdb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtracklayer", max_pin="x.x") }}' # Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-rcurl >=1.4-2' - 'r-restfulr >=0.0.13' @@ -38,17 +39,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - 'r-rcurl >=1.4-2' - 'r-restfulr >=0.0.13' diff --git a/recipes/bioconductor-rtreemix/meta.yaml b/recipes/bioconductor-rtreemix/meta.yaml index c454a93b616db..3fcbf4f2015c1 100644 --- a/recipes/bioconductor-rtreemix/meta.yaml +++ b/recipes/bioconductor-rtreemix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "Rtreemix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d05f9b9b4dce2e4a90fd273abcee669 + md5: 3a9bda84ad8cd784165f1b8ce1a43af7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtreemix", max_pin="x.x") }}' # Suggests: Rgraphviz requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-hmisc - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-hmisc build: diff --git a/recipes/bioconductor-rtrm/meta.yaml b/recipes/bioconductor-rtrm/meta.yaml index a0eff930f80c6..e12f221409eeb 100644 --- a/recipes/bioconductor-rtrm/meta.yaml +++ b/recipes/bioconductor-rtrm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "rTRM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6284b5e947d0c1b087ed858e85a80b11 + md5: 2804488949a044166efe737d4e25d9ac build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtrm", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-igraph >=1.0' - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - r-dbi - 'r-igraph >=1.0' diff --git a/recipes/bioconductor-rtrmui/meta.yaml b/recipes/bioconductor-rtrmui/meta.yaml index eb45f8922de4a..c92d5cb854754 100644 --- a/recipes/bioconductor-rtrmui/meta.yaml +++ b/recipes/bioconductor-rtrmui/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "rTRMui" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9255a3ec1721743cb12a993094fe52bb + md5: 6e1589a0f3e51870f4eb71a0eb56d915 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtrmui", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-motifdb >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtrm >=1.38.0,<1.39.0' + - 'bioconductor-motifdb >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtrm >=1.40.0,<1.41.0' - r-base - 'r-shiny >=0.9' run: - - 'bioconductor-motifdb >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rtrm >=1.38.0,<1.39.0' + - 'bioconductor-motifdb >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rtrm >=1.40.0,<1.41.0' - r-base - 'r-shiny >=0.9' test: diff --git a/recipes/bioconductor-rtu34.db/meta.yaml b/recipes/bioconductor-rtu34.db/meta.yaml index 3746466128099..fc5ff8cdaf925 100644 --- a/recipes/bioconductor-rtu34.db/meta.yaml +++ b/recipes/bioconductor-rtu34.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "rtu34.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f46c4763627f1a9e00cdc9d0af8c5f2e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtu34.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtu34cdf/meta.yaml b/recipes/bioconductor-rtu34cdf/meta.yaml index 687bfa4f11997..4c46f39a9d9c1 100644 --- a/recipes/bioconductor-rtu34cdf/meta.yaml +++ b/recipes/bioconductor-rtu34cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rtu34cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 317abfcca319d01eb14f16efa6d91da1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtu34cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rtu34probe/meta.yaml b/recipes/bioconductor-rtu34probe/meta.yaml index 6e82cebf7cdfb..85fe1dcc09abf 100644 --- a/recipes/bioconductor-rtu34probe/meta.yaml +++ b/recipes/bioconductor-rtu34probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "rtu34probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1778d857a61bf181b80b9fcf46ebd2c3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rtu34probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-runibic/meta.yaml b/recipes/bioconductor-runibic/meta.yaml index 7cca70531af16..2880440cd9bb6 100644 --- a/recipes/bioconductor-runibic/meta.yaml +++ b/recipes/bioconductor-runibic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "runibic" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a1dab58d1c0b9f7eab2bb787dcf09486 + md5: e67e1067d80c06f72208fca94d7a2e52 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-runibic", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, GEOquery, affy, airway, QUBIC # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biclust - 'r-rcpp >=0.12.12' @@ -29,7 +30,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biclust - 'r-rcpp >=0.12.12' diff --git a/recipes/bioconductor-ruvcorr/meta.yaml b/recipes/bioconductor-ruvcorr/meta.yaml index ea463f3c08a89..2579d63c4c8d9 100644 --- a/recipes/bioconductor-ruvcorr/meta.yaml +++ b/recipes/bioconductor-ruvcorr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RUVcorr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcabc6f20ae34007170c74c3687438f0 + md5: cfc2e185bc7d37f264843a6fa5ed7c6d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ruvcorr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, hgu133a2.db, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bladderbatch >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bladderbatch >=1.40.0,<1.41.0' - r-base - r-corrplot - r-gridextra @@ -32,8 +33,8 @@ requirements: - r-reshape2 - r-snowfall run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bladderbatch >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bladderbatch >=1.40.0,<1.41.0' - r-base - r-corrplot - r-gridextra diff --git a/recipes/bioconductor-ruvnormalize/meta.yaml b/recipes/bioconductor-ruvnormalize/meta.yaml index b4dec3a853f92..7c155c7112009 100644 --- a/recipes/bioconductor-ruvnormalize/meta.yaml +++ b/recipes/bioconductor-ruvnormalize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "RUVnormalize" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1c1270e40710ca88df4cd06f7b83436 + md5: 2d5d0d40d8720734dee3f8dc437c0756 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ruvnormalize", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ruvnormalizedata >=1.20.0,<1.21.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ruvnormalizedata >=1.22.0,<1.23.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-ruvnormalizedata >=1.20.0,<1.21.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-ruvnormalizedata >=1.22.0,<1.23.0' - r-base test: commands: diff --git a/recipes/bioconductor-ruvnormalizedata/meta.yaml b/recipes/bioconductor-ruvnormalizedata/meta.yaml index 84738d3293026..b4d2035842550 100644 --- a/recipes/bioconductor-ruvnormalizedata/meta.yaml +++ b/recipes/bioconductor-ruvnormalizedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RUVnormalizeData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 138ed1f796a9967fce840e1f751769a2 + md5: 5d7104746a5cac16500870312dd769a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ruvnormalizedata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ruvnormalizedata/post-link.sh b/recipes/bioconductor-ruvnormalizedata/post-link.sh index c3960ee3ad193..3d7a877bdd836 100644 --- a/recipes/bioconductor-ruvnormalizedata/post-link.sh +++ b/recipes/bioconductor-ruvnormalizedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ruvnormalizedata-1.20.0" +installBiocDataPackage.sh "ruvnormalizedata-1.22.0" diff --git a/recipes/bioconductor-ruvseq/meta.yaml b/recipes/bioconductor-ruvseq/meta.yaml index c8fc15fd77d19..2f25bffb6074b 100644 --- a/recipes/bioconductor-ruvseq/meta.yaml +++ b/recipes/bioconductor-ruvseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "RUVSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da6483e460647efa6a7f5754661e6254 + md5: eebbc7e6520dc1fb18f5d8f66de7b739 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ruvseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edaseq >=2.34.0,<2.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edaseq >=2.36.0,<2.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-rvisdiff/build.sh b/recipes/bioconductor-rvisdiff/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rvisdiff/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rvisdiff/meta.yaml b/recipes/bioconductor-rvisdiff/meta.yaml new file mode 100644 index 0000000000000..5b328f86ae0db --- /dev/null +++ b/recipes/bioconductor-rvisdiff/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "Rvisdiff" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3e3b8ccc9cb71388e2e7c17d60995cbe +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rvisdiff", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, DESeq2, limma, SummarizedExperiment, airway, BiocStyle, matrixTests, BiocManager +requirements: + host: + - 'bioconductor-edger >=4.0.0,<4.1.0' + - r-base + run: + - 'bioconductor-edger >=4.0.0,<4.1.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-2 | GPL-3' + summary: 'Interactive Graphs for Differential Expression' + description: 'Creates a muti-graph web page which allows the interactive exploration of differential expression results. The graphical web interface presents results as a table which is integrated with five interactive graphs: MA-plot, volcano plot, box plot, lines plot and cluster heatmap. Graphical aspect and information represented in the graphs can be customized by means of user controls. Final graphics can be exported as PNG format.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-rvs/meta.yaml b/recipes/bioconductor-rvs/meta.yaml index d01234acfc8da..0439a11c2393c 100644 --- a/recipes/bioconductor-rvs/meta.yaml +++ b/recipes/bioconductor-rvs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "RVS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c73fd33ebe8620d49b052656faf3988 + md5: 209870dca9bf6ebc9831014045ddbd42 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rvs", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation requirements: host: - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - r-genlib - r-grain - r-kinship2 run: - - 'bioconductor-snpstats >=1.50.0,<1.51.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' - r-base - r-genlib - r-grain diff --git a/recipes/bioconductor-rwgcod.db/meta.yaml b/recipes/bioconductor-rwgcod.db/meta.yaml index 59dede08fe2de..0fc2b8cb3aa76 100644 --- a/recipes/bioconductor-rwgcod.db/meta.yaml +++ b/recipes/bioconductor-rwgcod.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "rwgcod.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: c8d2fa81b6f03c4ee629a0883431e5fd build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rwgcod.db", max_pin="x.x") }}' noarch: generic # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rwikipathways/meta.yaml b/recipes/bioconductor-rwikipathways/meta.yaml index 36c370f0c00b4..f038e83886397 100644 --- a/recipes/bioconductor-rwikipathways/meta.yaml +++ b/recipes/bioconductor-rwikipathways/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.1" %} {% set name = "rWikiPathways" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bdab499f36c3811aaf36347c445bab3e + md5: 4a836092dcb14297a316efeb45de307d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rwikipathways", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - r-base - r-data.table + - r-dplyr - r-httr + - r-lubridate + - r-purrr - r-rcurl + - r-readr - r-rjson + - r-stringr - r-tidyr - r-xml run: - r-base - r-data.table + - r-dplyr - r-httr + - r-lubridate + - r-purrr - r-rcurl + - r-readr - r-rjson + - r-stringr - r-tidyr - r-xml test: diff --git a/recipes/bioconductor-s4arrays/meta.yaml b/recipes/bioconductor-s4arrays/meta.yaml index bd3614bd01d98..67a951397a9aa 100644 --- a/recipes/bioconductor-s4arrays/meta.yaml +++ b/recipes/bioconductor-s4arrays/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.4" %} +{% set version = "1.2.0" %} {% set name = "S4Arrays" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 60786b2573cb89bad3f57e4e9bb1e530 + md5: c77474b839251d19d31708831de3c1bf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-s4arrays", max_pin="x.x") }}' # Suggests: BiocParallel, SparseArray (>= 0.0.4), DelayedArray, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-abind - r-base - r-crayon - r-matrix - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-abind - r-base - r-crayon - r-matrix diff --git a/recipes/bioconductor-s4vectors/meta.yaml b/recipes/bioconductor-s4vectors/meta.yaml index fd70918e733e3..5f22a031ef513 100644 --- a/recipes/bioconductor-s4vectors/meta.yaml +++ b/recipes/bioconductor-s4vectors/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.1" %} +{% set version = "0.40.2" %} {% set name = "S4Vectors" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 683b1d01ccff0bb1c60087b4cb82f656 + md5: ee94f4f6c25dcaf7a50f5814495310e3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-s4vectors", max_pin="x.x") }}' # Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-safe/meta.yaml b/recipes/bioconductor-safe/meta.yaml index b7c5e1e2201ac..628005304fbab 100644 --- a/recipes/bioconductor-safe/meta.yaml +++ b/recipes/bioconductor-safe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.40.0" %} +{% set version = "3.42.0" %} {% set name = "safe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3207c6250626853ac244f56091f6b419 + md5: 70cc344ddfe65a9d0f3a021c565a1e8e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-safe", max_pin="x.x") }}' noarch: generic # Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-sparsem run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-sparsem test: diff --git a/recipes/bioconductor-sagenhaft/meta.yaml b/recipes/bioconductor-sagenhaft/meta.yaml index 561dd90c5992f..678694684b10b 100644 --- a/recipes/bioconductor-sagenhaft/meta.yaml +++ b/recipes/bioconductor-sagenhaft/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "sagenhaft" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c383e7a39b428ad34cf8ed33a4ca599f + md5: 4f27450a0e98b4f0f7396a784eb0e4e3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sagenhaft", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-saigegds/meta.yaml b/recipes/bioconductor-saigegds/meta.yaml index 487a7c010422c..ff7383e3f09cc 100644 --- a/recipes/bioconductor-saigegds/meta.yaml +++ b/recipes/bioconductor-saigegds/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.1" %} +{% set version = "2.2.0" %} {% set name = "SAIGEgds" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0d1a7a33eacf51e2b792ffe48a95a9d8 + md5: d5792543f5eba866f022723bad21b67e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-saigegds", max_pin="x.x") }}' # Suggests: parallel, crayon, CompQuadForm, survey, SNPRelate, RUnit, knitr, markdown, rmarkdown, ggmanh, BiocGenerics # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-matrix - r-rcpp @@ -31,8 +32,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-sampleclassifier/meta.yaml b/recipes/bioconductor-sampleclassifier/meta.yaml index 3ad85e51aa5cc..f2f2a849ce0a0 100644 --- a/recipes/bioconductor-sampleclassifier/meta.yaml +++ b/recipes/bioconductor-sampleclassifier/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "sampleClassifier" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2381e59b5ff80cd0f74a56ae644ca25 + md5: 7f17cc7eb566dcd27148ee400491b6c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sampleclassifier", max_pin="x.x") }}' noarch: generic # Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-mgfm >=1.34.0,<1.35.0' - - 'bioconductor-mgfr >=1.26.0,<1.27.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-mgfm >=1.36.0,<1.37.0' + - 'bioconductor-mgfr >=1.28.0,<1.29.0' - r-base - r-e1071 - r-ggplot2 run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-mgfm >=1.34.0,<1.35.0' - - 'bioconductor-mgfr >=1.26.0,<1.27.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-mgfm >=1.36.0,<1.37.0' + - 'bioconductor-mgfr >=1.28.0,<1.29.0' - r-base - r-e1071 - r-ggplot2 diff --git a/recipes/bioconductor-sampleclassifierdata/meta.yaml b/recipes/bioconductor-sampleclassifierdata/meta.yaml index 89ea031921117..a1b9746040b66 100644 --- a/recipes/bioconductor-sampleclassifierdata/meta.yaml +++ b/recipes/bioconductor-sampleclassifierdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "sampleClassifierData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4b0d64737358fad818a4a1cc71a27c8 + md5: 941790a92cde9051601206ed162f4151 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sampleclassifierdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sampleclassifierdata/post-link.sh b/recipes/bioconductor-sampleclassifierdata/post-link.sh index c6a957c0a883c..9b49079caf80f 100644 --- a/recipes/bioconductor-sampleclassifierdata/post-link.sh +++ b/recipes/bioconductor-sampleclassifierdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sampleclassifierdata-1.24.0" +installBiocDataPackage.sh "sampleclassifierdata-1.26.0" diff --git a/recipes/bioconductor-samspectral/meta.yaml b/recipes/bioconductor-samspectral/meta.yaml index 555bf904ed589..54499b23d8f09 100644 --- a/recipes/bioconductor-samspectral/meta.yaml +++ b/recipes/bioconductor-samspectral/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "SamSPECTRAL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c1cee5d6e3e0c2a3792b274772d14eb + md5: 2724bc54054c093fac88a672a6b173d6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-samspectral", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-sangeranalyser/meta.yaml b/recipes/bioconductor-sangeranalyser/meta.yaml index 3b1e01b66590c..3b746fd6bf70d 100644 --- a/recipes/bioconductor-sangeranalyser/meta.yaml +++ b/recipes/bioconductor-sangeranalyser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "sangeranalyseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 320b2dd2f4c63054bebd0a4c48dfd488 + md5: da4a748e4e8a1eaba322abafbd7aedad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sangeranalyser", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-sangerseqr >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' - r-ape - r-base - r-data.table @@ -48,10 +49,10 @@ requirements: - r-stringr - r-zeallot run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-sangerseqr >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' - r-ape - r-base - r-data.table diff --git a/recipes/bioconductor-sangerseqr/meta.yaml b/recipes/bioconductor-sangerseqr/meta.yaml index ecac53a019305..adeddccc55773 100644 --- a/recipes/bioconductor-sangerseqr/meta.yaml +++ b/recipes/bioconductor-sangerseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "sangerseqR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1fd0d600e418cf0e841f7aeb0cc70e0 + md5: efc55dbe39324b21b62910684962b86b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sangerseqr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-shiny - r-stringr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-shiny - r-stringr diff --git a/recipes/bioconductor-santa/meta.yaml b/recipes/bioconductor-santa/meta.yaml index 4c98dae1098bd..5c73501ad8a78 100644 --- a/recipes/bioconductor-santa/meta.yaml +++ b/recipes/bioconductor-santa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "SANTA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30c6e9de6ec8283380f691f2f2037378 + md5: 1b2b87312bb663905abbc444be13a056 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-santa", max_pin="x.x") }}' # Suggests: BiocGenerics, BioNet, DLBCL, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit requirements: host: diff --git a/recipes/bioconductor-sarc/build.sh b/recipes/bioconductor-sarc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sarc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sarc/meta.yaml b/recipes/bioconductor-sarc/meta.yaml new file mode 100644 index 0000000000000..168d1508d39d2 --- /dev/null +++ b/recipes/bioconductor-sarc/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.0" %} +{% set name = "SARC" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b3ccd1bbc820bc93c4b13ec4e3ec9705 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sarc", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments +requirements: + host: + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - r-base + - r-data.table + - r-desctools + - r-ggplot2 + - r-gridextra + - r-gtable + - r-metap + - r-plotly + - r-rcolorbrewer + - r-reshape2 + - r-scales + - r-tidyverse + run: + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - r-base + - r-data.table + - r-desctools + - r-ggplot2 + - r-gridextra + - r-gtable + - r-metap + - r-plotly + - r-rcolorbrewer + - r-reshape2 + - r-scales + - r-tidyverse +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Statistical Analysis of Regions with CNVs' + description: 'Imports a cov/coverage file (normalised read coverages from BAM files) and a cnv file (list of CNVs - similiar to a BED file) from WES/ WGS CNV (copy number variation) detection pipelines and utilises several metrics to weigh the likelihood of a sample containing a detected CNV being a true CNV or a false positive. Highly useful for diagnostic testing to filter out false positives to provide clinicians with fewer variants to interpret. SARC uniquely only used cov and csv (similiar to BED file) files which are the common CNV pipeline calling filetypes, and can be used as to supplement the Interactive Genome Browser (IGV) to generate many figures automatedly, which can be especially helpful in large cohorts with 100s-1000s of patients.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-sarks/meta.yaml b/recipes/bioconductor-sarks/meta.yaml index c5a227bf63b65..632d42d45814e 100644 --- a/recipes/bioconductor-sarks/meta.yaml +++ b/recipes/bioconductor-sarks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "sarks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c3c63006f7a3850821e4d2bbbcffe77 + md5: b6fc7553269237bea782582b858aaee5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sarks", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, ggplot2 # SystemRequirements: Java (>= 1.8) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-binom - r-cluster - r-rjava - openjdk run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-binom - r-cluster diff --git a/recipes/bioconductor-saturn/meta.yaml b/recipes/bioconductor-saturn/meta.yaml index 115cb8599eb59..56ea686073d4f 100644 --- a/recipes/bioconductor-saturn/meta.yaml +++ b/recipes/bioconductor-saturn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "satuRn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89d8bb9ce1b8397fba9a9ded087cd0a6 + md5: a0826944ab0aee6ff42127fa7eebf43c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-saturn", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-ggplot2 @@ -31,9 +32,9 @@ requirements: - r-matrix - r-pbapply run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-ggplot2 diff --git a/recipes/bioconductor-saureuscdf/meta.yaml b/recipes/bioconductor-saureuscdf/meta.yaml index 193995bd07b86..63b9008ca29cf 100644 --- a/recipes/bioconductor-saureuscdf/meta.yaml +++ b/recipes/bioconductor-saureuscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "saureuscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d01883e4c3dd99f32012e6dbab8cdb8b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-saureuscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-saureusprobe/meta.yaml b/recipes/bioconductor-saureusprobe/meta.yaml index 207987f0e84d0..7346b9ecb2da6 100644 --- a/recipes/bioconductor-saureusprobe/meta.yaml +++ b/recipes/bioconductor-saureusprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "saureusprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eb4e91b10a536cbde4ecc08951ddf4d3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-saureusprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sbgnview.data/meta.yaml b/recipes/bioconductor-sbgnview.data/meta.yaml index c96698e9c9057..aba842e7df3b8 100644 --- a/recipes/bioconductor-sbgnview.data/meta.yaml +++ b/recipes/bioconductor-sbgnview.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SBGNview.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab6acd3a8b3411fcba1cf7ab1bbbd370 + md5: 7e1bce0dfbc48b3cdc023d88e2ea7d9a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sbgnview.data", max_pin="x.x") }}' noarch: generic # Suggests: SummarizedExperiment requirements: @@ -31,7 +32,7 @@ requirements: - r-knitr - r-rmarkdown - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sbgnview.data/post-link.sh b/recipes/bioconductor-sbgnview.data/post-link.sh index e1f08a4c01f3d..b736f2bdd3bfd 100644 --- a/recipes/bioconductor-sbgnview.data/post-link.sh +++ b/recipes/bioconductor-sbgnview.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sbgnview.data-1.14.0" +installBiocDataPackage.sh "sbgnview.data-1.16.0" diff --git a/recipes/bioconductor-sbgnview/meta.yaml b/recipes/bioconductor-sbgnview/meta.yaml index 8f354e0856fdb..8c50f540bbd86 100644 --- a/recipes/bioconductor-sbgnview/meta.yaml +++ b/recipes/bioconductor-sbgnview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SBGNview" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e069957bf05ad05540c11fc90360a2cb + md5: 785b51f08ce7b40f23b6e9168ce1d1af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sbgnview", max_pin="x.x") }}' noarch: generic # Suggests: testthat, gage requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-sbgnview.data >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-sbgnview.data >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bookdown - r-httr @@ -36,11 +37,11 @@ requirements: - r-rsvg - r-xml2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-sbgnview.data >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-pathview >=1.42.0,<1.43.0' + - 'bioconductor-sbgnview.data >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bookdown - r-httr diff --git a/recipes/bioconductor-sbmlr/meta.yaml b/recipes/bioconductor-sbmlr/meta.yaml index 09aed6b74a822..2c7a8f8515985 100644 --- a/recipes/bioconductor-sbmlr/meta.yaml +++ b/recipes/bioconductor-sbmlr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.96.0" %} +{% set version = "1.98.0" %} {% set name = "SBMLR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fe40b590e4bfdb241a89787f0475ce7 + md5: 36433007d11730737942753523a9d91e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sbmlr", max_pin="x.x") }}' noarch: generic # Suggests: rsbml requirements: diff --git a/recipes/bioconductor-sc3/meta.yaml b/recipes/bioconductor-sc3/meta.yaml index bee00ba007ab8..87691107738fc 100644 --- a/recipes/bioconductor-sc3/meta.yaml +++ b/recipes/bioconductor-sc3/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.3" %} +{% set version = "1.30.0" %} {% set name = "SC3" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3621e7e5933a11aea8306f53389c85d4 + md5: c61e14eaf22ab5535ff11763d97e8c96 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sc3", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, mclust, scater, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-doparallel @@ -42,10 +43,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-doparallel diff --git a/recipes/bioconductor-scale4c/meta.yaml b/recipes/bioconductor-scale4c/meta.yaml index 46a8eca886c47..114860f5f9880 100644 --- a/recipes/bioconductor-scale4c/meta.yaml +++ b/recipes/bioconductor-scale4c/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "Scale4C" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 762ef20a76782aaf8526f4e4575b8188 + md5: 7897932085759a05ad185eaec2afcd13 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scale4c", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-smoothie run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-smoothie test: diff --git a/recipes/bioconductor-scaledmatrix/meta.yaml b/recipes/bioconductor-scaledmatrix/meta.yaml index 3055cb3574f0e..2c06205107872 100644 --- a/recipes/bioconductor-scaledmatrix/meta.yaml +++ b/recipes/bioconductor-scaledmatrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "ScaledMatrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 259cee9d8c815fc9760fa68a997fd12c + md5: 337f2af494241ac5def9fcae4dc12313 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scaledmatrix", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular, DelayedMatrixStats requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-scan.upc/meta.yaml b/recipes/bioconductor-scan.upc/meta.yaml index 66c8fd0a58c4a..bc6fddb7ec4c6 100644 --- a/recipes/bioconductor-scan.upc/meta.yaml +++ b/recipes/bioconductor-scan.upc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "SCAN.UPC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae3e59735107bb06928ac081fa52b308 + md5: 9da1b69c833d18db111112370bfe15ae build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scan.upc", max_pin="x.x") }}' noarch: generic # Suggests: pd.hg.u95a requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-foreach - r-mass run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-affyio >=1.70.0,<1.71.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-oligo >=1.64.0,<1.65.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-affyio >=1.72.0,<1.73.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-oligo >=1.66.0,<1.67.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-foreach - r-mass diff --git a/recipes/bioconductor-scanmir/meta.yaml b/recipes/bioconductor-scanmir/meta.yaml index e6d5d8f303248..97c1cf26883e9 100644 --- a/recipes/bioconductor-scanmir/meta.yaml +++ b/recipes/bioconductor-scanmir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scanMiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 043184d2269eeba5b620b4c97af9f33c + md5: a08199f29933bb3b0d1e9336b1b46a76 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scanmir", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table @@ -34,12 +35,12 @@ requirements: - r-ggseqlogo - r-stringi run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table diff --git a/recipes/bioconductor-scanmirapp/meta.yaml b/recipes/bioconductor-scanmirapp/meta.yaml index 760d5e52a1240..247186ca2ad89 100644 --- a/recipes/bioconductor-scanmirapp/meta.yaml +++ b/recipes/bioconductor-scanmirapp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scanMiRApp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 396fd2bf8dfcf6fc2a801c5ccaa0e3b0 + md5: 637ec69edde646093548d190325738fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scanmirapp", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn6 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scanmir >=1.6.0,<1.7.0' - - 'bioconductor-scanmirdata >=1.6.0,<1.7.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scanmir >=1.8.0,<1.9.0' + - 'bioconductor-scanmirdata >=1.8.0,<1.9.0' - r-base - r-data.table - r-digest @@ -51,20 +52,20 @@ requirements: - r-shinyjqui - r-waiter run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scanmir >=1.6.0,<1.7.0' - - 'bioconductor-scanmirdata >=1.6.0,<1.7.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scanmir >=1.8.0,<1.9.0' + - 'bioconductor-scanmirdata >=1.8.0,<1.9.0' - r-base - r-data.table - r-digest diff --git a/recipes/bioconductor-scanmirdata/meta.yaml b/recipes/bioconductor-scanmirdata/meta.yaml index 85e026948f7e0..0deef63b6ab5b 100644 --- a/recipes/bioconductor-scanmirdata/meta.yaml +++ b/recipes/bioconductor-scanmirdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scanMiRData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 163f0250a82df0c4fb402b756a3010d7 + md5: 4c717492a3c85bbcf199873e35190219 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scanmirdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-scanmir >=1.6.0,<1.7.0' + - 'bioconductor-scanmir >=1.8.0,<1.9.0' - r-base run: - - 'bioconductor-scanmir >=1.6.0,<1.7.0' + - 'bioconductor-scanmir >=1.8.0,<1.9.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scanmirdata/post-link.sh b/recipes/bioconductor-scanmirdata/post-link.sh index ef71048d18442..38be41e8fc92c 100644 --- a/recipes/bioconductor-scanmirdata/post-link.sh +++ b/recipes/bioconductor-scanmirdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scanmirdata-1.6.0" +installBiocDataPackage.sh "scanmirdata-1.8.0" diff --git a/recipes/bioconductor-scannotatr.models/meta.yaml b/recipes/bioconductor-scannotatr.models/meta.yaml index 5fa07ac9d2496..6f96a2629007b 100644 --- a/recipes/bioconductor-scannotatr.models/meta.yaml +++ b/recipes/bioconductor-scannotatr.models/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.10" %} {% set name = "scAnnotatR.models" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 77c6e16382645164d6413356c5ab52c5 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scannotatr.models", max_pin="x.x") }}' noarch: generic # Suggests: scAnnotatR, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scannotatr/meta.yaml b/recipes/bioconductor-scannotatr/meta.yaml index 939cb6786b62e..cf184bb7c972c 100644 --- a/recipes/bioconductor-scannotatr/meta.yaml +++ b/recipes/bioconductor-scannotatr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scAnnotatR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f99427ba417fd087195f719f781d499 + md5: 5474e416000bda50dc8273a09b41a54b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scannotatr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, scRNAseq, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-caret @@ -36,9 +37,9 @@ requirements: - r-rocr - r-seurat run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-caret diff --git a/recipes/bioconductor-scanvis/meta.yaml b/recipes/bioconductor-scanvis/meta.yaml index 1a5a2a0f2c982..507c7fb6aedb7 100644 --- a/recipes/bioconductor-scanvis/meta.yaml +++ b/recipes/bioconductor-scanvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SCANVIS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef9110c213faf5e20efba42cf2d7f3ae + md5: 36977f903eb019d8171d60519360cd9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scanvis", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-plotrix - r-rcurl run: - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-plotrix - r-rcurl diff --git a/recipes/bioconductor-scarray.sat/meta.yaml b/recipes/bioconductor-scarray.sat/meta.yaml index d7f2b2408acbb..b1f611aef2382 100644 --- a/recipes/bioconductor-scarray.sat/meta.yaml +++ b/recipes/bioconductor-scarray.sat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "SCArray.sat" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7e9d968f47394b45250bbfdd798e2a7 + md5: da0366cd6f3cc83e7acc0a45bf2d2389 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scarray.sat", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, knitr, markdown, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scarray >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scarray >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-seurat >=4.0' - 'r-seuratobject >=4.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scarray >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scarray >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-seurat >=4.0' - 'r-seuratobject >=4.0' diff --git a/recipes/bioconductor-scarray/meta.yaml b/recipes/bioconductor-scarray/meta.yaml index 141ecd2dc248e..2253c7eb3d251 100644 --- a/recipes/bioconductor-scarray/meta.yaml +++ b/recipes/bioconductor-scarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.2" %} +{% set version = "1.10.0" %} {% set name = "SCArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c456b74aefd2269839c207b8207bb99 + md5: c777bd1f1f52dd055b83830ed6da1f77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scarray", max_pin="x.x") }}' # Suggests: BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix build: diff --git a/recipes/bioconductor-scatac.explorer/meta.yaml b/recipes/bioconductor-scatac.explorer/meta.yaml index 988544a3cc48c..dc04d869c90f5 100644 --- a/recipes/bioconductor-scatac.explorer/meta.yaml +++ b/recipes/bioconductor-scatac.explorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scATAC.Explorer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 74c840082c522937d200169fcb963f71 + md5: 80927899a83bb06d19b0f9800c183b36 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scatac.explorer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-data.table - r-matrix run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-data.table - r-matrix - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scatac.explorer/post-link.sh b/recipes/bioconductor-scatac.explorer/post-link.sh index 9ae3e68b76fb3..e9ece7245fbbd 100644 --- a/recipes/bioconductor-scatac.explorer/post-link.sh +++ b/recipes/bioconductor-scatac.explorer/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scatac.explorer-1.6.0" +installBiocDataPackage.sh "scatac.explorer-1.8.0" diff --git a/recipes/bioconductor-scatedata/meta.yaml b/recipes/bioconductor-scatedata/meta.yaml index 811edf8de2da5..4682d43f3bac4 100644 --- a/recipes/bioconductor-scatedata/meta.yaml +++ b/recipes/bioconductor-scatedata/meta.yaml @@ -31,7 +31,7 @@ requirements: - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scater/meta.yaml b/recipes/bioconductor-scater/meta.yaml index 876940f11b334..06196151e19c6 100644 --- a/recipes/bioconductor-scater/meta.yaml +++ b/recipes/bioconductor-scater/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.1" %} {% set name = "scater" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f90f3937e49253c9abc23e88a0b65b8b + md5: c161043392323318c01792e2de828ad5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scater", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, snifter, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore +# Suggests: BiocStyle, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-densvis >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggbeeswarm - r-ggplot2 @@ -47,18 +47,17 @@ requirements: - r-uwot - r-viridis run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-densvis >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggbeeswarm - r-ggplot2 diff --git a/recipes/bioconductor-scatterhatch/meta.yaml b/recipes/bioconductor-scatterhatch/meta.yaml index b2c98f3629e72..7d4048dd2cdaa 100644 --- a/recipes/bioconductor-scatterhatch/meta.yaml +++ b/recipes/bioconductor-scatterhatch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scatterHatch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4e9a2d3f03e6a797fb2e5185083adfb + md5: d86cfd4fa0820f65efd6085edc997eed build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scatterhatch", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-scbfa/meta.yaml b/recipes/bioconductor-scbfa/meta.yaml index 18ef2f29a014d..9ab87c6d31b44 100644 --- a/recipes/bioconductor-scbfa/meta.yaml +++ b/recipes/bioconductor-scbfa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "scBFA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0be803eb4149ba1c7b717bbcc44d5f5d + md5: 7729a460da97e96d4da3957b959149db build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scbfa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, Rtsne requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - r-base - r-copula - r-ggplot2 @@ -32,10 +33,10 @@ requirements: - r-matrix - r-seurat run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - r-base - r-copula - r-ggplot2 diff --git a/recipes/bioconductor-scbn/meta.yaml b/recipes/bioconductor-scbn/meta.yaml index 8fc71321208ce..7da3092848b1b 100644 --- a/recipes/bioconductor-scbn/meta.yaml +++ b/recipes/bioconductor-scbn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SCBN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b458b6eb2e4734d08c20d943eb8d591 + md5: c58ee707d9418bd3374773e2675efad7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scbn", max_pin="x.x") }}' noarch: generic # Suggests: knitr,rmarkdown,BiocStyle,BiocManager requirements: diff --git a/recipes/bioconductor-scbubbletree/meta.yaml b/recipes/bioconductor-scbubbletree/meta.yaml index 21887483a2ea6..785fc8a629766 100644 --- a/recipes/bioconductor-scbubbletree/meta.yaml +++ b/recipes/bioconductor-scbubbletree/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "scBubbletree" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38f21dcba3b6a83f95b6aa770117b5fa + md5: d64f38622d8aec6ebb23e81231710134 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scbubbletree", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment # SystemRequirements: Python (>= 3.6), leidenalg (>= 0.8.2) requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-base - r-future @@ -34,7 +35,7 @@ requirements: - r-scales - r-seurat run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-base - r-future diff --git a/recipes/bioconductor-sccb2/meta.yaml b/recipes/bioconductor-sccb2/meta.yaml index 3de70972b457e..50528ac515db8 100644 --- a/recipes/bioconductor-sccb2/meta.yaml +++ b/recipes/bioconductor-sccb2/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "scCB2" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c89162a3736d26d21f71934c6cfe782e + md5: aaa88ac58fbc1b32bfc514cc72109ada build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sccb2", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown # SystemRequirements: C++11 requirements: host: - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-foreach @@ -34,11 +35,11 @@ requirements: - r-matrix - r-seurat run: - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-scclassify/build_failure.linux-64.yaml b/recipes/bioconductor-scclassify/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0c17e3a10137a --- /dev/null +++ b/recipes/bioconductor-scclassify/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5d9ecd6df4ab307246d9923f365939c559cf85122664ccc27d4a9200bf32c6b7 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - r-ggraph + - r-ggplot2 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-cluster + - r-base 4.3.* + - r-matrix + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-cepo >=1.8.0,<1.9.0 + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-cepo >=1.8.0,<1.9.0 + - r-mixtools + - r-igraph + - r-proxyc + - bioconductor-limma >=3.58.0,<3.59.0 + - r-minpack.lm + - r-diptest + - r-mgcv + - bioconductor-s4vectors >=0.40.0,<0.41.0 + - r-statmod + - bioconductor-hopach >=2.62.0,<2.63.0 + - r-proxy + - r-ggraph + - r-ggplot2 + - bioconductor-biocparallel >=1.36.0,<1.37.0 + - r-cluster + - r-base 4.3.* + - r-matrix + + with channels: + - file:///opt/host-conda-bld + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested bioconductor-cepo >=1.8.0,<1.9.0 + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-cepo[version='>=1.8.0,<1.9.0']")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-scclassify/meta.yaml b/recipes/bioconductor-scclassify/meta.yaml index b4a37a58ae136..c466f33922a97 100644 --- a/recipes/bioconductor-scclassify/meta.yaml +++ b/recipes/bioconductor-scclassify/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "scClassify" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4885483f204e79d0dc8b226030c92ec2 + md5: 6268da69185981088025702610fd424c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scclassify", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, pkgdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cepo >=1.6.0,<1.7.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cepo >=1.8.0,<1.9.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-diptest @@ -40,11 +41,11 @@ requirements: - r-proxyc - r-statmod run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cepo >=1.6.0,<1.7.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cepo >=1.8.0,<1.9.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-diptest diff --git a/recipes/bioconductor-sccomp/build_failure.linux-64.yaml b/recipes/bioconductor-sccomp/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..f18015f5e5ff0 --- /dev/null +++ b/recipes/bioconductor-sccomp/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: c6c86a551617ab192acea3543c4da0aa9ddee063ff6e7204b82211c508530538 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + package r-rstan-2.32.3-r43h884c59f_0 is excluded by strict repo priority +category: |- + dependency issue diff --git a/recipes/bioconductor-sccomp/build_failure.osx-64.yaml b/recipes/bioconductor-sccomp/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..2b6541107a2bf --- /dev/null +++ b/recipes/bioconductor-sccomp/build_failure.osx-64.yaml @@ -0,0 +1,7 @@ +recipe_sha: c6c86a551617ab192acea3543c4da0aa9ddee063ff6e7204b82211c508530538 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + nothing provides requested r-rstan >=2.26.0 +category: |- + dependency issue + diff --git a/recipes/bioconductor-sccomp/meta.yaml b/recipes/bioconductor-sccomp/meta.yaml index c48f9559a8aa2..60929b0dd67fd 100644 --- a/recipes/bioconductor-sccomp/meta.yaml +++ b/recipes/bioconductor-sccomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "sccomp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 583e84778aab5f72817a07565eab2b4c + md5: 8a24adb07d155b94645a5f684e1455f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sccomp", max_pin="x.x") }}' # Suggests: BiocStyle, testthat (>= 3.0.0), markdown, knitr, tidyseurat, tidySingleCellExperiment, loo # SystemRequirements: GNU make requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - 'r-bh >=1.66.0' - r-boot @@ -39,11 +40,11 @@ requirements: - 'r-rcppparallel >=5.0.1' - r-readr - r-rlang - - 'r-rstan >=2.18.1' + - 'r-rstan >=2.26.0' - 'r-rstantools >=2.1.1' - r-scales - r-seuratobject - - 'r-stanheaders >=2.18.0' + - 'r-stanheaders >=2.26.0' - r-stringr - r-tibble - r-tidyr @@ -51,7 +52,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - 'r-bh >=1.66.0' - r-boot @@ -69,11 +70,11 @@ requirements: - 'r-rcppparallel >=5.0.1' - r-readr - r-rlang - - 'r-rstan >=2.18.1' + - 'r-rstan >=2.26.0' - 'r-rstantools >=2.1.1' - r-scales - r-seuratobject - - 'r-stanheaders >=2.18.0' + - 'r-stanheaders >=2.26.0' - r-stringr - r-tibble - r-tidyr diff --git a/recipes/bioconductor-scdataviz/meta.yaml b/recipes/bioconductor-scdataviz/meta.yaml index fd5e523561ea4..655232cf0f529 100644 --- a/recipes/bioconductor-scdataviz/meta.yaml +++ b/recipes/bioconductor-scdataviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "scDataviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4970752cedf1f045d1c9e71ec15ae69f + md5: 71744390661cb39c6c12d920e7861d7f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scdataviz", max_pin="x.x") }}' noarch: generic # Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-corrplot - r-ggplot2 @@ -36,9 +37,9 @@ requirements: - r-seurat - r-umap run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-corrplot - r-ggplot2 diff --git a/recipes/bioconductor-scdblfinder/meta.yaml b/recipes/bioconductor-scdblfinder/meta.yaml index c45f71e9d8e46..42aaa31be2a5c 100644 --- a/recipes/bioconductor-scdblfinder/meta.yaml +++ b/recipes/bioconductor-scdblfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "scDblFinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,56 +11,57 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b69060db20baad2947be59b016056069 + md5: b833caa7cf87c1fb4cf9bf599f750ffa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scdblfinder", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-mass - r-matrix - r-xgboost run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-mass diff --git a/recipes/bioconductor-scdd/meta.yaml b/recipes/bioconductor-scdd/meta.yaml index 68ccda52d32b3..417177257b74a 100644 --- a/recipes/bioconductor-scdd/meta.yaml +++ b/recipes/bioconductor-scdd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "scDD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0020a2f90b2264d58527a49f0c467b02 + md5: 3c95209683b09f0584ab315a6fc1e779 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scdd", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, gridExtra requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-arm - r-base - r-fields @@ -34,12 +35,12 @@ requirements: - r-mclust - r-outliers run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-arm - r-base - r-fields diff --git a/recipes/bioconductor-scddboost/meta.yaml b/recipes/bioconductor-scddboost/meta.yaml index ba0f4ac4f8dfb..5268eed04fe71 100644 --- a/recipes/bioconductor-scddboost/meta.yaml +++ b/recipes/bioconductor-scddboost/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "scDDboost" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45a9eceba86f71915cb4f21a233a86f1 + md5: ac0cac5975ebe4025ea07ad00e132847 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scddboost", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat # SystemRequirements: c++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-oscope >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-oscope >=1.32.0,<1.33.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-cluster @@ -36,11 +37,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-ebseq >=1.40.0,<1.41.0' - - 'bioconductor-oscope >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - 'bioconductor-oscope >=1.32.0,<1.33.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-cluster diff --git a/recipes/bioconductor-scde/meta.yaml b/recipes/bioconductor-scde/meta.yaml index 738ebdeee2379..f4b90ef2f8f2c 100644 --- a/recipes/bioconductor-scde/meta.yaml +++ b/recipes/bioconductor-scde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.2" %} +{% set version = "2.30.0" %} {% set name = "scde" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46139e017c4865f6976c4ffd576f5c33 + md5: ee4cb04c3a1431fb088d8681ff950d49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scde", max_pin="x.x") }}' # Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - r-base - r-cairo - r-extremes @@ -40,9 +41,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - r-base - r-cairo - r-extremes diff --git a/recipes/bioconductor-scdesign3/build.sh b/recipes/bioconductor-scdesign3/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scdesign3/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scdesign3/meta.yaml b/recipes/bioconductor-scdesign3/meta.yaml new file mode 100644 index 0000000000000..a5b20677348d3 --- /dev/null +++ b/recipes/bioconductor-scdesign3/meta.yaml @@ -0,0 +1,73 @@ +{% set version = "1.0.0" %} +{% set name = "scDesign3" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 84c2f07635607b2167f24750f952745a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scdesign3", max_pin="x.x") }}' + noarch: generic +# Suggests: mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle +requirements: + host: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - r-gamlss + - r-gamlss.dist + - r-ggplot2 + - r-irlba + - r-matrix + - r-matrixstats + - r-mclust + - r-mgcv + - r-mvtnorm + - r-pbmcapply + - r-rvinecopulib + - r-tibble + - r-umap + - r-viridis + run: + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-dplyr + - r-gamlss + - r-gamlss.dist + - r-ggplot2 + - r-irlba + - r-matrix + - r-matrixstats + - r-mclust + - r-mgcv + - r-mvtnorm + - r-pbmcapply + - r-rvinecopulib + - r-tibble + - r-umap + - r-viridis +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics' + description: 'We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.' + license_file: LICENSE + diff --git a/recipes/bioconductor-scds/meta.yaml b/recipes/bioconductor-scds/meta.yaml index 9eb5e24d3a2a2..58c835c7336f2 100644 --- a/recipes/bioconductor-scds/meta.yaml +++ b/recipes/bioconductor-scds/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "scds" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 604b9f1136e4d2cfa79cc1ea1776e194 + md5: df6bd91f4acdd6ea2e54d2f20f632cbf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scds", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-matrix - r-proc - r-xgboost run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-matrix diff --git a/recipes/bioconductor-scfa/meta.yaml b/recipes/bioconductor-scfa/meta.yaml index 2aa546f1a74e0..1980760f8cd2b 100644 --- a/recipes/bioconductor-scfa/meta.yaml +++ b/recipes/bioconductor-scfa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SCFA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c694613f0dc42e223334903db005fcae + md5: c4e7d00ff20faff6a8a14eddde8e7a84 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scfa", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-cluster - r-coro @@ -34,7 +35,7 @@ requirements: - r-survival - 'r-torch >=0.3.0' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-cluster - r-coro diff --git a/recipes/bioconductor-scfeaturefilter/meta.yaml b/recipes/bioconductor-scfeaturefilter/meta.yaml index 7dbd32013e28f..ce5324266d06b 100644 --- a/recipes/bioconductor-scfeaturefilter/meta.yaml +++ b/recipes/bioconductor-scfeaturefilter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "scFeatureFilter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2bd744106dbac3e5ea1b17cdc17db357 + md5: f642025d766eb2cd17f406126e6fe0ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scfeaturefilter", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot requirements: diff --git a/recipes/bioconductor-scfeatures/meta.yaml b/recipes/bioconductor-scfeatures/meta.yaml index 2bcef4fd2f796..1b4a39426bc3a 100644 --- a/recipes/bioconductor-scfeatures/meta.yaml +++ b/recipes/bioconductor-scfeatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "scFeatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eaf120744a2b4c979aaf8ef6a0b56179 + md5: 00b3e1296507cdf60879fd6d112c1e53 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scfeatures", max_pin="x.x") }}' noarch: generic # Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler requirements: host: - - 'bioconductor-aucell >=1.22.0,<1.23.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' + - 'bioconductor-aucell >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - 'bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0' - 'bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellsignalr >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellsignalr >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-cli @@ -49,18 +50,18 @@ requirements: - r-spatstat.geom - r-tidyr run: - - 'bioconductor-aucell >=1.22.0,<1.23.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' + - 'bioconductor-aucell >=1.24.0,<1.25.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - 'bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0' - 'bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-singlecellsignalr >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-singlecellsignalr >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-cli diff --git a/recipes/bioconductor-scgps/meta.yaml b/recipes/bioconductor-scgps/meta.yaml index 64fd1c2a66667..c5ced940c31bd 100644 --- a/recipes/bioconductor-scgps/meta.yaml +++ b/recipes/bioconductor-scgps/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "scGPS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5470238c90cb59ccf891bd93de16774c + md5: 5d11fe3a4af0d56d3028d97c6090ccfb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scgps", max_pin="x.x") }}' # Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE # SystemRequirements: GNU make requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-caret >=6.0' - r-dplyr @@ -38,9 +39,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-caret >=6.0' - r-dplyr diff --git a/recipes/bioconductor-schex/meta.yaml b/recipes/bioconductor-schex/meta.yaml index 540fadf7b9012..c1c3dd9dbf16f 100644 --- a/recipes/bioconductor-schex/meta.yaml +++ b/recipes/bioconductor-schex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "schex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ed1bc17ff4de0560d1d36821b72b7ca2 + md5: 5be5dd9c76b2ee49cc894a728b08e2e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-schex", max_pin="x.x") }}' noarch: generic # Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-cluster - r-concaveman @@ -34,7 +35,7 @@ requirements: - r-seurat - r-shiny run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-cluster - r-concaveman diff --git a/recipes/bioconductor-schot/meta.yaml b/recipes/bioconductor-schot/meta.yaml index 40e0dc7962bde..c35c587215b4b 100644 --- a/recipes/bioconductor-schot/meta.yaml +++ b/recipes/bioconductor-schot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "scHOT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22cc889e9d524a0744ac6477d9e7dac9 + md5: 75f460d2a6c2d8bee223b64a05eb6224 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-schot", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggforce - r-ggplot2 @@ -33,11 +34,11 @@ requirements: - r-matrix - r-reshape run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggforce - r-ggplot2 diff --git a/recipes/bioconductor-scider/build.sh b/recipes/bioconductor-scider/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scider/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scider/meta.yaml b/recipes/bioconductor-scider/meta.yaml new file mode 100644 index 0000000000000..2dae5324cfcfe --- /dev/null +++ b/recipes/bioconductor-scider/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "scider" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d20e0e846be7368da2613650b3834957 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scider", max_pin="x.x") }}' + noarch: generic +# Suggests: edgeR, testthat (>= 3.0.0) +requirements: + host: + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-igraph + - r-isoband + - r-janitor + - r-knitr + - r-lwgeom + - r-pheatmap + - r-plotly + - r-rlang + - r-sf + - r-shiny + - r-spatstat.explore + - r-spatstat.geom + run: + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + - r-igraph + - r-isoband + - r-janitor + - r-knitr + - r-lwgeom + - r-pheatmap + - r-plotly + - r-rlang + - r-sf + - r-shiny + - r-spatstat.explore + - r-spatstat.geom +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Spatial cell-type inter-correlation by density in R' + description: 'scider is an user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.' + license_file: LICENSE + diff --git a/recipes/bioconductor-scifer/meta.yaml b/recipes/bioconductor-scifer/meta.yaml index 58e0dc58589ef..6f53163b0a43b 100644 --- a/recipes/bioconductor-scifer/meta.yaml +++ b/recipes/bioconductor-scifer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "scifer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e39ab9c9a71dd10992aedf09000f9848 + md5: 82fb184bec0c09d5f7067baf81f8fee1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scifer", max_pin="x.x") }}' noarch: generic # Suggests: fs, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-sangerseqr >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' - r-base - r-data.table - r-dplyr @@ -39,10 +40,10 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-flowcore >=2.12.0,<2.13.0' - - 'bioconductor-sangerseqr >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-sclcbam/meta.yaml b/recipes/bioconductor-sclcbam/meta.yaml index 407bca15aae77..974fda737ce12 100644 --- a/recipes/bioconductor-sclcbam/meta.yaml +++ b/recipes/bioconductor-sclcbam/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "SCLCBam" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca48c42a5e16460f72eb8bfbc697258f + md5: 660f11c1751b54cc942e91045884bfe6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sclcbam", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sclcbam/post-link.sh b/recipes/bioconductor-sclcbam/post-link.sh index bb942bfa1cea4..ebe08391743a4 100644 --- a/recipes/bioconductor-sclcbam/post-link.sh +++ b/recipes/bioconductor-sclcbam/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sclcbam-1.32.0" +installBiocDataPackage.sh "sclcbam-1.34.0" diff --git a/recipes/bioconductor-scmap/meta.yaml b/recipes/bioconductor-scmap/meta.yaml index 931d39e162095..747a349f39a63 100644 --- a/recipes/bioconductor-scmap/meta.yaml +++ b/recipes/bioconductor-scmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.3" %} +{% set version = "1.24.0" %} {% set name = "scmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a58a3a176f62d952dcd685a9027459bf + md5: de159d16de109a02a1c7cb3c85418b58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmap", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-e1071 @@ -39,11 +40,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-e1071 diff --git a/recipes/bioconductor-scmerge/meta.yaml b/recipes/bioconductor-scmerge/meta.yaml index 8387100c27930..e33892f3dba5d 100644 --- a/recipes/bioconductor-scmerge/meta.yaml +++ b/recipes/bioconductor-scmerge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "scMerge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cee90634720dffc0c35a55bb3b6cb95b + md5: d5b285890500ad5c781d33ab45282aca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmerge", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger requirements: host: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-m3drop >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-m3drop >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-cvtools @@ -41,18 +42,18 @@ requirements: - r-proxyc - r-ruv run: - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-m3drop >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-m3drop >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-cvtools diff --git a/recipes/bioconductor-scmet/meta.yaml b/recipes/bioconductor-scmet/meta.yaml index c8f7b35e4d3a1..9a2d2fce9889a 100644 --- a/recipes/bioconductor-scmet/meta.yaml +++ b/recipes/bioconductor-scmet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "scMET" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ade04cb98f2b5a74bdab738295cfabb + md5: 6420a2af7464f67eb676f06d20f9d5a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmet", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - 'r-bh >=1.66.0' @@ -48,10 +49,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - 'r-bh >=1.66.0' diff --git a/recipes/bioconductor-scmeth/meta.yaml b/recipes/bioconductor-scmeth/meta.yaml index 4502f17020d8e..97b16204b19f5 100644 --- a/recipes/bioconductor-scmeth/meta.yaml +++ b/recipes/bioconductor-scmeth/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "scmeth" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f3e27676cdd8c4eda10fd5004329a574 + md5: 52beac81d58da27e01cc5e1a0b6584b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmeth", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotatr >=1.26.0,<1.27.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-knitr - r-reshape2 - r-rmarkdown run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-annotatr >=1.26.0,<1.27.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-knitr diff --git a/recipes/bioconductor-scmultiome/build_failure.linux-64.yaml b/recipes/bioconductor-scmultiome/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3225ddc538d53 --- /dev/null +++ b/recipes/bioconductor-scmultiome/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 6724b9796e501ce375d77f605eb535671bf9bee68ee4a9d1873f64c6432b2905 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue +log: |2- + - bioconductor-genomicranges >=1.52.0,<1.53.0 + - r-base 4.3.* + - bioconductor-multiassayexperiment >=1.26.0,<1.27.0 + - bioconductor-experimenthub >=2.8.0,<2.9.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - r-checkmate + - bioconductor-hdf5array >=1.28.0,<1.29.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.26.0,<0.27.0 + - bioconductor-rhdf5 >=2.44.0,<2.45.0 + - bioconductor-annotationhub >=3.8.0,<3.9.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-azurestor + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested r-azurestor + - + + Leaving build/test directories: + Work: + /opt/conda/conda-bld/work + Test: + /opt/conda/conda-bld/test_tmp + Leaving build/test environments: + Test: + source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + Build: + source activate /opt/conda/conda-bld/_build_env + + + Traceback (most recent call last): + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions + solution = solver.solve_for_action(_specs, prefix) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action + t = self.solve(specs) + File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve + raise RuntimeError("Solver could not find solution." error_string) + RuntimeError: Solver could not find solution.Mamba failed to solve: + - bioconductor-genomicranges >=1.52.0,<1.53.0 + - r-base 4.3.* + - bioconductor-multiassayexperiment >=1.26.0,<1.27.0 + - bioconductor-experimenthub >=2.8.0,<2.9.0 + - bioconductor-s4vectors >=0.38.0,<0.39.0 + - r-checkmate + - bioconductor-hdf5array >=1.28.0,<1.29.0 + - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.26.0,<0.27.0 + - bioconductor-rhdf5 >=2.44.0,<2.45.0 + - bioconductor-annotationhub >=3.8.0,<3.9.0 + - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 + - r-azurestor + + with channels: + - conda-forge + - bioconda + - defaults + + The reported errors are: + - Encountered problems while solving: + - - nothing provides requested r-azurestor + - + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs + for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins(m, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files + deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, + File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies + actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions + raise err + conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-azurestor")} +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-scmultiome/meta.yaml b/recipes/bioconductor-scmultiome/meta.yaml index 4439589f6fb34..eaa4577ecd304 100644 --- a/recipes/bioconductor-scmultiome/meta.yaml +++ b/recipes/bioconductor-scmultiome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "scMultiome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22aceaa129afbecd400b2d16b6333d43 + md5: db13145ffc5eb5430eee8ac7212e1b7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmultiome", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi, testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-azurestor - r-base - r-checkmate run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-azurestor - r-base - r-checkmate - curl - - bioconductor-data-packages >=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scmultiome/post-link.sh b/recipes/bioconductor-scmultiome/post-link.sh index 3ce950ad4ac67..1324e5cb2e2c7 100644 --- a/recipes/bioconductor-scmultiome/post-link.sh +++ b/recipes/bioconductor-scmultiome/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scmultiome-1.0.0" +installBiocDataPackage.sh "scmultiome-1.2.0" diff --git a/recipes/bioconductor-scnorm/meta.yaml b/recipes/bioconductor-scnorm/meta.yaml index b9547849c0a78..c4058c473a397 100644 --- a/recipes/bioconductor-scnorm/meta.yaml +++ b/recipes/bioconductor-scnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "SCnorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5901d07a8f6feacfef451fc204de8eed + md5: cfac086eb57336e865c999c4c0b42a0c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scnorm", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-data.table @@ -34,11 +35,11 @@ requirements: - r-moments - r-quantreg run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-data.table diff --git a/recipes/bioconductor-scone/meta.yaml b/recipes/bioconductor-scone/meta.yaml index 7dbfa2a2f2363..07e654e223342 100644 --- a/recipes/bioconductor-scone/meta.yaml +++ b/recipes/bioconductor-scone/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "scone" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 03ca7a497be498bc8ba6ff313d121434 + md5: 0e7dd77999fc8cbf842fee6452c82a1b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scone", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData requirements: host: - - 'bioconductor-aroma.light >=3.30.0,<3.31.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-aroma.light >=3.32.0,<3.33.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-class @@ -44,15 +45,15 @@ requirements: - r-rarpack - r-rcolorbrewer run: - - 'bioconductor-aroma.light >=3.30.0,<3.31.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-aroma.light >=3.32.0,<3.33.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-boot - r-class diff --git a/recipes/bioconductor-sconify/meta.yaml b/recipes/bioconductor-sconify/meta.yaml index 26161eee8cbc4..c166731eb09ff 100644 --- a/recipes/bioconductor-sconify/meta.yaml +++ b/recipes/bioconductor-sconify/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "Sconify" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 730ac89643009501cab5346657dfe4a8 + md5: 61762bc5d7e8560ae818942a21da33a5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sconify", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-dplyr - r-fnn @@ -31,7 +32,7 @@ requirements: - r-rtsne - r-tibble run: - - 'bioconductor-flowcore >=2.12.0,<2.13.0' + - 'bioconductor-flowcore >=2.14.0,<2.15.0' - r-base - r-dplyr - r-fnn diff --git a/recipes/bioconductor-scope/meta.yaml b/recipes/bioconductor-scope/meta.yaml index a631ec984b3ab..3943cc3b77751 100644 --- a/recipes/bioconductor-scope/meta.yaml +++ b/recipes/bioconductor-scope/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SCOPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a727431edb54a52f5618b8273c73be24 + md5: b8e4ce76717f217322282d378de1b3bd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scope", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-desctools - r-doparallel @@ -38,16 +39,16 @@ requirements: - r-gplots - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-desctools - r-doparallel diff --git a/recipes/bioconductor-scoreinvhap/meta.yaml b/recipes/bioconductor-scoreinvhap/meta.yaml index a0e7f0f0f7dc2..2ce9837a52775 100644 --- a/recipes/bioconductor-scoreinvhap/meta.yaml +++ b/recipes/bioconductor-scoreinvhap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "scoreInvHap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3acda727fc5294ab60fa6badf682b337 + md5: 7505f8161571dcc7b9b752fc62dedce5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scoreinvhap", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-snpstats >=1.50.0,<1.51.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-scp/meta.yaml b/recipes/bioconductor-scp/meta.yaml index 914e612750fe1..c349acb3dacba 100644 --- a/recipes/bioconductor-scp/meta.yaml +++ b/recipes/bioconductor-scp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "scp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f16e9ca95ef9a6ff5df7dd223533d987 + md5: c4f759cfb996e6150ecec65b7de3e343 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scp", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr, BiocStyle, rmarkdown, patchwork, ggplot2, impute, scater, sva, preprocessCore, vsn, uwot +# Suggests: scpdata, testthat, knitr, BiocStyle, rmarkdown, ggplot2, patchwork, impute, scater, sva, preprocessCore, vsn, uwot requirements: host: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-magrittr - r-matrixstats run: - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-magrittr diff --git a/recipes/bioconductor-scpca/meta.yaml b/recipes/bioconductor-scpca/meta.yaml index 0d8b6478fc46d..61a413188a29a 100644 --- a/recipes/bioconductor-scpca/meta.yaml +++ b/recipes/bioconductor-scpca/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "scPCA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 573b440af9c8058ea71852420c36c695 + md5: e7058ad8f079f25d21ae55911652d01d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scpca", max_pin="x.x") }}' noarch: generic # Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - r-assertthat - r-base - r-cluster @@ -42,10 +43,10 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-scaledmatrix >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - r-assertthat - r-base - r-cluster diff --git a/recipes/bioconductor-scpdata/meta.yaml b/recipes/bioconductor-scpdata/meta.yaml index 8d5a56ba0bbb4..cf133817eeedf 100644 --- a/recipes/bioconductor-scpdata/meta.yaml +++ b/recipes/bioconductor-scpdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "scpdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a00beb40a6ae72de0364698c7a0129b + md5: eac9eae58fe9297359188c45a3dabd1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scpdata", max_pin="x.x") }}' noarch: generic # Suggests: scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-qfeatures >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-qfeatures >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scpdata/post-link.sh b/recipes/bioconductor-scpdata/post-link.sh index 25f2c1ee4adfb..6e55327fbf91f 100644 --- a/recipes/bioconductor-scpdata/post-link.sh +++ b/recipes/bioconductor-scpdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scpdata-1.8.0" +installBiocDataPackage.sh "scpdata-1.10.0" diff --git a/recipes/bioconductor-scpipe/meta.yaml b/recipes/bioconductor-scpipe/meta.yaml index 0b0bb5c2db301..9efcbe7c1cace 100644 --- a/recipes/bioconductor-scpipe/meta.yaml +++ b/recipes/bioconductor-scpipe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "scPipe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 460d566decff05a6ed6c304b1aa2a9ee + md5: 477ce2b2da9cc1ae5365c3140d6ed566 build: skip: True # [osx] number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scpipe", max_pin="x.x") }}' # Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr @@ -65,29 +66,30 @@ requirements: - r-testthat - r-tibble - r-tidyr + - 'r-vctrs >=0.5.2' - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dplyr @@ -111,6 +113,7 @@ requirements: - r-testthat - r-tibble - r-tidyr + - 'r-vctrs >=0.5.2' build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-scran/meta.yaml b/recipes/bioconductor-scran/meta.yaml index 9bff44d2d9e10..e1341546092cc 100644 --- a/recipes/bioconductor-scran/meta.yaml +++ b/recipes/bioconductor-scran/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.1" %} +{% set version = "1.30.0" %} {% set name = "scran" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46f41388ff6b8b0928f012dbf1e962fd + md5: f8cc4c59dde80171927b115dc09592af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scran", max_pin="x.x") }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle, Biobase, pheatmap, scater # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-dqrng @@ -45,20 +46,20 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-metapod >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-metapod >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-dqrng diff --git a/recipes/bioconductor-screclassify/meta.yaml b/recipes/bioconductor-screclassify/meta.yaml index a8888b9ef13c0..6ab9c50202c44 100644 --- a/recipes/bioconductor-screclassify/meta.yaml +++ b/recipes/bioconductor-screclassify/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scReClassify" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b0b6ffa809d9b206a9eecf23e3d4b23 + md5: 722bce944db1f380df35d68a47c4bef7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-screclassify", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-randomforest run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-randomforest diff --git a/recipes/bioconductor-screcover/meta.yaml b/recipes/bioconductor-screcover/meta.yaml index bfb98c8972abd..f0024c38fdf5e 100644 --- a/recipes/bioconductor-screcover/meta.yaml +++ b/recipes/bioconductor-screcover/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "scRecover" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b621333aa197e50352b5e297092ab2bb + md5: ebdc203b50818397a1856fdce417f10e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-screcover", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, SingleCellExperiment, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-bbmle >=1.0.18' - r-doparallel @@ -36,7 +37,7 @@ requirements: - r-rsvd - 'r-saver >=1.1.1' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - 'r-bbmle >=1.0.18' - r-doparallel diff --git a/recipes/bioconductor-screencounter/meta.yaml b/recipes/bioconductor-screencounter/meta.yaml index 05d9fc3635670..d706b51cee9f4 100644 --- a/recipes/bioconductor-screencounter/meta.yaml +++ b/recipes/bioconductor-screencounter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "screenCounter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5865a3dafb6a822adc5831b3c1fad028 + md5: 35bb89fb63853645e76facfc72e77522 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: Biostrings, BiocStyle, knitr, rmarkdown, testthat -# SystemRequirements: C++17 + run_exports: '{{ pin_subpackage("bioconductor-screencounter", max_pin="x.x") }}' +# Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat +# SystemRequirements: C++17, GNU make requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-rcpp build: diff --git a/recipes/bioconductor-screenr/meta.yaml b/recipes/bioconductor-screenr/meta.yaml index 46671016ada11..34203b1646f65 100644 --- a/recipes/bioconductor-screenr/meta.yaml +++ b/recipes/bioconductor-screenr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ScreenR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07fa63df60f427c8bacc15777075f113 + md5: bb8bd3276b17f7e0d63de9c19e64473d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-screenr", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle (>= 2.22.0), covr (>= 3.5) requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-dplyr >=1.0' - 'r-ggplot2 >=3.3' @@ -37,8 +38,8 @@ requirements: - 'r-tidyr >=1.2' - 'r-tidyselect >=1.1.2' run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-dplyr >=1.0' - 'r-ggplot2 >=3.3' diff --git a/recipes/bioconductor-screpertoire/meta.yaml b/recipes/bioconductor-screpertoire/meta.yaml index 9b5a1b165f172..e423553bb5630 100644 --- a/recipes/bioconductor-screpertoire/meta.yaml +++ b/recipes/bioconductor-screpertoire/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "scRepertoire" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d64c8e5caff50abe3de5ddf47f49598 + md5: 3debd173702ebe6c551ba6c572a76c25 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-screpertoire", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, circlize, scales, Seurat, scater requirements: host: - - 'bioconductor-powertcr >=1.20.0,<1.21.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-powertcr >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dplyr @@ -40,9 +41,9 @@ requirements: - r-tidygraph - r-vegan run: - - 'bioconductor-powertcr >=1.20.0,<1.21.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-powertcr >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-scrnaseq/meta.yaml b/recipes/bioconductor-scrnaseq/meta.yaml index 5fe75ed603bb6..8ac4a0edce522 100644 --- a/recipes/bioconductor-scrnaseq/meta.yaml +++ b/recipes/bioconductor-scrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "scRNAseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3adccc738839605191c0eda859e3d7c7 + md5: 55196cb10876aa15733c6a29ffc38100 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, BiocFileCache, testthat, rappdirs, tools requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scrnaseq/post-link.sh b/recipes/bioconductor-scrnaseq/post-link.sh index 95c672ef7f73a..25b040d1f3d7a 100644 --- a/recipes/bioconductor-scrnaseq/post-link.sh +++ b/recipes/bioconductor-scrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scrnaseq-2.14.0" +installBiocDataPackage.sh "scrnaseq-2.16.0" diff --git a/recipes/bioconductor-scrnaseqapp/meta.yaml b/recipes/bioconductor-scrnaseqapp/meta.yaml index cb79acb7eff21..d31492b6be478 100644 --- a/recipes/bioconductor-scrnaseqapp/meta.yaml +++ b/recipes/bioconductor-scrnaseqapp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.2" %} {% set name = "scRNAseqApp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 831fc1f4ceb49cfe0182b5c22312521f + md5: a9b64e980a9e0acef5ab93a44a35e124 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scrnaseqapp", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, testthat, BiocStyle requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' - r-base - r-bibtex - r-bslib @@ -57,18 +58,19 @@ requirements: - r-shiny - r-shinyhelper - r-shinymanager + - r-sortable - r-xfun - r-xml2 run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' - r-base - r-bibtex - r-bslib @@ -96,6 +98,7 @@ requirements: - r-shiny - r-shinyhelper - r-shinymanager + - r-sortable - r-xfun - r-xml2 test: diff --git a/recipes/bioconductor-scruff/meta.yaml b/recipes/bioconductor-scruff/meta.yaml index 0c226e6bef9eb..51177f8c27686 100644 --- a/recipes/bioconductor-scruff/meta.yaml +++ b/recipes/bioconductor-scruff/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "scruff" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,60 +11,63 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bad66b3a487c31db11e46744295fb017 + md5: cd21598690887291d1540e0a827fb6cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scruff", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-ggplot2 - r-ggthemes + - r-parallelly - r-plyr - r-scales - r-stringdist run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rsubread >=2.14.0,<2.15.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-ggplot2 - r-ggthemes + - r-parallelly - r-plyr - r-scales - r-stringdist diff --git a/recipes/bioconductor-scry/meta.yaml b/recipes/bioconductor-scry/meta.yaml index b979189a9b8a4..741c3bb267ea5 100644 --- a/recipes/bioconductor-scry/meta.yaml +++ b/recipes/bioconductor-scry/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "scry" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6887e89a51b1ea222901e82c6ae9c98b + md5: dbdcf37d35f52ba787d1d8d5f21e886e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scry", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat requirements: host: - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-glmpca >=0.2.0' - r-matrix run: - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-glmpca >=0.2.0' - r-matrix diff --git a/recipes/bioconductor-scshapes/meta.yaml b/recipes/bioconductor-scshapes/meta.yaml index 922a38b33bcd6..d12d4297ae966 100644 --- a/recipes/bioconductor-scshapes/meta.yaml +++ b/recipes/bioconductor-scshapes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scShapes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5284952d27abe9951426b826927589d + md5: 5a4954c320f7b1f30f8fbff6e9f5ad91 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scshapes", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-dgof - r-emdbook @@ -31,7 +32,7 @@ requirements: - r-pscl - r-vgam run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-dgof - r-emdbook diff --git a/recipes/bioconductor-sctensor/meta.yaml b/recipes/bioconductor-sctensor/meta.yaml index c4d7f96cb801e..a835706474c23 100644 --- a/recipes/bioconductor-sctensor/meta.yaml +++ b/recipes/bioconductor-sctensor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "scTensor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a026dfae8b4238cae3ff79142fc22cdb + md5: cfbb59a88b526fe373aacf4b1b1a5a97 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sctensor", max_pin="x.x") }}' noarch: generic # Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' - - 'bioconductor-meshr >=2.6.0,<2.7.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-schex >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' + - 'bioconductor-meshr >=2.8.0,<2.9.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-schex >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-biocmanager @@ -55,20 +56,20 @@ requirements: - r-tagcloud - r-visnetwork run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-category >=2.66.0,<2.67.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-meshdbi >=1.36.0,<1.37.0' - - 'bioconductor-meshr >=2.6.0,<2.7.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-schex >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-category >=2.68.0,<2.69.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-meshdbi >=1.38.0,<1.39.0' + - 'bioconductor-meshr >=2.8.0,<2.9.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-reactomepa >=1.46.0,<1.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-schex >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-abind - r-base - r-biocmanager diff --git a/recipes/bioconductor-sctgif/meta.yaml b/recipes/bioconductor-sctgif/meta.yaml index 42c82df750628..bc0285138b195 100644 --- a/recipes/bioconductor-sctgif/meta.yaml +++ b/recipes/bioconductor-sctgif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "scTGIF" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 374dde7d11795e274cfc50aed4fe792d + md5: 7fcf2fd9ff8c1d34aaa64399fa876f3a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sctgif", max_pin="x.x") }}' # Suggests: testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-schex >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-schex >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-igraph @@ -43,13 +44,13 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocstyle >=2.28.0,<2.29.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-schex >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-schex >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-igraph diff --git a/recipes/bioconductor-scthi.data/meta.yaml b/recipes/bioconductor-scthi.data/meta.yaml index 05d45aa099e78..d2c6c62b7e0c1 100644 --- a/recipes/bioconductor-scthi.data/meta.yaml +++ b/recipes/bioconductor-scthi.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "scTHI.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28e55c6ba60cb8527c376ca87993c95c + md5: 1fd101f8dc30262c323bdfa79810f6f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scthi.data", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-scthi.data/post-link.sh b/recipes/bioconductor-scthi.data/post-link.sh index 16c433ce6a893..7763769e34368 100644 --- a/recipes/bioconductor-scthi.data/post-link.sh +++ b/recipes/bioconductor-scthi.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scthi.data-1.12.0" +installBiocDataPackage.sh "scthi.data-1.14.0" diff --git a/recipes/bioconductor-scthi/meta.yaml b/recipes/bioconductor-scthi/meta.yaml index b4e4abeceb114..1e0797b2c9961 100644 --- a/recipes/bioconductor-scthi/meta.yaml +++ b/recipes/bioconductor-scthi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "scTHI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ebb6421876980b77128b35e11b44e86 + md5: c90e49b0aaed73dd76437e5236607e06 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scthi", max_pin="x.x") }}' noarch: generic # Suggests: scTHI.data, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-rtsne run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-rtsne test: diff --git a/recipes/bioconductor-sctreeviz/meta.yaml b/recipes/bioconductor-sctreeviz/meta.yaml index 39baa864da5fb..b05fd3b6f86e7 100644 --- a/recipes/bioconductor-sctreeviz/meta.yaml +++ b/recipes/bioconductor-sctreeviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scTreeViz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 927a1013984382aa44378cc9c728e2d4 + md5: 9e1a317862ad079f52876f54d7160bde build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sctreeviz", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb requirements: host: - - 'bioconductor-epivizr >=2.30.0,<2.31.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-epivizr >=2.32.0,<2.33.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clustree - r-data.table @@ -42,14 +43,14 @@ requirements: - r-seurat - r-sys run: - - 'bioconductor-epivizr >=2.30.0,<2.31.0' - - 'bioconductor-epivizrdata >=1.28.0,<1.29.0' - - 'bioconductor-epivizrserver >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-epivizr >=2.32.0,<2.33.0' + - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' + - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clustree - r-data.table diff --git a/recipes/bioconductor-scuttle/meta.yaml b/recipes/bioconductor-scuttle/meta.yaml index 9ce4f8ac5fa8f..a227c84e0e2c4 100644 --- a/recipes/bioconductor-scuttle/meta.yaml +++ b/recipes/bioconductor-scuttle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "scuttle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 55127c8e30fa4c15da7ba31721165165 + md5: b784ac30ef76b7c0cdac8b79be67b995 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scuttle", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran # SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-scvir/meta.yaml b/recipes/bioconductor-scvir/meta.yaml index 4608eb617c904..1c38e61212da1 100644 --- a/recipes/bioconductor-scvir/meta.yaml +++ b/recipes/bioconductor-scvir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "scviR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a3c949daf08cae151d0ffc4fe6918fb + md5: 71d6c427fcc042ac8b011a31935641df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scvir", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-pheatmap - r-reticulate - r-shiny run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-pheatmap - r-reticulate diff --git a/recipes/bioconductor-sdams/meta.yaml b/recipes/bioconductor-sdams/meta.yaml index 10f1e293bd99c..8ad0a22e4f270 100644 --- a/recipes/bioconductor-sdams/meta.yaml +++ b/recipes/bioconductor-sdams/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "SDAMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 70ceba01b2d6ce773d03ed13e393ee87 + md5: 27ac3a8046a94bf8473502ee2cd5afe1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sdams", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-trust run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-trust test: diff --git a/recipes/bioconductor-sechm/meta.yaml b/recipes/bioconductor-sechm/meta.yaml index 14b5526db7524..5d3d35924430b 100644 --- a/recipes/bioconductor-sechm/meta.yaml +++ b/recipes/bioconductor-sechm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "sechm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f1467f46edc1aa8f86c05aae81d2f368 + md5: 6935a759779eaf70e1cbf3f22c7a1358 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sechm", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-matrixstats - r-randomcolor - r-seriation run: - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circlize - r-matrixstats diff --git a/recipes/bioconductor-segmenter/meta.yaml b/recipes/bioconductor-segmenter/meta.yaml index c03b8b20a8a21..76cfdd42e39c9 100644 --- a/recipes/bioconductor-segmenter/meta.yaml +++ b/recipes/bioconductor-segmenter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "segmenter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 45997faeb651d2c6d5670b3713a8388d + md5: 8877dce2f35cc59e9c3d8b3fb38bf29e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-segmenter", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz requirements: host: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' - 'bioconductor-chromhmmdata >=0.99.0,<0.100.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-bamsignals >=1.32.0,<1.33.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' + - 'bioconductor-bamsignals >=1.34.0,<1.35.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' - 'bioconductor-chromhmmdata >=0.99.0,<0.100.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-segmentseq/build.sh b/recipes/bioconductor-segmentseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-segmentseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-segmentseq/meta.yaml b/recipes/bioconductor-segmentseq/meta.yaml new file mode 100644 index 0000000000000..e43eace8f35f7 --- /dev/null +++ b/recipes/bioconductor-segmentseq/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "2.36.0" %} +{% set name = "segmentSeq" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f86ecc00eba08e4f13412c624d98697c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-segmentseq", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, BiocGenerics +requirements: + host: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - r-abind + - r-base + run: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - r-abind + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Methods for identifying small RNA loci from high-throughput sequencing data' + description: 'High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-selectksigs/meta.yaml b/recipes/bioconductor-selectksigs/meta.yaml index 3455fc77d0785..15de6e1d4eb79 100644 --- a/recipes/bioconductor-selectksigs/meta.yaml +++ b/recipes/bioconductor-selectksigs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "selectKSigs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 730b7e4439fcf388eb775a220e23213f + md5: 95d84e53b480a52695c40071dfa9be68 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-selectksigs", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr requirements: host: - - 'bioconductor-hilda >=1.14.0,<1.15.0' + - 'bioconductor-hilda >=1.16.0,<1.17.0' - r-base - r-gtools - r-magrittr @@ -28,7 +29,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-hilda >=1.14.0,<1.15.0' + - 'bioconductor-hilda >=1.16.0,<1.17.0' - r-base - r-gtools - r-magrittr diff --git a/recipes/bioconductor-selex/meta.yaml b/recipes/bioconductor-selex/meta.yaml index 51229bf30d096..f722404705424 100644 --- a/recipes/bioconductor-selex/meta.yaml +++ b/recipes/bioconductor-selex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "SELEX" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37f1efe42a0799212df721e13d53dfe9 + md5: fdb39d601a2ce8c882e9a0e822ef014c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-selex", max_pin="x.x") }}' noarch: generic # SystemRequirements: Java (>= 1.5) requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-rjava >=0.5-0' - openjdk run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-rjava >=0.5-0' - openjdk diff --git a/recipes/bioconductor-semdist/meta.yaml b/recipes/bioconductor-semdist/meta.yaml index 221af1c2a8fe0..4d76de2af60bc 100644 --- a/recipes/bioconductor-semdist/meta.yaml +++ b/recipes/bioconductor-semdist/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "SemDist" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c69ea1b7da63b8c2dc2e99923dba8d3 + md5: b95a04e7daaae24fb22f3b2a40b17f5f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-semdist", max_pin="x.x") }}' noarch: generic # Suggests: GOSemSim requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' - r-base test: commands: diff --git a/recipes/bioconductor-semisup/meta.yaml b/recipes/bioconductor-semisup/meta.yaml index b857a81831940..e541f2fdda943 100644 --- a/recipes/bioconductor-semisup/meta.yaml +++ b/recipes/bioconductor-semisup/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "semisup" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2ff384fc0dbca3f33f519a4b8de74167 + md5: fb3d32c07acbfadbbee01f9a6c8333fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-semisup", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, SummarizedExperiment requirements: diff --git a/recipes/bioconductor-seq.hotspot/meta.yaml b/recipes/bioconductor-seq.hotspot/meta.yaml index 2f14c697b4d91..a2ea709167002 100644 --- a/recipes/bioconductor-seq.hotspot/meta.yaml +++ b/recipes/bioconductor-seq.hotspot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "seq.hotSPOT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20614c1b700f6efb77257e9ec89a13fe + md5: 37e04dc7e1bb05af58c50cb7701388c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seq.hotspot", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: diff --git a/recipes/bioconductor-seq2pathway.data/meta.yaml b/recipes/bioconductor-seq2pathway.data/meta.yaml index bb203b9c7cc5e..8410739a77c65 100644 --- a/recipes/bioconductor-seq2pathway.data/meta.yaml +++ b/recipes/bioconductor-seq2pathway.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "seq2pathway.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f5b47c139925e607c100f2e3e0292db0 + md5: b0035ff986391159c1329eac9fb96661 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seq2pathway.data", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-seq2pathway.data/post-link.sh b/recipes/bioconductor-seq2pathway.data/post-link.sh index 8d976f432fdf2..30b629ea74cff 100644 --- a/recipes/bioconductor-seq2pathway.data/post-link.sh +++ b/recipes/bioconductor-seq2pathway.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "seq2pathway.data-1.32.0" +installBiocDataPackage.sh "seq2pathway.data-1.34.0" diff --git a/recipes/bioconductor-seq2pathway/meta.yaml b/recipes/bioconductor-seq2pathway/meta.yaml index cd6d03f8af502..4dbc70fe6e390 100644 --- a/recipes/bioconductor-seq2pathway/meta.yaml +++ b/recipes/bioconductor-seq2pathway/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "seq2pathway" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 76098141614149c9fcc18823aeb3e359 + md5: 4aaa34232c40fdc31f493d67c72742c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seq2pathway", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-seq2pathway.data >=1.32.0,<1.33.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-seq2pathway.data >=1.34.0,<1.35.0' - r-base - r-gsa - r-nnet - r-wgcna run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-seq2pathway.data >=1.32.0,<1.33.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-seq2pathway.data >=1.34.0,<1.35.0' - r-base - r-gsa - r-nnet diff --git a/recipes/bioconductor-seqarchr/meta.yaml b/recipes/bioconductor-seqarchr/meta.yaml index b2d195646ee7e..228d43f42052d 100644 --- a/recipes/bioconductor-seqarchr/meta.yaml +++ b/recipes/bioconductor-seqarchr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "seqArchR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fecd57059a333de35b3509909921541c + md5: b991ca99e52e357f8ef95a3a75a1decc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqarchr", max_pin="x.x") }}' noarch: generic # Suggests: cowplot, hopach (>= 2.42.0), BiocStyle, knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>= 0.3.0) # SystemRequirements: Python (>= 3.5), scikit-learn (>= 0.21.2), packaging requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-cli - r-cluster @@ -38,8 +39,8 @@ requirements: - 'r-reshape2 >=1.4.3' - 'r-reticulate >=1.22' run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-cli - r-cluster diff --git a/recipes/bioconductor-seqarchrplus/meta.yaml b/recipes/bioconductor-seqarchrplus/meta.yaml index 73dd5f3d2a1b9..9c12d8beb187b 100644 --- a/recipes/bioconductor-seqarchrplus/meta.yaml +++ b/recipes/bioconductor-seqarchrplus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "seqArchRplus" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,57 +11,60 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35db67395c9e71a8e40360d5266a8e1f + md5: 9f20e2eed3e5b5a498564ea201b251d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqarchrplus", max_pin="x.x") }}' noarch: generic -# Suggests: BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2), covr, knitr (>= 1.22), org.Dm.eg.db, rmarkdown (>= 1.12), TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun +# Suggests: BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2), covr, knitr (>= 1.22), org.Dm.eg.db, pdftools, rmarkdown (>= 1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-heatmaps >=1.24.0,<1.25.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarchr >=1.4.0,<1.5.0' - - 'bioconductor-seqpattern >=1.32.0,<1.33.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-heatmaps >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarchr >=1.6.0,<1.7.0' + - 'bioconductor-seqpattern >=1.34.0,<1.35.0' - r-base - r-cli - r-cowplot - r-factoextra - - r-forcats + - r-ggimage - r-ggplot2 - r-gridextra + - r-magick - r-rcolorbrewer - r-scales run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-heatmaps >=1.24.0,<1.25.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarchr >=1.4.0,<1.5.0' - - 'bioconductor-seqpattern >=1.32.0,<1.33.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-chipseeker >=1.38.0,<1.39.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-heatmaps >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarchr >=1.6.0,<1.7.0' + - 'bioconductor-seqpattern >=1.34.0,<1.35.0' - r-base - r-cli - r-cowplot - r-factoextra - - r-forcats + - r-ggimage - r-ggplot2 - r-gridextra + - r-magick - r-rcolorbrewer - r-scales test: @@ -71,6 +74,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Downstream analyses of promoter sequence architectures and HTML report generation' - description: 'seqArchRplus facilitates downstream analyses of promoter sequence architectures/clusters identified by seqArchR (or any other tool/method). With additional available information such as the TPM values and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus can order the input promoter clusters by their shape (IQWs), and write the cluster information as browser/IGV track files. Provided visualizations are of two kind: per sample/stage and per cluster visualizations. Those of the first kind include: plot panels for each sample showing per cluster shape, TPM and other score distributions, sequence logos, and peak annotations. The second include per cluster chromosome-wise and strand distributions, motif occurrence heatmaps and GO term enrichments. Additionally, seqArchRplus can also generate HTML reports for easy viewing and comparison of promoter architectures between samples/stages (future).' + description: 'seqArchRplus facilitates downstream analyses of promoter sequence architectures/clusters identified by seqArchR (or any other tool/method). With additional available information such as the TPM values and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus can order the input promoter clusters by their shape (IQWs), and write the cluster information as browser/IGV track files. Provided visualizations are of two kind: per sample/stage and per cluster visualizations. Those of the first kind include: plot panels for each sample showing per cluster shape, TPM and other score distributions, sequence logos, and peak annotations. The second include per cluster chromosome-wise and strand distributions, motif occurrence heatmaps and GO term enrichments. Additionally, seqArchRplus can also generate HTML reports for easy viewing and comparison of promoter architectures between samples/stages.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-seqarray/meta.yaml b/recipes/bioconductor-seqarray/meta.yaml index cfd8a66707fd9..189913b7b1e3e 100644 --- a/recipes/bioconductor-seqarray/meta.yaml +++ b/recipes/bioconductor-seqarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.1" %} +{% set version = "1.42.0" %} {% set name = "SeqArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7fe9f3e22cc01b8c418d18e382b7a1c7 + md5: 9754225574380705e505629db229d41a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqarray", max_pin="x.x") }}' # Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-seqbias/meta.yaml b/recipes/bioconductor-seqbias/meta.yaml index 7ccf27fe16e38..68fec85f215e5 100644 --- a/recipes/bioconductor-seqbias/meta.yaml +++ b/recipes/bioconductor-seqbias/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "seqbias" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c5d17dfe8932ed8cd03a6b0428a74fd + md5: 0482c079ead497bdddd61be6bac445f7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqbias", max_pin="x.x") }}' # Suggests: Rsamtools, ggplot2 # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-seqc/meta.yaml b/recipes/bioconductor-seqc/meta.yaml index a24dc500afc1a..6da322827d369 100644 --- a/recipes/bioconductor-seqc/meta.yaml +++ b/recipes/bioconductor-seqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "seqc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 834e2a378860f1f6aea76581e87c876f + md5: 105a278c97aca90968641aec403c1219 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqc", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-seqc/post-link.sh b/recipes/bioconductor-seqc/post-link.sh index c4675267b71f1..9d67b6fc469d9 100644 --- a/recipes/bioconductor-seqc/post-link.sh +++ b/recipes/bioconductor-seqc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "seqc-1.34.0" +installBiocDataPackage.sh "seqc-1.36.0" diff --git a/recipes/bioconductor-seqcat/meta.yaml b/recipes/bioconductor-seqcat/meta.yaml index a3fe883852757..4c3f9796fbf43 100644 --- a/recipes/bioconductor-seqcat/meta.yaml +++ b/recipes/bioconductor-seqcat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "seqCAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28f42128bb177d143b80d274175364f0 + md5: a7694d3599501816a63d4b6e831af35d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqcat", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-dplyr >=0.5.0' - 'r-ggplot2 >=2.2.1' @@ -35,13 +36,13 @@ requirements: - 'r-scales >=0.4.1' - 'r-tidyr >=0.6.1' run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-dplyr >=0.5.0' - 'r-ggplot2 >=2.2.1' diff --git a/recipes/bioconductor-seqcna.annot/meta.yaml b/recipes/bioconductor-seqcna.annot/meta.yaml index b6742c5e3f45a..586086b68b240 100644 --- a/recipes/bioconductor-seqcna.annot/meta.yaml +++ b/recipes/bioconductor-seqcna.annot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "seqCNA.annot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: feee6a27f305149bdfec8a823e2134ec + md5: a61df6e0824d7c3c3f4c697b5bd73e30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqcna.annot", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-seqcna.annot/post-link.sh b/recipes/bioconductor-seqcna.annot/post-link.sh index d92e89050b20f..55de60d88d9ad 100644 --- a/recipes/bioconductor-seqcna.annot/post-link.sh +++ b/recipes/bioconductor-seqcna.annot/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "seqcna.annot-1.36.0" +installBiocDataPackage.sh "seqcna.annot-1.38.0" diff --git a/recipes/bioconductor-seqcna/meta.yaml b/recipes/bioconductor-seqcna/meta.yaml index 564887adce0e2..fbd5dc10071c8 100644 --- a/recipes/bioconductor-seqcna/meta.yaml +++ b/recipes/bioconductor-seqcna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "seqCNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dfe25506e95aa7a625d69e2e5420f168 + md5: 06ae9363110630b77cd3e5b4ae70b188 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqcna", max_pin="x.x") }}' # SystemRequirements: samtools requirements: host: - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-seqcna.annot >=1.36.0,<1.37.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-seqcna.annot >=1.38.0,<1.39.0' - 'r-adehabitatlt >=0.3.4' - r-base - 'r-dosnow >=1.0.5' @@ -29,8 +30,8 @@ requirements: - liblapack - samtools run: - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-seqcna.annot >=1.36.0,<1.37.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-seqcna.annot >=1.38.0,<1.39.0' - 'r-adehabitatlt >=0.3.4' - r-base - 'r-dosnow >=1.0.5' diff --git a/recipes/bioconductor-seqcombo/meta.yaml b/recipes/bioconductor-seqcombo/meta.yaml index 9f21f96fe79ad..4afa58a79f493 100644 --- a/recipes/bioconductor-seqcombo/meta.yaml +++ b/recipes/bioconductor-seqcombo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "seqcombo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ce813d4dc3284696f90d33e05f11f56 + md5: 76a401edd5e5583a94ab3a1b599b7a78 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqcombo", max_pin="x.x") }}' noarch: generic # Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble requirements: diff --git a/recipes/bioconductor-seqgate/meta.yaml b/recipes/bioconductor-seqgate/meta.yaml index 0d2e5925bdbe2..5ca65b1d94bf3 100644 --- a/recipes/bioconductor-seqgate/meta.yaml +++ b/recipes/bioconductor-seqgate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SeqGate" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: caca9e158a9bfe2b69e3423a86a81654 + md5: 786d9cf0f14de2b0056b9207daedbf45 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqgate", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-biocmanager test: diff --git a/recipes/bioconductor-seqgsea/meta.yaml b/recipes/bioconductor-seqgsea/meta.yaml index bd2c3d5d81d64..0d91107a888ec 100644 --- a/recipes/bioconductor-seqgsea/meta.yaml +++ b/recipes/bioconductor-seqgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "SeqGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c106db6ce0aeec4190b5f7fd7495a99a + md5: 13213924066a18535220d42938e923fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqgsea", max_pin="x.x") }}' noarch: generic # Suggests: GenomicRanges requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - r-base - r-doparallel run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - r-base - r-doparallel test: diff --git a/recipes/bioconductor-seqlogo/meta.yaml b/recipes/bioconductor-seqlogo/meta.yaml index 6ecaf507c15ab..7f32797f34d61 100644 --- a/recipes/bioconductor-seqlogo/meta.yaml +++ b/recipes/bioconductor-seqlogo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "seqLogo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea278495fc179bf6ef9309b2479b0671 + md5: 0771c35a7929a3e71aa5eebaf4a624ef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqlogo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-seqpattern/meta.yaml b/recipes/bioconductor-seqpattern/meta.yaml index e00aa28fe26ec..78b4fabd8eb99 100644 --- a/recipes/bioconductor-seqpattern/meta.yaml +++ b/recipes/bioconductor-seqpattern/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "seqPattern" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ae45cac8349ba8a6cf5114662c3dd7f + md5: 90ef37347887673ee80f12fa953e02f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqpattern", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth - r-plotrix run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-kernsmooth - r-plotrix diff --git a/recipes/bioconductor-seqsetvis/meta.yaml b/recipes/bioconductor-seqsetvis/meta.yaml index 3ae2dd43d0f62..fce6340743e95 100644 --- a/recipes/bioconductor-seqsetvis/meta.yaml +++ b/recipes/bioconductor-seqsetvis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "seqsetvis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0593e5b221ee0dcaa6edeabb195bb9ff + md5: 0119c8a5e2475e3a0d35059b3c35dfd6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqsetvis", max_pin="x.x") }}' noarch: generic # Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table @@ -39,16 +40,17 @@ requirements: - r-pbmcapply - r-png - r-rcolorbrewer + - r-scales - r-upsetr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-data.table @@ -59,6 +61,7 @@ requirements: - r-pbmcapply - r-png - r-rcolorbrewer + - r-scales - r-upsetr test: commands: diff --git a/recipes/bioconductor-seqsqc/meta.yaml b/recipes/bioconductor-seqsqc/meta.yaml index a47cc4ce41ef6..dfcf859b73495 100644 --- a/recipes/bioconductor-seqsqc/meta.yaml +++ b/recipes/bioconductor-seqsqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "SeqSQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 195f7e2bff5ce9fbd8e350f1022a530e + md5: 10e877d23b5c1572319af0515baca2c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqsqc", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base - r-e1071 - r-ggally @@ -36,12 +37,12 @@ requirements: - r-reshape2 - r-rmarkdown run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' - r-base - r-e1071 - r-ggally diff --git a/recipes/bioconductor-seqtools/meta.yaml b/recipes/bioconductor-seqtools/meta.yaml index 583d647382fcf..93a07f90dca3c 100644 --- a/recipes/bioconductor-seqtools/meta.yaml +++ b/recipes/bioconductor-seqtools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "seqTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fc462bf24881e9f121c7e8e734055ef + md5: be9be6eb0ee1ff4ab001720970d68da8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqtools", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-seqvartools/meta.yaml b/recipes/bioconductor-seqvartools/meta.yaml index b50ab43f0dadf..cd40a732cfeb5 100644 --- a/recipes/bioconductor-seqvartools/meta.yaml +++ b/recipes/bioconductor-seqvartools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "SeqVarTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f0de0a3c46d81cc184e94e9f9258a01d + md5: 160f56cd78339c2e4d4b5c0766a47846 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seqvartools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, RUnit, stringr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-data.table - r-gwasexacthw - r-logistf - r-matrix run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' - r-base - r-data.table - r-gwasexacthw diff --git a/recipes/bioconductor-serumstimulation/meta.yaml b/recipes/bioconductor-serumstimulation/meta.yaml index 08afdb968f69b..7304fb6ceb832 100644 --- a/recipes/bioconductor-serumstimulation/meta.yaml +++ b/recipes/bioconductor-serumstimulation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "serumStimulation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 642cc4d3939f4a05e331ef5d1f965835 + md5: 4d3f1a4e58f500d7e424eef0b22c05ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-serumstimulation", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-serumstimulation/post-link.sh b/recipes/bioconductor-serumstimulation/post-link.sh index 36e810aea6f28..f74707b1a8b74 100644 --- a/recipes/bioconductor-serumstimulation/post-link.sh +++ b/recipes/bioconductor-serumstimulation/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "serumstimulation-1.36.0" +installBiocDataPackage.sh "serumstimulation-1.38.0" diff --git a/recipes/bioconductor-sesame/meta.yaml b/recipes/bioconductor-sesame/meta.yaml index 5234aea678109..bef67f6a17dd4 100644 --- a/recipes/bioconductor-sesame/meta.yaml +++ b/recipes/bioconductor-sesame/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.4" %} +{% set version = "1.20.0" %} {% set name = "sesame" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d1f0f5e0d15b5b3e01160d6028497a58 + md5: 9bb9cc07a6c773f324fdee69d75a8427 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sesame", max_pin="x.x") }}' noarch: generic -# Suggests: scales, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals +# Suggests: scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sesamedata >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sesamedata >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -41,16 +42,16 @@ requirements: - r-tibble - 'r-wheatmap >=0.2.0' run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sesamedata >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sesamedata >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-sesamedata/meta.yaml b/recipes/bioconductor-sesamedata/meta.yaml index 60840cc790ad0..48d75153c0584 100644 --- a/recipes/bioconductor-sesamedata/meta.yaml +++ b/recipes/bioconductor-sesamedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "sesameData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4af907a4ed795d2493573b88d55fd4de + md5: 4cd44c4f5307d2775d94f2051b9a7f46 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sesamedata", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, sesame, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-readr - r-stringr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-readr - r-stringr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sesamedata/post-link.sh b/recipes/bioconductor-sesamedata/post-link.sh index 6efd3a74642d9..f5cc75f5ec748 100644 --- a/recipes/bioconductor-sesamedata/post-link.sh +++ b/recipes/bioconductor-sesamedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sesamedata-1.18.0" +installBiocDataPackage.sh "sesamedata-1.20.0" diff --git a/recipes/bioconductor-setools/meta.yaml b/recipes/bioconductor-setools/meta.yaml index c7e0e948dd6b9..364be9dc5ca55 100644 --- a/recipes/bioconductor-setools/meta.yaml +++ b/recipes/bioconductor-setools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SEtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e6a9df3ebf6eaacc2cce51d39040f13 + md5: 4b6f28a6fdf032d51f29793f25729114 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-setools", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, ggplot2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sechm >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sechm >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-circlize - r-data.table @@ -35,13 +36,13 @@ requirements: - r-openxlsx - r-pheatmap run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-sechm >=1.8.0,<1.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-sechm >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-circlize - r-data.table diff --git a/recipes/bioconductor-sevenbridges/meta.yaml b/recipes/bioconductor-sevenbridges/meta.yaml index cd03d3e9b99cd..66cb3290bcdbe 100644 --- a/recipes/bioconductor-sevenbridges/meta.yaml +++ b/recipes/bioconductor-sevenbridges/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "sevenbridges" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f09e6b0788100a89ac38eb13887d8993 + md5: 1c204add9c56d7518a5362b99111ec18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sevenbridges", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, readr requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-data.table @@ -33,7 +34,7 @@ requirements: - r-uuid - r-yaml run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-curl - r-data.table diff --git a/recipes/bioconductor-sevenc/meta.yaml b/recipes/bioconductor-sevenc/meta.yaml index 38be4b0ddbb31..e56d3a0da93e1 100644 --- a/recipes/bioconductor-sevenc/meta.yaml +++ b/recipes/bioconductor-sevenc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "sevenC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e943999c0ef7fc1049dd87b19bd4520e + md5: 575914dcdfdff58d10d7e926182801b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sevenc", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-boot >=1.3-20' - 'r-data.table >=1.10.4' - 'r-purrr >=0.2.2' - 'r-readr >=1.1.0' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-boot >=1.3-20' - 'r-data.table >=1.10.4' diff --git a/recipes/bioconductor-seventygenedata/meta.yaml b/recipes/bioconductor-seventygenedata/meta.yaml index f77017c68ad61..076afa9211ab5 100644 --- a/recipes/bioconductor-seventygenedata/meta.yaml +++ b/recipes/bioconductor-seventygenedata/meta.yaml @@ -25,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - bioconductor-data-packages >=20230706 test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sfedata/meta.yaml b/recipes/bioconductor-sfedata/meta.yaml index e7fd005710ab3..7b97631753e5d 100644 --- a/recipes/bioconductor-sfedata/meta.yaml +++ b/recipes/bioconductor-sfedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "SFEData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 405e15fbe6e99736481e40164abf3b04 + md5: 7f3376870c972cba309b26d52d24fcbb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sfedata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, SpatialFeatureExperiment, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sfedata/post-link.sh b/recipes/bioconductor-sfedata/post-link.sh index 05d7347ba3e7f..f690a3a41ff4f 100644 --- a/recipes/bioconductor-sfedata/post-link.sh +++ b/recipes/bioconductor-sfedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sfedata-1.2.0" +installBiocDataPackage.sh "sfedata-1.4.0" diff --git a/recipes/bioconductor-sgcp/meta.yaml b/recipes/bioconductor-sgcp/meta.yaml index 9af3e937efa45..eaaca7d8f94e0 100644 --- a/recipes/bioconductor-sgcp/meta.yaml +++ b/recipes/bioconductor-sgcp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "SGCP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34dc1d2d2ed37410c921ae70f7b10965 + md5: 46986c7dd18ef80a29c389500ed5023b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sgcp", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocManager requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-desctools @@ -43,14 +44,14 @@ requirements: - r-rspectra - r-xtable run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gostats >=2.66.0,<2.67.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gostats >=2.68.0,<2.69.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-caret - r-desctools diff --git a/recipes/bioconductor-sgseq/meta.yaml b/recipes/bioconductor-sgseq/meta.yaml index b4fc72a14d8b6..a88e1160be342 100644 --- a/recipes/bioconductor-sgseq/meta.yaml +++ b/recipes/bioconductor-sgseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "SGSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ffeb95713ad100a5988daf418801096 + md5: 874492401a4a17bf0836f9fa011f459a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sgseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-runit run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-runit diff --git a/recipes/bioconductor-sharedobject/build.sh b/recipes/bioconductor-sharedobject/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sharedobject/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sharedobject/meta.yaml b/recipes/bioconductor-sharedobject/meta.yaml new file mode 100644 index 0000000000000..849fb0abf9871 --- /dev/null +++ b/recipes/bioconductor-sharedobject/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.16.0" %} +{% set name = "SharedObject" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7c47265b6a5f61385088d6146c7e4879 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sharedobject", max_pin="x.x") }}' +# Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle +# SystemRequirements: GNU make, C++11 +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - r-base + - r-bh + - r-rcpp + - libblas + - liblapack + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - r-base + - r-bh + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Sharing R objects across multiple R processes without memory duplication' + description: 'This package is developed for facilitating parallel computing in R. It is capable to create an R object in the shared memory space and share the data across multiple R processes. It avoids the overhead of memory dulplication and data transfer, which make sharing big data object across many clusters possible.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-shdz.db/meta.yaml b/recipes/bioconductor-shdz.db/meta.yaml index db050bfdcd0ac..b7927519c0bdf 100644 --- a/recipes/bioconductor-shdz.db/meta.yaml +++ b/recipes/bioconductor-shdz.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "SHDZ.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 63c4439a272a5cd0c4746e9e53a7bdc7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-shdz.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-shinyepico/meta.yaml b/recipes/bioconductor-shinyepico/meta.yaml index d2a600fdca1a7..352d8232c1e6f 100644 --- a/recipes/bioconductor-shinyepico/meta.yaml +++ b/recipes/bioconductor-shinyepico/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "shinyepico" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4eb22bc9e04f69e4d52faf1dafc43809 + md5: 044010b7c6b7570adb28be7374473f82 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-shinyepico", max_pin="x.x") }}' noarch: generic # Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-data.table >=1.13.0' - 'r-doparallel >=1.0.0' @@ -47,10 +48,10 @@ requirements: - 'r-tidyr >=1.2.0' - 'r-zip >=2.1.0' run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - 'r-data.table >=1.13.0' - 'r-doparallel >=1.0.0' diff --git a/recipes/bioconductor-shinymethyl/meta.yaml b/recipes/bioconductor-shinymethyl/meta.yaml index 505a32b6f3332..09cdddcbcd8cc 100644 --- a/recipes/bioconductor-shinymethyl/meta.yaml +++ b/recipes/bioconductor-shinymethyl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "shinyMethyl" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f8531aa5c428db361db5abf32e59111 + md5: 21f2fe819a72a5c4db3694a22dcda934 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-shinymethyl", max_pin="x.x") }}' noarch: generic # Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-htmltools - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' - r-base - r-htmltools - r-rcolorbrewer diff --git a/recipes/bioconductor-shinymethyldata/meta.yaml b/recipes/bioconductor-shinymethyldata/meta.yaml index 11cedfd25f71c..e41c94e7ad9f3 100644 --- a/recipes/bioconductor-shinymethyldata/meta.yaml +++ b/recipes/bioconductor-shinymethyldata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "shinyMethylData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f633d8b104a4f61c393b15f59671039b + md5: 46f32db849aaa1467d09b0a371769374 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-shinymethyldata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-shinymethyldata/post-link.sh b/recipes/bioconductor-shinymethyldata/post-link.sh index 51a237e07d36e..3d514dc1f7ffc 100644 --- a/recipes/bioconductor-shinymethyldata/post-link.sh +++ b/recipes/bioconductor-shinymethyldata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "shinymethyldata-1.20.0" +installBiocDataPackage.sh "shinymethyldata-1.22.0" diff --git a/recipes/bioconductor-shortread/meta.yaml b/recipes/bioconductor-shortread/meta.yaml index 3aada6e844fcc..9b4eee6ba99c3 100644 --- a/recipes/bioconductor-shortread/meta.yaml +++ b/recipes/bioconductor-shortread/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "ShortRead" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8547be10c12f7765d3e25a4a735af39 + md5: 480786b1db8f8138a7a4e8c36f9bdfc4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-shortread", max_pin="x.x") }}' # Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-hwriter - r-lattice @@ -40,19 +41,19 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-hwriter - r-lattice diff --git a/recipes/bioconductor-siamcat/meta.yaml b/recipes/bioconductor-siamcat/meta.yaml index 956cab8ec228e..d94c3be14962d 100644 --- a/recipes/bioconductor-siamcat/meta.yaml +++ b/recipes/bioconductor-siamcat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "SIAMCAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38b6d1bc1d77495fe3faf0efc44cabb5 + md5: 36938473e8b2bd9b269fae69ec312e8d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-siamcat", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, optparse, testthat, knitr, rmarkdown, tidyverse, ggpubr +# Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr requirements: host: - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-beanplot - r-corrplot @@ -44,7 +45,7 @@ requirements: - r-scales - r-stringr run: - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - r-base - r-beanplot - r-corrplot diff --git a/recipes/bioconductor-sictools/build.sh b/recipes/bioconductor-sictools/build.sh index 8ed8c159a97a0..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sictools/build.sh +++ b/recipes/bioconductor-sictools/build.sh @@ -2,10 +2,10 @@ mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R -echo -e "CC=$CC -I$PREFIX/include -L$PREFIX/lib +echo -e "CC=$CC FC=$FC -CXX=$CXX -I$PREFIX/include -L$PREFIX/lib +CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -MAKE="make LIBCURSES=-lncurses" $R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sictools/build_failure.linux-64.yaml b/recipes/bioconductor-sictools/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c447c0a1d2387 --- /dev/null +++ b/recipes/bioconductor-sictools/build_failure.linux-64.yaml @@ -0,0 +1,37 @@ +recipe_sha: d0341aa6f0be4917a820c67382d360ac5f5e76815434d7cecb1769b617051f44 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bgzf.h:33:10: fatal error: zlib.h: No such file or directory +category: |- + compiler error +log: |- + 13:35:37 BIOCONDA INFO (OUT) In file included from bgzf.c:32: + 13:35:37 BIOCONDA INFO (OUT) bgzf.h:33:10: fatal error: zlib.h: No such file or directory + 13:35:37 BIOCONDA INFO (OUT) 33 | #include + 13:35:37 BIOCONDA INFO (OUT) | ^~~~~~~~ + 13:35:37 BIOCONDA INFO (OUT) compilation terminated. + 13:35:37 BIOCONDA INFO (OUT) make[2]: *** [Makefile:56: bgzf.o] Error 1 + 13:35:37 BIOCONDA INFO (OUT) make[2]: Leaving directory '$SRC_DIR/src' + 13:35:37 BIOCONDA INFO (OUT) make[1]: *** [Makefile:27: lib-recur] Error 1 + 13:35:37 BIOCONDA INFO (OUT) make[1]: Leaving directory '$SRC_DIR/src' + 13:35:37 BIOCONDA INFO (OUT) make: *** [Makefile:27: all-recur] Error 1 + 13:35:37 BIOCONDA INFO (OUT) ERROR: compilation failed for package ‘SICtools’ + 13:35:37 BIOCONDA INFO (OUT) * removing ‘/opt/conda/conda-bld/bioconductor-sictools_1702301527486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/SICtools’ + 13:35:38 BIOCONDA INFO (OUT) Traceback (most recent call last): + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in + 13:35:38 BIOCONDA INFO (OUT) sys.exit(main()) + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 13:35:38 BIOCONDA INFO (OUT) call_conda_build(action, config) + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 13:35:38 BIOCONDA INFO (OUT) result = api.build( + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 13:35:38 BIOCONDA INFO (OUT) return build_tree( + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + 13:35:38 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + 13:35:38 BIOCONDA INFO (OUT) utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + 13:35:38 BIOCONDA INFO (OUT) return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + 13:35:38 BIOCONDA INFO (OUT) raise subprocess.CalledProcessError(proc.returncode, _args) + 13:35:38 BIOCONDA INFO (OUT) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-sictools_1702301527486/work/conda_build.sh']' returned non-zero exit status 1. diff --git a/recipes/bioconductor-sictools/meta.yaml b/recipes/bioconductor-sictools/meta.yaml index ffcbe6f486b4f..12a5dc2cb5ca8 100644 --- a/recipes/bioconductor-sictools/meta.yaml +++ b/recipes/bioconductor-sictools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "SICtools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b83944eeafc064c998ad1c3acfa3b0e + md5: 1df54634cb8bc00e60963b0ca10886d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sictools", max_pin="x.x") }}' # Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-doparallel >=1.0.8' - 'r-matrixstats >=0.10.0' @@ -31,20 +32,16 @@ requirements: - 'r-stringr >=0.6.2' - libblas - liblapack - - zlib - - ncurses run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - 'r-doparallel >=1.0.8' - 'r-matrixstats >=0.10.0' - 'r-plyr >=1.8.3' - 'r-stringr >=0.6.2' - - zlib - - ncurses build: - {{ compiler('c') }} - make diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml b/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml index c7d63153dc4b1..63f65568f82da 100644 --- a/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml +++ b/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.2" %} {% set name = "SIFT.Hsapiens.dbSNP132" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,24 +13,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c374f0bf4c99357cfe99e0b192c00d75 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sift.hsapiens.dbsnp132", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml b/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml index c422913f4d133..f0f7108912e36 100644 --- a/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml +++ b/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.0.0" %} {% set name = "SIFT.Hsapiens.dbSNP137" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,24 +13,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3c3e73f826399af5ff368d1aab12cfd1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sift.hsapiens.dbsnp137", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-rsqlite >=0.11.0' - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sigcheck/meta.yaml b/recipes/bioconductor-sigcheck/meta.yaml index c2a7a7a09e7c3..d0bf27e007237 100644 --- a/recipes/bioconductor-sigcheck/meta.yaml +++ b/recipes/bioconductor-sigcheck/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "SigCheck" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a66d9ee5f9009f29346bdfca24346288 + md5: 0c956bbf06058a0a494f887fbdf6549f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sigcheck", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, breastCancerNKI, qusage requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mlinterfaces >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' - r-base - r-e1071 - r-survival run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-mlinterfaces >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' - r-base - r-e1071 - r-survival diff --git a/recipes/bioconductor-sigfeature/meta.yaml b/recipes/bioconductor-sigfeature/meta.yaml index 0f6d1c3a4c5b4..9c09d518d848e 100644 --- a/recipes/bioconductor-sigfeature/meta.yaml +++ b/recipes/bioconductor-sigfeature/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "sigFeature" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63592ed4b877d9961ce62abd53541a7c + md5: 96249637034c39dc1924cd78c1a0ba58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sigfeature", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-matrix @@ -33,9 +34,9 @@ requirements: - r-rcolorbrewer - r-sparsem run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocviews >=1.68.0,<1.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocviews >=1.70.0,<1.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-matrix diff --git a/recipes/bioconductor-sigfuge/meta.yaml b/recipes/bioconductor-sigfuge/meta.yaml index 2966d00f7cd0c..b5a313692d97c 100644 --- a/recipes/bioconductor-sigfuge/meta.yaml +++ b/recipes/bioconductor-sigfuge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "SigFuge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 474286ce316b812744a7f7b2ed8a49d4 + md5: cb03ecb39c2df4b4f5e1b49f8ba5d594 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sigfuge", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-ggplot2 - r-matlab - r-reshape - r-sigclust run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - r-ggplot2 - r-matlab diff --git a/recipes/bioconductor-siggenes/meta.yaml b/recipes/bioconductor-siggenes/meta.yaml index ab2e1e6eaead6..7b70075ae924b 100644 --- a/recipes/bioconductor-siggenes/meta.yaml +++ b/recipes/bioconductor-siggenes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "siggenes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a4eb4fbc80332b7d40a1c74e92243af6 + md5: ae9899f2a3587a423169a27502868709 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-siggenes", max_pin="x.x") }}' noarch: generic # Suggests: affy, annotate, genefilter, KernSmooth requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-scrime >=1.2.5' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' - r-base - 'r-scrime >=1.2.5' test: diff --git a/recipes/bioconductor-sights/meta.yaml b/recipes/bioconductor-sights/meta.yaml index c98adcfb1b0ac..6e11b18225760 100644 --- a/recipes/bioconductor-sights/meta.yaml +++ b/recipes/bioconductor-sights/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "sights" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 290c43f8616319bdca706779a2e7ad05 + md5: 566e869c884c7b12f1a42a9dbaeec05a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sights", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.0' - 'r-lattice >=0.2' - 'r-mass >=7.3' - 'r-reshape2 >=1.4' run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - 'r-ggplot2 >=2.0' - 'r-lattice >=0.2' diff --git a/recipes/bioconductor-signaturesearch/meta.yaml b/recipes/bioconductor-signaturesearch/meta.yaml index 561e436f8b679..f1ab00dc3f3f6 100644 --- a/recipes/bioconductor-signaturesearch/meta.yaml +++ b/recipes/bioconductor-signaturesearch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "signatureSearch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a35d0c11a34a2880ca935789599bd02 + md5: 9585172c7764e755ee67aee1c5a1adba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-signaturesearch", max_pin="x.x") }}' # Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT # SystemRequirements: C++11 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -53,21 +54,21 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-signaturesearchdata/meta.yaml b/recipes/bioconductor-signaturesearchdata/meta.yaml index 25ed2008fb3b8..c53b81dce19ae 100644 --- a/recipes/bioconductor-signaturesearchdata/meta.yaml +++ b/recipes/bioconductor-signaturesearchdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "signatureSearchData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b3174e0e3af77fea49a107ef423adb3 + md5: b30a7f1715a7525279c47db6df5ad995 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-signaturesearchdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-dplyr - r-magrittr - r-r.utils run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - r-base - r-dplyr - r-magrittr - r-r.utils - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-signaturesearchdata/post-link.sh b/recipes/bioconductor-signaturesearchdata/post-link.sh index 3151921fff67c..505a2c08ce197 100644 --- a/recipes/bioconductor-signaturesearchdata/post-link.sh +++ b/recipes/bioconductor-signaturesearchdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "signaturesearchdata-1.14.0" +installBiocDataPackage.sh "signaturesearchdata-1.16.0" diff --git a/recipes/bioconductor-signer/meta.yaml b/recipes/bioconductor-signer/meta.yaml index 0619c6c177669..8c8f0364b486a 100644 --- a/recipes/bioconductor-signer/meta.yaml +++ b/recipes/bioconductor-signer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.1" %} +{% set version = "2.4.0" %} {% set name = "signeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90a383b5dfb52f507eec10ac958b1c53 + md5: 36ca120021611cebddf20efa74c6bbf7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-signer", max_pin="x.x") }}' # Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-ada - r-base - r-bsplus @@ -77,15 +78,15 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-ada - r-base - r-bsplus @@ -141,7 +142,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Empirical Bayesian approach to mutational signature discovery' - description: 'The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variaton (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.' + description: 'The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variation (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: diff --git a/recipes/bioconductor-signifinder/meta.yaml b/recipes/bioconductor-signifinder/meta.yaml index 5699d1c83b780..13db755d08530 100644 --- a/recipes/bioconductor-signifinder/meta.yaml +++ b/recipes/bioconductor-signifinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "signifinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa726b8d8e8127426f3eb6f883b36bed + md5: f24a46dbbbc9b688450e9f2a0e2e221e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-signifinder", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, kableExtra, testthat (>= 3.0.0), edgeR, limma requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusov >=1.22.0,<1.23.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusov >=1.24.0,<1.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-cowplot - r-dgeobj.utils @@ -48,17 +50,18 @@ requirements: - r-survminer - r-viridis run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-consensusov >=1.22.0,<1.23.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-consensusov >=1.24.0,<1.25.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-cowplot - r-dgeobj.utils diff --git a/recipes/bioconductor-sigspack/meta.yaml b/recipes/bioconductor-sigspack/meta.yaml index 46326eaad55d4..4b9d64c027d97 100644 --- a/recipes/bioconductor-sigspack/meta.yaml +++ b/recipes/bioconductor-sigspack/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SigsPack" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb7c27412e07f6a833b6a46af887b508 + md5: 5fde29d53a470944ef9a4ba82bcca75d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sigspack", max_pin="x.x") }}' noarch: generic # Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-quadprog >=1.5-5' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-quadprog >=1.5-5' test: diff --git a/recipes/bioconductor-sigsquared/meta.yaml b/recipes/bioconductor-sigsquared/meta.yaml index 135799c1f6676..2970f841bef59 100644 --- a/recipes/bioconductor-sigsquared/meta.yaml +++ b/recipes/bioconductor-sigsquared/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "sigsquared" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9d98cbf7704581f4c430ba2b5e8a00ec + md5: f7dfbb4c066df8fe146b2b73f8180195 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sigsquared", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-survival test: diff --git a/recipes/bioconductor-sim/meta.yaml b/recipes/bioconductor-sim/meta.yaml index a3b8f14087b87..b5f1d18e0e31c 100644 --- a/recipes/bioconductor-sim/meta.yaml +++ b/recipes/bioconductor-sim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "SIM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d3c5c65ce115197dca40594a4b16b539 + md5: 72c2ca38244f4d53842bece2abdfadee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sim", max_pin="x.x") }}' # Suggests: biomaRt, RColorBrewer requirements: host: - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base - r-quantreg - libblas - liblapack run: - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-quantsmooth >=1.66.0,<1.67.0' + - 'bioconductor-globaltest >=5.56.0,<5.57.0' + - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' - r-base - r-quantreg build: diff --git a/recipes/bioconductor-simat/meta.yaml b/recipes/bioconductor-simat/meta.yaml index 0eea27535c90e..c8c53947eb7d9 100644 --- a/recipes/bioconductor-simat/meta.yaml +++ b/recipes/bioconductor-simat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "SIMAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a58d1eff9379ec914d5895269592ca8e + md5: 4482fbb67b81a5c0c2ed553f6b44faa2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simat", max_pin="x.x") }}' # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-ggplot2 - 'r-rcpp >=0.11.3' @@ -28,7 +29,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-ggplot2 - 'r-rcpp >=0.11.3' diff --git a/recipes/bioconductor-simbenchdata/meta.yaml b/recipes/bioconductor-simbenchdata/meta.yaml index 777409b6375f3..a21401c5931bd 100644 --- a/recipes/bioconductor-simbenchdata/meta.yaml +++ b/recipes/bioconductor-simbenchdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SimBenchData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b2d78e96922a7935cbe5ba91a129b0f + md5: c801056ea68c668cd98230e8956d551b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simbenchdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, Seurat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-simbenchdata/post-link.sh b/recipes/bioconductor-simbenchdata/post-link.sh index f1b9f38693847..29b22974ec81f 100644 --- a/recipes/bioconductor-simbenchdata/post-link.sh +++ b/recipes/bioconductor-simbenchdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "simbenchdata-1.8.0" +installBiocDataPackage.sh "simbenchdata-1.10.0" diff --git a/recipes/bioconductor-simbindprofiles/meta.yaml b/recipes/bioconductor-simbindprofiles/meta.yaml index 52de2f9221cf6..5ad27d6918d6d 100644 --- a/recipes/bioconductor-simbindprofiles/meta.yaml +++ b/recipes/bioconductor-simbindprofiles/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "SimBindProfiles" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa3f1e8271ff94bd2590512f9c80073d + md5: 9785a8acda5c3423edaefd09f14e6ca2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simbindprofiles", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' - r-base - r-mclust run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ringo >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ringo >=1.66.0,<1.67.0' - r-base - r-mclust test: diff --git a/recipes/bioconductor-simbu/meta.yaml b/recipes/bioconductor-simbu/meta.yaml index cc46b06a2ea82..122d2cdc3c9af 100644 --- a/recipes/bioconductor-simbu/meta.yaml +++ b/recipes/bioconductor-simbu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "SimBu" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fef87275d51f572073a477f69bfbb0f + md5: 50f7ac0bde39513f3ca816495b7ec9fc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simbu", max_pin="x.x") }}' noarch: generic # Suggests: curl, knitr, matrixStats, rmarkdown, Seurat, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr @@ -37,11 +38,11 @@ requirements: - r-reticulate - r-tidyr run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr diff --git a/recipes/bioconductor-simd/meta.yaml b/recipes/bioconductor-simd/meta.yaml index f268f9b562fe7..a50dbbec80a87 100644 --- a/recipes/bioconductor-simd/meta.yaml +++ b/recipes/bioconductor-simd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SIMD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2931556d02416a254a308886a78297fe + md5: 3fa4a3f26b9c42aa5026f0a22956195b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simd", max_pin="x.x") }}' # Suggests: BiocStyle, knitr,rmarkdown requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-methylmnm >=1.38.0,<1.39.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-methylmnm >=1.40.0,<1.41.0' - r-base - r-statmod - libblas - liblapack run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-methylmnm >=1.38.0,<1.39.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-methylmnm >=1.40.0,<1.41.0' - r-base - r-statmod build: diff --git a/recipes/bioconductor-simffpe/meta.yaml b/recipes/bioconductor-simffpe/meta.yaml index df7db42d051fd..8e72d0c1e17b1 100644 --- a/recipes/bioconductor-simffpe/meta.yaml +++ b/recipes/bioconductor-simffpe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SimFFPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6741039d6c2006d51a571456d16cf063 + md5: 95d6710ea184127f659f0c6f7786234c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simffpe", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-doparallel - r-dplyr - r-foreach - r-truncnorm run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-similarpeak/meta.yaml b/recipes/bioconductor-similarpeak/meta.yaml index 6860b904508b4..9f2da87d43c8c 100644 --- a/recipes/bioconductor-similarpeak/meta.yaml +++ b/recipes/bioconductor-similarpeak/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "similaRpeak" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35dd8b1abb325af118f05e56c1ebdb8f + md5: 3d91ba41941b12c9f93e77872e444c4d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-similarpeak", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-simlr/meta.yaml b/recipes/bioconductor-simlr/meta.yaml index 4851267fb6058..ab2a37047dc77 100644 --- a/recipes/bioconductor-simlr/meta.yaml +++ b/recipes/bioconductor-simlr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.0" %} {% set name = "SIMLR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f02d88ffc083881d030ff8f24e2d790 + md5: 9692308a74c8781b41b55409edf594ce build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simlr", max_pin="x.x") }}' # Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph requirements: host: diff --git a/recipes/bioconductor-simona/build.sh b/recipes/bioconductor-simona/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-simona/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-simona/meta.yaml b/recipes/bioconductor-simona/meta.yaml new file mode 100644 index 0000000000000..7cbbb253de34d --- /dev/null +++ b/recipes/bioconductor-simona/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.0.2" %} +{% set name = "simona" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: be691f3b2b1908a5af3180d4c9e47232 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simona", max_pin="x.x") }}' +# Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png +# SystemRequirements: Perl, Java +requirements: + host: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-circlize + - r-getoptlong + - r-globaloptions + - r-igraph + - r-matrixstats + - r-polychrome + - r-rcpp + - 'r-xml2 >=1.3.3' + - libblas + - liblapack + - 'perl >=5.6.0' + run: + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - r-base + - r-circlize + - r-getoptlong + - r-globaloptions + - r-igraph + - r-matrixstats + - r-polychrome + - r-rcpp + - 'r-xml2 >=1.3.3' + - 'perl >=5.6.0' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Semantic Similarity in Bio-Ontologies' + description: 'This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.' + license_file: LICENSE + diff --git a/recipes/bioconductor-simpintlists/meta.yaml b/recipes/bioconductor-simpintlists/meta.yaml index 12cae66ad17f9..a51d0edccc031 100644 --- a/recipes/bioconductor-simpintlists/meta.yaml +++ b/recipes/bioconductor-simpintlists/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "simpIntLists" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb06f66a10c4e02738fdfaff769c2dfd + md5: 9dbe0a1f390843a49bb11d05ac5f2e28 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simpintlists", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-simpintlists/post-link.sh b/recipes/bioconductor-simpintlists/post-link.sh index 9a5168f1dc3f2..20fa4fcd46724 100644 --- a/recipes/bioconductor-simpintlists/post-link.sh +++ b/recipes/bioconductor-simpintlists/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "simpintlists-1.36.0" +installBiocDataPackage.sh "simpintlists-1.38.0" diff --git a/recipes/bioconductor-simpleseg/meta.yaml b/recipes/bioconductor-simpleseg/meta.yaml index 75e64bc6223f9..37f94dc135935 100644 --- a/recipes/bioconductor-simpleseg/meta.yaml +++ b/recipes/bioconductor-simpleseg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "simpleSeg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 341edd78b0499ac89cb89fe2ed0882f4 + md5: d0e40e9be3d3e9c8a16d0390040f3da8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simpleseg", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-spatstat.geom - r-terra run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-cytomapper >=1.12.0,<1.13.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-cytomapper >=1.14.0,<1.15.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-spatstat.geom - r-terra diff --git a/recipes/bioconductor-simplifyenrichment/meta.yaml b/recipes/bioconductor-simplifyenrichment/meta.yaml index 4bd40b28cab06..83eeed1cbd3c8 100644 --- a/recipes/bioconductor-simplifyenrichment/meta.yaml +++ b/recipes/bioconductor-simplifyenrichment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "simplifyEnrichment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00527c9634ea2aa7918e582ad61af42c + md5: d54c7188ca88dd43802296650e5b80e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simplifyenrichment", max_pin="x.x") }}' noarch: generic # Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-circlize - r-clue @@ -40,12 +41,12 @@ requirements: - r-slam - r-tm run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-circlize - r-clue diff --git a/recipes/bioconductor-sincell/meta.yaml b/recipes/bioconductor-sincell/meta.yaml index 15a94a94e5060..f42dbd1131da1 100644 --- a/recipes/bioconductor-sincell/meta.yaml +++ b/recipes/bioconductor-sincell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "sincell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ba6ef4928190ede2dd94b4775f66387b + md5: 308aa15c851a99b7f345dbd0af122f07 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sincell", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, biomaRt, stringr, monocle requirements: host: diff --git a/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml b/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml index bcaef7e34a460..d9ce115024fa4 100644 --- a/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml +++ b/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Single.mTEC.Transcriptomes" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11ebbf5ecaf89f0433719a71a8df67b2 + md5: 574ee45ff1177688d68e6ae8295e67a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-single.mtec.transcriptomes", max_pin="x.x") }}' noarch: generic # Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr, BiocParallel requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh b/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh index ccdcaffe7f29a..c09b613681aa7 100644 --- a/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh +++ b/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "single.mtec.transcriptomes-1.28.0" +installBiocDataPackage.sh "single.mtec.transcriptomes-1.30.0" diff --git a/recipes/bioconductor-single/meta.yaml b/recipes/bioconductor-single/meta.yaml index 0443a953bc07d..4bde20f315321 100644 --- a/recipes/bioconductor-single/meta.yaml +++ b/recipes/bioconductor-single/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "single" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 60fe993d492e1e3354f4a4d066cbd78e + md5: 61242086622646ed92a4304d33bc1457 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-single", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dplyr - r-reshape2 @@ -33,11 +34,11 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dplyr - r-reshape2 diff --git a/recipes/bioconductor-singlecellexperiment/meta.yaml b/recipes/bioconductor-singlecellexperiment/meta.yaml index e62fc8618dab0..3f8eefc75d7b5 100644 --- a/recipes/bioconductor-singlecellexperiment/meta.yaml +++ b/recipes/bioconductor-singlecellexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "SingleCellExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0d2806a0547fdcea6688a4d96bdfa5a8 + md5: ef057b77f40efba992f311486e83448b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlecellexperiment", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-singlecellmultimodal/meta.yaml b/recipes/bioconductor-singlecellmultimodal/meta.yaml index 52e2bf35b2f0f..7a3421ef82fa5 100644 --- a/recipes/bioconductor-singlecellmultimodal/meta.yaml +++ b/recipes/bioconductor-singlecellmultimodal/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "SingleCellMultiModal" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 599f48321756805173d2069623a0319d + md5: e397bc4fbd9ea63f6660758f01d01d38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlecellmultimodal", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-singlecellmultimodal/post-link.sh b/recipes/bioconductor-singlecellmultimodal/post-link.sh index a8c1076f77b7e..a9af6b4051d35 100644 --- a/recipes/bioconductor-singlecellmultimodal/post-link.sh +++ b/recipes/bioconductor-singlecellmultimodal/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "singlecellmultimodal-1.12.2" +installBiocDataPackage.sh "singlecellmultimodal-1.14.0" diff --git a/recipes/bioconductor-singlecellsignalr/meta.yaml b/recipes/bioconductor-singlecellsignalr/meta.yaml index 547b3ca6726fc..65343241fe4ed 100644 --- a/recipes/bioconductor-singlecellsignalr/meta.yaml +++ b/recipes/bioconductor-singlecellsignalr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SingleCellSignalR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bbced887bff155cb16721818e1614e98 + md5: d00060a859db9cd8c87ce9673cc9d886 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlecellsignalr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-biocmanager - r-circlize @@ -36,10 +37,10 @@ requirements: - r-rtsne - r-stringr run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' - r-base - r-biocmanager - r-circlize diff --git a/recipes/bioconductor-singlecelltk/meta.yaml b/recipes/bioconductor-singlecelltk/meta.yaml index 1e6c259583316..9455db96d8260 100644 --- a/recipes/bioconductor-singlecelltk/meta.yaml +++ b/recipes/bioconductor-singlecelltk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "singleCellTK" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,55 +11,57 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd24cbf92dd3998cb79b244fd070910a + md5: 5efaf76211a6a623f6657383677474bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlecelltk", max_pin="x.x") }}' noarch: generic # Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-celda >=1.16.0,<1.17.0' - - 'bioconductor-celldex >=1.10.0,<1.11.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-eds >=1.2.0,<1.3.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-gsvadata >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scdblfinder >=1.14.0,<1.15.0' - - 'bioconductor-scds >=1.16.0,<1.17.0' - - 'bioconductor-scmerge >=1.16.0,<1.17.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scrnaseq >=2.14.0,<2.15.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-singler >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-tenxpbmcdata >=1.18.0,<1.19.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' - - 'bioconductor-tscan >=1.38.0,<1.39.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-zellkonverter >=1.10.0,<1.11.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-celda >=1.18.0,<1.19.0' + - 'bioconductor-celldex >=1.12.0,<1.13.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-eds >=1.4.0,<1.5.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-gsvadata >=1.38.0,<1.39.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scdblfinder >=1.16.0,<1.17.0' + - 'bioconductor-scds >=1.18.0,<1.19.0' + - 'bioconductor-scmerge >=1.18.0,<1.19.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scrnaseq >=2.16.0,<2.17.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-singler >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-tenxpbmcdata >=1.20.0,<1.21.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - 'bioconductor-tscan >=1.40.0,<1.41.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' + - r-anndata - r-ape - r-base - r-circlize @@ -70,7 +72,7 @@ requirements: - r-data.table - r-dplyr - r-dt - - r-enrichr + - 'r-enrichr >=3.2' - r-fields - r-ggplot2 - r-ggplotify @@ -103,45 +105,46 @@ requirements: - r-withr - r-yaml run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-batchelor >=1.16.0,<1.17.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-celda >=1.16.0,<1.17.0' - - 'bioconductor-celldex >=1.10.0,<1.11.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-eds >=1.2.0,<1.3.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-gsvadata >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mast >=1.26.0,<1.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scdblfinder >=1.14.0,<1.15.0' - - 'bioconductor-scds >=1.16.0,<1.17.0' - - 'bioconductor-scmerge >=1.16.0,<1.17.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scrnaseq >=2.14.0,<2.15.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-singler >=2.2.0,<2.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-tenxpbmcdata >=1.18.0,<1.19.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' - - 'bioconductor-tscan >=1.38.0,<1.39.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-zellkonverter >=1.10.0,<1.11.0' - - 'bioconductor-zinbwave >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-batchelor >=1.18.0,<1.19.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-celda >=1.18.0,<1.19.0' + - 'bioconductor-celldex >=1.12.0,<1.13.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-eds >=1.4.0,<1.5.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-gsvadata >=1.38.0,<1.39.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mast >=1.28.0,<1.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scdblfinder >=1.16.0,<1.17.0' + - 'bioconductor-scds >=1.18.0,<1.19.0' + - 'bioconductor-scmerge >=1.18.0,<1.19.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scrnaseq >=2.16.0,<2.17.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-singler >=2.4.0,<2.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' + - 'bioconductor-tenxpbmcdata >=1.20.0,<1.21.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - 'bioconductor-tscan >=1.40.0,<1.41.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' + - 'bioconductor-zinbwave >=1.24.0,<1.25.0' + - r-anndata - r-ape - r-base - r-circlize @@ -152,7 +155,7 @@ requirements: - r-data.table - r-dplyr - r-dt - - r-enrichr + - 'r-enrichr >=3.2' - r-fields - r-ggplot2 - r-ggplotify diff --git a/recipes/bioconductor-singlemoleculefootprinting/meta.yaml b/recipes/bioconductor-singlemoleculefootprinting/meta.yaml index 7e1a72be15812..0a49754cd4e22 100644 --- a/recipes/bioconductor-singlemoleculefootprinting/meta.yaml +++ b/recipes/bioconductor-singlemoleculefootprinting/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SingleMoleculeFootprinting" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6f36357ed42062a6d48b14986fb50aa + md5: dcdbbace0f6394ce22397640da1dd03f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlemoleculefootprinting", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-quasr >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-quasr >=1.42.0,<1.43.0' - r-base - r-data.table - r-plyr - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-quasr >=1.40.0,<1.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-quasr >=1.42.0,<1.43.0' - r-base - r-data.table - r-plyr diff --git a/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml b/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml index 9f59a0011a77f..6a54bd67dd050 100644 --- a/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml +++ b/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SingleMoleculeFootprintingData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc061d235ffc26615634a650aedd4ac0 + md5: 451ecbdbb964607afbbe3b778b290246 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlemoleculefootprintingdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh b/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh index 178987ba30e16..a016eff25036b 100644 --- a/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh +++ b/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "singlemoleculefootprintingdata-1.8.0" +installBiocDataPackage.sh "singlemoleculefootprintingdata-1.10.0" diff --git a/recipes/bioconductor-singler/meta.yaml b/recipes/bioconductor-singler/meta.yaml index b0b34a8280eff..8bf68ce82b2b1 100644 --- a/recipes/bioconductor-singler/meta.yaml +++ b/recipes/bioconductor-singler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "SingleR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58b4a0cd038cc175cd966a32f0195f30 + md5: 83651106a9f823febc5859dff16b48a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singler", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex # SystemRequirements: C++17 requirements: host: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-beachmat >=2.16.0,<2.17.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-beachmat >=2.18.0,<2.19.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-singscore/meta.yaml b/recipes/bioconductor-singscore/meta.yaml index 1266b324ae624..9fb6b973e6177 100644 --- a/recipes/bioconductor-singscore/meta.yaml +++ b/recipes/bioconductor-singscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "singscore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 79764544605a5b1de41856c897375ad2 + md5: c3ab598fd61c5bb54a842f9738133d24 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singscore", max_pin="x.x") }}' noarch: generic # Suggests: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel @@ -39,12 +40,12 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-sipsic/meta.yaml b/recipes/bioconductor-sipsic/meta.yaml index b89be2584da1b..b7be8ce59689b 100644 --- a/recipes/bioconductor-sipsic/meta.yaml +++ b/recipes/bioconductor-sipsic/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "SiPSiC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a749994a28fcd113adbf13ff1fdb9e6 + md5: e85e0e9b34b9a1e0a93dd653868061ef build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sipsic", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-matrix run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-sitadela/meta.yaml b/recipes/bioconductor-sitadela/meta.yaml index d18d8e6cb05de..81f00ad65a55e 100644 --- a/recipes/bioconductor-sitadela/meta.yaml +++ b/recipes/bioconductor-sitadela/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "sitadela" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a9e771d4e00d39c87e1731fcdaa3999 + md5: 109b3096c37f30906c8c009097e45c59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sitadela", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rsqlite run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rsqlite test: diff --git a/recipes/bioconductor-sitepath/meta.yaml b/recipes/bioconductor-sitepath/meta.yaml index 5485b4e65b010..9470f4a08a362 100644 --- a/recipes/bioconductor-sitepath/meta.yaml +++ b/recipes/bioconductor-sitepath/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "sitePath" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,17 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f713347fa5b74763d60d1f91db80838 + md5: f5742fbe513f4d3cec29d3d3ee714d13 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sitepath", max_pin="x.x") }}' # Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-aplot - r-base @@ -34,7 +35,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - r-ape - r-aplot - r-base diff --git a/recipes/bioconductor-sizepower/meta.yaml b/recipes/bioconductor-sizepower/meta.yaml index 49ff669f27e7b..bdcda1851859b 100644 --- a/recipes/bioconductor-sizepower/meta.yaml +++ b/recipes/bioconductor-sizepower/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "sizepower" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f168cdc6e987a88dda51d11e9fabfa1a + md5: 4edf7f08a26ccaa8ae0d08e17b6ef0cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sizepower", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-skewr/meta.yaml b/recipes/bioconductor-skewr/meta.yaml index 8d4c837add74c..4c0aea4605a0e 100644 --- a/recipes/bioconductor-skewr/meta.yaml +++ b/recipes/bioconductor-skewr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "skewr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c00d797ae9ac8e4b1f40a352409df4cb + md5: 083671e386afa1b9ec5766e6a8c50bba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-skewr", max_pin="x.x") }}' noarch: generic # Suggests: GEOquery, knitr, minfiData requirements: host: - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base - r-mixsmsn - r-rcolorbrewer run: - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-minfi >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-watermelon >=2.8.0,<2.9.0' - r-base - r-mixsmsn - r-rcolorbrewer diff --git a/recipes/bioconductor-slalom/meta.yaml b/recipes/bioconductor-slalom/meta.yaml index cb544f8714472..9a66e56b5ce25 100644 --- a/recipes/bioconductor-slalom/meta.yaml +++ b/recipes/bioconductor-slalom/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "slalom" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 398713b48231b0d9d9197f0a8af1e6f7 + md5: cf8b2aec440cd0fd79260a1f0199db2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-slalom", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat requirements: host: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-ggplot2 @@ -32,9 +33,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-bh - r-ggplot2 diff --git a/recipes/bioconductor-slingshot/meta.yaml b/recipes/bioconductor-slingshot/meta.yaml index c9b05a6884e98..6031c6d4802c9 100644 --- a/recipes/bioconductor-slingshot/meta.yaml +++ b/recipes/bioconductor-slingshot/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "slingshot" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2f610f3a1f4538cff7e7f17240e2c3fb + md5: 556fe5835a602547c3475065eb5c11d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-slingshot", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-igraph - r-matrixstats - 'r-princurve >=2.0.4' run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-igraph - r-matrixstats diff --git a/recipes/bioconductor-slqpcr/meta.yaml b/recipes/bioconductor-slqpcr/meta.yaml index d802eb5b5b6be..51064b62afbb9 100644 --- a/recipes/bioconductor-slqpcr/meta.yaml +++ b/recipes/bioconductor-slqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "SLqPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7929611dce4a5093abfd58b6df35039 + md5: 72759fb6b62f3852f458e695318c0f6f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-slqpcr", max_pin="x.x") }}' noarch: generic # Suggests: RColorBrewer requirements: diff --git a/recipes/bioconductor-smad/meta.yaml b/recipes/bioconductor-smad/meta.yaml index 138e48d614390..1fe978fb29b01 100644 --- a/recipes/bioconductor-smad/meta.yaml +++ b/recipes/bioconductor-smad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SMAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c224400a2f1d4715e3a4274544b34915 + md5: 65f0eba6ed0bf086797b95b2c9da6dd6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-smad", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: diff --git a/recipes/bioconductor-smap/meta.yaml b/recipes/bioconductor-smap/meta.yaml index fa97b77650cb6..85c8a5cbef687 100644 --- a/recipes/bioconductor-smap/meta.yaml +++ b/recipes/bioconductor-smap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "SMAP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e90b812af45d9a171b490e282d28f91 + md5: f29ffdead8f34c2f531dd7ea764febe0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-smap", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-smite/meta.yaml b/recipes/bioconductor-smite/meta.yaml index 8084f012aca37..84c7ff35a230a 100644 --- a/recipes/bioconductor-smite/meta.yaml +++ b/recipes/bioconductor-smite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "SMITE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 611558066283955f055323c81446ec75 + md5: 47c578785a426c3c7850880ed58033e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-smite", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bionet >=1.60.0,<1.61.0' - - 'bioconductor-genelendatabase >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bionet >=1.62.0,<1.63.0' + - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-hmisc @@ -39,17 +40,17 @@ requirements: - r-plyr - r-scales run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bionet >=1.60.0,<1.61.0' - - 'bioconductor-genelendatabase >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactome.db >=1.84.0,<1.85.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-bionet >=1.62.0,<1.63.0' + - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-goseq >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-hmisc diff --git a/recipes/bioconductor-smokingmouse/meta.yaml b/recipes/bioconductor-smokingmouse/meta.yaml new file mode 100644 index 0000000000000..95d226795b7e7 --- /dev/null +++ b/recipes/bioconductor-smokingmouse/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.0.0" %} +{% set name = "smokingMouse" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0c2fad6bf0e911ae8c140c02bc29150e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-smokingmouse", max_pin="x.x") }}' + noarch: generic +# Suggests: ExperimentHub, AnnotationHubData, BiocStyle, covr, ExperimentHubData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) +requirements: + host: + - r-base + run: + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides access to smokingMouse project data' + description: 'This is an ExperimentHub package that provides access to the data at the gene, exon, transcript and junction level used in the analyses of the smokingMouse project. See https://github.com/LieberInstitute/smokingMouse_Indirects. This datasets contain the expression counts of genes, transcripts, exons and exon-exon junctions across 208 mice samples from pup and adult brains and adult blood. They also contain relevant information of these samples and features, such as conditions, QC metrics and if they were used after filtering steps and also if the features were differently expressed in the different experiments.' + diff --git a/recipes/bioconductor-smokingmouse/post-link.sh b/recipes/bioconductor-smokingmouse/post-link.sh new file mode 100644 index 0000000000000..d023daf8a973e --- /dev/null +++ b/recipes/bioconductor-smokingmouse/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "smokingmouse-1.0.0" diff --git a/recipes/bioconductor-smokingmouse/pre-unlink.sh b/recipes/bioconductor-smokingmouse/pre-unlink.sh new file mode 100644 index 0000000000000..aa46890e613d8 --- /dev/null +++ b/recipes/bioconductor-smokingmouse/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ smokingMouse diff --git a/recipes/bioconductor-snadata/meta.yaml b/recipes/bioconductor-snadata/meta.yaml index e787901ae7435..326d0f4f2d6e1 100644 --- a/recipes/bioconductor-snadata/meta.yaml +++ b/recipes/bioconductor-snadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "SNAData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d83f5e312b308aacb8c9c83d3226115 + md5: bfbd447afa550db44aa1db55e227cc10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snadata", max_pin="x.x") }}' noarch: generic # Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snadata/post-link.sh b/recipes/bioconductor-snadata/post-link.sh index 2b6df30c5257c..15572eae53e04 100644 --- a/recipes/bioconductor-snadata/post-link.sh +++ b/recipes/bioconductor-snadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "snadata-1.46.0" +installBiocDataPackage.sh "snadata-1.48.0" diff --git a/recipes/bioconductor-snagee/meta.yaml b/recipes/bioconductor-snagee/meta.yaml index 1834a5bc44880..88fa7034220c6 100644 --- a/recipes/bioconductor-snagee/meta.yaml +++ b/recipes/bioconductor-snagee/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "SNAGEE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 352732bbf9406a70370117c7ac521fa5 + md5: faadcab23b170f71a29ac7fd67b2a5d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snagee", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-snageedata >=1.36.0,<1.37.0' + - 'bioconductor-snageedata >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-snageedata >=1.36.0,<1.37.0' + - 'bioconductor-snageedata >=1.38.0,<1.39.0' - r-base test: commands: diff --git a/recipes/bioconductor-snageedata/meta.yaml b/recipes/bioconductor-snageedata/meta.yaml index 45c4aa8bef0f0..06c4621e7b240 100644 --- a/recipes/bioconductor-snageedata/meta.yaml +++ b/recipes/bioconductor-snageedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "SNAGEEdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7786160ad882aea9132d3fb2ba77789 + md5: bfd0a2689cb9ac612cb2f8995c3a03d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snageedata", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db, SNAGEE requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snageedata/post-link.sh b/recipes/bioconductor-snageedata/post-link.sh index a2bcecbea365f..5e8bb8a522c3c 100644 --- a/recipes/bioconductor-snageedata/post-link.sh +++ b/recipes/bioconductor-snageedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "snageedata-1.36.0" +installBiocDataPackage.sh "snageedata-1.38.0" diff --git a/recipes/bioconductor-snapcgh/meta.yaml b/recipes/bioconductor-snapcgh/meta.yaml index d34947ac5d13e..e534b5ccc7b74 100644 --- a/recipes/bioconductor-snapcgh/meta.yaml +++ b/recipes/bioconductor-snapcgh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.70.0" %} +{% set version = "1.72.0" %} {% set name = "snapCGH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7484b0baccb980c615fb9ecd6fb86ab9 + md5: d21dbae207756cb76e04cadbcfa8b086 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snapcgh", max_pin="x.x") }}' requirements: host: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base - r-cluster - libblas - liblapack run: - - 'bioconductor-acgh >=1.78.0,<1.79.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-glad >=2.64.0,<2.65.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-tilingarray >=1.78.0,<1.79.0' + - 'bioconductor-acgh >=1.80.0,<1.81.0' + - 'bioconductor-dnacopy >=1.76.0,<1.77.0' + - 'bioconductor-glad >=2.66.0,<2.67.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-tilingarray >=1.80.0,<1.81.0' - r-base - r-cluster build: diff --git a/recipes/bioconductor-snapcount/meta.yaml b/recipes/bioconductor-snapcount/meta.yaml index 8ec421e639259..e40c86fed787a 100644 --- a/recipes/bioconductor-snapcount/meta.yaml +++ b/recipes/bioconductor-snapcount/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "snapcount" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1a80d0c735e1b5059c4f0376f75fa61a + md5: 8efa036bfe73acf9c31a279b3c365ae7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snapcount", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-data.table @@ -36,9 +37,9 @@ requirements: - r-rlang - r-stringr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-data.table diff --git a/recipes/bioconductor-snifter/meta.yaml b/recipes/bioconductor-snifter/meta.yaml index 8de266ad1bedc..2da36a360a549 100644 --- a/recipes/bioconductor-snifter/meta.yaml +++ b/recipes/bioconductor-snifter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "snifter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 105db4c0e2b10570d93fe359524beccc + md5: a6cfc8a05013cd2d050a1adba2b3fe4d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snifter", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-assertthat - r-base - r-irlba - r-reticulate run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' - r-assertthat - r-base - r-irlba diff --git a/recipes/bioconductor-snm/meta.yaml b/recipes/bioconductor-snm/meta.yaml index 5ec09c740d1f3..16a1786338618 100644 --- a/recipes/bioconductor-snm/meta.yaml +++ b/recipes/bioconductor-snm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "snm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1585a1bef1fe800b8ce9fd1dab014e9b + md5: 103ab8eb4cca35d12c53c48615ebd5da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snm", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-snpediar/meta.yaml b/recipes/bioconductor-snpediar/meta.yaml index 682d2d3ff2b7e..163a5977bdb6d 100644 --- a/recipes/bioconductor-snpediar/meta.yaml +++ b/recipes/bioconductor-snpediar/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "SNPediaR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4335833edff43f6406eeed4294fa83ff + md5: 25d5eec5081ccfac687eba26102eb826 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snpediar", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-snphood/meta.yaml b/recipes/bioconductor-snphood/meta.yaml index c3cddcd6c75bf..9b8303698581a 100644 --- a/recipes/bioconductor-snphood/meta.yaml +++ b/recipes/bioconductor-snphood/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "SNPhood" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95aecf97b2fc6fda26705f4c0b7f83b9 + md5: f5a30ae405bebdb97e51cb2782debcbf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snphood", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-checkmate - r-cluster @@ -43,17 +44,17 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-checkmate - r-cluster diff --git a/recipes/bioconductor-snphooddata/meta.yaml b/recipes/bioconductor-snphooddata/meta.yaml index 13452dc4c61f6..b7e1b79ba3652 100644 --- a/recipes/bioconductor-snphooddata/meta.yaml +++ b/recipes/bioconductor-snphooddata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "SNPhoodData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fbc9419fda8d78b06f76e62df5639ae9 + md5: 72ac86008c225c71df946cc8a7de1fa1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snphooddata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,knitr,rmarkdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snphooddata/post-link.sh b/recipes/bioconductor-snphooddata/post-link.sh index fdf543333018e..7fd81f93fc969 100644 --- a/recipes/bioconductor-snphooddata/post-link.sh +++ b/recipes/bioconductor-snphooddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "snphooddata-1.30.0" +installBiocDataPackage.sh "snphooddata-1.32.0" diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml index 327d00aae5fcf..9e6b83fb2ab62 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh37" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bd338bb583cacc18f210e871dac79ebf build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp144.grch37", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml index d54fe98d34148..62e24e4082892 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 128c95e327adf72ae137fb5ae58270fc build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp144.grch38", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml index d70675ec90785..f6a6fc11e513c 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP149.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8cf749a8649a53449066b54160a3745c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp149.grch38", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml index 6d37b8ed2a26f..f066bc2eeae6b 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP150.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 575a7aaa9125d52ca0634b3ac586c9a7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp150.grch38", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml index b62ab1e5462cc..64217e319f370 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.24" %} {% set name = "SNPlocs.Hsapiens.dbSNP155.GRCh37" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -17,27 +17,28 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp155.grch37", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml index 7c427bc75106a..cfda415a59962 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.24" %} {% set name = "SNPlocs.Hsapiens.dbSNP155.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -17,27 +17,28 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp155.grch38", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-snprelate/meta.yaml b/recipes/bioconductor-snprelate/meta.yaml index fb0f78bb75ad3..a0e37b7d6801a 100644 --- a/recipes/bioconductor-snprelate/meta.yaml +++ b/recipes/bioconductor-snprelate/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "SNPRelate" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8392e87cb9c26212c12cebd76de12cf + md5: f4e5095c6b99014e02d770e7f4bd5617 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snprelate", max_pin="x.x") }}' # Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics requirements: host: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - r-base - libblas - liblapack run: - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-snpstats/meta.yaml b/recipes/bioconductor-snpstats/meta.yaml index c5ed6fbea506f..0203a1cda4481 100644 --- a/recipes/bioconductor-snpstats/meta.yaml +++ b/recipes/bioconductor-snpstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "snpStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fba193a357b1be45597d537425b2c62f + md5: 0625c920470937a31fd278cf8bd8982a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-snpstats", max_pin="x.x") }}' # Suggests: hexbin requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-matrix - r-survival - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-matrix - r-survival diff --git a/recipes/bioconductor-soggi/meta.yaml b/recipes/bioconductor-soggi/meta.yaml index fddf936914ea7..b4b76b787681f 100644 --- a/recipes/bioconductor-soggi/meta.yaml +++ b/recipes/bioconductor-soggi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "soGGi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,46 +11,47 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3e73483964e8c438966ac51a33187c0 + md5: 6b8a823ad7812fdda198d38b28c00f6f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-soggi", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-reshape2 diff --git a/recipes/bioconductor-somascan.db/meta.yaml b/recipes/bioconductor-somascan.db/meta.yaml new file mode 100644 index 0000000000000..06a3f52706efd --- /dev/null +++ b/recipes/bioconductor-somascan.db/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "0.99.7" %} +{% set name = "SomaScan.db" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aa52f4f12dfb2f0aa4c7fe3633de4646 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-somascan.db", max_pin="x.x") }}' + noarch: generic +# Suggests: annotate, BiocStyle, dplyr, GO.db, hgu95av2.db, KEGGREST, knitr, rmarkdown, SomaDataIO, testthat (>= 3.0.0), withr +requirements: + host: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - r-base + - r-dbi + run: + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - r-base + - r-dbi + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Somalogic SomaScan Annotation Data' + description: 'An R package providing extended biological annotations for the SomaScan Assay, a proteomics platform developed by SomaLogic Operating Co., Inc. The annotations in this package were assembled using data from public repositories. For more information about the SomaScan assay and its data, please reference the ''SomaLogic/SomaLogic-Data'' GitHub repository.' + license_file: LICENSE + diff --git a/recipes/bioconductor-somascan.db/post-link.sh b/recipes/bioconductor-somascan.db/post-link.sh new file mode 100644 index 0000000000000..5a86e22124d74 --- /dev/null +++ b/recipes/bioconductor-somascan.db/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "somascan.db-0.99.7" diff --git a/recipes/bioconductor-somascan.db/pre-unlink.sh b/recipes/bioconductor-somascan.db/pre-unlink.sh new file mode 100644 index 0000000000000..2bd6437f78149 --- /dev/null +++ b/recipes/bioconductor-somascan.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SomaScan.db diff --git a/recipes/bioconductor-somaticadata/meta.yaml b/recipes/bioconductor-somaticadata/meta.yaml index 6f7e9ab2135e6..00bdf05078a09 100644 --- a/recipes/bioconductor-somaticadata/meta.yaml +++ b/recipes/bioconductor-somaticadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "SomatiCAData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ec746e24a46ea58a782f2d7e18b9c29 + md5: 31d9100d6b5fa5f95c59eda9995f2684 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-somaticadata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-somaticadata/post-link.sh b/recipes/bioconductor-somaticadata/post-link.sh index e0381f4000f6d..ae240efdbcd9e 100644 --- a/recipes/bioconductor-somaticadata/post-link.sh +++ b/recipes/bioconductor-somaticadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "somaticadata-1.38.0" +installBiocDataPackage.sh "somaticadata-1.40.0" diff --git a/recipes/bioconductor-somaticcanceralterations/meta.yaml b/recipes/bioconductor-somaticcanceralterations/meta.yaml index 6dfdcd891ec29..45d47329efb01 100644 --- a/recipes/bioconductor-somaticcanceralterations/meta.yaml +++ b/recipes/bioconductor-somaticcanceralterations/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "SomaticCancerAlterations" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09b8e014009801826dde224175c1f774 + md5: 77b2b0312705c2a9581cdf7aab591db8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-somaticcanceralterations", max_pin="x.x") }}' noarch: generic # Suggests: testthat, ggbio, ggplot2, knitr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-somaticcanceralterations/post-link.sh b/recipes/bioconductor-somaticcanceralterations/post-link.sh index 6fe8d5d9a642b..d63db0e4c80a7 100644 --- a/recipes/bioconductor-somaticcanceralterations/post-link.sh +++ b/recipes/bioconductor-somaticcanceralterations/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "somaticcanceralterations-1.36.0" +installBiocDataPackage.sh "somaticcanceralterations-1.38.0" diff --git a/recipes/bioconductor-somaticsignatures/meta.yaml b/recipes/bioconductor-somaticsignatures/meta.yaml index c455794f053be..9db50d019bf36 100644 --- a/recipes/bioconductor-somaticsignatures/meta.yaml +++ b/recipes/bioconductor-somaticsignatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "SomaticSignatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c70a8ab04a25f675f456adae05f672a3 + md5: 46d14334be0098323bc956bade5d5e9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-somaticsignatures", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-nmf - r-proxy - r-reshape2 run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-ggbio >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-pcamethods >=1.92.0,<1.93.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-ggbio >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggplot2 - r-nmf diff --git a/recipes/bioconductor-somnibus/meta.yaml b/recipes/bioconductor-somnibus/meta.yaml index 391796666a2c9..3d26442edc700 100644 --- a/recipes/bioconductor-somnibus/meta.yaml +++ b/recipes/bioconductor-somnibus/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.7.0" %} +{% set version = "1.10.0" %} {% set name = "SOMNiBUS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,52 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3686657266b274a93233dd24d23f1294 + md5: 0865c015122f915127302bf751a10812 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-somnibus", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat +# Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, requirements: host: + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base + - r-biocmanager + - r-data.table + - r-ggplot2 - r-matrix - r-mgcv + - r-reshape2 + - r-tidyr - r-vgam + - r-yaml run: + - 'bioconductor-annotatr >=1.28.0,<1.29.0' + - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base + - r-biocmanager + - r-data.table + - r-ggplot2 - r-matrix - r-mgcv + - r-reshape2 + - r-tidyr - r-vgam + - r-yaml test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-soybeancdf/meta.yaml b/recipes/bioconductor-soybeancdf/meta.yaml index ebd6fea315882..fa809e0be223a 100644 --- a/recipes/bioconductor-soybeancdf/meta.yaml +++ b/recipes/bioconductor-soybeancdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "soybeancdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: a18e0ba5dbcf2291bdec91091dc528e6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-soybeancdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-soybeanprobe/meta.yaml b/recipes/bioconductor-soybeanprobe/meta.yaml index 21b5bdee97dbd..37c26efb68ab5 100644 --- a/recipes/bioconductor-soybeanprobe/meta.yaml +++ b/recipes/bioconductor-soybeanprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "soybeanprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3057a5c387ff35b6c647c4db27041a13 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-soybeanprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spacepac/meta.yaml b/recipes/bioconductor-spacepac/meta.yaml index da89c68eb3064..af052e29be413 100644 --- a/recipes/bioconductor-spacepac/meta.yaml +++ b/recipes/bioconductor-spacepac/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "SpacePAC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ff52a3613f9c0d46581f626a41a29f9 + md5: aa35450e9ef0b3cd7ca3d90262d36ddf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spacepac", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, rgl requirements: host: - - 'bioconductor-ipac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-ipac >=1.44.0,<1.45.0' + - 'bioconductor-ipac >=1.46.0,<1.47.0' - r-base test: commands: diff --git a/recipes/bioconductor-spaniel/meta.yaml b/recipes/bioconductor-spaniel/meta.yaml index cb7b2d8a46f9d..5dbb8445371d2 100644 --- a/recipes/bioconductor-spaniel/meta.yaml +++ b/recipes/bioconductor-spaniel/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Spaniel" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a456611860cdb19712e117ca3bb5811 + md5: fb29666756a1db567f16b5c72420de4c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spaniel", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, devtools requirements: host: - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -38,12 +39,12 @@ requirements: - r-seurat - r-shiny run: - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dropletutils >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-sparrow/meta.yaml b/recipes/bioconductor-sparrow/meta.yaml index cb8a9b9527ac9..5d45dc6ab1c96 100644 --- a/recipes/bioconductor-sparrow/meta.yaml +++ b/recipes/bioconductor-sparrow/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "sparrow" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d48cb1cab6f2032d3e8101f5ff9b527a + md5: 072ccf02fa2cc42410000f238dce492b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sparrow", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocset >=1.14.0,<1.15.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocset >=1.16.0,<1.17.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - 'r-babelgene >=21.4' - r-base - r-checkmate @@ -40,14 +41,14 @@ requirements: - 'r-plotly >=4.9.0' - r-viridis run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocset >=1.14.0,<1.15.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocset >=1.16.0,<1.17.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - 'r-babelgene >=21.4' - r-base - r-checkmate diff --git a/recipes/bioconductor-sparsearray/meta.yaml b/recipes/bioconductor-sparsearray/meta.yaml index f5acf6cd63e10..b055e619a974e 100644 --- a/recipes/bioconductor-sparsearray/meta.yaml +++ b/recipes/bioconductor-sparsearray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.10" %} +{% set version = "1.2.2" %} {% set name = "SparseArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e5ecc9eaa58af506cbf7340f9c890f1 + md5: a73b2e316ce8135de81af01a9a9610ec build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sparsearray", max_pin="x.x") }}' # Suggests: DelayedArray, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-matrix - r-matrixstats - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-matrix - r-matrixstats diff --git a/recipes/bioconductor-sparsematrixstats/meta.yaml b/recipes/bioconductor-sparsematrixstats/meta.yaml index 2f11958509062..5b0186e8e00f3 100644 --- a/recipes/bioconductor-sparsematrixstats/meta.yaml +++ b/recipes/bioconductor-sparsematrixstats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "sparseMatrixStats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7669451759bb18ece433548b067ac73e + md5: 4319e6fb04b91467bd08cc4ce2ad609c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sparsematrixstats", max_pin="x.x") }}' # Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle # SystemRequirements: C++11 requirements: host: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - r-base - r-matrix - 'r-matrixstats >=0.60.0' @@ -29,7 +30,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - r-base - r-matrix - 'r-matrixstats >=0.60.0' diff --git a/recipes/bioconductor-sparsenetgls/meta.yaml b/recipes/bioconductor-sparsenetgls/meta.yaml index 3492a6b81e9fd..9568b17a7c9b5 100644 --- a/recipes/bioconductor-sparsenetgls/meta.yaml +++ b/recipes/bioconductor-sparsenetgls/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "sparsenetgls" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e3b4604f61dbbc07c2acdad62b980e2f + md5: 32b8f3b9fe86b40386aee23ac4ea55fd build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sparsenetgls", max_pin="x.x") }}' noarch: generic # Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) # SystemRequirements: GNU make diff --git a/recipes/bioconductor-sparsesignatures/meta.yaml b/recipes/bioconductor-sparsesignatures/meta.yaml index 313e0c984a18a..5f81cb9307a38 100644 --- a/recipes/bioconductor-sparsesignatures/meta.yaml +++ b/recipes/bioconductor-sparsesignatures/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "SparseSignatures" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eaa4a346f4ce804bdd6e4f684a8889f5 + md5: 832b206679a06252fa3b76f2700a70e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sparsesignatures", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table - r-ggplot2 @@ -35,11 +36,11 @@ requirements: - r-nnls - r-reshape2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-spasim/meta.yaml b/recipes/bioconductor-spasim/meta.yaml index c899699a568f0..4189527c513c5 100644 --- a/recipes/bioconductor-spasim/meta.yaml +++ b/recipes/bioconductor-spasim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "spaSim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a6294d1b8bfe4bacae22708e5043fa8f + md5: d69e70975aaaa9bffc5e52f95885e59c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spasim", max_pin="x.x") }}' noarch: generic # Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown requirements: host: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -30,8 +31,8 @@ requirements: - r-spatstat.geom - r-spatstat.random run: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-spatialcpie/meta.yaml b/recipes/bioconductor-spatialcpie/meta.yaml index ccddfc1fa8f6c..2a26cea000a99 100644 --- a/recipes/bioconductor-spatialcpie/meta.yaml +++ b/recipes/bioconductor-spatialcpie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SpatialCPie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5b9f134b000016e4ac3171cb99f9bfc + md5: f7f622f0a9e08b387870bddc9a52cfc2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialcpie", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-colorspace >=1.3-2' - 'r-data.table >=1.12.2' @@ -45,7 +46,7 @@ requirements: - 'r-tidyselect >=0.2.4' - 'r-zeallot >=0.1.0' run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-colorspace >=1.3-2' - 'r-data.table >=1.12.2' diff --git a/recipes/bioconductor-spatialdatasets/meta.yaml b/recipes/bioconductor-spatialdatasets/meta.yaml new file mode 100644 index 0000000000000..59eeabf7949e9 --- /dev/null +++ b/recipes/bioconductor-spatialdatasets/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "SpatialDatasets" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 36fd913ef0d7109d0be40afbc1255548 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialdatasets", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - r-base + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Collection of spatial omics datasets' + description: 'This is a collection of publically available spatial omics datasets. Where possible we have curated these datasets as either SpatialExperiments, MoleculeExperiments or CytoImageLists and included annotations of the sample characteristics.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-spatialdatasets/post-link.sh b/recipes/bioconductor-spatialdatasets/post-link.sh new file mode 100644 index 0000000000000..072e49b3171c7 --- /dev/null +++ b/recipes/bioconductor-spatialdatasets/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "spatialdatasets-1.0.0" diff --git a/recipes/bioconductor-spatialdatasets/pre-unlink.sh b/recipes/bioconductor-spatialdatasets/pre-unlink.sh new file mode 100644 index 0000000000000..b5bdda7982391 --- /dev/null +++ b/recipes/bioconductor-spatialdatasets/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SpatialDatasets diff --git a/recipes/bioconductor-spatialde/meta.yaml b/recipes/bioconductor-spatialde/meta.yaml index 9229b7cb57066..113377b6f586e 100644 --- a/recipes/bioconductor-spatialde/meta.yaml +++ b/recipes/bioconductor-spatialde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "spatialDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62f672c7a70d4a0d0b4895b103e73379 + md5: 4227d5d446ef2399e1b325cfa7ef65b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialde", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-ggplot2 @@ -33,9 +34,9 @@ requirements: - r-reticulate - r-scales run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-ggplot2 diff --git a/recipes/bioconductor-spatialdecon/meta.yaml b/recipes/bioconductor-spatialdecon/meta.yaml index c6f443962be21..dd83c38cceac5 100644 --- a/recipes/bioconductor-spatialdecon/meta.yaml +++ b/recipes/bioconductor-spatialdecon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SpatialDecon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6fb182168a8f4c35626e71f3f9ad301 + md5: a3dd72587ea55dc018231523782d225f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialdecon", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, qpdf requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' - r-base - 'r-lognormreg >=0.4' - r-matrix - r-repmis - r-seuratobject run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' - r-base - 'r-lognormreg >=0.4' - r-matrix diff --git a/recipes/bioconductor-spatialdmelxsim/meta.yaml b/recipes/bioconductor-spatialdmelxsim/meta.yaml index 9141957e86303..2e4dbaa680488 100644 --- a/recipes/bioconductor-spatialdmelxsim/meta.yaml +++ b/recipes/bioconductor-spatialdmelxsim/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "spatialDmelxsim" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f999976552a56f39d49fd9ee186b017 + md5: 2fec38c7672022e76f2b7a7ba7b9a677 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialdmelxsim", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230713 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spatialdmelxsim/post-link.sh b/recipes/bioconductor-spatialdmelxsim/post-link.sh index 73a1e9d948c9a..b6c6cfed4f1e5 100644 --- a/recipes/bioconductor-spatialdmelxsim/post-link.sh +++ b/recipes/bioconductor-spatialdmelxsim/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spatialdmelxsim-1.6.1" +installBiocDataPackage.sh "spatialdmelxsim-1.8.0" diff --git a/recipes/bioconductor-spatialexperiment/meta.yaml b/recipes/bioconductor-spatialexperiment/meta.yaml index 470bebc56e1f2..61e7e4da5902d 100644 --- a/recipes/bioconductor-spatialexperiment/meta.yaml +++ b/recipes/bioconductor-spatialexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SpatialExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9541a84eef622297d0a26bc0de26da03 + md5: 7dbd7938c005104df763ecf3d016154f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialexperiment", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix +# Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-magick - r-rjson run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-dropletutils >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-magick - r-rjson diff --git a/recipes/bioconductor-spatialfeatureexperiment/meta.yaml b/recipes/bioconductor-spatialfeatureexperiment/meta.yaml index 7ae7a555748f0..72a314a96d05f 100644 --- a/recipes/bioconductor-spatialfeatureexperiment/meta.yaml +++ b/recipes/bioconductor-spatialfeatureexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "SpatialFeatureExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6b58208d533b7d157f3f736da0c77bd + md5: 56d4ad5144861bea16c2f677e096ac75 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialfeatureexperiment", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, dplyr, DropletUtils, knitr, rhdf5, rmarkdown, sfarrow, SFEData, vroom, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rjson @@ -36,13 +37,13 @@ requirements: - 'r-spdep >=1.1-7' - r-terra run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rjson diff --git a/recipes/bioconductor-spatialheatmap/meta.yaml b/recipes/bioconductor-spatialheatmap/meta.yaml index cb8a49efac777..d4edc6ad928bf 100644 --- a/recipes/bioconductor-spatialheatmap/meta.yaml +++ b/recipes/bioconductor-spatialheatmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "spatialHeatmap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,83 +11,68 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 99f9415e7f96f98c824aac703586776b + md5: 2fe3c68f9bbfb419d0afd3d329e65747 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialheatmap", max_pin="x.x") }}' noarch: generic -# Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, distinct, dendextend, DT, HDF5Array, htmltools, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, rmarkdown, rols, rappdirs, RUnit, Rtsne, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, uwot +# Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, distinct, dendextend, DT, dynamicTreeCut, flashClust, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, yaml requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr - - r-dynamictreecut - - r-flashclust - - r-ggdendro - r-ggplot2 - r-ggplotify - r-gplots - r-gridextra - r-grimport - - r-htmlwidgets - r-igraph - r-matrix - - r-plotly - r-reshape2 - r-rsvg - r-shiny - r-shinydashboard + - 'r-spscomps >=0.3.3.0' - r-tibble - - r-upsetr - - r-visnetwork - - r-wgcna - r-xml2 - - r-yaml run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scran >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scran >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-dplyr - - r-dynamictreecut - - r-flashclust - - r-ggdendro - r-ggplot2 - r-ggplotify - r-gplots - r-gridextra - r-grimport - - r-htmlwidgets - r-igraph - r-matrix - - r-plotly - r-reshape2 - r-rsvg - r-shiny - r-shinydashboard + - 'r-spscomps >=0.3.3.0' - r-tibble - - r-upsetr - - r-visnetwork - - r-wgcna - r-xml2 - - r-yaml test: commands: - '$R -e "library(''{{ name }}'')"' @@ -95,5 +80,5 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: spatialHeatmap - description: 'The spatialHeatmap package provides functionalities for visualizing cell-, tissue- and organ-specific data of biological assays by coloring the corresponding spatial features defined in anatomical images according to a numeric color key.' + description: 'The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data.' diff --git a/recipes/bioconductor-spatiallibd/meta.yaml b/recipes/bioconductor-spatiallibd/meta.yaml index 30f9d535b5b41..9c66105422f97 100644 --- a/recipes/bioconductor-spatiallibd/meta.yaml +++ b/recipes/bioconductor-spatiallibd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.1" %} {% set name = "spatialLIBD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c14166eb3d988b152448d770f491507 + md5: cd8c85a03e555f2dfdeb1627f7087002 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatiallibd", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr +# Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-benchmarkme - r-cowplot @@ -57,21 +58,21 @@ requirements: - r-tibble - r-viridislite run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-benchmarkme - r-cowplot @@ -93,7 +94,7 @@ requirements: - r-tibble - r-viridislite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spatiallibd/post-link.sh b/recipes/bioconductor-spatiallibd/post-link.sh index ef2ee65ad274e..9ef1f36f1b430 100644 --- a/recipes/bioconductor-spatiallibd/post-link.sh +++ b/recipes/bioconductor-spatiallibd/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spatiallibd-1.12.0" +installBiocDataPackage.sh "spatiallibd-1.14.1" diff --git a/recipes/bioconductor-spatialomicsoverlay/meta.yaml b/recipes/bioconductor-spatialomicsoverlay/meta.yaml index a65ec0d5984ba..8d46d91ef4271 100644 --- a/recipes/bioconductor-spatialomicsoverlay/meta.yaml +++ b/recipes/bioconductor-spatialomicsoverlay/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.1" %} {% set name = "SpatialOmicsOverlay" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 596d07d8c2f6f59deafd7d6d3f24162e + md5: 149a968f19aa22b57caca243b3480378 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialomicsoverlay", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' - - 'bioconductor-rbioformats >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' + - 'bioconductor-rbioformats >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-base64enc - r-data.table @@ -41,12 +42,12 @@ requirements: - r-stringr - r-xml run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-geomxtools >=3.4.0,<3.5.0' - - 'bioconductor-rbioformats >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-geomxtools >=3.5.0,<3.6.0' + - 'bioconductor-rbioformats >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-base64enc - r-data.table diff --git a/recipes/bioconductor-spatzie/meta.yaml b/recipes/bioconductor-spatzie/meta.yaml index 30b812f536f85..98199da5b24e6 100644 --- a/recipes/bioconductor-spatzie/meta.yaml +++ b/recipes/bioconductor-spatzie/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "spatzie" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 001f0345a1039c53f6f585f2950ef7f7 + md5: fa887a71329c75cde9ab0b1aaeb0d481 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatzie", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, Biostrings, knitr, pheatmap, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicinteractions >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-motifmatchr >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tfbstools >=1.38.0,<1.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - r-base - r-ggplot2 - r-matrixstats diff --git a/recipes/bioconductor-speckle/meta.yaml b/recipes/bioconductor-speckle/meta.yaml index 5f7896bf030f5..76d5d70a76e25 100644 --- a/recipes/bioconductor-speckle/meta.yaml +++ b/recipes/bioconductor-speckle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "speckle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f95c51e61cd908d7bdc1c09c0f818eea + md5: 4603cad300c83d6e6374e5989b5fe32a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-speckle", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-seurat run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-seurat diff --git a/recipes/bioconductor-specl/meta.yaml b/recipes/bioconductor-specl/meta.yaml index 64f32842e8a77..df05401abb956 100644 --- a/recipes/bioconductor-specl/meta.yaml +++ b/recipes/bioconductor-specl/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "specL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94afc529140346a23f2b1b46026b482b + md5: a3a436585f26f8353106b030a26cbf98 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-specl", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) requirements: diff --git a/recipes/bioconductor-specond/meta.yaml b/recipes/bioconductor-specond/meta.yaml index 59647e5a09f72..dce56f3e7bbba 100644 --- a/recipes/bioconductor-specond/meta.yaml +++ b/recipes/bioconductor-specond/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "SpeCond" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b33052af7d4b397953ca36153d07a8d + md5: f189b2d0a72f0fb1b7a99bd0b2bb73ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-specond", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fields - 'r-hwriter >=1.1' - 'r-mclust >=3.3.1' - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-fields - 'r-hwriter >=1.1' diff --git a/recipes/bioconductor-spectra/meta.yaml b/recipes/bioconductor-spectra/meta.yaml index 436634bf9685e..dd269b5bb66be 100644 --- a/recipes/bioconductor-spectra/meta.yaml +++ b/recipes/bioconductor-spectra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "Spectra" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 617b4d14b39808599e781280c128fe1e + md5: 32589596593389b703c87d7a05479fe3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spectra", max_pin="x.x") }}' noarch: generic -# Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0) +# Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fs run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-fs test: diff --git a/recipes/bioconductor-spectraltad/meta.yaml b/recipes/bioconductor-spectraltad/meta.yaml index 763c5722c6bf4..dc69aaf8e4fd8 100644 --- a/recipes/bioconductor-spectraltad/meta.yaml +++ b/recipes/bioconductor-spectraltad/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SpectralTAD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39074ac3986665a8f47831b0931adcca + md5: 359760e22303de30ab396fcc7d5938af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spectraltad", max_pin="x.x") }}' noarch: generic # Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-base - r-cluster - r-dplyr @@ -31,9 +32,9 @@ requirements: - r-matrix - r-primme run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-base - r-cluster - r-dplyr diff --git a/recipes/bioconductor-spem/meta.yaml b/recipes/bioconductor-spem/meta.yaml index 0e0876ae2f0af..a841243035900 100644 --- a/recipes/bioconductor-spem/meta.yaml +++ b/recipes/bioconductor-spem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "SPEM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 785ed40eb3c06926a7e4dc2d327d6d74 + md5: 2b0ef40bd2428559cf559dfeb2a384f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spem", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rsolnp run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-rsolnp test: diff --git a/recipes/bioconductor-spia/meta.yaml b/recipes/bioconductor-spia/meta.yaml index 3fd1d648db072..dc1d20edf94e0 100644 --- a/recipes/bioconductor-spia/meta.yaml +++ b/recipes/bioconductor-spia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.52.0" %} +{% set version = "2.54.0" %} {% set name = "SPIA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 108b8d0a425842f59317eb392085a48c + md5: 1a03ed18c41344eb23d6836cb337b9dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spia", max_pin="x.x") }}' noarch: generic # Suggests: graph, Rgraphviz, hgu133plus2.db requirements: host: - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - r-base run: - - 'bioconductor-kegggraph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - r-base test: commands: diff --git a/recipes/bioconductor-spiat/meta.yaml b/recipes/bioconductor-spiat/meta.yaml index a6bb194d78112..584c9b01bc639 100644 --- a/recipes/bioconductor-spiat/meta.yaml +++ b/recipes/bioconductor-spiat/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.2" %} +{% set version = "1.4.1" %} {% set name = "SPIAT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9cfee83cf9df8a5f738501c50a9deb30 + md5: 45342ea9b5cbfbc01e38d6c7b7866852 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spiat", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, rlang, ComplexHeatmap, elsa +# Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa requirements: host: - - 'bioconductor-dittoseq >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dittoseq >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-apcluster >=1.4.7' - r-base - 'r-dbscan >=1.1-5' @@ -36,15 +37,16 @@ requirements: - 'r-rann >=2.6.1' - r-raster - 'r-reshape2 >=1.4.3' + - r-rlang - r-sp - r-spatstat.explore - r-spatstat.geom - 'r-tibble >=2.1.3' - r-vroom run: - - 'bioconductor-dittoseq >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-dittoseq >=1.14.0,<1.15.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'r-apcluster >=1.4.7' - r-base - 'r-dbscan >=1.1-5' @@ -57,6 +59,7 @@ requirements: - 'r-rann >=2.6.1' - r-raster - 'r-reshape2 >=1.4.3' + - r-rlang - r-sp - r-spatstat.explore - r-spatstat.geom @@ -67,7 +70,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 + license: 'Artistic-2.0 + file LICENSE' summary: 'Spatial Image Analysis of Tissues' description: 'SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.' + license_file: LICENSE diff --git a/recipes/bioconductor-spicyr/meta.yaml b/recipes/bioconductor-spicyr/meta.yaml index 758db5f04d27a..cac91262c0ec4 100644 --- a/recipes/bioconductor-spicyr/meta.yaml +++ b/recipes/bioconductor-spicyr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.2" %} {% set name = "spicyR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce45c72613383f9d7f5502ac6856060b + md5: 36cba4820e1206ad3a7220e0430b245f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spicyr", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, pkgdown +# Suggests: BiocStyle, knitr, rmarkdown, pkgdown, imcRtools requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-classifyr >=3.6.0,<3.7.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-concaveman - r-data.table - r-dplyr - r-ggforce - r-ggplot2 - - r-lme4 - r-lmertest - r-mgcv - r-pheatmap @@ -42,22 +43,23 @@ requirements: - r-scam - r-spatstat.explore - r-spatstat.geom + - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-classifyr >=3.6.0,<3.7.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-concaveman - r-data.table - r-dplyr - r-ggforce - r-ggplot2 - - r-lme4 - r-lmertest - r-mgcv - r-pheatmap @@ -65,6 +67,7 @@ requirements: - r-scam - r-spatstat.explore - r-spatstat.geom + - r-tibble - r-tidyr test: commands: @@ -73,6 +76,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Spatial analysis of in situ cytometry data' - description: 'spicyR provides a series of functions to aid in the analysis of both immunofluorescence and mass cytometry imaging data as well as other assays that can deeply phenotype individual cells and their spatial location.' + description: 'The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-spidermir/meta.yaml b/recipes/bioconductor-spidermir/meta.yaml index bdf9c8b33201c..efa9330b4c45e 100644 --- a/recipes/bioconductor-spidermir/meta.yaml +++ b/recipes/bioconductor-spidermir/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "SpidermiR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 611d3128b08997448bf2f5b68f7c646e + md5: 86d54ea72377eb5f3fc8f92ba3b55374 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spidermir", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-mirnatap >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-mirnatap >=1.36.0,<1.37.0' - 'bioconductor-mirnatap.db >=0.99.0,<0.100.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-gdata - r-httr - r-igraph run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-mirnatap >=1.34.0,<1.35.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-mirnatap >=1.36.0,<1.37.0' - 'bioconductor-mirnatap.db >=0.99.0,<0.100.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-gdata - r-httr diff --git a/recipes/bioconductor-spikein/meta.yaml b/recipes/bioconductor-spikein/meta.yaml index b44831908e204..f995b553eabe6 100644 --- a/recipes/bioconductor-spikein/meta.yaml +++ b/recipes/bioconductor-spikein/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "SpikeIn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e738872c55386dae6334ee399c4674a3 + md5: 439f9d2eda54024edb7c1c81862d74c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spikein", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spikein/post-link.sh b/recipes/bioconductor-spikein/post-link.sh index 57a7e13c948a6..2b5335dd03814 100644 --- a/recipes/bioconductor-spikein/post-link.sh +++ b/recipes/bioconductor-spikein/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spikein-1.42.0" +installBiocDataPackage.sh "spikein-1.44.0" diff --git a/recipes/bioconductor-spikeinsubset/meta.yaml b/recipes/bioconductor-spikeinsubset/meta.yaml index 7737f7b5325e7..1cbb90bd6c7ae 100644 --- a/recipes/bioconductor-spikeinsubset/meta.yaml +++ b/recipes/bioconductor-spikeinsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "SpikeInSubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25b553c357880acdabf962253d55d69b + md5: 0c9b5af679c89a1468c9a6f581202e2b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spikeinsubset", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spikeinsubset/post-link.sh b/recipes/bioconductor-spikeinsubset/post-link.sh index 7151258b59659..0c176d193c9ac 100644 --- a/recipes/bioconductor-spikeinsubset/post-link.sh +++ b/recipes/bioconductor-spikeinsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spikeinsubset-1.40.0" +installBiocDataPackage.sh "spikeinsubset-1.42.0" diff --git a/recipes/bioconductor-spikeli/meta.yaml b/recipes/bioconductor-spikeli/meta.yaml index fe565d7c8c501..eaaa49bf1b204 100644 --- a/recipes/bioconductor-spikeli/meta.yaml +++ b/recipes/bioconductor-spikeli/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.60.0" %} +{% set version = "2.62.0" %} {% set name = "spikeLI" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7922faf962c15610b2a0f116187e1b1a + md5: 15e5851707938b83c34b9d5667d62f79 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spikeli", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-spiky/meta.yaml b/recipes/bioconductor-spiky/meta.yaml index bb24ac3af4889..e7f1720f0e287 100644 --- a/recipes/bioconductor-spiky/meta.yaml +++ b/recipes/bioconductor-spiky/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "spiky" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,38 +11,39 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 55cbf8a3742386f0db93aadf07b4306f + md5: 8f710d2ecca4f24247ab38805d665b41 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spiky", max_pin="x.x") }}' noarch: generic # Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-bamlss - r-base - r-blandaltmanleh - r-ggplot2 - r-scales run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-bamlss - r-base - r-blandaltmanleh diff --git a/recipes/bioconductor-spktools/meta.yaml b/recipes/bioconductor-spktools/meta.yaml index d604e37b7aa86..e82233da53f09 100644 --- a/recipes/bioconductor-spktools/meta.yaml +++ b/recipes/bioconductor-spktools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "spkTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a32ef23d5786b41a3428e9b84edda198 + md5: 9cc7d56d0cf0eec1e65d47d262525ba1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spktools", max_pin="x.x") }}' noarch: generic # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gtools - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-gtools - r-rcolorbrewer diff --git a/recipes/bioconductor-splatter/meta.yaml b/recipes/bioconductor-splatter/meta.yaml index c196f33726a43..15276553de261 100644 --- a/recipes/bioconductor-splatter/meta.yaml +++ b/recipes/bioconductor-splatter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "splatter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a5dfb529cb37945588d026098a760bea + md5: 1afec799cae913802068b5b20b32a598 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splatter", max_pin="x.x") }}' noarch: generic # Suggests: BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), IRanges, igraph, knitr, limSolve, lme4, magick, mfa, phenopath, progress, preprocessCore, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave, requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-checkmate >=2.0.0' - r-crayon @@ -37,13 +38,13 @@ requirements: - r-rlang - r-withr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-checkmate >=2.0.0' - r-crayon diff --git a/recipes/bioconductor-splicewiz/meta.yaml b/recipes/bioconductor-splicewiz/meta.yaml index c949a95ada69b..9a264cf06a4ec 100644 --- a/recipes/bioconductor-splicewiz/meta.yaml +++ b/recipes/bioconductor-splicewiz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.2" %} +{% set version = "1.4.0" %} {% set name = "SpliceWiz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14454891d1a6d00f4b3935681f0619de + md5: 95ad1603bebc847d12b7dc715aef923a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splicewiz", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, openssl, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, fgsea, Rsubread # SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-nxtirfdata >=1.6.0,<1.7.0' - - 'bioconductor-ompbam >=1.4.0,<1.5.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-nxtirfdata >=1.8.0,<1.9.0' + - 'bioconductor-ompbam >=1.6.0,<1.7.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dt @@ -69,26 +70,26 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-nxtirfdata >=1.6.0,<1.7.0' - - 'bioconductor-ompbam >=1.4.0,<1.5.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-nxtirfdata >=1.8.0,<1.9.0' + - 'bioconductor-ompbam >=1.6.0,<1.7.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-data.table - r-dt diff --git a/recipes/bioconductor-splicingfactory/meta.yaml b/recipes/bioconductor-splicingfactory/meta.yaml index 2a3a973d23961..79a03bd119400 100644 --- a/recipes/bioconductor-splicingfactory/meta.yaml +++ b/recipes/bioconductor-splicingfactory/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SplicingFactory" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 597502530bf80359bb918678702bb2b7 + md5: 354167193190b04ec94fac9c097b4503 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splicingfactory", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-splicinggraphs/meta.yaml b/recipes/bioconductor-splicinggraphs/meta.yaml index 70cfb611423c8..dd2329883597e 100644 --- a/recipes/bioconductor-splicinggraphs/meta.yaml +++ b/recipes/bioconductor-splicinggraphs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "SplicingGraphs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d15a3c6a52e0cf2e5821f90fd992053 + md5: 04e2a057bc1c6935ee13333acdf5ba52 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splicinggraphs", max_pin="x.x") }}' noarch: generic # Suggests: igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-igraph run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-igraph test: diff --git a/recipes/bioconductor-splinetimer/meta.yaml b/recipes/bioconductor-splinetimer/meta.yaml index add5dbe8d4d52..19a7f65b4f424 100644 --- a/recipes/bioconductor-splinetimer/meta.yaml +++ b/recipes/bioconductor-splinetimer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "splineTimeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cad5d2654b4b510de7aba9fefd73e46b + md5: 09454e29df75ff3f9d9e3f2780fb5db6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splinetimer", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fis >=1.28.0,<1.29.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fis >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-genenet >=1.2.13' - r-gtools - r-igraph - 'r-longitudinal >=1.1.12' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fis >=1.28.0,<1.29.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-fis >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - 'r-genenet >=1.2.13' - r-gtools diff --git a/recipes/bioconductor-splinter/meta.yaml b/recipes/bioconductor-splinter/meta.yaml index 76c565ec2b60b..e96e229c81b4a 100644 --- a/recipes/bioconductor-splinter/meta.yaml +++ b/recipes/bioconductor-splinter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "SPLINTER" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,44 +11,45 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfa5400f767658eb668ccf62c50f4914 + md5: f328ebcc0e4d27dee8a98c2e230bd8dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splinter", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base - r-ggplot2 - r-googlevis - r-plyr - r-stringr run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - r-base - r-ggplot2 - r-googlevis diff --git a/recipes/bioconductor-splots/meta.yaml b/recipes/bioconductor-splots/meta.yaml index bb84e57882648..adc7ad8e35825 100644 --- a/recipes/bioconductor-splots/meta.yaml +++ b/recipes/bioconductor-splots/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "splots" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,14 +11,15 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6b86fd185efeaeb6bb38515bf577b0e2 + md5: 5f497af3c7a5fcdbba178a1ff3b411b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-splots", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI +# Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr, ggplot2 requirements: host: - r-base @@ -33,7 +34,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Visualization of high-throughput assays in microtitre plate or slide format' - description: 'This package is provided to support legacy code and reverse dependencies, but it should not be used as a dependency for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package on CRAN (https://cran.r-project.org/package=platetools and https://github.com/Swarchal/platetools), or generic ggplot2 graphics functionality.' + description: 'This package is here to support legacy usages of it, but it should not be used for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package on CRAN (https://cran.r-project.org/package=platetools and https://github.com/Swarchal/platetools), or ggplot2 (geom_raster, facet_wrap) as exemplified in the vignette of this package.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: identifiers: diff --git a/recipes/bioconductor-spotclean/meta.yaml b/recipes/bioconductor-spotclean/meta.yaml index e8d0b89ae307f..8832e69eae5ea 100644 --- a/recipes/bioconductor-spotclean/meta.yaml +++ b/recipes/bioconductor-spotclean/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.1" %} {% set name = "SpotClean" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 649c0a781c17b134925269f6696e8bf0 + md5: b6e7be89394d959837993f3fd385ad55 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spotclean", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling requirements: host: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -37,10 +38,10 @@ requirements: - r-tibble - r-viridis run: - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-spotlight/meta.yaml b/recipes/bioconductor-spotlight/meta.yaml index 898bf91b3f4fe..a29d88c4d27da 100644 --- a/recipes/bioconductor-spotlight/meta.yaml +++ b/recipes/bioconductor-spotlight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.3" %} {% set name = "SPOTlight" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3cf368e27ab8dba4f20ca904271c4ea + md5: 00759051612f8f17697afd03507d6d8c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spotlight", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, colorBlindness, ExperimentHub, DelayedArray, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, Seurat, SeuratObject, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat +# Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, Seurat, SeuratObject, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-matrix @@ -29,7 +30,7 @@ requirements: - r-nmf - r-nnls run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-ggplot2 - r-matrix diff --git a/recipes/bioconductor-spqn/meta.yaml b/recipes/bioconductor-spqn/meta.yaml index 6dd80e885fe8d..c6aa1696bc6a1 100644 --- a/recipes/bioconductor-spqn/meta.yaml +++ b/recipes/bioconductor-spqn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "spqn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d36cc99c0915e86aba64cafad9a690af + md5: 63599cd8ebe97287b176d98cb3d9de43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spqn", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggridges - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggridges diff --git a/recipes/bioconductor-spqndata/meta.yaml b/recipes/bioconductor-spqndata/meta.yaml index e8d06d0ab7422..efac37f68f5cb 100644 --- a/recipes/bioconductor-spqndata/meta.yaml +++ b/recipes/bioconductor-spqndata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "spqnData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1588ea6c755eb468f60af1a67712cac0 + md5: 453bf944ea40956afef2bd868f92d747 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spqndata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-spqndata/post-link.sh b/recipes/bioconductor-spqndata/post-link.sh index eb0052e45a644..4468f52ef6133 100644 --- a/recipes/bioconductor-spqndata/post-link.sh +++ b/recipes/bioconductor-spqndata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spqndata-1.12.0" +installBiocDataPackage.sh "spqndata-1.14.0" diff --git a/recipes/bioconductor-spsimseq/meta.yaml b/recipes/bioconductor-spsimseq/meta.yaml index c327a1072ec78..e85f49127980d 100644 --- a/recipes/bioconductor-spsimseq/meta.yaml +++ b/recipes/bioconductor-spsimseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SPsimSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 433fef1a4f51ce4bbe425b88d9b7eec7 + md5: 1ccc188618b92dcf94489a00d7faa5b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spsimseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, LSD, testthat, BiocStyle requirements: host: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-fitdistrplus - r-hmisc - r-mvtnorm - r-wgcna run: - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-phyloseq >=1.44.0,<1.45.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-fitdistrplus - r-hmisc diff --git a/recipes/bioconductor-sqldataframe/meta.yaml b/recipes/bioconductor-sqldataframe/meta.yaml index 911d736933457..4ab1d6af33f2c 100644 --- a/recipes/bioconductor-sqldataframe/meta.yaml +++ b/recipes/bioconductor-sqldataframe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SQLDataFrame" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e85f08b5a38073be4f7ae655d57c139f + md5: 4153fe66ee281c087e77c6706a2b2faf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sqldataframe", max_pin="x.x") }}' noarch: generic -# Suggests: RMySQL, bigrquery, testthat, knitr, rmarkdown, DelayedArray +# Suggests: RMySQL, bigrquery, testthat, knitr, rmarkdown, DelayedArray, GenomicRanges requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - 'r-dbplyr >=1.4.0' @@ -31,8 +32,8 @@ requirements: - r-rsqlite - r-tibble run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dbi - 'r-dbplyr >=1.4.0' diff --git a/recipes/bioconductor-squadd/meta.yaml b/recipes/bioconductor-squadd/meta.yaml index ad4a8ea5b03e9..0a8548a01dd6e 100644 --- a/recipes/bioconductor-squadd/meta.yaml +++ b/recipes/bioconductor-squadd/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "SQUADD" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07c942ac0b69c5a285a49341451afb5f + md5: 8837e27ab065ddae145da3cc5ca2ad32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-squadd", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-sracipe/meta.yaml b/recipes/bioconductor-sracipe/meta.yaml index 858cccbb7efec..3b7c215452e39 100644 --- a/recipes/bioconductor-sracipe/meta.yaml +++ b/recipes/bioconductor-sracipe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "sRACIPE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b032be2639312a58690b6190dca69d2f + md5: 84a1b79b944741fc6ecab26168020841 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sracipe", max_pin="x.x") }}' # Suggests: knitr, BiocStyle, rmarkdown, tinytest, doFuture requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-gplots @@ -37,9 +38,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-gplots diff --git a/recipes/bioconductor-sradb/meta.yaml b/recipes/bioconductor-sradb/meta.yaml index d88957529f1e9..25db5e723e5ca 100644 --- a/recipes/bioconductor-sradb/meta.yaml +++ b/recipes/bioconductor-sradb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "SRAdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a74df8413362db72d8e415e5bb2dcdf + md5: 6bc0aa8bd176c1b388f4da270b4f668b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sradb", max_pin="x.x") }}' noarch: generic # Suggests: Rgraphviz requirements: host: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-rcurl - r-rsqlite run: - - 'bioconductor-geoquery >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-rcurl - r-rsqlite diff --git a/recipes/bioconductor-srnadiff/build.sh b/recipes/bioconductor-srnadiff/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-srnadiff/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-srnadiff/meta.yaml b/recipes/bioconductor-srnadiff/meta.yaml new file mode 100644 index 0000000000000..916fb53ca5359 --- /dev/null +++ b/recipes/bioconductor-srnadiff/meta.yaml @@ -0,0 +1,79 @@ +{% set version = "1.22.0" %} +{% set name = "srnadiff" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0125777227eab34f7839615139aacb91 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-srnadiff", max_pin="x.x") }}' +# Suggests: knitr, rmarkdown, testthat, BiocManager, BiocStyle +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-biocmanager + - r-devtools + - 'r-rcpp >=0.12.8' + - libblas + - liblapack + run: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-biocmanager + - r-devtools + - 'r-rcpp >=0.12.8' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Finding differentially expressed unannotated genomic regions from RNA-seq data' + description: 'srnadiff is a package that finds differently expressed regions from RNA-seq data at base-resolution level without relying on existing annotation. To do so, the package implements the identify-then-annotate methodology that builds on the idea of combining two pipelines approachs differential expressed regions detection and differential expression quantification. It reads BAM files as input, and outputs a list differentially regions, together with the adjusted p-values.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-sscu/meta.yaml b/recipes/bioconductor-sscu/meta.yaml index 674ac072e84b2..2d4fb8c20013f 100644 --- a/recipes/bioconductor-sscu/meta.yaml +++ b/recipes/bioconductor-sscu/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "sscu" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 361e476bdd720a428c36c352bccb9802 + md5: 3856e06321ac866e2664573b452c6a85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sscu", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-seqinr >=3.1-3' run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - 'r-seqinr >=3.1-3' test: diff --git a/recipes/bioconductor-sseq/meta.yaml b/recipes/bioconductor-sseq/meta.yaml index 0e4be979404ea..2ecb6cdba2b18 100644 --- a/recipes/bioconductor-sseq/meta.yaml +++ b/recipes/bioconductor-sseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "sSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43ed8739950672325635df07770212a3 + md5: 9276919acd944871a6e05a8dbeed6b9f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sseq", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-ssize/meta.yaml b/recipes/bioconductor-ssize/meta.yaml index cb93b69f91109..e7e2942a52185 100644 --- a/recipes/bioconductor-ssize/meta.yaml +++ b/recipes/bioconductor-ssize/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "ssize" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4b0c875620b8d1a31e166b27a3538a6d + md5: b61fbe78b68fecd3090e1c658a284b83 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ssize", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-ssnappy/meta.yaml b/recipes/bioconductor-ssnappy/meta.yaml index 7160a4a6be7a5..5b49df2a9511a 100644 --- a/recipes/bioconductor-ssnappy/meta.yaml +++ b/recipes/bioconductor-ssnappy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.1" %} {% set name = "sSNAPPY" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,61 +11,55 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 263387c3d870cf83e91c5da6a2cbac8c + md5: 15f7a550e110c069710c3f6572a06e83 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocManager, BiocStyle, cowplot, DT, htmltools, knitr, pander, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse + run_exports: '{{ pin_subpackage("bioconductor-ssnappy", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=1.1' - r-ggforce - r-ggplot2 - r-ggraph + - r-gtools - r-igraph - r-magrittr - r-pheatmap - - r-rcpp - - r-rcpparmadillo - r-reshape2 - r-rlang - r-stringr - r-tibble - - libblas - - liblapack + - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=1.1' - r-ggforce - r-ggplot2 - r-ggraph + - r-gtools - r-igraph - r-magrittr - r-pheatmap - - r-rcpp - - r-rcpparmadillo - r-reshape2 - r-rlang - r-stringr - r-tibble - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-tidyr test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sspaths/meta.yaml b/recipes/bioconductor-sspaths/meta.yaml index c9f863931d308..e7f074e25161c 100644 --- a/recipes/bioconductor-sspaths/meta.yaml +++ b/recipes/bioconductor-sspaths/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "ssPATHS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 31fd9abb3ebbad68e476099511cd0161 + md5: 121909c57596e3cd0d817cac2deb22c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sspaths", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dml - r-mess - r-rocr run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dml - r-mess diff --git a/recipes/bioconductor-ssrch/meta.yaml b/recipes/bioconductor-ssrch/meta.yaml index 04d1b9d146627..b3495f2f86488 100644 --- a/recipes/bioconductor-ssrch/meta.yaml +++ b/recipes/bioconductor-ssrch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "ssrch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4cb99d0771a2949808a20c55c687044e + md5: 095c153ce56b89d040c929a8c1af6840 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ssrch", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-ssviz/meta.yaml b/recipes/bioconductor-ssviz/meta.yaml index 717d098cdee5d..87ac9b79c48bf 100644 --- a/recipes/bioconductor-ssviz/meta.yaml +++ b/recipes/bioconductor-ssviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "ssviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3d62d00ec992873217d787aa0aee02e6 + md5: 00bd4a7d6a57af51b74187993bdf84c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ssviz", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-ggplot2 - r-rcolorbrewer - r-reshape run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-ggplot2 - r-rcolorbrewer diff --git a/recipes/bioconductor-stager/meta.yaml b/recipes/bioconductor-stager/meta.yaml index 170a3ed5a0ef3..afdbee6634400 100644 --- a/recipes/bioconductor-stager/meta.yaml +++ b/recipes/bioconductor-stager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "stageR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53be8e8637660075a5dd3a5788bb887e + md5: cdbf6ab3c35c3e019b0ce786ad85eb38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stager", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-standr/meta.yaml b/recipes/bioconductor-standr/meta.yaml index 976227bf60283..c54e0c516383c 100644 --- a/recipes/bioconductor-standr/meta.yaml +++ b/recipes/bioconductor-standr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.2" %} +{% set version = "1.6.0" %} {% set name = "standR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a59d4f2ed1a9301c835e2c4bf83d74ea + md5: 94e29a2001fbb9d0bfa1488ae7039aa7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-standr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggalluvial @@ -42,15 +43,15 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-ruvseq >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-ruvseq >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggalluvial diff --git a/recipes/bioconductor-starank/meta.yaml b/recipes/bioconductor-starank/meta.yaml index e820622caca23..684cceb9f69d6 100644 --- a/recipes/bioconductor-starank/meta.yaml +++ b/recipes/bioconductor-starank/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "staRank" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0125b4deecba9bf4db3f9bcac2326be7 + md5: 6284ebc665a24e39437e707b4fc1ad80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-starank", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' - r-base run: - - 'bioconductor-cellhts2 >=2.64.0,<2.65.0' + - 'bioconductor-cellhts2 >=2.66.0,<2.67.0' - r-base test: commands: diff --git a/recipes/bioconductor-starbiotrek/meta.yaml b/recipes/bioconductor-starbiotrek/meta.yaml index 6e426df618368..1ca02bc22bc51 100644 --- a/recipes/bioconductor-starbiotrek/meta.yaml +++ b/recipes/bioconductor-starbiotrek/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "StarBioTrek" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cba511d5a1ac1494e491455c893ed3d9 + md5: a1a892a63f09a57e18eb825ab8a0ec7e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-starbiotrek", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, qgraph, png, grid requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-spidermir >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-spidermir >=1.32.0,<1.33.0' - r-base - r-e1071 - r-ggplot2 @@ -32,9 +33,9 @@ requirements: - r-reshape2 - r-rocr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-graphite >=1.46.0,<1.47.0' - - 'bioconductor-spidermir >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-graphite >=1.48.0,<1.49.0' + - 'bioconductor-spidermir >=1.32.0,<1.33.0' - r-base - r-e1071 - r-ggplot2 diff --git a/recipes/bioconductor-stategra/meta.yaml b/recipes/bioconductor-stategra/meta.yaml index 8693cc153ae6b..21e069eaf1b45 100644 --- a/recipes/bioconductor-stategra/meta.yaml +++ b/recipes/bioconductor-stategra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "STATegRa" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c23bae33718cd7c94ef30beb97344cb0 + md5: be42ca7786d4b038ad3f706492c74022 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stategra", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-calibrate - r-foreach @@ -33,10 +34,10 @@ requirements: - r-gridextra - r-mass run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-calibrate - r-foreach diff --git a/recipes/bioconductor-statial/meta.yaml b/recipes/bioconductor-statial/meta.yaml index aeef3a2b9c3cd..d414780320fc2 100644 --- a/recipes/bioconductor-statial/meta.yaml +++ b/recipes/bioconductor-statial/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.5" %} {% set name = "Statial" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,60 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef5801f844d0bc314ecf0e208e2a29f0 + md5: e7151f23bb952401803e4d239390c210 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-statial", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, testthat (>= 3.0.0) +# Suggests: BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-concaveman - r-data.table - r-dplyr - r-ggplot2 + - r-magrittr + - r-plotly + - r-purrr + - r-ranger - r-spatstat.explore - r-spatstat.geom - r-stringr - r-tibble - r-tidyr - r-tidyselect - - r-tidyverse run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-concaveman - r-data.table - r-dplyr - r-ggplot2 + - r-magrittr + - r-plotly + - r-purrr + - r-ranger - r-spatstat.explore - r-spatstat.geom - r-stringr - r-tibble - r-tidyr - r-tidyselect - - r-tidyverse test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-stattarget/meta.yaml b/recipes/bioconductor-stattarget/meta.yaml index ae19bb6675d09..c3b72f32f6d1c 100644 --- a/recipes/bioconductor-stattarget/meta.yaml +++ b/recipes/bioconductor-stattarget/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "statTarget" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bebae7ea2293cdbc8e26baddba59605c + md5: 8a504e674b8756201ca93b590dd0b078 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stattarget", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-pdist - r-pls @@ -30,8 +31,8 @@ requirements: - r-randomforest - r-rrcov run: - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-pdist - r-pls diff --git a/recipes/bioconductor-stdeconvolve/build_failure.linux-64.yaml b/recipes/bioconductor-stdeconvolve/build_failure.linux-64.yaml index d06518ec443cf..46b164e797e06 100644 --- a/recipes/bioconductor-stdeconvolve/build_failure.linux-64.yaml +++ b/recipes/bioconductor-stdeconvolve/build_failure.linux-64.yaml @@ -1,4 +1,4 @@ -recipe_sha: 8b208f8587b5f20c9475a1a086aa90016f4f780fe772c97b3e6a7391f4848065 # The commit at which this recipe failed to build. +recipe_sha: b11c54aa8b5803ac796aadaf1ab911295658038c435eea768cf62514aa5c4e79 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- r-vctrs: 0.6.3-r43ha503ecb_0 conda-forge @@ -102,3 +102,7 @@ log: |2- raise subprocess.CalledProcessError(proc.returncode, _args) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-stdeconvolve_1689833080445/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. +reason: |- + 07:50:52 BIOCONDA INFO (OUT) ERROR: dependency ‘liger’ is not available for package ‘STdeconvolve’ +category: |- + dependency issue diff --git a/recipes/bioconductor-stdeconvolve/meta.yaml b/recipes/bioconductor-stdeconvolve/meta.yaml index 1834a810f856e..0e9d14b87e1da 100644 --- a/recipes/bioconductor-stdeconvolve/meta.yaml +++ b/recipes/bioconductor-stdeconvolve/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "STdeconvolve" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a5cf6d8c89d292cd28df0c245c25d51 + md5: 2908e0d59713b2c3ef6c7bc549d0d123 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stdeconvolve", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots, gridExtra, hash, dplyr, parallel requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-clue - r-ggplot2 @@ -34,7 +35,7 @@ requirements: - r-topicmodels - r-viridis run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-clue - r-ggplot2 diff --git a/recipes/bioconductor-stemhypoxia/meta.yaml b/recipes/bioconductor-stemhypoxia/meta.yaml index c3a6d2e8b2cfc..1bf4c404eb5a3 100644 --- a/recipes/bioconductor-stemhypoxia/meta.yaml +++ b/recipes/bioconductor-stemhypoxia/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "stemHypoxia" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53b049bafffb969dea77f35479720221 + md5: 22ec9d76cac05ac7118873f7815225ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stemhypoxia", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-stemhypoxia/post-link.sh b/recipes/bioconductor-stemhypoxia/post-link.sh index c47b0e4558bb3..519f3ce64e7b7 100644 --- a/recipes/bioconductor-stemhypoxia/post-link.sh +++ b/recipes/bioconductor-stemhypoxia/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "stemhypoxia-1.36.0" +installBiocDataPackage.sh "stemhypoxia-1.38.0" diff --git a/recipes/bioconductor-stepnorm/meta.yaml b/recipes/bioconductor-stepnorm/meta.yaml index 3b3f5a1ca9c77..a109683e28058 100644 --- a/recipes/bioconductor-stepnorm/meta.yaml +++ b/recipes/bioconductor-stepnorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "stepNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a7edda3646c8d02d776e7e8b62ef64d + md5: a8f357efcff85a6d723734d6e0a91ba0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stepnorm", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-mass run: - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-stexampledata/meta.yaml b/recipes/bioconductor-stexampledata/meta.yaml index 60acf470da223..422e84e76f070 100644 --- a/recipes/bioconductor-stexampledata/meta.yaml +++ b/recipes/bioconductor-stexampledata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "STexampleData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21ccea26e0677e8ff1ec5ddfe7da0a32 + md5: 5fa4bfb2e58e7f6bbcd957aa1aa7e938 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stexampledata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, BumpyMatrix requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-stexampledata/post-link.sh b/recipes/bioconductor-stexampledata/post-link.sh index 20643afbd8feb..6dea914d714c1 100644 --- a/recipes/bioconductor-stexampledata/post-link.sh +++ b/recipes/bioconductor-stexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "stexampledata-1.8.0" +installBiocDataPackage.sh "stexampledata-1.10.0" diff --git a/recipes/bioconductor-stjoincount/meta.yaml b/recipes/bioconductor-stjoincount/meta.yaml index 9de2419b16348..38b3392c1fcd2 100644 --- a/recipes/bioconductor-stjoincount/meta.yaml +++ b/recipes/bioconductor-stjoincount/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "stJoincount" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6bf5da007b58f88706124d298422dde7 + md5: 85dd3f81a773ede72a70185cb4132d2b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stjoincount", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 @@ -33,8 +34,8 @@ requirements: - r-sp - r-spdep run: - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-stjudem/meta.yaml b/recipes/bioconductor-stjudem/meta.yaml index e49fa8565cb43..f224b6a78e11d 100644 --- a/recipes/bioconductor-stjudem/meta.yaml +++ b/recipes/bioconductor-stjudem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "stjudem" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d793d5b3f5abf684f188723111097faf + md5: 4c6868a60726df51408834a227e551bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stjudem", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-stjudem/post-link.sh b/recipes/bioconductor-stjudem/post-link.sh index 98f05a794211c..bbadc4df501c3 100644 --- a/recipes/bioconductor-stjudem/post-link.sh +++ b/recipes/bioconductor-stjudem/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "stjudem-1.40.0" +installBiocDataPackage.sh "stjudem-1.42.0" diff --git a/recipes/bioconductor-strandcheckr/meta.yaml b/recipes/bioconductor-strandcheckr/meta.yaml index efba83d3688df..21ce40d74e7fd 100644 --- a/recipes/bioconductor-strandcheckr/meta.yaml +++ b/recipes/bioconductor-strandcheckr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "strandCheckR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3212c9f0350eb46edfa4d2aed1741f3f + md5: d9544940bb53aa96ca4e14fda712581d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-strandcheckr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-dplyr - r-ggplot2 @@ -38,14 +39,14 @@ requirements: - r-rmarkdown - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-streamer/meta.yaml b/recipes/bioconductor-streamer/meta.yaml index 683510919b546..b98467148e69a 100644 --- a/recipes/bioconductor-streamer/meta.yaml +++ b/recipes/bioconductor-streamer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "Streamer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d23715dbf4aec29873e6c2bfd6257817 + md5: d41ea52d04a44b0705846078ffe3b1e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-streamer", max_pin="x.x") }}' # Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-stringdb/meta.yaml b/recipes/bioconductor-stringdb/meta.yaml index b7c61cecb2c7e..64027a236667d 100644 --- a/recipes/bioconductor-stringdb/meta.yaml +++ b/recipes/bioconductor-stringdb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "STRINGdb" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 099f3db99ae7033c75db37df090e8d3e + md5: 6dc5819519574f0656e4b811e4618db7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stringdb", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, BiocGenerics requirements: diff --git a/recipes/bioconductor-struct/meta.yaml b/recipes/bioconductor-struct/meta.yaml index 92e18d7183956..6436c5e2462f7 100644 --- a/recipes/bioconductor-struct/meta.yaml +++ b/recipes/bioconductor-struct/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "struct" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 63b865919a93b7112c758393c9b9795b + md5: ef5fb8febc9f7bfed87fba9bc24cbebc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-struct", max_pin="x.x") }}' noarch: generic # Suggests: testthat, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx, ggplot2, magick requirements: host: - - 'bioconductor-rols >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rols >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-knitr - r-ontologyindex run: - - 'bioconductor-rols >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-rols >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-knitr - r-ontologyindex diff --git a/recipes/bioconductor-structstrings/meta.yaml b/recipes/bioconductor-structstrings/meta.yaml index 64c50442ec9f0..adcd3be37235e 100644 --- a/recipes/bioconductor-structstrings/meta.yaml +++ b/recipes/bioconductor-structstrings/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Structstrings" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30a130dd232ccb09f2680746ae3c65f2 + md5: 8d4afbd61a5546b52947869b7912eecb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-structstrings", max_pin="x.x") }}' # Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon - r-stringi @@ -32,11 +33,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-crayon - r-stringi diff --git a/recipes/bioconductor-structtoolbox/meta.yaml b/recipes/bioconductor-structtoolbox/meta.yaml index 085906542fe3f..4a6d887b6e887 100644 --- a/recipes/bioconductor-structtoolbox/meta.yaml +++ b/recipes/bioconductor-structtoolbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.2" %} +{% set version = "1.14.0" %} {% set name = "structToolbox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,16 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c6bb1a435086c8f3fb3462c38e50fcd + md5: d6e4aa6631f797571a7ec07348cfbd30 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-structtoolbox", max_pin="x.x") }}' noarch: generic +# Suggests: agricolae, BiocFileCache, BiocStyle, car, covr, cowplot, e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls, pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs requirements: host: - - 'bioconductor-struct >=1.12.0,<1.13.0' + - 'bioconductor-struct >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggthemes @@ -28,34 +30,13 @@ requirements: - r-scales - r-sp run: - - 'bioconductor-struct >=1.12.0,<1.13.0' + - 'bioconductor-struct >=1.14.0,<1.15.0' - r-base - r-ggplot2 - r-ggthemes - r-gridextra - r-scales - r-sp - - bioconductor-BiocFileCache - - bioconductor-BiocStyle - - bioconductor-pmp - - bioconductor-ropls - - r-agricolae - - r-car - - r-covr - - r-cowplot - - r-e1071 - - r-emmeans - - r-ggdendro - - r-knitr - - r-magick - - r-nlme - - r-openxlsx - - r-pls - - r-reshape2 - - r-rmarkdown - - r-rtsne - - r-testthat - - r-rappdirs test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-structuralvariantannotation/meta.yaml b/recipes/bioconductor-structuralvariantannotation/meta.yaml index 56b5c9d69db2d..33f925708abe9 100644 --- a/recipes/bioconductor-structuralvariantannotation/meta.yaml +++ b/recipes/bioconductor-structuralvariantannotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "StructuralVariantAnnotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,42 +11,43 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b202869069b95a7fc763f81e45a20f5d + md5: d72d8c88083ed0fc9319afa075360841 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-structuralvariantannotation", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-subcellbarcode/meta.yaml b/recipes/bioconductor-subcellbarcode/meta.yaml index 2bc92431495c5..e6f6ea30837ae 100644 --- a/recipes/bioconductor-subcellbarcode/meta.yaml +++ b/recipes/bioconductor-subcellbarcode/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SubCellBarCode" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d51692e771904243e46346f6db1229b + md5: 9b3f34495b8132c4cbdc426e27ffc740 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-subcellbarcode", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-caret - r-e1071 @@ -33,8 +34,8 @@ requirements: - r-rtsne - r-scatterplot3d run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-caret - r-e1071 diff --git a/recipes/bioconductor-subseq/meta.yaml b/recipes/bioconductor-subseq/meta.yaml index 5296f6e59b98d..f482cf4d343f7 100644 --- a/recipes/bioconductor-subseq/meta.yaml +++ b/recipes/bioconductor-subseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "subSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 01708051b6affd954eb9c2b625d6c0db + md5: 81acfd896fc4e8c52e50475dca2c1519 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-subseq", max_pin="x.x") }}' noarch: generic # Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-data.table - r-digest @@ -31,8 +32,8 @@ requirements: - r-magrittr - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-data.table - r-digest diff --git a/recipes/bioconductor-sugarcanecdf/meta.yaml b/recipes/bioconductor-sugarcanecdf/meta.yaml index 98084152b6f97..f35923e94468a 100644 --- a/recipes/bioconductor-sugarcanecdf/meta.yaml +++ b/recipes/bioconductor-sugarcanecdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "sugarcanecdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f66d51868068f83d3693d3cb05be418a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sugarcanecdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-sugarcaneprobe/meta.yaml b/recipes/bioconductor-sugarcaneprobe/meta.yaml index 3c7b6e3a9c55b..206f4292a4db3 100644 --- a/recipes/bioconductor-sugarcaneprobe/meta.yaml +++ b/recipes/bioconductor-sugarcaneprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "sugarcaneprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 66c101ac73e9235d258b9f996c42778e build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sugarcaneprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-suitor/meta.yaml b/recipes/bioconductor-suitor/meta.yaml index 707ed676d00f7..2c3b4b7017d9d 100644 --- a/recipes/bioconductor-suitor/meta.yaml +++ b/recipes/bioconductor-suitor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "SUITOR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e3df0f3c1651702438aecf49a67fb7f + md5: 5f4a5ea607ef7551025cf8b425d20bc7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-suitor", max_pin="x.x") }}' # Suggests: devtools, MutationalPatterns, RUnit, BiocManager, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ggplot2 - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-ggplot2 build: diff --git a/recipes/bioconductor-summarizedbenchmark/meta.yaml b/recipes/bioconductor-summarizedbenchmark/meta.yaml index ff5f061ec8208..fc6634da01088 100644 --- a/recipes/bioconductor-summarizedbenchmark/meta.yaml +++ b/recipes/bioconductor-summarizedbenchmark/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "SummarizedBenchmark" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e72a284cb81ab58625cbc15c12b891fb + md5: f967c7e3db84713c2db5a2b0f1999ce4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-summarizedbenchmark", max_pin="x.x") }}' noarch: generic # Suggests: iCOBRA, BiocStyle, rmarkdown, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - r-digest @@ -38,10 +39,10 @@ requirements: - r-tidyr - r-upsetr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - r-digest diff --git a/recipes/bioconductor-summarizedexperiment/meta.yaml b/recipes/bioconductor-summarizedexperiment/meta.yaml index e2e9d98423b38..26284256593de 100644 --- a/recipes/bioconductor-summarizedexperiment/meta.yaml +++ b/recipes/bioconductor-summarizedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.2" %} +{% set version = "1.32.0" %} {% set name = "SummarizedExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3785779b5e61a51d2be4f71c46e3b67a + md5: cf4b430247b40acb2be8e6c9ecf3aac7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-summarizedexperiment", max_pin="x.x") }}' noarch: generic # Suggests: HDF5Array (>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite, rhdf5, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4arrays >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4arrays >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-summix/meta.yaml b/recipes/bioconductor-summix/meta.yaml index 494356af38ef0..9426ca82a1bea 100644 --- a/recipes/bioconductor-summix/meta.yaml +++ b/recipes/bioconductor-summix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "Summix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d845748231aaea3953d1bb4814764356 + md5: 74d3140f7f5db9a648955b81abdfb769 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-summix", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, markdown, knitr requirements: diff --git a/recipes/bioconductor-supersigs/meta.yaml b/recipes/bioconductor-supersigs/meta.yaml index d75f2dbbc2cc4..7eb7f89d459f7 100644 --- a/recipes/bioconductor-supersigs/meta.yaml +++ b/recipes/bioconductor-supersigs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "supersigs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 42a9e56f253261e8adece79a7db5eb2a + md5: 35df3e9fd0272854b23baf15d93d300f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-supersigs", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-caret @@ -31,8 +32,8 @@ requirements: - r-rsample - r-tidyr run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-caret diff --git a/recipes/bioconductor-suprahex/meta.yaml b/recipes/bioconductor-suprahex/meta.yaml index 04eb6c4e30369..e36b5c278da3e 100644 --- a/recipes/bioconductor-suprahex/meta.yaml +++ b/recipes/bioconductor-suprahex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "supraHex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e336ff1cb8560472beba7d8ccf5a09f + md5: 19685808f18718a58889c70e476888d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-suprahex", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-surfaltr/meta.yaml b/recipes/bioconductor-surfaltr/meta.yaml index 2ed649c1aa0a6..fec35c9c96474 100644 --- a/recipes/bioconductor-surfaltr/meta.yaml +++ b/recipes/bioconductor-surfaltr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "surfaltr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3a4fb02609853c9949dd59b780178915 + md5: 69ea67dd32fffa5376607fa6fa5c7e9f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-surfaltr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, devtools, kableExtra requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - 'r-dplyr >=1.0.6' - 'r-ggplot2 >=3.3.2' @@ -35,9 +36,9 @@ requirements: - 'r-testthat >=3.0.0' - 'r-xml2 >=1.3.2' run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msa >=1.32.0,<1.33.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msa >=1.34.0,<1.35.0' - r-base - 'r-dplyr >=1.0.6' - 'r-ggplot2 >=3.3.2' diff --git a/recipes/bioconductor-survcomp/meta.yaml b/recipes/bioconductor-survcomp/meta.yaml index 2f2780ca4ccff..52adadac760d3 100644 --- a/recipes/bioconductor-survcomp/meta.yaml +++ b/recipes/bioconductor-survcomp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "survcomp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf071254fe286a0ece30502f89c7a76a + md5: 5026589c50042751474d3474dc24847d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-survcomp", max_pin="x.x") }}' # Suggests: Hmisc, clinfun, xtable, Biobase, BiocManager requirements: host: diff --git a/recipes/bioconductor-survtype/meta.yaml b/recipes/bioconductor-survtype/meta.yaml index 12039d62d24df..1d4612397856c 100644 --- a/recipes/bioconductor-survtype/meta.yaml +++ b/recipes/bioconductor-survtype/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "survtype" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 639c5a6fcc3ff8139f8c46a3cefd2e84 + md5: e939bd3726a715cb0a817d0541ff86ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-survtype", max_pin="x.x") }}' noarch: generic # Suggests: maftools, scales, knitr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clustvarsel - r-pheatmap - r-survival - r-survminer run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-clustvarsel - r-pheatmap diff --git a/recipes/bioconductor-sva/meta.yaml b/recipes/bioconductor-sva/meta.yaml index 2e4dcb6704fdf..22e62492bff10 100644 --- a/recipes/bioconductor-sva/meta.yaml +++ b/recipes/bioconductor-sva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.48.0" %} +{% set version = "3.50.0" %} {% set name = "sva" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a2553ec4e50d85e75a764a83b8dc74b + md5: 8c42cd3e23be4d24f072d98394931552 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sva", max_pin="x.x") }}' # Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-matrixstats - r-mgcv - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-matrixstats - r-mgcv diff --git a/recipes/bioconductor-svanumt/meta.yaml b/recipes/bioconductor-svanumt/meta.yaml index 3dba97073f8ec..03b3aa0e409af 100644 --- a/recipes/bioconductor-svanumt/meta.yaml +++ b/recipes/bioconductor-svanumt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "svaNUMT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b4ce1b0c7f1224d6703e8681aa643fa4 + md5: 1f25f8632f0e52d0826ee0b1b8a1fe28 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-svanumt", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structuralvariantannotation >=1.16.0,<1.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structuralvariantannotation >=1.16.0,<1.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-svaretro/meta.yaml b/recipes/bioconductor-svaretro/meta.yaml index b4fa14e5bae17..176e5ea539cc2 100644 --- a/recipes/bioconductor-svaretro/meta.yaml +++ b/recipes/bioconductor-svaretro/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "svaRetro" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b746169da6f49e96d3f4f50a2826f577 + md5: 56da2ed056a7078a5d9f2883885d5be5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-svaretro", max_pin="x.x") }}' noarch: generic # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structuralvariantannotation >=1.16.0,<1.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structuralvariantannotation >=1.16.0,<1.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-assertthat - r-base - r-dplyr diff --git a/recipes/bioconductor-svm2crmdata/meta.yaml b/recipes/bioconductor-svm2crmdata/meta.yaml index ea67ef2e8f814..7e8ea729d45d5 100644 --- a/recipes/bioconductor-svm2crmdata/meta.yaml +++ b/recipes/bioconductor-svm2crmdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "SVM2CRMdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e1d44ea0446ba41c2f9264ab088461e2 + md5: ce0c6615bfbb9a5a7cf4eeab0bd6199d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-svm2crmdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-svm2crmdata/post-link.sh b/recipes/bioconductor-svm2crmdata/post-link.sh index eb5d1751d701d..b48dec842f852 100644 --- a/recipes/bioconductor-svm2crmdata/post-link.sh +++ b/recipes/bioconductor-svm2crmdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "svm2crmdata-1.32.0" +installBiocDataPackage.sh "svm2crmdata-1.34.0" diff --git a/recipes/bioconductor-svmdo/meta.yaml b/recipes/bioconductor-svmdo/meta.yaml index 37e37aa503896..81368ffa43b1b 100644 --- a/recipes/bioconductor-svmdo/meta.yaml +++ b/recipes/bioconductor-svmdo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "SVMDO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1eb944647d9a94e7d36c9c9b94f03ab4 + md5: 3edf50ad6544537845fe263bb490b9e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-svmdo", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.1.6), BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bsda >=1.2.1' - 'r-caret >=6.0-93' @@ -41,10 +42,10 @@ requirements: - 'r-sjmisc >=2.8.9' - 'r-survival >=3.4-0' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-bsda >=1.2.1' - 'r-caret >=6.0-93' diff --git a/recipes/bioconductor-swath2stats/meta.yaml b/recipes/bioconductor-swath2stats/meta.yaml index 4af9facf1e894..8a7eef17ac912 100644 --- a/recipes/bioconductor-swath2stats/meta.yaml +++ b/recipes/bioconductor-swath2stats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.1" %} +{% set version = "1.32.0" %} {% set name = "SWATH2stats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 78daf29b8044f381022c2ffe6090c9d1 + md5: 3853f9f81af8bc0732ff0e2ceaf43441 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-swath2stats", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-data.table - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-swathxtend/meta.yaml b/recipes/bioconductor-swathxtend/meta.yaml index 60b0a2a5ede76..23a30c62141a5 100644 --- a/recipes/bioconductor-swathxtend/meta.yaml +++ b/recipes/bioconductor-swathxtend/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "SwathXtend" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff355cc022731be52c04ba7c3642fbff + md5: 64b04f78ca92078b9ad63cee65bf012f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-swathxtend", max_pin="x.x") }}' noarch: generic requirements: host: diff --git a/recipes/bioconductor-swfdr/meta.yaml b/recipes/bioconductor-swfdr/meta.yaml index 18c52df32692d..5b1503ab08784 100644 --- a/recipes/bioconductor-swfdr/meta.yaml +++ b/recipes/bioconductor-swfdr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "swfdr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 81f7760a0a60bf0b4316d3c4331254c9 + md5: f873820993a9785dbca1c825b291abfb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-swfdr", max_pin="x.x") }}' noarch: generic # Suggests: dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat requirements: diff --git a/recipes/bioconductor-switchbox/meta.yaml b/recipes/bioconductor-switchbox/meta.yaml index d4d07d56b234b..a1db6b69845ce 100644 --- a/recipes/bioconductor-switchbox/meta.yaml +++ b/recipes/bioconductor-switchbox/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "switchBox" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7459e39ae728ff2ea86be9d8b7dabe7 + md5: 29de2be8446a4f686acf75635f1539b9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-switchbox", max_pin="x.x") }}' requirements: host: - r-base diff --git a/recipes/bioconductor-switchde/meta.yaml b/recipes/bioconductor-switchde/meta.yaml index 34886fcb98e1f..7bd82e5a01c55 100644 --- a/recipes/bioconductor-switchde/meta.yaml +++ b/recipes/bioconductor-switchde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "switchde" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d51bc2a4680829c8c892a5338e9f3357 + md5: 9017dd3162508b4412c30ae21eef9328 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-switchde", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr requirements: host: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 run: - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-synapsis/meta.yaml b/recipes/bioconductor-synapsis/meta.yaml index f0d3daec91acd..448748a38bafa 100644 --- a/recipes/bioconductor-synapsis/meta.yaml +++ b/recipes/bioconductor-synapsis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "synapsis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e13bb0dbe8bcba4ac4dffa389ec31ed8 + md5: 592572937da010f5fbd70fb7fc8e80d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synapsis", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse, BiocStyle requirements: host: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base run: - - 'bioconductor-ebimage >=4.42.0,<4.43.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' - r-base test: commands: diff --git a/recipes/bioconductor-synapter/meta.yaml b/recipes/bioconductor-synapter/meta.yaml index 6f7e59fa0a2d8..74524f15fc539 100644 --- a/recipes/bioconductor-synapter/meta.yaml +++ b/recipes/bioconductor-synapter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "synapter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a1b7bdc0e115bb14644630fdbb324ef + md5: a6c9ade32fbe35d5cb85adc0e9a5322c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synapter", max_pin="x.x") }}' noarch: generic # Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-cleaver >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-cleaver >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-lattice - r-rcolorbrewer - 'r-readr >=0.2' - 'r-rmarkdown >=1.0' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-cleaver >=1.38.0,<1.39.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-cleaver >=1.40.0,<1.41.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-lattice - r-rcolorbrewer diff --git a/recipes/bioconductor-synapterdata/meta.yaml b/recipes/bioconductor-synapterdata/meta.yaml index 032f55aa8709c..a49f7875e36cd 100644 --- a/recipes/bioconductor-synapterdata/meta.yaml +++ b/recipes/bioconductor-synapterdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "synapterdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cfc22e448bd4d28d06535acfc93cea7b + md5: 255aa756f0b6c0c1d95cdfbc889a67a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synapterdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-synapter >=2.24.0,<2.25.0' + - 'bioconductor-synapter >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-synapter >=2.24.0,<2.25.0' + - 'bioconductor-synapter >=2.26.0,<2.27.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-synapterdata/post-link.sh b/recipes/bioconductor-synapterdata/post-link.sh index 2f003cfbef0d2..a426a8749af10 100644 --- a/recipes/bioconductor-synapterdata/post-link.sh +++ b/recipes/bioconductor-synapterdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "synapterdata-1.38.0" +installBiocDataPackage.sh "synapterdata-1.40.0" diff --git a/recipes/bioconductor-synaptome.data/meta.yaml b/recipes/bioconductor-synaptome.data/meta.yaml index 43d4767182ffc..d7106934d6d10 100644 --- a/recipes/bioconductor-synaptome.data/meta.yaml +++ b/recipes/bioconductor-synaptome.data/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.6" %} {% set name = "synaptome.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,21 +13,22 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 4388c63219782a9aa3e384fcdb51ed47 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synaptome.data", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-synaptome.db/meta.yaml b/recipes/bioconductor-synaptome.db/meta.yaml index 95ca7d6cb55e6..1ee54ad6b3834 100644 --- a/recipes/bioconductor-synaptome.db/meta.yaml +++ b/recipes/bioconductor-synaptome.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.99.12" %} +{% set version = "0.99.15" %} {% set name = "synaptome.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 383e2a16688e13d40d1f8e2efd3168ef + md5: 7ed11d61ac8dca86372eeec59b5ab03b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synaptome.db", max_pin="x.x") }}' noarch: generic -# Suggests: rmarkdown, knitr, pander, testthat, devtools, markdown +# Suggests: rmarkdown, knitr, pander, testthat, devtools, markdown, ggplot2 requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - 'bioconductor-synaptome.data >=0.99.0,<0.100.0' - r-base - r-dbi @@ -31,7 +32,7 @@ requirements: - r-rdpack - r-rsqlite run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - 'bioconductor-synaptome.data >=0.99.0,<0.100.0' - r-base - r-dbi @@ -41,7 +42,7 @@ requirements: - r-rdpack - r-rsqlite - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-synaptome.db/post-link.sh b/recipes/bioconductor-synaptome.db/post-link.sh index b5043fedb70cd..f2b7062f649b3 100644 --- a/recipes/bioconductor-synaptome.db/post-link.sh +++ b/recipes/bioconductor-synaptome.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "synaptome.db-0.99.12" +installBiocDataPackage.sh "synaptome.db-0.99.15" diff --git a/recipes/bioconductor-synergyfinder/meta.yaml b/recipes/bioconductor-synergyfinder/meta.yaml index 14e3d5a448a85..9eb18914024ce 100644 --- a/recipes/bioconductor-synergyfinder/meta.yaml +++ b/recipes/bioconductor-synergyfinder/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.8.2" %} +{% set version = "3.10.0" %} {% set name = "synergyfinder" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6323a009044409b49239020be9cb7431 + md5: 8b511fc821bd8e8b344a439f5c641a72 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synergyfinder", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-synextend/meta.yaml b/recipes/bioconductor-synextend/meta.yaml index c2ef67d7cee4d..f46ea364894f7 100644 --- a/recipes/bioconductor-synextend/meta.yaml +++ b/recipes/bioconductor-synextend/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "SynExtend" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e01e05a7fad5a006ee4fa765002a728 + md5: f7ee0b985a06dbd6040329dd264648f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synextend", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, igraph, markdown, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-decipher >=2.28.0,<2.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-decipher >=2.30.0,<2.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-synlet/meta.yaml b/recipes/bioconductor-synlet/meta.yaml index 06b0e3a65a979..42f0e6cfbeb87 100644 --- a/recipes/bioconductor-synlet/meta.yaml +++ b/recipes/bioconductor-synlet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "synlet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ca162c2dc8ffc6452cd92f618e06c010 + md5: f56c634faaae3a0de5e46d18e6617d11 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synlet", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-rankprod >=3.26.0,<3.27.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' - r-base - r-data.table - r-ggplot2 @@ -29,7 +30,7 @@ requirements: - r-patchwork - r-rcolorbrewer run: - - 'bioconductor-rankprod >=3.26.0,<3.27.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' - r-base - r-data.table - r-ggplot2 diff --git a/recipes/bioconductor-synmut/meta.yaml b/recipes/bioconductor-synmut/meta.yaml index 2f76cc1ccdc30..e2cd14510aeba 100644 --- a/recipes/bioconductor-synmut/meta.yaml +++ b/recipes/bioconductor-synmut/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SynMut" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a3be12d75414cd7bcaf19df34e812cc + md5: 485dd0770e2c64ad7ace9a3edf957fe8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-synmut", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-seqinr - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-seqinr - r-stringr diff --git a/recipes/bioconductor-syntenet/meta.yaml b/recipes/bioconductor-syntenet/meta.yaml index d11bda0b6b26f..58a7b99d243ea 100644 --- a/recipes/bioconductor-syntenet/meta.yaml +++ b/recipes/bioconductor-syntenet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.4" %} +{% set version = "1.4.0" %} {% set name = "syntenet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 81bd02bbba83fcb7f62098b5fd2a1fc6 + md5: ab56b637f74d79cfba3dd6aab80b7ac9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-syntenet", max_pin="x.x") }}' # Suggests: BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-ggnetwork - r-ggplot2 @@ -38,10 +39,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - r-base - r-ggnetwork - r-ggplot2 diff --git a/recipes/bioconductor-systempiper/meta.yaml b/recipes/bioconductor-systempiper/meta.yaml index dc1a2c0c6014b..2690b4fb73a2c 100644 --- a/recipes/bioconductor-systempiper/meta.yaml +++ b/recipes/bioconductor-systempiper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.3" %} +{% set version = "2.8.0" %} {% set name = "systemPipeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5abc2d7529b19cae2029a906ab790dde + md5: 67456347870d6c358e1209658cb930d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-systempiper", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools, GenomicFeatures (>= 1.31.3), VariantAnnotation (>= 1.25.11) # SystemRequirements: systemPipeR can be used to run external command-line software (e.g. short read aligners), but the corresponding tool needs to be installed on a system. requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - r-ggplot2 @@ -37,13 +38,13 @@ requirements: - r-stringr - r-yaml run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - r-ggplot2 @@ -58,7 +59,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'systemPipeR: workflow management and report generation environment' - description: 'systemPipeR is a generic data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.' + description: 'systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.' extra: identifiers: - biotools:systempiper diff --git a/recipes/bioconductor-systempiperdata/meta.yaml b/recipes/bioconductor-systempiperdata/meta.yaml index 54390564b9f98..40deed2560a71 100644 --- a/recipes/bioconductor-systempiperdata/meta.yaml +++ b/recipes/bioconductor-systempiperdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "systemPipeRdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: afa259f7cd53e2252902a48dd32df1b9 + md5: 1af59929fb95c3a017b88fce32a4c833 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-systempiperdata", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-jsonlite - r-remotes run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - r-base - r-jsonlite - r-remotes - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-systempiperdata/post-link.sh b/recipes/bioconductor-systempiperdata/post-link.sh index f66ddefe81cd4..5e959d6d140be 100644 --- a/recipes/bioconductor-systempiperdata/post-link.sh +++ b/recipes/bioconductor-systempiperdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "systempiperdata-2.4.0" +installBiocDataPackage.sh "systempiperdata-2.6.0" diff --git a/recipes/bioconductor-systempipeshiny/meta.yaml b/recipes/bioconductor-systempipeshiny/meta.yaml index b2a420c776120..6a0d1fa4130e8 100644 --- a/recipes/bioconductor-systempipeshiny/meta.yaml +++ b/recipes/bioconductor-systempipeshiny/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "systemPipeShiny" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ac48a618b74b5c41efcec02c40c6690 + md5: 8880796c4c2bf213ffa98df7f3f8d164 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-systempipeshiny", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>= 2.2.0), systemPipeRdata (>= 2.0.0), rhandsontable, zip, callr, pushbar, fs, readr, R.utils, DESeq2, SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne, UpSetR, tidyr, esquisse (>= 1.1.0), cicerone requirements: @@ -47,7 +48,7 @@ requirements: - r-shinyjs - r-shinytoastr - r-shinywidgets - - 'r-spscomps >=0.3.2' + - 'r-spscomps >=0.3.3' - 'r-spsutil >=0.2.2' - r-stringr - r-styler @@ -81,7 +82,7 @@ requirements: - r-shinyjs - r-shinytoastr - r-shinywidgets - - 'r-spscomps >=0.3.2' + - 'r-spscomps >=0.3.3' - 'r-spsutil >=0.2.2' - r-stringr - r-styler diff --git a/recipes/bioconductor-systempipetools/meta.yaml b/recipes/bioconductor-systempipetools/meta.yaml index a2aee49bccd5b..f406794a6855d 100644 --- a/recipes/bioconductor-systempipetools/meta.yaml +++ b/recipes/bioconductor-systempipetools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "systemPipeTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9a22e57ab20cf5f5412adaee75b50c2 + md5: e0f74af8b351b49c68cbfed4e9e00adc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-systempipetools", max_pin="x.x") }}' noarch: generic # Suggests: systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocGenerics, Biostrings, methods requirements: host: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-dplyr @@ -38,9 +39,9 @@ requirements: - r-rtsne - r-tibble run: - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-ape - r-base - r-dplyr diff --git a/recipes/bioconductor-tabulamurisdata/meta.yaml b/recipes/bioconductor-tabulamurisdata/meta.yaml index e2cfdf8ef3cd9..c226941259d34 100644 --- a/recipes/bioconductor-tabulamurisdata/meta.yaml +++ b/recipes/bioconductor-tabulamurisdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "TabulaMurisData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c198946ebcce0c1e6c79c65f52a11642 + md5: 39c27cc6646ea3bcdb4637a226b219b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tabulamurisdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tabulamurisdata/post-link.sh b/recipes/bioconductor-tabulamurisdata/post-link.sh index 4f3b46aad6d18..fb80612c77662 100644 --- a/recipes/bioconductor-tabulamurisdata/post-link.sh +++ b/recipes/bioconductor-tabulamurisdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tabulamurisdata-1.18.0" +installBiocDataPackage.sh "tabulamurisdata-1.20.0" diff --git a/recipes/bioconductor-tabulamurissenisdata/meta.yaml b/recipes/bioconductor-tabulamurissenisdata/meta.yaml index 092094204d602..0a4e957526051 100644 --- a/recipes/bioconductor-tabulamurissenisdata/meta.yaml +++ b/recipes/bioconductor-tabulamurissenisdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "TabulaMurisSenisData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6a42dc2dc0bbabe7cfd25c91e11f050 + md5: 6d6120b18adce70e943a3da8e0e577b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tabulamurissenisdata", max_pin="x.x") }}' noarch: generic # Suggests: ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gdata run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-gdata - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tabulamurissenisdata/post-link.sh b/recipes/bioconductor-tabulamurissenisdata/post-link.sh index 8c408f1ad763f..946a2b411a203 100644 --- a/recipes/bioconductor-tabulamurissenisdata/post-link.sh +++ b/recipes/bioconductor-tabulamurissenisdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tabulamurissenisdata-1.6.0" +installBiocDataPackage.sh "tabulamurissenisdata-1.8.0" diff --git a/recipes/bioconductor-tadar/build.sh b/recipes/bioconductor-tadar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tadar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tadar/meta.yaml b/recipes/bioconductor-tadar/meta.yaml new file mode 100644 index 0000000000000..a4d1aea0a2232 --- /dev/null +++ b/recipes/bioconductor-tadar/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "tadar" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 88c91583a351bef3f3d8ca38b51c0c04 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tadar", max_pin="x.x") }}' + noarch: generic +# Suggests: BiocStyle, covr, knitr, limma, rmarkdown, testthat (>= 3.0.0), tidyverse +requirements: + host: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-ggplot2 + - r-rlang + run: + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - r-base + - r-ggplot2 + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Transcriptome Analysis of Differential Allelic Representation' + description: 'This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + diff --git a/recipes/bioconductor-tadcompare/meta.yaml b/recipes/bioconductor-tadcompare/meta.yaml index 7bde3530ca42a..db49b519eb40d 100644 --- a/recipes/bioconductor-tadcompare/meta.yaml +++ b/recipes/bioconductor-tadcompare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "TADCompare" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e72268cea3f87bc16d914b4907ebcf4 + md5: 92966a38a0c202cfe7dbd09bb83b23b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tadcompare", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, rGREAT, SpectralTAD requirements: host: - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-base - r-cluster - r-cowplot @@ -35,7 +36,7 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-hiccompare >=1.22.0,<1.23.0' + - 'bioconductor-hiccompare >=1.24.0,<1.25.0' - r-base - r-cluster - r-cowplot diff --git a/recipes/bioconductor-tanggle/meta.yaml b/recipes/bioconductor-tanggle/meta.yaml index 695da10676f27..f1e803a007b94 100644 --- a/recipes/bioconductor-tanggle/meta.yaml +++ b/recipes/bioconductor-tanggle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "tanggle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5582a23deea9db3af347e42b327e895f + md5: d23bc70f7c920e00bb14a3d05e8cfdea build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tanggle", max_pin="x.x") }}' noarch: generic # Suggests: tinytest, BiocStyle, ggimage, knitr, rmarkdown requirements: host: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - 'r-ape >=5.0' - r-base - 'r-ggplot2 >=2.2.0' - 'r-phangorn >=2.5' run: - - 'bioconductor-ggtree >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' - 'r-ape >=5.0' - r-base - 'r-ggplot2 >=2.2.0' diff --git a/recipes/bioconductor-tapseq/meta.yaml b/recipes/bioconductor-tapseq/meta.yaml index 112e6d082f8aa..39c94bc15447d 100644 --- a/recipes/bioconductor-tapseq/meta.yaml +++ b/recipes/bioconductor-tapseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.1" %} {% set name = "TAPseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,41 +11,42 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0acc6577f95cf45253359a38029de75a + md5: 423853e9c2015594d616f9315d5c217d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tapseq", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle # SystemRequirements: Primer3 (>= 2.5.0), BLAST+ (>=2.6.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-tidyr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-dplyr - r-tidyr diff --git a/recipes/bioconductor-target/meta.yaml b/recipes/bioconductor-target/meta.yaml index 48f960fb213e3..9a6b3f33d033d 100644 --- a/recipes/bioconductor-target/meta.yaml +++ b/recipes/bioconductor-target/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "target" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5d1cce236aa72d723a2b0db48f97fb88 + md5: 96ca9fa7bed738941cd930b5e7491bc2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-target", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-matrixstats - r-shiny run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-matrixstats - r-shiny diff --git a/recipes/bioconductor-targetdecoy/meta.yaml b/recipes/bioconductor-targetdecoy/meta.yaml index 6a31ddf07787a..a48d89bad2795 100644 --- a/recipes/bioconductor-targetdecoy/meta.yaml +++ b/recipes/bioconductor-targetdecoy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "TargetDecoy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5b99cde4bb8d267e2f094778feac42c + md5: ff49065b40e049f06bbe1ad9c74200fc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetdecoy", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra, testthat (>= 3.0.0), covr requirements: host: - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-ggpubr - r-miniui - r-shiny run: - - 'bioconductor-mzid >=1.38.0,<1.39.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' + - 'bioconductor-mzid >=1.40.0,<1.41.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-ggpubr diff --git a/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml index 3ad409739d7ea..1a5256aad3781 100644 --- a/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.1" %} {% set name = "targetscan.Hs.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d10569315400f6c1b95ad2688632b6de build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetscan.hs.eg.db", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml b/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml index 3a214e634c698..0a4db556725a7 100644 --- a/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.1" %} {% set name = "targetscan.Mm.eg.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1830815c9d1383739f1ff152da0508c5 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetscan.mm.eg.db", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetscore/meta.yaml b/recipes/bioconductor-targetscore/meta.yaml index c50e4e01c9a53..b57d457d83c63 100644 --- a/recipes/bioconductor-targetscore/meta.yaml +++ b/recipes/bioconductor-targetscore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "TargetScore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11b4e6f2896e28dac5a4b08485769f2a + md5: 92d3b6ca138c6c3081262a758ec63766 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetscore", max_pin="x.x") }}' noarch: generic # Suggests: TargetScoreData, gplots, Biobase, GEOquery requirements: diff --git a/recipes/bioconductor-targetscoredata/meta.yaml b/recipes/bioconductor-targetscoredata/meta.yaml index d519bd5b385f1..2da4addce3f26 100644 --- a/recipes/bioconductor-targetscoredata/meta.yaml +++ b/recipes/bioconductor-targetscoredata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "TargetScoreData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63ccf68833f45d1a853a719046cf9def + md5: 61084f230f2c3dedb27988867f07f50f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetscoredata", max_pin="x.x") }}' noarch: generic # Suggests: TargetScore, gplots requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetscoredata/post-link.sh b/recipes/bioconductor-targetscoredata/post-link.sh index ffe6ca3e5bfb0..80e2477b8de59 100644 --- a/recipes/bioconductor-targetscoredata/post-link.sh +++ b/recipes/bioconductor-targetscoredata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "targetscoredata-1.36.0" +installBiocDataPackage.sh "targetscoredata-1.38.0" diff --git a/recipes/bioconductor-targetsearch/meta.yaml b/recipes/bioconductor-targetsearch/meta.yaml index a118d4918a513..c554006c9e67c 100644 --- a/recipes/bioconductor-targetsearch/meta.yaml +++ b/recipes/bioconductor-targetsearch/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.1" %} {% set name = "TargetSearch" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2ecd6d2c39b8705b55009a4e383dcf5 + md5: 652009cfa3df492780c9ea45715df0b9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetsearch", max_pin="x.x") }}' # Suggests: TargetSearchData, BiocStyle, knitr, tinytest requirements: host: diff --git a/recipes/bioconductor-targetsearchdata/meta.yaml b/recipes/bioconductor-targetsearchdata/meta.yaml index 91fb3650656ea..df32deec7a9b3 100644 --- a/recipes/bioconductor-targetsearchdata/meta.yaml +++ b/recipes/bioconductor-targetsearchdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "TargetSearchData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6dd9996121d44e6f753ce68434de7aad + md5: 96bbec70706d8adcf4ee321261620d79 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-targetsearchdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-targetsearchdata/post-link.sh b/recipes/bioconductor-targetsearchdata/post-link.sh index d1539a16f580a..1f74c111549e7 100644 --- a/recipes/bioconductor-targetsearchdata/post-link.sh +++ b/recipes/bioconductor-targetsearchdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "targetsearchdata-1.38.0" +installBiocDataPackage.sh "targetsearchdata-1.40.0" diff --git a/recipes/bioconductor-tartare/meta.yaml b/recipes/bioconductor-tartare/meta.yaml index 0e552a41f409a..880886341b0d0 100644 --- a/recipes/bioconductor-tartare/meta.yaml +++ b/recipes/bioconductor-tartare/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "tartare" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 10b4601e60890e48d47840d2a4f03a22 + md5: 869743e16f05bc962de518ca925750d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tartare", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, tools requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tartare/post-link.sh b/recipes/bioconductor-tartare/post-link.sh index 41396cdf35cae..0017d5f89c426 100644 --- a/recipes/bioconductor-tartare/post-link.sh +++ b/recipes/bioconductor-tartare/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tartare-1.14.0" +installBiocDataPackage.sh "tartare-1.16.0" diff --git a/recipes/bioconductor-tbsignatureprofiler/meta.yaml b/recipes/bioconductor-tbsignatureprofiler/meta.yaml index 14eb668a3cdfd..4ef88100aca8b 100644 --- a/recipes/bioconductor-tbsignatureprofiler/meta.yaml +++ b/recipes/bioconductor-tbsignatureprofiler/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "TBSignatureProfiler" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a00e9d71be544060c7eda4f08ba8322e + md5: 1cd38948c20b0f43904a8ff204f2940d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tbsignatureprofiler", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, caret, circlize, class, covr, dplyr, e1071, glmnet, HGNChelper, impute, knitr, lintr, MASS, plyr, pROC, randomForest, rmarkdown, shiny, spelling, sva, testthat requirements: host: - - 'bioconductor-assign >=1.36.0,<1.37.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singscore >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-assign >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singscore >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-gdata @@ -40,15 +41,15 @@ requirements: - r-rlang - r-rocit run: - - 'bioconductor-assign >=1.36.0,<1.37.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singscore >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-assign >=1.38.0,<1.39.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singscore >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-gdata diff --git a/recipes/bioconductor-tbx20bamsubset/meta.yaml b/recipes/bioconductor-tbx20bamsubset/meta.yaml index cb3222da9f6b5..18a9421aaee7e 100644 --- a/recipes/bioconductor-tbx20bamsubset/meta.yaml +++ b/recipes/bioconductor-tbx20bamsubset/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "TBX20BamSubset" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b8761f75b20b32450d6cae46dc063a9 + md5: c158901ec6203e85569c600efb335ccf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tbx20bamsubset", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-xtable run: - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-xtable - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tbx20bamsubset/post-link.sh b/recipes/bioconductor-tbx20bamsubset/post-link.sh index fbddcded07bfd..7c52406af39b8 100644 --- a/recipes/bioconductor-tbx20bamsubset/post-link.sh +++ b/recipes/bioconductor-tbx20bamsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tbx20bamsubset-1.36.0" +installBiocDataPackage.sh "tbx20bamsubset-1.38.0" diff --git a/recipes/bioconductor-tcc/build.sh b/recipes/bioconductor-tcc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tcc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tcc/meta.yaml b/recipes/bioconductor-tcc/meta.yaml new file mode 100644 index 0000000000000..a070ac06036b2 --- /dev/null +++ b/recipes/bioconductor-tcc/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.42.0" %} +{% set name = "TCC" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e36a17d628a68654296227603e0678da +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcc", max_pin="x.x") }}' + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' + - r-base + run: + - 'bioconductor-bayseq >=2.36.0,<2.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'TCC: Differential expression analysis for tag count data with robust normalization strategies' + description: 'This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in depended packages.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + diff --git a/recipes/bioconductor-tcgabiolinks/meta.yaml b/recipes/bioconductor-tcgabiolinks/meta.yaml index 97ec14cf72ff7..a5d528634ec4a 100644 --- a/recipes/bioconductor-tcgabiolinks/meta.yaml +++ b/recipes/bioconductor-tcgabiolinks/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.28.3" %} +{% set version = "2.30.0" %} {% set name = "TCGAbiolinks" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef3da29fc90f15d770fef2ae20629127 + md5: 91536d6234ebd992dac8102393c363d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgabiolinks", max_pin="x.x") }}' noarch: generic # Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinksgui.data >=1.20.0,<1.21.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinksgui.data >=1.22.0,<1.23.0' - r-base - r-data.table - 'r-downloader >=0.4' @@ -46,12 +47,12 @@ requirements: - 'r-xml >=3.98.0' - r-xml2 run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tcgabiolinksgui.data >=1.20.0,<1.21.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tcgabiolinksgui.data >=1.22.0,<1.23.0' - r-base - r-data.table - 'r-downloader >=0.4' diff --git a/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml b/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml index cf31353641906..a599989612e1c 100644 --- a/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml +++ b/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TCGAbiolinksGUI.data" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0764549e842b85e9ed17bb0e27b1c54 + md5: bd2042c0064583d666364a52ce3be17e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgabiolinksgui.data", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, readr, DT requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh b/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh index cd1bdb8413e09..3ce61f3013f98 100644 --- a/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh +++ b/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgabiolinksgui.data-1.20.0" +installBiocDataPackage.sh "tcgabiolinksgui.data-1.22.0" diff --git a/recipes/bioconductor-tcgacrcmirna/meta.yaml b/recipes/bioconductor-tcgacrcmirna/meta.yaml index 77c92d198b9ee..d5aa585eae22e 100644 --- a/recipes/bioconductor-tcgacrcmirna/meta.yaml +++ b/recipes/bioconductor-tcgacrcmirna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TCGAcrcmiRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a286cf4adf594bccf4910c3445e2901c + md5: 451d09b5ec341d7e92211a1d42c35947 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgacrcmirna", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgacrcmirna/post-link.sh b/recipes/bioconductor-tcgacrcmirna/post-link.sh index 5a4a98bea980a..8c432e9a0c322 100644 --- a/recipes/bioconductor-tcgacrcmirna/post-link.sh +++ b/recipes/bioconductor-tcgacrcmirna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgacrcmirna-1.20.0" +installBiocDataPackage.sh "tcgacrcmirna-1.22.0" diff --git a/recipes/bioconductor-tcgacrcmrna/meta.yaml b/recipes/bioconductor-tcgacrcmrna/meta.yaml index f8b1e5d7b7be0..e4c24ff6fed90 100644 --- a/recipes/bioconductor-tcgacrcmrna/meta.yaml +++ b/recipes/bioconductor-tcgacrcmrna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TCGAcrcmRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d3f199714f9dba5ed0838af4e6646c7e + md5: bb9300e6ad6e4e5435a31487fdc22ed6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgacrcmrna", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgacrcmrna/post-link.sh b/recipes/bioconductor-tcgacrcmrna/post-link.sh index 5efda522e33cd..53b5ac1ad6709 100644 --- a/recipes/bioconductor-tcgacrcmrna/post-link.sh +++ b/recipes/bioconductor-tcgacrcmrna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgacrcmrna-1.20.0" +installBiocDataPackage.sh "tcgacrcmrna-1.22.0" diff --git a/recipes/bioconductor-tcgamethylation450k/meta.yaml b/recipes/bioconductor-tcgamethylation450k/meta.yaml index 3bb05d8e97048..521516a508d02 100644 --- a/recipes/bioconductor-tcgamethylation450k/meta.yaml +++ b/recipes/bioconductor-tcgamethylation450k/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "TCGAMethylation450k" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d230a3e839f3ac33e404453c46dfa4f + md5: e913aa3b85d5cd1d0b27a346daf8c9ee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgamethylation450k", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgamethylation450k/post-link.sh b/recipes/bioconductor-tcgamethylation450k/post-link.sh index da7290bd32706..7b0a1b521a206 100644 --- a/recipes/bioconductor-tcgamethylation450k/post-link.sh +++ b/recipes/bioconductor-tcgamethylation450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgamethylation450k-1.36.0" +installBiocDataPackage.sh "tcgamethylation450k-1.38.0" diff --git a/recipes/bioconductor-tcgautils/meta.yaml b/recipes/bioconductor-tcgautils/meta.yaml index 946c3853a6883..472458d809d70 100644 --- a/recipes/bioconductor-tcgautils/meta.yaml +++ b/recipes/bioconductor-tcgautils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.2" %} +{% set version = "1.22.0" %} {% set name = "TCGAutils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61dc029c8eecfc34d14907b19d396360 + md5: 33d917253a210382a92537383bb4ee4f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgautils", max_pin="x.x") }}' noarch: generic -# Suggests: AnnotationHub, BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene +# Suggests: AnnotationHub, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicdatacommons >=1.24.0,<1.25.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rvest - r-stringr - r-xml2 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicdatacommons >=1.24.0,<1.25.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-rvest - r-stringr diff --git a/recipes/bioconductor-tcgaworkflowdata/meta.yaml b/recipes/bioconductor-tcgaworkflowdata/meta.yaml index 4401e938f7cc9..8987d3058c1b2 100644 --- a/recipes/bioconductor-tcgaworkflowdata/meta.yaml +++ b/recipes/bioconductor-tcgaworkflowdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "TCGAWorkflowData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12be13d34d28928864db32c639257777 + md5: cbba498f1922aeedadf96a1911a81751 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcgaworkflowdata", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, pander, testthat +# Suggests: knitr, rmarkdown, pander, testthat, BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tcgaworkflowdata/post-link.sh b/recipes/bioconductor-tcgaworkflowdata/post-link.sh index 66078bdc1c486..1f5635c08afec 100644 --- a/recipes/bioconductor-tcgaworkflowdata/post-link.sh +++ b/recipes/bioconductor-tcgaworkflowdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgaworkflowdata-1.24.0" +installBiocDataPackage.sh "tcgaworkflowdata-1.26.0" diff --git a/recipes/bioconductor-tcseq/meta.yaml b/recipes/bioconductor-tcseq/meta.yaml index bd5393e7d4a55..59a57399ee0d5 100644 --- a/recipes/bioconductor-tcseq/meta.yaml +++ b/recipes/bioconductor-tcseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.23.0" %} +{% set version = "1.26.0" %} {% set name = "TCseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0bd128ed62aa6f6d75ea1083747b9f60 + md5: f5b63a6d1b40c82f8ddc86cc2abdb89b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tcseq", max_pin="x.x") }}' noarch: generic # Suggests: testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-e1071 @@ -35,13 +36,13 @@ requirements: - r-locfit - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cluster - r-e1071 @@ -55,6 +56,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Time course sequencing data analysis' - description: 'Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of temporal patterns of time course data.' + description: 'Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of the temporal patterns of time course data.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-tdbasedufe/meta.yaml b/recipes/bioconductor-tdbasedufe/meta.yaml index 0cc6b899026b0..52baeee1720db 100644 --- a/recipes/bioconductor-tdbasedufe/meta.yaml +++ b/recipes/bioconductor-tdbasedufe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "TDbasedUFE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1e0064920f4edfe8d052c3db37c7b2f + md5: 5557e1128d1d6ffab09670bf90b8947c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tdbasedufe", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-mofadata >=1.16.0,<1.17.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-tximportdata >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-mofadata >=1.18.0,<1.19.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-tximportdata >=1.30.0,<1.31.0' - r-base - r-readr - r-rtensor - r-shiny run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-mofadata >=1.16.0,<1.17.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' - - 'bioconductor-tximportdata >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-mofadata >=1.18.0,<1.19.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' + - 'bioconductor-tximportdata >=1.30.0,<1.31.0' - r-base - r-readr - r-rtensor diff --git a/recipes/bioconductor-tdbasedufeadv/meta.yaml b/recipes/bioconductor-tdbasedufeadv/meta.yaml index 9cc8358eef686..3ec6ded747c03 100644 --- a/recipes/bioconductor-tdbasedufeadv/meta.yaml +++ b/recipes/bioconductor-tdbasedufeadv/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "TDbasedUFEadv" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f2dc73b489be0993668b18e618fbb3d + md5: 6f873403b62f756c6b8424cfeb2409c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tdbasedufeadv", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 3.0.0), RTCGA.rnaseq, RTCGA.clinical, BiocStyle, MOFAdata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtcga >=1.30.0,<1.31.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-tdbasedufe >=1.0.0,<1.1.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-tdbasedufe >=1.2.0,<1.3.0' - r-base - r-enrichr - r-hash - r-rtensor - r-shiny run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-enrichplot >=1.20.0,<1.21.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rtcga >=1.30.0,<1.31.0' - - 'bioconductor-stringdb >=2.12.0,<2.13.0' - - 'bioconductor-tdbasedufe >=1.0.0,<1.1.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-dose >=3.28.0,<3.29.0' + - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - 'bioconductor-tdbasedufe >=1.2.0,<1.3.0' - r-base - r-enrichr - r-hash diff --git a/recipes/bioconductor-tekrabber/meta.yaml b/recipes/bioconductor-tekrabber/meta.yaml index 4e1051f1e4808..14842af5d7cd6 100644 --- a/recipes/bioconductor-tekrabber/meta.yaml +++ b/recipes/bioconductor-tekrabber/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "TEKRABber" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20b586d92efd367abd9c29d48d4fb9c7 + md5: 145026d8a5e02ec94f8a2a1f5405851e build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, ggpubr, rmarkdown, shiny, knitr, testthat (>= 3.0.0) + run_exports: '{{ pin_subpackage("bioconductor-tekrabber", max_pin="x.x") }}' +# Suggests: BiocStyle, bslib, ggplot2, ggpubr, plotly, rmarkdown, shiny, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-scbn >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-scbn >=1.20.0,<1.21.0' - r-base - r-dplyr - r-magrittr @@ -32,11 +32,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-apeglm >=1.22.0,<1.23.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-scbn >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-apeglm >=1.24.0,<1.25.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-scbn >=1.20.0,<1.21.0' - r-base - r-dplyr - r-magrittr @@ -50,8 +49,8 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'LGPL (>=3)' summary: 'An R package estimates the correlations of orthologs and transposable elements between two species' description: 'TEKRABber is made to provide a user-friendly pipeline for comparing orthologs and transposable elements (TEs) between two species. It considers the orthology confidence between two species from BioMart to normalize expression counts and detect differentially expressed orthologs/TEs. Then it provides one to one correlation analysis for desired orthologs and TEs. There is also an app function to have a first insight on the result. Users can prepare orthologs/TEs RNA-seq expression data by their own preference to run TEKRABber following the data structure mentioned in the vignettes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' diff --git a/recipes/bioconductor-tenxbraindata/meta.yaml b/recipes/bioconductor-tenxbraindata/meta.yaml index db75aa07a19f1..58bd199e51f1a 100644 --- a/recipes/bioconductor-tenxbraindata/meta.yaml +++ b/recipes/bioconductor-tenxbraindata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TENxBrainData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 74f64ec6654482787dcdc4d6edf085c0 + md5: 1fa1b93ab8d144b860c83dc5741490a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxbraindata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tenxbraindata/post-link.sh b/recipes/bioconductor-tenxbraindata/post-link.sh index a8864917b11ce..5358e416f4cff 100644 --- a/recipes/bioconductor-tenxbraindata/post-link.sh +++ b/recipes/bioconductor-tenxbraindata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxbraindata-1.20.0" +installBiocDataPackage.sh "tenxbraindata-1.22.0" diff --git a/recipes/bioconductor-tenxbusdata/meta.yaml b/recipes/bioconductor-tenxbusdata/meta.yaml index 6460871ebb1bd..6b7ec47703e37 100644 --- a/recipes/bioconductor-tenxbusdata/meta.yaml +++ b/recipes/bioconductor-tenxbusdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "TENxBUSData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ef9324a12e6e70e28a16def5f6e8f8f + md5: 35be2bd3c806b055fc9463e8f135dd32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxbusdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tenxbusdata/post-link.sh b/recipes/bioconductor-tenxbusdata/post-link.sh index 097377fc14852..dc2ed75ffb6a5 100644 --- a/recipes/bioconductor-tenxbusdata/post-link.sh +++ b/recipes/bioconductor-tenxbusdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxbusdata-1.14.0" +installBiocDataPackage.sh "tenxbusdata-1.16.0" diff --git a/recipes/bioconductor-tenxio/meta.yaml b/recipes/bioconductor-tenxio/meta.yaml index 3b6ee3533653c..d48c1bc5f0f43 100644 --- a/recipes/bioconductor-tenxio/meta.yaml +++ b/recipes/bioconductor-tenxio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "TENxIO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 156715deb84301cc0c1deaf2bea74a59 + md5: 98a845f55877d89b82b9a153fe54a41f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxio", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, DropletTestFiles, ExperimentHub, HDF5Array, knitr, RaggedExperiment, rhdf5, rmarkdown, Rsamtools, tinytest requirements: host: - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-r.utils - r-rcurl - r-readr run: - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocio >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocio >=1.12.0,<1.13.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-r.utils diff --git a/recipes/bioconductor-tenxpbmcdata/meta.yaml b/recipes/bioconductor-tenxpbmcdata/meta.yaml index 0663453a17cb5..7b29159a6f5b5 100644 --- a/recipes/bioconductor-tenxpbmcdata/meta.yaml +++ b/recipes/bioconductor-tenxpbmcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "TENxPBMCData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6902ddadd45f76cce7e73228ed4bdcaf + md5: 3e6c961a01998667f37de542858dbc09 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxpbmcdata", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, snow, BiocFileCache, BiocParallel requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tenxpbmcdata/post-link.sh b/recipes/bioconductor-tenxpbmcdata/post-link.sh index 21c88cd40324e..eb9fbb18d674f 100644 --- a/recipes/bioconductor-tenxpbmcdata/post-link.sh +++ b/recipes/bioconductor-tenxpbmcdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxpbmcdata-1.18.0" +installBiocDataPackage.sh "tenxpbmcdata-1.20.0" diff --git a/recipes/bioconductor-tenxplore/meta.yaml b/recipes/bioconductor-tenxplore/meta.yaml index cc37d8d989d1f..f2c5019b0eebf 100644 --- a/recipes/bioconductor-tenxplore/meta.yaml +++ b/recipes/bioconductor-tenxplore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "tenXplore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96c18d808ccb0106111ce4bf1d00ec5c + md5: 13e1778f8b644661a521bb832af6e7d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxplore", max_pin="x.x") }}' noarch: generic # Suggests: org.Hs.eg.db, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-ontoproc >=1.22.0,<1.23.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-restfulse >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-ontoproc >=1.24.0,<1.25.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-restfulse >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrixstats - r-shiny run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-ontoproc >=1.22.0,<1.23.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-restfulse >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-ontoproc >=1.24.0,<1.25.0' + - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-restfulse >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrixstats - r-shiny diff --git a/recipes/bioconductor-tenxvisiumdata/meta.yaml b/recipes/bioconductor-tenxvisiumdata/meta.yaml index 449adeb44e95b..6c8051114d57a 100644 --- a/recipes/bioconductor-tenxvisiumdata/meta.yaml +++ b/recipes/bioconductor-tenxvisiumdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "TENxVisiumData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd391f3b1849f658578a44cfe2aec13b + md5: f578add429847efff027a61b1749b9b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tenxvisiumdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tenxvisiumdata/post-link.sh b/recipes/bioconductor-tenxvisiumdata/post-link.sh index 2d628409ccf36..1921065bf2398 100644 --- a/recipes/bioconductor-tenxvisiumdata/post-link.sh +++ b/recipes/bioconductor-tenxvisiumdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxvisiumdata-1.8.0" +installBiocDataPackage.sh "tenxvisiumdata-1.10.0" diff --git a/recipes/bioconductor-teqc/meta.yaml b/recipes/bioconductor-teqc/meta.yaml index a85b72af6bb87..062c2e16d092a 100644 --- a/recipes/bioconductor-teqc/meta.yaml +++ b/recipes/bioconductor-teqc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "4.22.0" %} +{% set version = "4.24.0" %} {% set name = "TEQC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1972bf594cded1f47f9fe7d9e6c9e2a0 + md5: 02976837ccda44f13a0a43b9de17ea81 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-teqc", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-hwriter run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-hwriter test: diff --git a/recipes/bioconductor-ternarynet/meta.yaml b/recipes/bioconductor-ternarynet/meta.yaml index 629108221b0ee..bd39c481f7479 100644 --- a/recipes/bioconductor-ternarynet/meta.yaml +++ b/recipes/bioconductor-ternarynet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "ternarynet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1aa77c1b9619ead34f9b06e00d761028 + md5: 1ee0ac867354eedf8cf756d94be52589 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ternarynet", max_pin="x.x") }}' # Suggests: testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-igraph - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - r-base - r-igraph build: diff --git a/recipes/bioconductor-terratcgadata/meta.yaml b/recipes/bioconductor-terratcgadata/meta.yaml index 2cf2e42ef005b..d5498e1fc2f25 100644 --- a/recipes/bioconductor-terratcgadata/meta.yaml +++ b/recipes/bioconductor-terratcgadata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "terraTCGAdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,36 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fceb4c4282a26c126a6b91f30c130904 + md5: b5803a78627bbe874b8cd8ae0a147979 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-terratcgadata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-anvil >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-dplyr - r-readr - r-tidyr run: - - 'bioconductor-anvil >=1.12.0,<1.13.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-raggedexperiment >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-tcgautils >=1.20.0,<1.21.0' + - 'bioconductor-anvil >=1.14.0,<1.15.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-tcgautils >=1.22.0,<1.23.0' - r-base - r-dplyr - r-readr diff --git a/recipes/bioconductor-test1cdf/meta.yaml b/recipes/bioconductor-test1cdf/meta.yaml index a2679d123c71d..9cf00a9e907da 100644 --- a/recipes/bioconductor-test1cdf/meta.yaml +++ b/recipes/bioconductor-test1cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8c94708b49ccc7bbf127485155970b9b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-test1cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-test2cdf/meta.yaml b/recipes/bioconductor-test2cdf/meta.yaml index 4ac7f876c924e..74ae9fa6eb04c 100644 --- a/recipes/bioconductor-test2cdf/meta.yaml +++ b/recipes/bioconductor-test2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0d1c20d6450dfc83d62214be9dc46b5f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-test2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-test3cdf/meta.yaml b/recipes/bioconductor-test3cdf/meta.yaml index 9316b144dff78..4f62a9f138b91 100644 --- a/recipes/bioconductor-test3cdf/meta.yaml +++ b/recipes/bioconductor-test3cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test3cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9904e7fa6599f68400a9b77d0caa159a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-test3cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-test3probe/meta.yaml b/recipes/bioconductor-test3probe/meta.yaml index 06620f2d8c54c..4cf7c7451737f 100644 --- a/recipes/bioconductor-test3probe/meta.yaml +++ b/recipes/bioconductor-test3probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "test3probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ffcbfee4e5c486fd03b2b9b64820340c build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-test3probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tfarm/meta.yaml b/recipes/bioconductor-tfarm/meta.yaml index 05573723829ec..f68855b990209 100644 --- a/recipes/bioconductor-tfarm/meta.yaml +++ b/recipes/bioconductor-tfarm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TFARM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8cd4be3928a6737c36ae2a17d8d52d3 + md5: bf2876d47da6baa42642dc5492ef7a94 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tfarm", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, plyr requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-arules - r-base - r-fields - r-gplots - r-stringr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-arules - r-base - r-fields diff --git a/recipes/bioconductor-tfbstools/meta.yaml b/recipes/bioconductor-tfbstools/meta.yaml index 21998ea8662db..73200d3f9cb99 100644 --- a/recipes/bioconductor-tfbstools/meta.yaml +++ b/recipes/bioconductor-tfbstools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "TFBSTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0973f29eb2d02f3bbcdf438e79b6414 + md5: f2395c8153c4820e3cebb53a9eda94d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tfbstools", max_pin="x.x") }}' # Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0), rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cner >=1.36.0,<1.37.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cner >=1.38.0,<1.39.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-catools >=1.17.1' - 'r-dbi >=0.6' @@ -44,20 +45,20 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-cner >=1.36.0,<1.37.0' - - 'bioconductor-dirichletmultinomial >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqlogo >=1.66.0,<1.67.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-cner >=1.38.0,<1.39.0' + - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - 'r-catools >=1.17.1' - 'r-dbi >=0.6' diff --git a/recipes/bioconductor-tfea.chip/meta.yaml b/recipes/bioconductor-tfea.chip/meta.yaml index b3dc30610b2c9..de5695cd80ca7 100644 --- a/recipes/bioconductor-tfea.chip/meta.yaml +++ b/recipes/bioconductor-tfea.chip/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TFEA.ChIP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c3bebfd9a9424c0585ba6351e1ebfca + md5: 86f7ae5bb16ceaf9fbdc01d0cc606c42 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tfea.chip", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-dplyr - r-r.utils run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - r-dplyr - r-r.utils diff --git a/recipes/bioconductor-tfhaz/meta.yaml b/recipes/bioconductor-tfhaz/meta.yaml index 95a094ff1d190..62729c28422f7 100644 --- a/recipes/bioconductor-tfhaz/meta.yaml +++ b/recipes/bioconductor-tfhaz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TFHAZ" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c80ec5e4711cc07bf27ff180942cc78c + md5: 4befbb77bb7eb52b220a2472010cab25 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tfhaz", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-orfik >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-orfik >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-orfik >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-orfik >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-tfutils/meta.yaml b/recipes/bioconductor-tfutils/meta.yaml index c5d9167c87b4c..e81f9833f5aea 100644 --- a/recipes/bioconductor-tfutils/meta.yaml +++ b/recipes/bioconductor-tfutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TFutils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f91497509b64adadcb5babf7a2cc2f86 + md5: a2e83bbaafa0e47d7dbbd17385bd15fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tfutils", max_pin="x.x") }}' noarch: generic # Suggests: knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dplyr - r-dt @@ -36,11 +37,11 @@ requirements: - r-rjson - r-shiny run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - r-base - r-dplyr - r-dt diff --git a/recipes/bioconductor-tidybulk/meta.yaml b/recipes/bioconductor-tidybulk/meta.yaml index 0840813a280b1..af300d3308e74 100644 --- a/recipes/bioconductor-tidybulk/meta.yaml +++ b/recipes/bioconductor-tidybulk/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.2" %} {% set name = "tidybulk" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bdaa13b16dbafba7b0bbcc13ff4d810f + md5: e1a43f9392049059ec6b67930277df16 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidybulk", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA +# Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - - r-dplyr + - 'r-dplyr >=1.1.0' - r-lifecycle - r-magrittr + - r-matrix - r-purrr - r-readr - r-rlang @@ -39,16 +41,18 @@ requirements: - r-tibble - r-tidyr - r-tidyselect + - 'r-ttservice >=0.3.6' run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-crayon - - r-dplyr + - 'r-dplyr >=1.1.0' - r-lifecycle - r-magrittr + - r-matrix - r-purrr - r-readr - r-rlang @@ -58,6 +62,7 @@ requirements: - r-tibble - r-tidyr - r-tidyselect + - 'r-ttservice >=0.3.6' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tidysinglecellexperiment/meta.yaml b/recipes/bioconductor-tidysinglecellexperiment/meta.yaml index b73d09371bcbe..e37d659138088 100644 --- a/recipes/bioconductor-tidysinglecellexperiment/meta.yaml +++ b/recipes/bioconductor-tidysinglecellexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "tidySingleCellExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6cf2a2b42418731f758bce9df31de473 + md5: 4f0e61cb23c56df988e1a731a452eb2d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidysinglecellexperiment", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, testthat, knitr, markdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, EnsDb.Hsapiens.v86 +# Suggests: BiocStyle, testthat, knitr, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-dplyr @@ -34,6 +35,7 @@ requirements: - r-magrittr - r-matrix - r-pillar + - r-pkgconfig - r-plotly - r-purrr - r-rlang @@ -41,12 +43,12 @@ requirements: - r-tibble - r-tidyr - r-tidyselect - - r-ttservice + - 'r-ttservice >=0.3.8' - r-vctrs run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-dplyr @@ -57,6 +59,7 @@ requirements: - r-magrittr - r-matrix - r-pillar + - r-pkgconfig - r-plotly - r-purrr - r-rlang @@ -64,7 +67,7 @@ requirements: - r-tibble - r-tidyr - r-tidyselect - - r-ttservice + - 'r-ttservice >=0.3.8' - r-vctrs test: commands: @@ -73,6 +76,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Brings SingleCellExperiment to the Tidyverse' - description: 'tidySingleCellExperiment is an adapter that abstracts the ''SingleCellExperiment'' container in the form of a tibble and allows the data manipulation, plotting and nesting using ''tidyverse''.' + description: '''tidySingleCellExperiment'' is an adapter that abstracts the ''SingleCellExperiment'' container in the form of a ''tibble''. This allows *tidy* data manipulation, nesting, and plotting. For example, a ''tidySingleCellExperiment'' is directly compatible with functions from ''tidyverse'' packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-tidysummarizedexperiment/meta.yaml b/recipes/bioconductor-tidysummarizedexperiment/meta.yaml index 9f720354b8f60..e1c10a2c75d43 100644 --- a/recipes/bioconductor-tidysummarizedexperiment/meta.yaml +++ b/recipes/bioconductor-tidysummarizedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "tidySummarizedExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4776d530e2487d78c6b502823d963c48 + md5: a7962f90a1d5e582e22a5c6e1f5e46da build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidysummarizedexperiment", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, markdown requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-dplyr @@ -32,6 +33,7 @@ requirements: - r-lifecycle - r-magrittr - r-pillar + - r-pkgconfig - r-plotly - r-purrr - r-rlang @@ -39,10 +41,11 @@ requirements: - 'r-tibble >=3.0.4' - r-tidyr - r-tidyselect + - r-ttservice - r-vctrs run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-dplyr @@ -52,6 +55,7 @@ requirements: - r-lifecycle - r-magrittr - r-pillar + - r-pkgconfig - r-plotly - r-purrr - r-rlang @@ -59,6 +63,7 @@ requirements: - 'r-tibble >=3.0.4' - r-tidyr - r-tidyselect + - r-ttservice - r-vctrs test: commands: @@ -67,6 +72,6 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Brings SummarizedExperiment to the Tidyverse' - description: 'tidySummarizedExperiment is an adapter that abstracts the ''SummarizedExperiment'' container in the form of tibble and allows the data manipulation, plotting and nesting using ''tidyverse''' + description: 'The tidySummarizedExperiment package provides a set of tools for creating and manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment is a widely used data structure in bioinformatics for storing high-throughput genomic data, such as gene expression or DNA sequencing data. The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. It allows users to convert their data into a tidy format, where each observation is a row and each variable is a column. This tidy representation simplifies data manipulation, integration with other tidyverse packages, and enables seamless integration with the broader ecosystem of tidy tools for data analysis.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/bioconductor-tigre/meta.yaml b/recipes/bioconductor-tigre/meta.yaml index eae63f5c1f1ff..3d755d26318d8 100644 --- a/recipes/bioconductor-tigre/meta.yaml +++ b/recipes/bioconductor-tigre/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "tigre" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0edc8e7589fc2380307610089d22178c + md5: d6bc46b9552c8c910c05c2ab705710d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tigre", max_pin="x.x") }}' # Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dbi - r-gplots @@ -31,10 +32,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-dbi - r-gplots diff --git a/recipes/bioconductor-tiledbarray/meta.yaml b/recipes/bioconductor-tiledbarray/meta.yaml index 2db05e47c4179..64c48ae9123a5 100644 --- a/recipes/bioconductor-tiledbarray/meta.yaml +++ b/recipes/bioconductor-tiledbarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "TileDBArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a54b516115c12a5cec2574c0b383f1a0 + md5: 7bb6ef67d882031ac2ebfcb3c1873dd2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tiledbarray", max_pin="x.x") }}' # Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcpp - r-tiledb - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-rcpp - r-tiledb diff --git a/recipes/bioconductor-tilingarray/meta.yaml b/recipes/bioconductor-tilingarray/meta.yaml index f34d6ad123d96..1cc59e0adddee 100644 --- a/recipes/bioconductor-tilingarray/meta.yaml +++ b/recipes/bioconductor-tilingarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "tilingArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dad60f0e34a7b8edec674e76ef7373c + md5: ef9c26009f7990175b320386fcfeeb5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tilingarray", max_pin="x.x") }}' requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-pixmap - r-rcolorbrewer @@ -30,10 +31,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-pixmap - r-rcolorbrewer diff --git a/recipes/bioconductor-timecourse/meta.yaml b/recipes/bioconductor-timecourse/meta.yaml index 58f5c9575973b..dac5e6130e637 100644 --- a/recipes/bioconductor-timecourse/meta.yaml +++ b/recipes/bioconductor-timecourse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "timecourse" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: feb399cff346d2361c9a1c47cc0df9e4 + md5: 4a760d4bcf875bb5c0069cbef4a1af32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timecourse", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-mass test: diff --git a/recipes/bioconductor-timecoursedata/meta.yaml b/recipes/bioconductor-timecoursedata/meta.yaml index c162f817abc10..96f0a9f45922b 100644 --- a/recipes/bioconductor-timecoursedata/meta.yaml +++ b/recipes/bioconductor-timecoursedata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "timecoursedata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7f2ad9b14757098a934109a0597a630b + md5: a5b9f962c12d69003eff9b6949d2b0af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timecoursedata", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr, BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-timecoursedata/post-link.sh b/recipes/bioconductor-timecoursedata/post-link.sh index b36c8fe9fe8cd..4e773c67621b2 100644 --- a/recipes/bioconductor-timecoursedata/post-link.sh +++ b/recipes/bioconductor-timecoursedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "timecoursedata-1.10.0" +installBiocDataPackage.sh "timecoursedata-1.12.0" diff --git a/recipes/bioconductor-timeomics/meta.yaml b/recipes/bioconductor-timeomics/meta.yaml index 79e6e5b19eaef..9c8c950e0f52f 100644 --- a/recipes/bioconductor-timeomics/meta.yaml +++ b/recipes/bioconductor-timeomics/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "timeOmics" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd8990e7f9a92ec1208b598bc7091c37 + md5: ddea6709cf6d8d977b998f458e7938fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timeomics", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots requirements: host: - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - r-dplyr - r-ggplot2 @@ -34,7 +35,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-mixomics >=6.24.0,<6.25.0' + - 'bioconductor-mixomics >=6.26.0,<6.27.0' - r-base - r-dplyr - r-ggplot2 diff --git a/recipes/bioconductor-timerquant/meta.yaml b/recipes/bioconductor-timerquant/meta.yaml index 219c222b5396a..1a46726437cd3 100644 --- a/recipes/bioconductor-timerquant/meta.yaml +++ b/recipes/bioconductor-timerquant/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "TimerQuant" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8cbdff0672ae0d06372f36e5de1dc86c + md5: 7033d0ae9a0731af8bafecbbfa5398c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timerquant", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, reshape2, knitr, shinyBS requirements: @@ -37,7 +38,7 @@ requirements: - r-locfit - r-shiny - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-timerquant/post-link.sh b/recipes/bioconductor-timerquant/post-link.sh index 89a811d4052cc..c834f2b1641a0 100644 --- a/recipes/bioconductor-timerquant/post-link.sh +++ b/recipes/bioconductor-timerquant/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "timerquant-1.30.0" +installBiocDataPackage.sh "timerquant-1.32.0" diff --git a/recipes/bioconductor-timescape/meta.yaml b/recipes/bioconductor-timescape/meta.yaml index 4efb191116023..2b92ef17d1383 100644 --- a/recipes/bioconductor-timescape/meta.yaml +++ b/recipes/bioconductor-timescape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "timescape" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3ed14459b64d92e1cb55934105941db0 + md5: 1a409bde946cb8ed4c7e8e6a334158de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timescape", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: diff --git a/recipes/bioconductor-timirgen/meta.yaml b/recipes/bioconductor-timirgen/meta.yaml index 41a7f31ddd10d..4e6c7b1d5d457 100644 --- a/recipes/bioconductor-timirgen/meta.yaml +++ b/recipes/bioconductor-timirgen/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.11.0" %} {% set name = "TimiRGeN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5b8016f4edda9b0a5b863ce86204b98 + md5: 87bc148544059ef1b52ff839557d8a48 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-timirgen", max_pin="x.x") }}' noarch: generic # Suggests: BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db, org.Mm.eg.db, testthat, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-mfuzz >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' - r-base - 'r-dplyr >=0.8.4' - r-freqprof @@ -42,12 +43,12 @@ requirements: - 'r-stringr >=1.4.0' - 'r-tidyr >=1.0.2' run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-mfuzz >=2.60.0,<2.61.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' - - 'bioconductor-rwikipathways >=1.20.0,<1.21.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' + - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' - r-base - 'r-dplyr >=0.8.4' - r-freqprof diff --git a/recipes/bioconductor-tin/meta.yaml b/recipes/bioconductor-tin/meta.yaml index 83630014fdd92..1acc38ee9a11d 100644 --- a/recipes/bioconductor-tin/meta.yaml +++ b/recipes/bioconductor-tin/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "TIN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5693eb6bc1804b53b77dc4a3d58b14fb + md5: 33dbf5f6f5fada307f20f5a9b8d6f8a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tin", max_pin="x.x") }}' noarch: generic # Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics requirements: host: - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-aroma.affymetrix - r-base - r-data.table @@ -29,7 +30,7 @@ requirements: - r-stringr - r-wgcna run: - - 'bioconductor-impute >=1.74.0,<1.75.0' + - 'bioconductor-impute >=1.76.0,<1.77.0' - r-aroma.affymetrix - r-base - r-data.table diff --git a/recipes/bioconductor-tinesath1cdf/meta.yaml b/recipes/bioconductor-tinesath1cdf/meta.yaml index cf5445ee14152..73e31ef2a3a0c 100644 --- a/recipes/bioconductor-tinesath1cdf/meta.yaml +++ b/recipes/bioconductor-tinesath1cdf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "tinesath1cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e3235aa047fc3dc7d77437a0afa5b71 + md5: a58177f0ed4976f52370b35e13818ce3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tinesath1cdf", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tinesath1cdf/post-link.sh b/recipes/bioconductor-tinesath1cdf/post-link.sh index 5e3512aab7972..12e58ab694e6c 100644 --- a/recipes/bioconductor-tinesath1cdf/post-link.sh +++ b/recipes/bioconductor-tinesath1cdf/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tinesath1cdf-1.38.0" +installBiocDataPackage.sh "tinesath1cdf-1.40.0" diff --git a/recipes/bioconductor-tinesath1probe/meta.yaml b/recipes/bioconductor-tinesath1probe/meta.yaml index 894c1271e9b65..6f2f2c78341f2 100644 --- a/recipes/bioconductor-tinesath1probe/meta.yaml +++ b/recipes/bioconductor-tinesath1probe/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "tinesath1probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d3dc0686f2651dff52a201923e73a751 + md5: abd9396a4f17a0044018702394b62933 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tinesath1probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tinesath1probe/post-link.sh b/recipes/bioconductor-tinesath1probe/post-link.sh index 116840a9029b2..1e35a8d90f622 100644 --- a/recipes/bioconductor-tinesath1probe/post-link.sh +++ b/recipes/bioconductor-tinesath1probe/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tinesath1probe-1.38.0" +installBiocDataPackage.sh "tinesath1probe-1.40.0" diff --git a/recipes/bioconductor-tissueenrich/meta.yaml b/recipes/bioconductor-tissueenrich/meta.yaml index e5835cf899280..e98619fb7169a 100644 --- a/recipes/bioconductor-tissueenrich/meta.yaml +++ b/recipes/bioconductor-tissueenrich/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "TissueEnrich" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25b74b3d262fc3ccd8aded6ad6cc24c5 + md5: 5cc00925f523a6d82b216343e7f4b81a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tissueenrich", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=0.7.3' - 'r-ensurer >=1.1.0' - 'r-ggplot2 >=2.2.1' - 'r-tidyr >=0.8.0' run: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-dplyr >=0.7.3' - 'r-ensurer >=1.1.0' diff --git a/recipes/bioconductor-tissuetreg/meta.yaml b/recipes/bioconductor-tissuetreg/meta.yaml index c8c75229a235e..78f702a37065e 100644 --- a/recipes/bioconductor-tissuetreg/meta.yaml +++ b/recipes/bioconductor-tissuetreg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "tissueTreg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9755c73b171a371afea8927b7d229a78 + md5: 5d975c08b7a19af832c4468ecb04c58b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tissuetreg", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment +# Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment, ggplot2, reshape2 requirements: host: - r-base run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tissuetreg/post-link.sh b/recipes/bioconductor-tissuetreg/post-link.sh index 332df6472065a..407a1fd8a9db4 100644 --- a/recipes/bioconductor-tissuetreg/post-link.sh +++ b/recipes/bioconductor-tissuetreg/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tissuetreg-1.20.0" +installBiocDataPackage.sh "tissuetreg-1.22.0" diff --git a/recipes/bioconductor-titancna/meta.yaml b/recipes/bioconductor-titancna/meta.yaml index 3265c545f77b7..05bd29c21bf16 100644 --- a/recipes/bioconductor-titancna/meta.yaml +++ b/recipes/bioconductor-titancna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "TitanCNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9048b13844f8aa903f158f087e6199d5 + md5: ce40de587ae35a22c583019e6a85dbc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-titancna", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-data.table >=1.10.4' - 'r-dplyr >=0.5.0' @@ -31,11 +32,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - 'r-data.table >=1.10.4' - 'r-dplyr >=0.5.0' diff --git a/recipes/bioconductor-tkwidgets/meta.yaml b/recipes/bioconductor-tkwidgets/meta.yaml index ddd9322e0b027..81145b1f4f180 100644 --- a/recipes/bioconductor-tkwidgets/meta.yaml +++ b/recipes/bioconductor-tkwidgets/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "tkWidgets" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b031940a2ac5599748b67348cc0c693 + md5: 044f7f3666426cbac3929eb9af1ce9d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tkwidgets", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, hgu95av2 requirements: host: - - 'bioconductor-dyndoc >=1.78.0,<1.79.0' - - 'bioconductor-widgettools >=1.78.0,<1.79.0' + - 'bioconductor-dyndoc >=1.80.0,<1.81.0' + - 'bioconductor-widgettools >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-dyndoc >=1.78.0,<1.79.0' - - 'bioconductor-widgettools >=1.78.0,<1.79.0' + - 'bioconductor-dyndoc >=1.80.0,<1.81.0' + - 'bioconductor-widgettools >=1.80.0,<1.81.0' - r-base test: commands: diff --git a/recipes/bioconductor-tloh/meta.yaml b/recipes/bioconductor-tloh/meta.yaml index abd9163085ee3..72917842a802d 100644 --- a/recipes/bioconductor-tloh/meta.yaml +++ b/recipes/bioconductor-tloh/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "tLOH" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6bea4dcf39c695fb5bc82f9be70e166 + md5: 1693fc28c2855f1af11159ec1051e2df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tloh", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-bestnormalize - r-data.table @@ -35,9 +36,9 @@ requirements: - r-scales - r-stringr run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-bestnormalize - r-data.table diff --git a/recipes/bioconductor-tmexplorer/meta.yaml b/recipes/bioconductor-tmexplorer/meta.yaml index b009d57e535b4..016c668957311 100644 --- a/recipes/bioconductor-tmexplorer/meta.yaml +++ b/recipes/bioconductor-tmexplorer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "TMExplorer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14411a5488789b44b63a2bc2b88cf33e + md5: 48b11be99739e61f54d9b442af739d49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tmexplorer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-matrix run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-base - r-matrix - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tmexplorer/post-link.sh b/recipes/bioconductor-tmexplorer/post-link.sh index 5c6491ca754e0..7bb935ca65385 100644 --- a/recipes/bioconductor-tmexplorer/post-link.sh +++ b/recipes/bioconductor-tmexplorer/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tmexplorer-1.10.0" +installBiocDataPackage.sh "tmexplorer-1.12.0" diff --git a/recipes/bioconductor-tmixclust/meta.yaml b/recipes/bioconductor-tmixclust/meta.yaml index 5ab363076bb68..4542db2ccca41 100644 --- a/recipes/bioconductor-tmixclust/meta.yaml +++ b/recipes/bioconductor-tmixclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TMixClust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94b58831f2ce8e936e4c048369ce0bd6 + md5: 3e0e6852e806722f305ed45332c23179 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tmixclust", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-spem >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-spem >=1.42.0,<1.43.0' - r-base - r-cluster - r-flexclust @@ -31,9 +32,9 @@ requirements: - r-mvtnorm - r-zoo run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-spem >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-spem >=1.42.0,<1.43.0' - r-base - r-cluster - r-flexclust diff --git a/recipes/bioconductor-tnbc.cms/meta.yaml b/recipes/bioconductor-tnbc.cms/meta.yaml index 9a94c2592fff3..30db981ea98a1 100644 --- a/recipes/bioconductor-tnbc.cms/meta.yaml +++ b/recipes/bioconductor-tnbc.cms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "TNBC.CMS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46d15e4ca09ee831aff446cf62da575e + md5: a0cf09eed274d5cd812076d4f000e1bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tnbc.cms", max_pin="x.x") }}' noarch: generic # Suggests: knitr requirements: host: - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-forestplot @@ -36,8 +37,8 @@ requirements: - r-rcolorbrewer - r-survival run: - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-gsva >=1.50.0,<1.51.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-e1071 - r-forestplot diff --git a/recipes/bioconductor-tnt/meta.yaml b/recipes/bioconductor-tnt/meta.yaml index 371856141ba03..eb73b9746ce6e 100644 --- a/recipes/bioconductor-tnt/meta.yaml +++ b/recipes/bioconductor-tnt/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TnT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e47b8605d300517fe691c3b8dc6c4124 + md5: 1afe4c0018eb0c5026c72dcfe2120045 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tnt", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-htmlwidgets - r-jsonlite - r-knitr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-htmlwidgets diff --git a/recipes/bioconductor-toast/meta.yaml b/recipes/bioconductor-toast/meta.yaml index 8b3d92d6d7d5b..45a9580d13cd1 100644 --- a/recipes/bioconductor-toast/meta.yaml +++ b/recipes/bioconductor-toast/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "TOAST" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43fb520992045f40b5a505dcc9f20468 + md5: 7161d25bca2e95e8f83aea1f7d0bba6d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-toast", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix requirements: host: - - 'bioconductor-epidish >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-epidish >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-corpcor - r-doparallel @@ -33,9 +34,9 @@ requirements: - r-quadprog - r-tidyr run: - - 'bioconductor-epidish >=2.16.0,<2.17.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-epidish >=2.18.0,<2.19.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-corpcor - r-doparallel diff --git a/recipes/bioconductor-tofsimsdata/meta.yaml b/recipes/bioconductor-tofsimsdata/meta.yaml index 9e04978e4694b..d77787901bee4 100644 --- a/recipes/bioconductor-tofsimsdata/meta.yaml +++ b/recipes/bioconductor-tofsimsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "tofsimsData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5eccad99f9e3cdfb3813eb1243926142 + md5: 57fe35de7b03ee4f3ca07540949a6b5e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tofsimsdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, tools requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tofsimsdata/post-link.sh b/recipes/bioconductor-tofsimsdata/post-link.sh index 4d3ff1631bd37..2165ad029b1c3 100644 --- a/recipes/bioconductor-tofsimsdata/post-link.sh +++ b/recipes/bioconductor-tofsimsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tofsimsdata-1.28.0" +installBiocDataPackage.sh "tofsimsdata-1.30.0" diff --git a/recipes/bioconductor-tomatocdf/meta.yaml b/recipes/bioconductor-tomatocdf/meta.yaml index d6de1c8b55b55..18ad431e15afa 100644 --- a/recipes/bioconductor-tomatocdf/meta.yaml +++ b/recipes/bioconductor-tomatocdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "tomatocdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 200efc0637788d4bd3263fc9183c1aa6 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tomatocdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tomatoprobe/meta.yaml b/recipes/bioconductor-tomatoprobe/meta.yaml index b8621403ff105..da018906e552d 100644 --- a/recipes/bioconductor-tomatoprobe/meta.yaml +++ b/recipes/bioconductor-tomatoprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "tomatoprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 72020469f35c19399fd0be9eaffd8e77 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tomatoprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tomoda/meta.yaml b/recipes/bioconductor-tomoda/meta.yaml index 5dc661aa786e3..ef22967e0bd24 100644 --- a/recipes/bioconductor-tomoda/meta.yaml +++ b/recipes/bioconductor-tomoda/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "tomoda" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9f15c43bd46119d2474f1224994e00b5 + md5: 49b8009bc1e0c7c7567b75be6fbde6c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tomoda", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel @@ -30,7 +31,7 @@ requirements: - r-rtsne - r-umap run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-ggrepel diff --git a/recipes/bioconductor-tomoseqr/meta.yaml b/recipes/bioconductor-tomoseqr/meta.yaml index 6d4c07423adc0..10dee3d515805 100644 --- a/recipes/bioconductor-tomoseqr/meta.yaml +++ b/recipes/bioconductor-tomoseqr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "tomoseqr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: abd0e85f5aaac89d5b86bd41a929b5df + md5: b881e4b272396cc4696d840658ec0ef5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tomoseqr", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-animation - r-base - r-dplyr @@ -33,7 +34,7 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - r-animation - r-base - r-dplyr diff --git a/recipes/bioconductor-top/meta.yaml b/recipes/bioconductor-top/meta.yaml index 2feec788acdb4..47810af59cec0 100644 --- a/recipes/bioconductor-top/meta.yaml +++ b/recipes/bioconductor-top/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.0" %} +{% set version = "1.2.0" %} {% set name = "TOP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67cf959128704d96b21c8f04c0b94a2a + md5: af6712369d58630bdcc2b05d7dc06b52 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-top", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse requirements: host: - - 'bioconductor-classifyr >=3.4.0,<3.5.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-classifyr >=3.6.0,<3.7.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-assertthat - r-base - r-caret @@ -50,8 +51,8 @@ requirements: - r-tidygraph - r-tidyr run: - - 'bioconductor-classifyr >=3.4.0,<3.5.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-classifyr >=3.6.0,<3.7.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-assertthat - r-base - r-caret diff --git a/recipes/bioconductor-topconfects/meta.yaml b/recipes/bioconductor-topconfects/meta.yaml index 9d70091f33ace..eb8e8b3ac1e1d 100644 --- a/recipes/bioconductor-topconfects/meta.yaml +++ b/recipes/bioconductor-topconfects/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "topconfects" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 30084c826e12d985bd00e1f4722ed54c + md5: 222a043b78c72f00d0dee0d6658d9284 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-topconfects", max_pin="x.x") }}' noarch: generic # Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle requirements: diff --git a/recipes/bioconductor-topdownr/meta.yaml b/recipes/bioconductor-topdownr/meta.yaml index b7c363a52e8f7..ae46358e6c952 100644 --- a/recipes/bioconductor-topdownr/meta.yaml +++ b/recipes/bioconductor-topdownr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "topdownr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 51f610645fd9c00ef8b2719f9c16c476 + md5: 9aa08f9983d77f0794cd1cce6c1b8085 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-topdownr", max_pin="x.x") }}' noarch: generic # Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ggplot2 >=2.2.1' - 'r-matrix >=1.4-2' run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-ggplot2 >=2.2.1' - 'r-matrix >=1.4-2' diff --git a/recipes/bioconductor-topdownrdata/meta.yaml b/recipes/bioconductor-topdownrdata/meta.yaml index 6a7ed7f87e303..fd7e915295c84 100644 --- a/recipes/bioconductor-topdownrdata/meta.yaml +++ b/recipes/bioconductor-topdownrdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "topdownrdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c105c5a497f0270c574b757c55eea433 + md5: 28e746b858956bea0967344bfe363e7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-topdownrdata", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-topdownr >=1.22.0,<1.23.0' + - 'bioconductor-topdownr >=1.24.0,<1.25.0' - r-base run: - - 'bioconductor-topdownr >=1.22.0,<1.23.0' + - 'bioconductor-topdownr >=1.24.0,<1.25.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-topdownrdata/post-link.sh b/recipes/bioconductor-topdownrdata/post-link.sh index 59251b5778340..b9614922d0e2b 100644 --- a/recipes/bioconductor-topdownrdata/post-link.sh +++ b/recipes/bioconductor-topdownrdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "topdownrdata-1.22.0" +installBiocDataPackage.sh "topdownrdata-1.24.0" diff --git a/recipes/bioconductor-topgo/meta.yaml b/recipes/bioconductor-topgo/meta.yaml index 1671a148aacec..1f934d3e45795 100644 --- a/recipes/bioconductor-topgo/meta.yaml +++ b/recipes/bioconductor-topgo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.52.0" %} +{% set version = "2.54.0" %} {% set name = "topGO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca3c35559129d3dac81b5bbea27f1334 + md5: 62aeda25dfb89dfd466ddc749e52a422 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-topgo", max_pin="x.x") }}' noarch: generic # Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-dbi - r-lattice - r-matrixstats - 'r-sparsem >=0.73' run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - r-dbi - r-lattice diff --git a/recipes/bioconductor-toxicogx/meta.yaml b/recipes/bioconductor-toxicogx/meta.yaml index 0c75eea26690c..94042954f8fd5 100644 --- a/recipes/bioconductor-toxicogx/meta.yaml +++ b/recipes/bioconductor-toxicogx/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "ToxicoGx" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d6a576970e3646d89131996935da8c6 + md5: 2be22f48c0e155c94f9af6e6157a0333 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-toxicogx", max_pin="x.x") }}' noarch: generic # Suggests: rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-catools @@ -42,13 +43,13 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-coregx >=2.4.0,<2.5.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-coregx >=2.6.0,<2.7.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-assertthat - r-base - r-catools diff --git a/recipes/bioconductor-tpp/meta.yaml b/recipes/bioconductor-tpp/meta.yaml index 09ee0e38eb63d..573be703abd26 100644 --- a/recipes/bioconductor-tpp/meta.yaml +++ b/recipes/bioconductor-tpp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.28.0" %} +{% set version = "3.30.0" %} {% set name = "TPP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1a08b79403e297acb280cf185a5855b + md5: 4a0ea50f7969045d710d3bfef371af62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tpp", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biobroom >=1.32.0,<1.33.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biobroom >=1.34.0,<1.35.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-broom - r-data.table @@ -51,9 +52,9 @@ requirements: - r-venndiagram - r-vgam run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biobroom >=1.32.0,<1.33.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biobroom >=1.34.0,<1.35.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-broom - r-data.table diff --git a/recipes/bioconductor-tpp2d/meta.yaml b/recipes/bioconductor-tpp2d/meta.yaml index 906db98ec1583..c7c16fb5161cc 100644 --- a/recipes/bioconductor-tpp2d/meta.yaml +++ b/recipes/bioconductor-tpp2d/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "TPP2D" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c0319843d11772fdf950a5da576a4396 + md5: b10330822e1c629c04c568ab155b4ee1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tpp2d", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-doparallel - r-dplyr @@ -34,8 +35,8 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-doparallel - r-dplyr diff --git a/recipes/bioconductor-tracktables/meta.yaml b/recipes/bioconductor-tracktables/meta.yaml index b1b396afebb77..58b77cb8dd7a6 100644 --- a/recipes/bioconductor-tracktables/meta.yaml +++ b/recipes/bioconductor-tracktables/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "tracktables" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fddfa8e48265ccc4fa82c31e9a028457 + md5: 0726840a7d7c0252dc163cfe065cefa0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tracktables", max_pin="x.x") }}' noarch: generic # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-rcolorbrewer - r-stringr - r-tractor.base - r-xml run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-rcolorbrewer - r-stringr diff --git a/recipes/bioconductor-trackviewer/meta.yaml b/recipes/bioconductor-trackviewer/meta.yaml index 9e959ab78163d..fa2657452ff77 100644 --- a/recipes/bioconductor-trackviewer/meta.yaml +++ b/recipes/bioconductor-trackviewer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.2" %} +{% set version = "1.38.1" %} {% set name = "trackViewer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0be10d11abe74066bbfc8bd026c998a + md5: c0004e0bdb49b5d051e486f73a79a245 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trackviewer", max_pin="x.x") }}' noarch: generic # Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-grimport - r-htmlwidgets @@ -43,21 +44,21 @@ requirements: - r-scales - r-strawr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-interactionset >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' - - 'bioconductor-rhdf5 >=2.44.0,<2.45.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-grimport - r-htmlwidgets diff --git a/recipes/bioconductor-tradeseq/meta.yaml b/recipes/bioconductor-tradeseq/meta.yaml index 1775b5406d426..cc3a8829e413c 100644 --- a/recipes/bioconductor-tradeseq/meta.yaml +++ b/recipes/bioconductor-tradeseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "tradeSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0bc724474103ac1b4f2f70e1bc65cda7 + md5: 5de25ecb5472b592837cd3937ff467c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tradeseq", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment, DelayedMatrixStats requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-ggplot2 - r-igraph @@ -43,14 +44,14 @@ requirements: - r-tibble - r-viridis run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-ggplot2 - r-igraph diff --git a/recipes/bioconductor-trajectorygeometry/meta.yaml b/recipes/bioconductor-trajectorygeometry/meta.yaml index abd4de676597e..b8e7e01e6f772 100644 --- a/recipes/bioconductor-trajectorygeometry/meta.yaml +++ b/recipes/bioconductor-trajectorygeometry/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "TrajectoryGeometry" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75158a6b92d1dc27580a4b7fd7ee6df1 + md5: a955410c20ec9cbae97e2d60a8c9b46f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trajectorygeometry", max_pin="x.x") }}' noarch: generic # Suggests: dplyr, knitr, RColorBrewer, rmarkdown requirements: diff --git a/recipes/bioconductor-trajectoryutils/meta.yaml b/recipes/bioconductor-trajectoryutils/meta.yaml index dbac9c6191216..b5d17afac2d84 100644 --- a/recipes/bioconductor-trajectoryutils/meta.yaml +++ b/recipes/bioconductor-trajectoryutils/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "TrajectoryUtils" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14277b55869f2bf8089e8608826b8f62 + md5: 8d29813e2befc86d418f15a3e594f37b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trajectoryutils", max_pin="x.x") }}' noarch: generic # Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-igraph - r-matrix diff --git a/recipes/bioconductor-transcriptogramer/meta.yaml b/recipes/bioconductor-transcriptogramer/meta.yaml index 44fed3619f14a..987323d84bf10 100644 --- a/recipes/bioconductor-transcriptogramer/meta.yaml +++ b/recipes/bioconductor-transcriptogramer/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "transcriptogramer" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 98ed3dbfd9f93632f97f126df7db63cb + md5: 6c6b8c13ec29ef0e6e5552cbbd49f14d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transcriptogramer", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics # SystemRequirements: Java Runtime Environment (>= 6) requirements: host: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-data.table - r-dosnow @@ -37,10 +38,10 @@ requirements: - r-tidyr - openjdk run: - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-reder >=2.4.0,<2.5.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-data.table - r-dosnow diff --git a/recipes/bioconductor-transcriptr/meta.yaml b/recipes/bioconductor-transcriptr/meta.yaml index 61642c5bb8a20..9dbdcebc52b50 100644 --- a/recipes/bioconductor-transcriptr/meta.yaml +++ b/recipes/bioconductor-transcriptr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "transcriptR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 85c8f7e9e4267dc2fa7710e4db391144 + md5: a60b381f153539a74fa743f4f5edac43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transcriptr", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-e1071 @@ -38,16 +39,16 @@ requirements: - r-proc - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-chipseq >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-chipseq >=1.52.0,<1.53.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-caret - r-e1071 diff --git a/recipes/bioconductor-transformgampoi/meta.yaml b/recipes/bioconductor-transformgampoi/meta.yaml index 9e578d6873ee2..baecaa012883b 100644 --- a/recipes/bioconductor-transformgampoi/meta.yaml +++ b/recipes/bioconductor-transformgampoi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "transformGamPoi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 26f9f4a793ca9e8a3107831974857260 + md5: ec9683fa0efb74c2fae2e8721f265f0b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transformgampoi", max_pin="x.x") }}' # Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-glmgampoi >=1.12.0,<1.13.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-glmgampoi >=1.12.0,<1.13.0' - - 'bioconductor-hdf5array >=1.28.0,<1.29.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-rcpp diff --git a/recipes/bioconductor-transite/meta.yaml b/recipes/bioconductor-transite/meta.yaml index 382d05db034b8..a5da73a5f57c1 100644 --- a/recipes/bioconductor-transite/meta.yaml +++ b/recipes/bioconductor-transite/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "transite" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fca53e0a3e5747c2fc0950fd8103234c + md5: 14ac71ed8ae01023f28aaed2d93f83b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transite", max_pin="x.x") }}' # Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) # SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - 'r-dplyr >=0.7.6' - 'r-ggplot2 >=3.0.0' @@ -35,9 +36,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - 'r-dplyr >=0.7.6' - 'r-ggplot2 >=3.0.0' diff --git a/recipes/bioconductor-translatome/meta.yaml b/recipes/bioconductor-translatome/meta.yaml index 0087dc14cc434..500e767a03429 100644 --- a/recipes/bioconductor-translatome/meta.yaml +++ b/recipes/bioconductor-translatome/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "tRanslatome" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,39 +11,40 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a126654549808e184a6fd2b915bf8726 + md5: 6dabe57675cc4250a3b38f9d309a6816 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-translatome", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-anota >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-heatplus >=3.8.0,<3.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-anota >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-heatplus >=3.10.0,<3.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-gplots - r-plotrix run: - - 'bioconductor-anota >=1.48.0,<1.49.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-heatplus >=3.8.0,<3.9.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rankprod >=3.26.0,<3.27.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-anota >=1.50.0,<1.51.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-heatplus >=3.10.0,<3.11.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-gplots - r-plotrix diff --git a/recipes/bioconductor-transomics2cytoscape/meta.yaml b/recipes/bioconductor-transomics2cytoscape/meta.yaml index 82cdcca2598c5..656868a7687e9 100644 --- a/recipes/bioconductor-transomics2cytoscape/meta.yaml +++ b/recipes/bioconductor-transomics2cytoscape/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "transomics2cytoscape" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 19293f16a9fd2d5f64e7da38a9871ea0 + md5: 17325dd51ab6dfcc10dff97e98be6e91 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transomics2cytoscape", max_pin="x.x") }}' noarch: generic # Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown -# SystemRequirements: Cytoscape >= 3.9.1 +# SystemRequirements: Cytoscape >= 3.10.0 requirements: host: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-dplyr + - r-pbapply - r-purrr - r-tibble run: - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-rcy3 >=2.20.0,<2.21.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - r-base - r-dplyr + - r-pbapply - r-purrr - r-tibble test: diff --git a/recipes/bioconductor-transview/meta.yaml b/recipes/bioconductor-transview/meta.yaml index 6dc1578b222ee..361542fb3d1c1 100644 --- a/recipes/bioconductor-transview/meta.yaml +++ b/recipes/bioconductor-transview/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "TransView" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a37e697eb98a5b1244563306577befb + md5: 39d2c9d2471bb732b294b68f3997eab2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transview", max_pin="x.x") }}' # Suggests: RUnit, pasillaBamSubset, BiocManager # SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-gplots - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-gplots build: diff --git a/recipes/bioconductor-traser/meta.yaml b/recipes/bioconductor-traser/meta.yaml index 3bba0ceecb4e6..cc53d2c42bb9d 100644 --- a/recipes/bioconductor-traser/meta.yaml +++ b/recipes/bioconductor-traser/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "traseR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 472e1ac5ad2ccb5a07ea3b046a3727e8 + md5: 2af018d9562b672f6701de644617856b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-traser", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle,RUnit, BiocGenerics requirements: host: - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base run: - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base test: commands: diff --git a/recipes/bioconductor-traviz/build_failure.linux-64.yaml b/recipes/bioconductor-traviz/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..f1ffa5ab49f58 --- /dev/null +++ b/recipes/bioconductor-traviz/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 68cc108a4ebdc4305e3060a475e85276df2f244592455f0f29263f603f48ba51 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libxdamage-cos6-x86_64: 1.1.3-h9b0a68f_1105 conda-forge + libxxf86vm-cos6-x86_64: 1.1.3-h9b0a68f_1105 conda-forge + mesa-dri-drivers-cos6-x86_64: 11.0.7-h9b0a68f_1105 conda-forge + mesa-dri1-drivers-cos6-x86_64: 7.11-h9b0a68f_1105 conda-forge + mesa-libgl-cos6-x86_64: 11.0.7-h9b0a68f_1105 conda-forge + mesa-libgl-devel-cos6-x86_64: 11.0.7-h9b0a68f_1105 conda-forge + pthread-stubs: 0.4-h36c2ea0_1001 conda-forge + sysroot_linux-64: 2.12-he073ed8_16 conda-forge + xorg-fixesproto: 5.0-h7f98852_1002 conda-forge + xorg-kbproto: 1.0.7-h7f98852_1002 conda-forge + xorg-libx11: 1.8.7-h8ee46fc_0 conda-forge + xorg-libxau: 1.0.11-hd590300_0 conda-forge + xorg-libxdmcp: 1.1.3-h7f98852_0 conda-forge + xorg-libxfixes: 5.0.3-h7f98852_1004 conda-forge + xorg-xextproto: 7.3.0-h0b41bf4_1003 conda-forge + xorg-xproto: 7.0.31-h7f98852_1007 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: traviz_1.8.0_65f0bdfccd.tar.gz + INFO:conda_build.source:Downloading source to cache: traviz_1.8.0_65f0bdfccd.tar.gz + Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/traviz_1.8.0.tar.gz + INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/traviz_1.8.0.tar.gz + Success + INFO:conda_build.source:Success + Extracting download + source tree in: /opt/conda/conda-bld/bioconductor-traviz_1703280230725/work + export PREFIX=/opt/conda/conda-bld/bioconductor-traviz_1703280230725/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-traviz_1703280230725/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-traviz_1703280230725/work + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-traviz_1703280230725/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library + * installing *source* package traviz ... + ** using staged installation + ** R + ** data + ** inst + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. + ** help + *** installing help indices + ** building package indices + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** installing vignettes + ** testing if installed package can be loaded from temporary location + During startup - Warning message: + Setting LC_TIME failed, using "C" + Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. + ** testing if installed package can be loaded from final location + During startup - Warning message: + Setting LC_TIME failed, using "C" + Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. + ** testing if installed package keeps a record of temporary installation path + * creating tarball + packaged installation of traviz as traviz_1.8.0_R_x86_64-conda-linux-gnu.tar.gz + * DONE (traviz) + + Resource usage statistics from building bioconductor-traviz: + Process count: 6 + CPU time: Sys=0:00:02.2, User=0:00:14.0 + Memory: 729.5M + Disk usage: 7.8K + Time elapsed: 0:00:19.3 + + + Packaging bioconductor-traviz + INFO:conda_build.build:Packaging bioconductor-traviz + Packaging bioconductor-traviz-1.8.0-r43hdfd78af_0 + INFO:conda_build.build:Packaging bioconductor-traviz-1.8.0-r43hdfd78af_0 + number of files: 32 + Fixing permissions + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2358, in build + newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1672, in bundle_conda + output['checksums'] = create_info_files(metadata, replacements, files, prefix=metadata.config.host_prefix) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1272, in create_info_files + copy_license(m) + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 762, in copy_license + generic_copy(m, "license", "license_file") + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 800, in generic_copy + raise ValueError( + ValueError: License file given in about/license_file (/opt/recipe/LICENSE) does not exist in source root dir or in recipe root dir (with meta.yaml) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-traviz/meta.yaml b/recipes/bioconductor-traviz/meta.yaml index 893bd6a022e8c..dc8c8ce9fe896 100644 --- a/recipes/bioconductor-traviz/meta.yaml +++ b/recipes/bioconductor-traviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "traviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1958b9031af3abdc0e7018dc5a425cab + md5: 65f0bdfccd1faa4d9b61bef77e686155 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-traviz", max_pin="x.x") }}' noarch: generic # Suggests: scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors, rmarkdown, knitr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-mgcv @@ -33,10 +34,10 @@ requirements: - r-rgl - r-viridis run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-slingshot >=2.8.0,<2.9.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-slingshot >=2.10.0,<2.11.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggplot2 - r-mgcv @@ -59,6 +60,7 @@ about: license: 'MIT + file LICENSE' summary: 'Trajectory functions for visualization and interpretation.' description: 'traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in reduced dimension, as well as averge gene expression smoothers as a function of pseudotime. Asides from general utility functions, traviz also allows plotting trajectories estimated by Slingshot, as well as smoothers estimated by tradeSeq. Furthermore, it allows for visualization of Slingshot trajectories using ggplot2.' + license_file: LICENSE extra: container: extended-base: true diff --git a/recipes/bioconductor-treeandleaf/meta.yaml b/recipes/bioconductor-treeandleaf/meta.yaml index 1e11fc2fd2bad..f5ae24bf9b602 100644 --- a/recipes/bioconductor-treeandleaf/meta.yaml +++ b/recipes/bioconductor-treeandleaf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "TreeAndLeaf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e4076b533cb176f32d5498aa923752a + md5: 066beb0c7f15d3b6a853bcb68c682f73 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-treeandleaf", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer requirements: host: - - 'bioconductor-reder >=2.4.0,<2.5.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' - r-ape - r-base - r-igraph run: - - 'bioconductor-reder >=2.4.0,<2.5.0' + - 'bioconductor-reder >=2.6.0,<2.7.0' - r-ape - r-base - r-igraph diff --git a/recipes/bioconductor-treeio/meta.yaml b/recipes/bioconductor-treeio/meta.yaml index 423d81525fb03..f7107d562170d 100644 --- a/recipes/bioconductor-treeio/meta.yaml +++ b/recipes/bioconductor-treeio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "treeio" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,35 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b7d57a69b1ed07beec128f756261ff95 + md5: 583758f88bf0d8efa0749407f4183567 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-treeio", max_pin="x.x") }}' noarch: generic -# Suggests: Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml, purrr +# Suggests: Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml, purrr, cli requirements: host: - r-ape - r-base - - r-cli - r-dplyr - r-jsonlite - r-magrittr - r-rlang - r-tibble - - 'r-tidytree >=0.3.9' + - 'r-tidytree >=0.4.5' run: - r-ape - r-base - - r-cli - r-dplyr - r-jsonlite - r-magrittr - r-rlang - r-tibble - - 'r-tidytree >=0.3.9' + - 'r-tidytree >=0.4.5' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-treekor/meta.yaml b/recipes/bioconductor-treekor/meta.yaml index 62937050696a4..4eb3c5f1947e7 100644 --- a/recipes/bioconductor-treekor/meta.yaml +++ b/recipes/bioconductor-treekor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "treekoR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fdd0132593952c3eed82ef2d3c425d38 + md5: c1b9ce26aa6252f5cb1fe9cd07c3245f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-treekor", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-ape - r-base - r-data.table @@ -37,11 +38,11 @@ requirements: - r-patchwork - r-tidyr run: - - 'bioconductor-diffcyt >=1.20.0,<1.21.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-ggtree >=3.8.0,<3.9.0' - - 'bioconductor-hopach >=2.60.0,<2.61.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-diffcyt >=1.22.0,<1.23.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - 'bioconductor-hopach >=2.62.0,<2.63.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - r-ape - r-base - r-data.table diff --git a/recipes/bioconductor-treesummarizedexperiment/meta.yaml b/recipes/bioconductor-treesummarizedexperiment/meta.yaml index a70dc907b0ff1..c507405f02a1b 100644 --- a/recipes/bioconductor-treesummarizedexperiment/meta.yaml +++ b/recipes/bioconductor-treesummarizedexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "TreeSummarizedExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a78e6a2d70a7fe7eaa12b1ca77bc832e + md5: 595842345af9cb4136aea17bdfdceb3f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-treesummarizedexperiment", max_pin="x.x") }}' noarch: generic # Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-base - r-dplyr - r-rlang run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-treeio >=1.24.0,<1.25.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-treeio >=1.26.0,<1.27.0' - r-ape - r-base - r-dplyr diff --git a/recipes/bioconductor-treg/meta.yaml b/recipes/bioconductor-treg/meta.yaml index 29dffb113ff6f..dfeb2c614796a 100644 --- a/recipes/bioconductor-treg/meta.yaml +++ b/recipes/bioconductor-treg/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "TREG" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90ee1d8dc737b34549f2ed915c97f833 + md5: d76ba3f3707e1810e6491d04013d6e7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-treg", max_pin="x.x") }}' noarch: generic # Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-purrr - r-rafalib run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-purrr diff --git a/recipes/bioconductor-trendy/meta.yaml b/recipes/bioconductor-trendy/meta.yaml index 61b8ce5881abe..aab3bd13ca6aa 100644 --- a/recipes/bioconductor-trendy/meta.yaml +++ b/recipes/bioconductor-trendy/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.1" %} {% set name = "Trendy" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ee8425a1de6db2081ac61e8252a6382 + md5: 00e5de9c46c116f4adc3caf3708608df build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trendy", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-gplots @@ -32,9 +33,9 @@ requirements: - r-shiny - r-shinyfiles run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dt - r-gplots diff --git a/recipes/bioconductor-tress/meta.yaml b/recipes/bioconductor-tress/meta.yaml index 0af5bbd36984e..a3e9ebd429ed9 100644 --- a/recipes/bioconductor-tress/meta.yaml +++ b/recipes/bioconductor-tress/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "TRESS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b75e6e03b1b95b420e30bf9a7d8ed2d5 + md5: f0a0a2bbb1b989970231d8ac23ecfaaa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tress", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown,BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix - r-matrixstats run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-matrix - r-matrixstats diff --git a/recipes/bioconductor-tricycle/meta.yaml b/recipes/bioconductor-tricycle/meta.yaml index c1b797eb2e8a2..e1fdcf85c0706 100644 --- a/recipes/bioconductor-tricycle/meta.yaml +++ b/recipes/bioconductor-tricycle/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "tricycle" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 33bba6617090b97414304b1b8697b0af + md5: 6a6a35c0a2cd9f279395e046b98a79f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tricycle", max_pin="x.x") }}' noarch: generic # Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circular - r-dplyr @@ -36,13 +37,13 @@ requirements: - r-rcolorbrewer - r-scattermore run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-circular - r-dplyr diff --git a/recipes/bioconductor-trigger/meta.yaml b/recipes/bioconductor-trigger/meta.yaml index c03ddcc99624f..e17c679057855 100644 --- a/recipes/bioconductor-trigger/meta.yaml +++ b/recipes/bioconductor-trigger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "trigger" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7944a3dc498b593e76945f84bad02cfb + md5: d8cb2a76223f510ff08d9dcbf1d6210c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trigger", max_pin="x.x") }}' requirements: host: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-corpcor - r-qtl - libblas - liblapack run: - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-sva >=3.50.0,<3.51.0' - r-base - r-corpcor - r-qtl diff --git a/recipes/bioconductor-trio/meta.yaml b/recipes/bioconductor-trio/meta.yaml index 4170c29e5b51b..26c7056d86138 100644 --- a/recipes/bioconductor-trio/meta.yaml +++ b/recipes/bioconductor-trio/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.38.0" %} +{% set version = "3.40.0" %} {% set name = "trio" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 659fd698018b3f4f5a9e7c6c56112ec4 + md5: cd87ad1a66fe181df937dd7a8edfda56 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trio", max_pin="x.x") }}' noarch: generic # Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation requirements: host: - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - 'r-logicreg >=1.6.1' - r-survival run: - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - 'r-logicreg >=1.6.1' - r-survival diff --git a/recipes/bioconductor-triplex/meta.yaml b/recipes/bioconductor-triplex/meta.yaml index 4954147c5afdf..008158d2d995b 100644 --- a/recipes/bioconductor-triplex/meta.yaml +++ b/recipes/bioconductor-triplex/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "triplex" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 94c2754156770fdcc42d7ade7fe9b04c + md5: c66a6990486e7a4873b256d08eff9933 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-triplex", max_pin="x.x") }}' # Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-tripr/meta.yaml b/recipes/bioconductor-tripr/meta.yaml index d6d784902f055..727c7544b3cdb 100644 --- a/recipes/bioconductor-tripr/meta.yaml +++ b/recipes/bioconductor-tripr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "tripr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 115f039f182a6543c5bb99714e64401e + md5: 6682fcae99b44178612cdf8ebc48d045 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tripr", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr requirements: diff --git a/recipes/bioconductor-trna/meta.yaml b/recipes/bioconductor-trna/meta.yaml index 9c111ee141651..1c6f912b7393d 100644 --- a/recipes/bioconductor-trna/meta.yaml +++ b/recipes/bioconductor-trna/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "tRNA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0870ee6c0b51fc8533a2128c939e9ec4 + md5: 52f5648075d6e9b6cb9ca2db65b5509f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trna", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-ggplot2 - r-scales - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-ggplot2 - r-scales diff --git a/recipes/bioconductor-trnadbimport/meta.yaml b/recipes/bioconductor-trnadbimport/meta.yaml index f878de839dcbb..4306e7ec1e88a 100644 --- a/recipes/bioconductor-trnadbimport/meta.yaml +++ b/recipes/bioconductor-trnadbimport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "tRNAdbImport" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,37 +11,38 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7fe475fbdfc05e6a9d1593d6289f3da + md5: 4610dcee69d8555572652b0193cc5cd3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trnadbimport", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-trna >=1.18.0,<1.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-trna >=1.20.0,<1.21.0' - r-base - r-httr - r-stringr - r-xml2 run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-modstrings >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-trna >=1.18.0,<1.19.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-modstrings >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-trna >=1.20.0,<1.21.0' - r-base - r-httr - r-stringr diff --git a/recipes/bioconductor-trnascanimport/meta.yaml b/recipes/bioconductor-trnascanimport/meta.yaml index ce72bfc877041..87b8afa53958f 100644 --- a/recipes/bioconductor-trnascanimport/meta.yaml +++ b/recipes/bioconductor-trnascanimport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "tRNAscanImport" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,44 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc67c78b9d8ec78f964b095933f36a30 + md5: 49f872c7de9b6cba139c7758330efa8c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-trnascanimport", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-trna >=1.18.0,<1.19.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-trna >=1.20.0,<1.21.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-structstrings >=1.16.0,<1.17.0' - - 'bioconductor-trna >=1.18.0,<1.19.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-structstrings >=1.18.0,<1.19.0' + - 'bioconductor-trna >=1.20.0,<1.21.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-stringr test: diff --git a/recipes/bioconductor-tronco/meta.yaml b/recipes/bioconductor-tronco/meta.yaml index 36d229b2a642e..58d3d0dadd395 100644 --- a/recipes/bioconductor-tronco/meta.yaml +++ b/recipes/bioconductor-tronco/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "TRONCO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80ed49d7d0ed5d5078c3029fdefed2e4 + md5: 0e137e734d0e5552bdcaa25ccdd4df08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tronco", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick requirements: host: - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-bnlearn - r-circlize @@ -37,7 +38,7 @@ requirements: - r-scales - r-xtable run: - - 'bioconductor-rgraphviz >=2.44.0,<2.45.0' + - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - r-base - r-bnlearn - r-circlize diff --git a/recipes/bioconductor-tsar/build.sh b/recipes/bioconductor-tsar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tsar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tsar/meta.yaml b/recipes/bioconductor-tsar/meta.yaml new file mode 100644 index 0000000000000..b6aae8910eb01 --- /dev/null +++ b/recipes/bioconductor-tsar/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "TSAR" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7cc8589151c5b03e247590bbd7dc04dd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tsar", max_pin="x.x") }}' + noarch: generic +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - r-base + - 'r-dplyr >=1.0.7' + - 'r-ggplot2 >=3.3.5' + - 'r-ggpubr >=0.4.0' + - 'r-jsonlite >=1.8.7' + - 'r-magrittr >=2.0.3' + - 'r-mgcv >=1.8.38' + - 'r-minpack.lm >=1.2.3' + - 'r-openxlsx >=4.2.5.2' + - 'r-plotly >=4.10.2' + - 'r-readxl >=1.4.0' + - 'r-rhandsontable >=0.3.8' + - 'r-shiny >=1.7.4.1' + - 'r-shinyjs >=2.1.0' + - 'r-shinywidgets >=0.7.6' + - 'r-stringr >=1.4.0' + - 'r-tidyr >=1.1.4' + run: + - r-base + - 'r-dplyr >=1.0.7' + - 'r-ggplot2 >=3.3.5' + - 'r-ggpubr >=0.4.0' + - 'r-jsonlite >=1.8.7' + - 'r-magrittr >=2.0.3' + - 'r-mgcv >=1.8.38' + - 'r-minpack.lm >=1.2.3' + - 'r-openxlsx >=4.2.5.2' + - 'r-plotly >=4.10.2' + - 'r-readxl >=1.4.0' + - 'r-rhandsontable >=0.3.8' + - 'r-shiny >=1.7.4.1' + - 'r-shinyjs >=2.1.0' + - 'r-shinywidgets >=0.7.6' + - 'r-stringr >=1.4.0' + - 'r-tidyr >=1.1.4' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: AGPL-3 + summary: 'Thermal Shift Analysis in R' + description: 'This package automates analysis workflow for Thermal Shift Analysis (TSAS) data. Processing, analyzing, and visualizing data through both shiny applications and command lines. Package aims to simplify data analysis and offer front to end workflow, from raw data to multiple trial analysis.' + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + diff --git a/recipes/bioconductor-tscan/meta.yaml b/recipes/bioconductor-tscan/meta.yaml index 4cf037f190b49..2ea54e7791685 100644 --- a/recipes/bioconductor-tscan/meta.yaml +++ b/recipes/bioconductor-tscan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "TSCAN" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ac450a8f8e95d90e0da330379af5bb0 + md5: 018be0d6197c80dbf2ce7832a3f9c49d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tscan", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-combinat - r-fastica @@ -38,11 +39,11 @@ requirements: - r-plyr - r-shiny run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-trajectoryutils >=1.8.0,<1.9.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - r-base - r-combinat - r-fastica diff --git a/recipes/bioconductor-ttgsea/meta.yaml b/recipes/bioconductor-ttgsea/meta.yaml index f9a1edcf172c9..9266a10fd6ed4 100644 --- a/recipes/bioconductor-ttgsea/meta.yaml +++ b/recipes/bioconductor-ttgsea/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ttgsea" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 666f5cb46746a27a71312a8bedee2a49 + md5: 0b38c9baea88905217b9ed667c80c26f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ttgsea", max_pin="x.x") }}' noarch: generic # Suggests: fgsea, knitr, testthat, reticulate, rmarkdown requirements: diff --git a/recipes/bioconductor-ttmap/meta.yaml b/recipes/bioconductor-ttmap/meta.yaml index af509427b8eb8..bcb28bc41745f 100644 --- a/recipes/bioconductor-ttmap/meta.yaml +++ b/recipes/bioconductor-ttmap/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "TTMap" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 053ab5b1d1b45af48c5338ebffb4eaf8 + md5: 9fb52b78486eff55cc91ef0f8116633b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ttmap", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, airway requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colorramps - r-rgl run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-colorramps - r-rgl diff --git a/recipes/bioconductor-tuberculosis/meta.yaml b/recipes/bioconductor-tuberculosis/meta.yaml index b9e7d08b36705..019d16095c2ba 100644 --- a/recipes/bioconductor-tuberculosis/meta.yaml +++ b/recipes/bioconductor-tuberculosis/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "tuberculosis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9f3fd16d5debb8705f56bf714fc3e860 + md5: 154cd343b8fba727ecf80a671a6a112d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tuberculosis", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, ggplot2, hrbrthemes, knitr, readr, rmarkdown, scater, usethis, utils requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-magrittr @@ -34,10 +35,10 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-dplyr - r-magrittr @@ -47,7 +48,7 @@ requirements: - r-tibble - r-tidyr - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tuberculosis/post-link.sh b/recipes/bioconductor-tuberculosis/post-link.sh index 5d70a601472ac..387c3ba762b5d 100644 --- a/recipes/bioconductor-tuberculosis/post-link.sh +++ b/recipes/bioconductor-tuberculosis/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tuberculosis-1.6.0" +installBiocDataPackage.sh "tuberculosis-1.8.0" diff --git a/recipes/bioconductor-tumourmethdata/meta.yaml b/recipes/bioconductor-tumourmethdata/meta.yaml new file mode 100644 index 0000000000000..0258769ad47df --- /dev/null +++ b/recipes/bioconductor-tumourmethdata/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.0.0" %} +{% set name = "TumourMethData" %} +{% set bioc = "3.18" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7b4ba6a8a59379a3b7f368e6c26fa0a6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tumourmethdata", max_pin="x.x") }}' + noarch: generic +# Suggests: ggplot2, knitr, rmarkdown +requirements: + host: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-r.utils + run: + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - r-base + - r-r.utils + - curl + - 'bioconductor-data-packages >=20231203' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples' + description: 'TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies.' + diff --git a/recipes/bioconductor-tumourmethdata/post-link.sh b/recipes/bioconductor-tumourmethdata/post-link.sh new file mode 100644 index 0000000000000..8e6c2a8a145a1 --- /dev/null +++ b/recipes/bioconductor-tumourmethdata/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "tumourmethdata-1.0.0" diff --git a/recipes/bioconductor-tumourmethdata/pre-unlink.sh b/recipes/bioconductor-tumourmethdata/pre-unlink.sh new file mode 100644 index 0000000000000..6eb78cbb96c43 --- /dev/null +++ b/recipes/bioconductor-tumourmethdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TumourMethData diff --git a/recipes/bioconductor-turbonorm/meta.yaml b/recipes/bioconductor-turbonorm/meta.yaml index e5b09163eae71..0818a2addd0ac 100644 --- a/recipes/bioconductor-turbonorm/meta.yaml +++ b/recipes/bioconductor-turbonorm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "TurboNorm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82bdd2f9cb32c4366ba0c8983e31acc8 + md5: 6df6da83bc36e4ce202d91888feaafa7 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, affydata + run_exports: '{{ pin_subpackage("bioconductor-turbonorm", max_pin="x.x") }}' +# Suggests: BiocStyle, affydata, hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-convert >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-convert >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-lattice - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-convert >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-convert >=1.78.0,<1.79.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - r-lattice build: diff --git a/recipes/bioconductor-tvtb/meta.yaml b/recipes/bioconductor-tvtb/meta.yaml index d7bcadb51de52..6955abe0f5030 100644 --- a/recipes/bioconductor-tvtb/meta.yaml +++ b/recipes/bioconductor-tvtb/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "TVTB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,51 +11,52 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e1e1dc3b593cb5f838eb3a40ffb59d0 + md5: 64da00f3c21bf3f9a82dc32e451395a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tvtb", max_pin="x.x") }}' noarch: generic # Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander requirements: host: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-ensemblvep >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-ensemblvep >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggally - r-ggplot2 - r-reshape2 run: - - 'bioconductor-annotationfilter >=1.24.0,<1.25.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-ensemblvep >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-ensemblvep >=1.44.0,<1.45.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-ggally - r-ggplot2 diff --git a/recipes/bioconductor-tweedeseq/meta.yaml b/recipes/bioconductor-tweedeseq/meta.yaml index 646f74165d5b7..2005ab0221e0d 100644 --- a/recipes/bioconductor-tweedeseq/meta.yaml +++ b/recipes/bioconductor-tweedeseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.45.0" %} +{% set version = "1.48.0" %} {% set name = "tweeDEseq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9cc6b9ec2db1052d2ed270dbb1f6ec1 + md5: 1a919ba1b3c5709068bc126336b77826 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tweedeseq", max_pin="x.x") }}' # Suggests: tweeDEseqCountData, xtable requirements: host: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-mass + - 'r-rcpp >=1.0.10' - libblas - liblapack run: - - 'bioconductor-cqn >=1.46.0,<1.47.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-cqn >=1.48.0,<1.49.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-mass + - 'r-rcpp >=1.0.10' build: - {{ compiler('c') }} + - {{ compiler('cxx') }} - make test: commands: @@ -43,7 +47,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'RNA-seq data analysis using the Poisson-Tweedie family of distributions' - description: 'Differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.' + description: 'Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: diff --git a/recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml b/recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3e36ab5993f41 --- /dev/null +++ b/recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml @@ -0,0 +1,44 @@ +recipe_sha: e9ea10dec9b205dbce587c85515bdb5db1c152a2def749ed83d0b124ea0cec27 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + WARNING:conda_build.build:No files or script found for output bioconductor-tweedeseqcountdata +category: |- + source download error +log: |- + 08:56:10 BIOCONDA INFO (OUT) Downloading https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tweeDEseqCountData_1.40.0.tar.gz + 08:56:10 BIOCONDA INFO (OUT) INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tweeDEseqCountData_1.40.0.tar.gz + 08:56:11 BIOCONDA INFO (OUT) Success + 08:56:11 BIOCONDA INFO (OUT) INFO:conda_build.source:Success + 08:56:11 BIOCONDA INFO (OUT) Extracting download + 08:56:11 BIOCONDA INFO (OUT) source tree in: /opt/conda/conda-bld/bioconductor-tweedeseqcountdata_1702025598887/work + 08:56:11 BIOCONDA INFO (OUT) Packaging bioconductor-tweedeseqcountdata + 08:56:11 BIOCONDA INFO (OUT) INFO:conda_build.build:Packaging bioconductor-tweedeseqcountdata + 08:56:11 BIOCONDA INFO (OUT) Packaging bioconductor-tweedeseqcountdata-1.40.0-r43hdfd78af_0 + 08:56:11 BIOCONDA INFO (OUT) INFO:conda_build.build:Packaging bioconductor-tweedeseqcountdata-1.40.0-r43hdfd78af_0 + 08:56:11 BIOCONDA INFO (OUT) No files or script found for output bioconductor-tweedeseqcountdata + 08:56:11 BIOCONDA INFO (OUT) WARNING:conda_build.build:No files or script found for output bioconductor-tweedeseqcountdata + 08:56:12 BIOCONDA INFO (OUT) number of files: 2 + 08:56:12 BIOCONDA INFO (OUT) Fixing permissions + 08:56:12 BIOCONDA INFO (OUT) Traceback (most recent call last): + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in + 08:56:12 BIOCONDA INFO (OUT) sys.exit(main()) + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + 08:56:12 BIOCONDA INFO (OUT) call_conda_build(action, config) + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + 08:56:12 BIOCONDA INFO (OUT) result = api.build( + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + 08:56:12 BIOCONDA INFO (OUT) return build_tree( + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + 08:56:12 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2358, in build + 08:56:12 BIOCONDA INFO (OUT) newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1672, in bundle_conda + 08:56:12 BIOCONDA INFO (OUT) output['checksums'] = create_info_files(metadata, replacements, files, prefix=metadata.config.host_prefix) + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1272, in create_info_files + 08:56:12 BIOCONDA INFO (OUT) copy_license(m) + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 762, in copy_license + 08:56:12 BIOCONDA INFO (OUT) generic_copy(m, "license", "license_file") + 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 800, in generic_copy + 08:56:12 BIOCONDA INFO (OUT) raise ValueError( + 08:56:12 BIOCONDA INFO (OUT) ValueError: License file given in about/license_file (/opt/recipe/LICENSE) does not exist in source root dir or in recipe root dir (with meta.yaml) + .08:56:20 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmpbp4seh01/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-tweedeseqcountdata:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:2.11.0 /bin/bash /opt/build_script.bash diff --git a/recipes/bioconductor-tweedeseqcountdata/meta.yaml b/recipes/bioconductor-tweedeseqcountdata/meta.yaml index e98b6cb1fc0f6..4cec84b4097ed 100644 --- a/recipes/bioconductor-tweedeseqcountdata/meta.yaml +++ b/recipes/bioconductor-tweedeseqcountdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "tweeDEseqCountData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b48baebaa2abe35419bad4110d7523ec + md5: d63e819cedf93ffbe115ed518bc9feaf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tweedeseqcountdata", max_pin="x.x") }}' noarch: generic +# Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' + license: 'MIT + file LICENSE' summary: 'RNA-seq count data employed in the vignette of the tweeDEseq package' description: 'RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + license_file: LICENSE diff --git a/recipes/bioconductor-tweedeseqcountdata/post-link.sh b/recipes/bioconductor-tweedeseqcountdata/post-link.sh index ee220691d0a70..5418d98cd3da2 100644 --- a/recipes/bioconductor-tweedeseqcountdata/post-link.sh +++ b/recipes/bioconductor-tweedeseqcountdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tweedeseqcountdata-1.38.0" +installBiocDataPackage.sh "tweedeseqcountdata-1.40.0" diff --git a/recipes/bioconductor-twilight/meta.yaml b/recipes/bioconductor-twilight/meta.yaml index 4c5e88db6a0e8..42a74a2994831 100644 --- a/recipes/bioconductor-twilight/meta.yaml +++ b/recipes/bioconductor-twilight/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.76.0" %} +{% set version = "1.78.0" %} {% set name = "twilight" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9b97614549c3048f37ee8db280fe7602 + md5: fa6b01126ace9423edfc04757f6392b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-twilight", max_pin="x.x") }}' # Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-twoddpcr/meta.yaml b/recipes/bioconductor-twoddpcr/meta.yaml index 4a2997ce8842d..1de09201d6a1c 100644 --- a/recipes/bioconductor-twoddpcr/meta.yaml +++ b/recipes/bioconductor-twoddpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "twoddpcr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 598cbdea40a78c70568965c4a87019c4 + md5: bbdb2cd12a3bd6f756b700d1216043ee build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-twoddpcr", max_pin="x.x") }}' noarch: generic # Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-class - r-ggplot2 @@ -30,7 +31,7 @@ requirements: - r-scales - r-shiny run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-class - r-ggplot2 diff --git a/recipes/bioconductor-txcutr/meta.yaml b/recipes/bioconductor-txcutr/meta.yaml index 708de4be2a766..0e45c92ea1d02 100644 --- a/recipes/bioconductor-txcutr/meta.yaml +++ b/recipes/bioconductor-txcutr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "txcutr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,36 +11,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: da702f8e8c123e0745674ba4610a1a05 + md5: 10d81d02156a45cebc08845455180010 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txcutr", max_pin="x.x") }}' noarch: generic # Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base test: commands: diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml index 8011c9090a8ad..a6886a0920dd4 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.0.1" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart22" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3bab54295e300fedba99eef521220e50 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart22", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml index 2ff8cad569c54..eda07b96d60d3 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.1.3" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart25" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: eb007c07317b9717c76949e5ed999978 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart25", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml index 9aba3d36ac6ed..63dab73960eb5 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart28" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9ed52284f01e08fc382db179b544bb17 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart28", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml index 2e048e1293d01..d69be5548db43 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.0" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart51" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c623af555537bfd9958f8f9573308103 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart51", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml index 46d445c651fb0..4a642c4756fcb 100644 --- a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Btaurus.UCSC.bosTau8.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 2112b91fbecabf9c89d1b0a48d88ce03 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.btaurus.ucsc.bostau8.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml b/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml index 7f89af6557ccc..a6ba08db8eca3 100644 --- a/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Btaurus.UCSC.bosTau9.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fe443d123b0b788e1e450f4e60036788 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.btaurus.ucsc.bostau9.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml index 1db5d62f78fb1..b4921754ff83d 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.15.0" %} {% set name = "TxDb.Celegans.UCSC.ce11.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1b4d61d06ac8acb27e57d1fafc5b79ce build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.celegans.ucsc.ce11.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml index 28e829fb1aca1..25dfa74d6898a 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Celegans.UCSC.ce11.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3765169432e745aff5e85afd239066ca build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.celegans.ucsc.ce11.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml index 957e6b067aaf1..039511fff6c9e 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Celegans.UCSC.ce6.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 215c2edd440a3df8229fe6a75b431aa8 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.celegans.ucsc.ce6.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml index c647963377fb5..18ad135c029fc 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.11.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam3.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bf6af84c14a30ad5d01f3678246b1180 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml index c45c3264a26d4..b46d02cb2c06d 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam4.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0b47072fa79cf8e99f8563002a0998cb build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml index 65c1b1d17f91e..ddec9ac42b39b 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam5.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fc3d84569c092b74e5e0bccb785db8b6 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml index 1a6043e0ea30e..59b9744aeb5b0 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.17.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam6.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9279204329323191fbb72717a57b13aa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml index c42688c4f3d01..d1f4e9fba8f5e 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm3.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 46b7ffe0c516edf8a2a3b5d78e0d8b67 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml index 4d1aafa9dbaa7..e336c647d474a 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm6.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bec18a1fb2768347e907e3171d5332ca build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml index 6068ea11a32d2..fca8354c5912c 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Drerio.UCSC.danRer10.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fef9bbec3809e1b69991516988f146fb build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.drerio.ucsc.danrer10.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml index 24e329bb6164b..f95557448c480 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Drerio.UCSC.danRer11.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3d4ded4cec068a807b8b86b31389b677 build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.drerio.ucsc.danrer11.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml index 0bcae1e37f595..a4d1e1a9d9a08 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ggallus.UCSC.galGal4.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d50eb467227cd9077a7a690ae6934d11 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ggallus.ucsc.galgal4.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml index a5619d77db894..c539c071a4343 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ggallus.UCSC.galGal5.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0df53cd4f8e29705df75867a427de56e build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ggallus.ucsc.galgal5.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml index 22dded94e5395..9a465cc414e93 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Ggallus.UCSC.galGal6.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4d81026ecb786abf1fe0cb548238214c build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ggallus.ucsc.galgal6.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml b/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml index 68ed5a6e6c194..3dbd6d642a0c9 100644 --- a/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.3.2" %} {% set name = "TxDb.Hsapiens.BioMart.igis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 75b793928d29bcd3f069b5986bc2cfae build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.biomart.igis", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml index 766497a9f5d34..1e389329cbe79 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg18.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: e8b32a672e87345c72bb30be73d1e2d6 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg18.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml index 664361974a4c3..09de8f7c38a1f 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 61be88a81433958571b57d0952be48a0 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg19.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml index 40debb03a2b43..4559792f7c905 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a0d61cd90639c40b3d0bb6bdb043cf12 build: - number: 17 + number: 18 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml index 4d52500d1e3c9..618385aa5a855 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "TxDb.Hsapiens.UCSC.hg38.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9b7cfbf5ed7d9ef129c84abdd7858dc + md5: 2344dbd2878c82c6c860ed6529a700b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg38.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh index 989c79064a838..7e845c2497808 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.knowngene-3.17.0" +installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.knowngene-3.18.0" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml index 62180f04d9b91..fbea99b3dbea6 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.15.0" %} +{% set version = "3.18.0" %} {% set name = "TxDb.Hsapiens.UCSC.hg38.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50e7c4ce068c4ca2d77a3c0b46a3ab45 + md5: 7ec982095ea795b99d53b6549d7ba4d4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg38.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh index 0b664dac3262c..165899b5e92d6 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.refgene-3.15.0" +installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.refgene-3.18.0" diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml index 22bf3eb855a3e..71ee0e7b1156c 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.14.0" %} {% set name = "TxDb.Mmulatta.UCSC.rheMac10.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 81b01b07d87ae91b4d9a269a2baf616e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml index 4e21a38d6ccda..0534539bc09fe 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Mmulatta.UCSC.rheMac3.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: db84a9e85d613635d74002f11df41e1f build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml index 584c9a333cb06..bc41e0d7a744b 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Mmulatta.UCSC.rheMac8.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8437e0a05ffd28b667c7b740e0db68a7 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml index 459b32c3a98bb..d32fc6e7daded 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 88d65b714d1f86b456aee2b8524e9d84 build: - number: 16 + number: 17 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm10.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml index fa8fefd0a88e2..1466d7f497572 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 129b610bf05ec77451731196baa55bcc build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm10.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml index d06a04e2188f3..7d5fc68376690 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm39.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca2e9ed7dc7fe96ef98b18e3c7e3245a + md5: 5ceb110ce3327d44f45bf5118ec7f3af build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm39.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh index b53c424d92c0a..40c86bb8d84f5 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.knowngene-3.17.0" +installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.knowngene-3.18.0" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml index 04ef013177696..9734f2b6f61c1 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.12.0" %} +{% set version = "3.18.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm39.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2525799b85e0a52bf274ab5eed51cd84 + md5: 2fd64557d5f1bade11432b666c63f33a build: - number: 6 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm39.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh index 2fc5b5d65dd07..039d2293e91ed 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.refgene-3.12.0" +installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.refgene-3.18.0" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml index a1ef79d8b7a66..4b3641897a188 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Mmusculus.UCSC.mm9.knownGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cb72af039b011033477363bda8ed9104 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm9.knowngene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml index 93301e0d981e2..45f0301d0133b 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ptroglodytes.UCSC.panTro4.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9bdd3ba81561550f50250368d7d52eaa build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml index 351b5edc41946..e46a4701dd0a3 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ptroglodytes.UCSC.panTro5.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 76ee1d253d1c8e54c12e8d5b9db93303 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml index f25065559cccb..7e50c87b44421 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Ptroglodytes.UCSC.panTro6.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 48a88973fe0e5117cadd5c816a46e6e9 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml index d1310743d20d7..072131a10520b 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.3.2" %} {% set name = "TxDb.Rnorvegicus.BioMart.igis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: eaf695f63cd021074d68c76d148cdfb7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.biomart.igis", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml index 8e1e7c08903b2..87c5843fcb54e 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn4.ensGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6bf2ebc522c2828c036e52b2028792c1 build: - number: 15 + number: 16 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml index f9c1a81bab905..7a4c200fb093a 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn5.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8a93a15b37bf73e5c529c976c4561537 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml index ac1b3853eb920..a891c74d515a3 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6660ee000fbc956541728c6dadf1fca7 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml index 4cc98f3db3ee6..18c8a1da4b97b 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn6.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ea525daa75bcf165eb24f6e93f4dbf6c build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml index d383b75fe0cbd..50c4b8f2e2f3f 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.15.0" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn7.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 589dc0f8f4c6ee8f5ed11aeb95a74a7d build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml index 4a09a8c215b8e..15d753d9f15d2 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer2.sgdGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8ce83ef2ba6cfc69f9b4435a0a047819 build: - number: 18 + number: 19 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml index e84ce9f6c0dd3..c404797fc5a6d 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: afb23b3265730b9e59c2f07ab37cc3a0 build: - number: 21 + number: 22 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml index 58510c515e0d2..0aac7bae47394 100644 --- a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Sscrofa.UCSC.susScr11.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a6c5a2c402ad904a2f55099e391d18de build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.sscrofa.ucsc.susscr11.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml index 522da876b179d..dafdf280b2985 100644 --- a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Sscrofa.UCSC.susScr3.refGene" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,22 +13,23 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 981602dc706e545d5acdf7590e222ca7 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdb.sscrofa.ucsc.susscr3.refgene", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tximeta/meta.yaml b/recipes/bioconductor-tximeta/meta.yaml index d1564f35f1dbd..f258f1c4275af 100644 --- a/recipes/bioconductor-tximeta/meta.yaml +++ b/recipes/bioconductor-tximeta/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.1" %} {% set name = "tximeta" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c1de1419dbe0b129421a1a7ada21fe8 + md5: 20a7fe1f7efc9be9ab420325932b8c0b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tximeta", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-jsonlite - r-matrix - r-tibble run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-ensembldb >=2.24.0,<2.25.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-tximport >=1.28.0,<1.29.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-tximport >=1.30.0,<1.31.0' - r-base - r-jsonlite - r-matrix @@ -61,7 +62,7 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Transcript Quantification Import with Automatic Metadata' - description: 'Transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.' + description: 'Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: parent_recipe: diff --git a/recipes/bioconductor-tximport/meta.yaml b/recipes/bioconductor-tximport/meta.yaml index cdda57ad44ec5..0cac1468cec2d 100644 --- a/recipes/bioconductor-tximport/meta.yaml +++ b/recipes/bioconductor-tximport/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "tximport" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,14 +11,15 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6b52b54d5477b1612e7be93cfd08d796 + md5: 8bbe549dafbf5b0dfe626f327910a893 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tximport", max_pin="x.x") }}' noarch: generic -# Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds +# Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds requirements: host: - r-base diff --git a/recipes/bioconductor-tximportdata/meta.yaml b/recipes/bioconductor-tximportdata/meta.yaml index c468adfd7aa19..67efaa786b0ac 100644 --- a/recipes/bioconductor-tximportdata/meta.yaml +++ b/recipes/bioconductor-tximportdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "tximportData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b5ef0f4b63bcd11c21a8389af32fa1f + md5: 4494d764fc087333e5c04ee7977c85c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tximportdata", max_pin="x.x") }}' noarch: generic # Suggests: knitr, markdown requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-tximportdata/post-link.sh b/recipes/bioconductor-tximportdata/post-link.sh index 5ec2e04af174c..d17909a301ad8 100644 --- a/recipes/bioconductor-tximportdata/post-link.sh +++ b/recipes/bioconductor-tximportdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tximportdata-1.28.0" +installBiocDataPackage.sh "tximportdata-1.30.0" diff --git a/recipes/bioconductor-typeinfo/meta.yaml b/recipes/bioconductor-typeinfo/meta.yaml index 5b60c14bd9cf1..11ddbcbf2414b 100644 --- a/recipes/bioconductor-typeinfo/meta.yaml +++ b/recipes/bioconductor-typeinfo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "TypeInfo" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13936395f272715de70454397c80d7eb + md5: a2c4ab8a27a1d9c5a463a18cd0e37356 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-typeinfo", max_pin="x.x") }}' noarch: generic # Suggests: Biobase requirements: diff --git a/recipes/bioconductor-u133aaofav2cdf/meta.yaml b/recipes/bioconductor-u133aaofav2cdf/meta.yaml index 7f158e92ca7e6..68e66f5114324 100644 --- a/recipes/bioconductor-u133aaofav2cdf/meta.yaml +++ b/recipes/bioconductor-u133aaofav2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "u133aaofav2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 716483ddb6664b8b7f0c58cd21136e8b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-u133aaofav2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-u133x3p.db/meta.yaml b/recipes/bioconductor-u133x3p.db/meta.yaml index a315d9457b0e8..141cf64856d0d 100644 --- a/recipes/bioconductor-u133x3p.db/meta.yaml +++ b/recipes/bioconductor-u133x3p.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "u133x3p.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1a36a09dc64b94728bf6ac75600b40c6 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-u133x3p.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-u133x3pcdf/meta.yaml b/recipes/bioconductor-u133x3pcdf/meta.yaml index 52b3580ddceb0..c14b372731fdb 100644 --- a/recipes/bioconductor-u133x3pcdf/meta.yaml +++ b/recipes/bioconductor-u133x3pcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "u133x3pcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ee4e62041bc8c63813e8cf8400ece2f3 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-u133x3pcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-u133x3pprobe/meta.yaml b/recipes/bioconductor-u133x3pprobe/meta.yaml index 000ab40decaa2..2d940a22ec63b 100644 --- a/recipes/bioconductor-u133x3pprobe/meta.yaml +++ b/recipes/bioconductor-u133x3pprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "u133x3pprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 81e2b00985688160805147bef0c638be build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-u133x3pprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ucell/meta.yaml b/recipes/bioconductor-ucell/meta.yaml index e858d65a0d465..584900adb879c 100644 --- a/recipes/bioconductor-ucell/meta.yaml +++ b/recipes/bioconductor-ucell/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.2" %} {% set name = "UCell" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3b3b2f541a098357e0d324a468cc5fa + md5: c02318fc6a9ac12b0d902460be5204d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ucell", max_pin="x.x") }}' noarch: generic # Suggests: Seurat, scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.13.6' - r-matrix run: - - 'bioconductor-biocneighbors >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - 'r-data.table >=1.13.6' - r-matrix diff --git a/recipes/bioconductor-ucscrepeatmasker/meta.yaml b/recipes/bioconductor-ucscrepeatmasker/meta.yaml index 2cec4f1d771cf..732e819f62c2b 100644 --- a/recipes/bioconductor-ucscrepeatmasker/meta.yaml +++ b/recipes/bioconductor-ucscrepeatmasker/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.15.2" %} {% set name = "UCSCRepeatMasker" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,27 +13,28 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: ad19a6fbd936e478af88fa21bc918a29 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ucscrepeatmasker", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-rcurl - r-xml run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - r-base - r-rcurl - r-xml - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ularcirc/meta.yaml b/recipes/bioconductor-ularcirc/meta.yaml index 8ca10d19bda19..1007d484742c7 100644 --- a/recipes/bioconductor-ularcirc/meta.yaml +++ b/recipes/bioconductor-ularcirc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Ularcirc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b82a3d2b16ce13cc2c3c354aec4f1e77 + md5: dee64401e02d9e5884a6399d7ab122b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ularcirc", max_pin="x.x") }}' noarch: generic # Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-mirbase.db >=1.2.0,<1.3.0' - - 'bioconductor-organism.dplyr >=1.28.0,<1.29.0' - - 'bioconductor-plotgardener >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-organism.dplyr >=1.30.0,<1.31.0' + - 'bioconductor-plotgardener >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-data.table >=1.9.4' - r-dt @@ -49,20 +50,20 @@ requirements: - r-shinyjs - r-yaml run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - 'bioconductor-mirbase.db >=1.2.0,<1.3.0' - - 'bioconductor-organism.dplyr >=1.28.0,<1.29.0' - - 'bioconductor-plotgardener >=1.6.0,<1.7.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-organism.dplyr >=1.30.0,<1.31.0' + - 'bioconductor-plotgardener >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-data.table >=1.9.4' - r-dt diff --git a/recipes/bioconductor-umi4cats/meta.yaml b/recipes/bioconductor-umi4cats/meta.yaml index 3e76de3805dc8..caa73d85038c4 100644 --- a/recipes/bioconductor-umi4cats/meta.yaml +++ b/recipes/bioconductor-umi4cats/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "UMI4Cats" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84b4b4be278891d3503c78e20d3dfa6c + md5: bfadc67d7452919fe1e4a63684692442 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-umi4cats", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat requirements: host: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-cowplot @@ -56,24 +57,24 @@ requirements: - r-stringr - r-zoo run: - - 'bioconductor-annotate >=1.78.0,<1.79.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rbowtie2 >=2.6.0,<2.7.0' - - 'bioconductor-regioner >=1.32.0,<1.33.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-shortread >=1.58.0,<1.59.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-annotate >=1.80.0,<1.81.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' + - 'bioconductor-regioner >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-shortread >=1.60.0,<1.61.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-cowplot diff --git a/recipes/bioconductor-uncoverapplib/meta.yaml b/recipes/bioconductor-uncoverapplib/meta.yaml index 85e9b6269cd56..1a28223113b02 100644 --- a/recipes/bioconductor-uncoverapplib/meta.yaml +++ b/recipes/bioconductor-uncoverapplib/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "uncoverappLib" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec3e240519cd29c9a91154e0c38bf211 + md5: 2aa395f92e95d5ff7e67612c6a2c0021 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-uncoverapplib", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-condformat - r-dt @@ -48,18 +49,18 @@ requirements: - r-shinywidgets - r-stringr run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-organismdbi >=1.42.0,<1.43.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - 'bioconductor-organismdbi >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.17.0,<3.18.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - r-base - r-condformat - r-dt diff --git a/recipes/bioconductor-undo/meta.yaml b/recipes/bioconductor-undo/meta.yaml index 30cd162fb9e37..f214965e0b298 100644 --- a/recipes/bioconductor-undo/meta.yaml +++ b/recipes/bioconductor-undo/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "UNDO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a8de0b0595afb75551a7186b00b45bf + md5: a94665c036a09fbf3728f0a1ad220dfa build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-undo", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-boot - r-mass - r-nnls run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-boot - r-mass diff --git a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml index 92fae1b55a09a..9c7b8e08be53a 100644 --- a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml +++ b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "unifiedWMWqPCR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5014bd5d35c03623b142b02ac2599eaa + md5: d9a09d196f72dc2246328247851dd24a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-unifiedwmwqpcr", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-htqpcr >=1.54.0,<1.55.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-htqpcr >=1.56.0,<1.57.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-htqpcr >=1.54.0,<1.55.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-htqpcr >=1.56.0,<1.57.0' - r-base test: commands: diff --git a/recipes/bioconductor-uniprot.ws/meta.yaml b/recipes/bioconductor-uniprot.ws/meta.yaml index 095637e68a890..07e01957f1b4c 100644 --- a/recipes/bioconductor-uniprot.ws/meta.yaml +++ b/recipes/bioconductor-uniprot.ws/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.40.1" %} +{% set version = "2.42.0" %} {% set name = "UniProt.ws" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19942d736d5f87dcb885720b524ce954 + md5: 47d9ee4038c5dcaf66229e4e1e07c052 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-uniprot.ws", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httpcache - r-httr @@ -33,10 +34,10 @@ requirements: - r-rjsoncons - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biocbaseutils >=1.2.0,<1.3.0' - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - r-base - r-httpcache - r-httr diff --git a/recipes/bioconductor-uniprotkeywords/meta.yaml b/recipes/bioconductor-uniprotkeywords/meta.yaml index d14358fb3dfa3..e997cfd605a01 100644 --- a/recipes/bioconductor-uniprotkeywords/meta.yaml +++ b/recipes/bioconductor-uniprotkeywords/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.99.4" %} +{% set version = "0.99.7" %} {% set name = "UniProtKeywords" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f3f91ac1b8eca20fabcf46cae4348ea5 + md5: b2cda32dda256fb0d110192e194af838 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-uniprotkeywords", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, markdown, testthat requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-uniprotkeywords/post-link.sh b/recipes/bioconductor-uniprotkeywords/post-link.sh index 5a72202c55dd6..2f90ff95a700c 100644 --- a/recipes/bioconductor-uniprotkeywords/post-link.sh +++ b/recipes/bioconductor-uniprotkeywords/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "uniprotkeywords-0.99.4" +installBiocDataPackage.sh "uniprotkeywords-0.99.7" diff --git a/recipes/bioconductor-uniquorn/meta.yaml b/recipes/bioconductor-uniquorn/meta.yaml index 74ffa08b92ef2..3bcbea9f536d0 100644 --- a/recipes/bioconductor-uniquorn/meta.yaml +++ b/recipes/bioconductor-uniquorn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "Uniquorn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca181ab420669fd785a9984d9c3a03e1 + md5: 63658e23af6991784cdd4b038f2d1268 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-uniquorn", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-doparallel @@ -32,9 +33,9 @@ requirements: - r-stringr - r-writexls run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-data.table - r-doparallel diff --git a/recipes/bioconductor-universalmotif/meta.yaml b/recipes/bioconductor-universalmotif/meta.yaml index d828d62f4b536..3e87affe747df 100644 --- a/recipes/bioconductor-universalmotif/meta.yaml +++ b/recipes/bioconductor-universalmotif/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "universalmotif" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 53ef747289e457e4097ced1d46199854 + md5: fe680a8d988fce6bfde0af9fdce148de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-universalmotif", max_pin="x.x") }}' # Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-mass @@ -35,11 +36,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-ggplot2 - r-mass diff --git a/recipes/bioconductor-updateobject/meta.yaml b/recipes/bioconductor-updateobject/meta.yaml index e6901ad19b093..0ac250a75a4ef 100644 --- a/recipes/bioconductor-updateobject/meta.yaml +++ b/recipes/bioconductor-updateobject/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "updateObject" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7a6ae09fcd22300d35d2ff503ce9f08 + md5: 0d69cbbcd4bd9c5f31d905a47f6af212 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-updateobject", max_pin="x.x") }}' noarch: generic # Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, TimiRGeN, testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: git requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-digest run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-digest test: diff --git a/recipes/bioconductor-usort/meta.yaml b/recipes/bioconductor-usort/meta.yaml index c3367d77d2e81..5783b25934ca6 100644 --- a/recipes/bioconductor-usort/meta.yaml +++ b/recipes/bioconductor-usort/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "uSORT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fb4c6b3706ad7e264a9f106c5519169 + md5: 0c89e7d86bb2f37b99ce32989b121110 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-usort", max_pin="x.x") }}' noarch: generic # Suggests: knitr, RUnit, testthat, ggplot2 requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' - r-base - r-cluster - r-fpc @@ -35,9 +36,9 @@ requirements: - r-rspectra - r-vgam run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-monocle >=2.28.0,<2.29.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-monocle >=2.30.0,<2.31.0' - r-base - r-cluster - r-fpc diff --git a/recipes/bioconductor-vaexprs/meta.yaml b/recipes/bioconductor-vaexprs/meta.yaml index 12718521e4783..41a54d8a833b0 100644 --- a/recipes/bioconductor-vaexprs/meta.yaml +++ b/recipes/bioconductor-vaexprs/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "VAExprs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f66a09bd4ecba61a3bb6a4931f9a2ff + md5: 6f9ed6eba476abd7908d6849381b545c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vaexprs", max_pin="x.x") }}' noarch: generic # Suggests: SC3, knitr, testthat, reticulate, rmarkdown requirements: host: - - 'bioconductor-deeppincs >=1.8.0,<1.9.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deeppincs >=1.10.0,<1.11.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-catencoders - r-diagrammer @@ -33,10 +34,10 @@ requirements: - r-purrr - r-tensorflow run: - - 'bioconductor-deeppincs >=1.8.0,<1.9.0' - - 'bioconductor-scater >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-deeppincs >=1.10.0,<1.11.0' + - 'bioconductor-scater >=1.30.0,<1.31.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-catencoders - r-diagrammer diff --git a/recipes/bioconductor-vanillaice/meta.yaml b/recipes/bioconductor-vanillaice/meta.yaml index 0b037492191c2..ef2b66554d491 100644 --- a/recipes/bioconductor-vanillaice/meta.yaml +++ b/recipes/bioconductor-vanillaice/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "VanillaICE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e1544c4961ab0be39a24130c53fce392 + md5: 557131c410cc7474d15a4cc9a7d940de build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vanillaice", max_pin="x.x") }}' # Suggests: RUnit, human610quadv1bCrlmm requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - - 'bioconductor-crlmm >=1.58.0,<1.59.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-crlmm >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-foreach @@ -39,17 +40,17 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - - 'bioconductor-crlmm >=1.58.0,<1.59.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-oligoclasses >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-crlmm >=1.60.0,<1.61.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-foreach diff --git a/recipes/bioconductor-varcon/meta.yaml b/recipes/bioconductor-varcon/meta.yaml index dd6f12bfb8cbe..409d0dc24a003 100644 --- a/recipes/bioconductor-varcon/meta.yaml +++ b/recipes/bioconductor-varcon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "VarCon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0ded1a90369093a4576e0d86660ca32 + md5: 843e95d7843d7611c222d8cbca8814b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-varcon", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-shiny - r-shinycssloaders - r-shinyfiles run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' - r-base - r-ggplot2 - r-shiny diff --git a/recipes/bioconductor-variancepartition/meta.yaml b/recipes/bioconductor-variancepartition/meta.yaml index 9e8cf690075ff..ff40c729611e6 100644 --- a/recipes/bioconductor-variancepartition/meta.yaml +++ b/recipes/bioconductor-variancepartition/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.30.2" %} +{% set version = "1.32.2" %} {% set name = "variancePartition" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,57 +11,58 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea2b29627ac9a4e7c039319af82a2caf + md5: 75a8e840769ba62b9f175c73aba9c99a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-variancepartition", max_pin="x.x") }}' noarch: generic -# Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, Rfast, zenith, RUnit, statmod, BiocGenerics, r2glmm, readr +# Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-aod - r-base - - r-doparallel - - r-foreach + - r-corpcor + - r-fancova - r-ggplot2 - r-gplots - r-iterators - - 'r-lme4 >=1.1-10' + - 'r-lme4 >=1.1.33' - r-lmertest - r-mass - 'r-matrix >=1.4.0' + - r-matrixstats - 'r-pbkrtest >=0.4-4' - - r-progress - r-rdpack - - 'r-remacor >=0.0.11' + - 'r-remacor >=0.0.15' - r-reshape2 - r-rhpcblasctl - r-rlang - r-scales run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-aod - r-base - - r-doparallel - - r-foreach + - r-corpcor + - r-fancova - r-ggplot2 - r-gplots - r-iterators - - 'r-lme4 >=1.1-10' + - 'r-lme4 >=1.1.33' - r-lmertest - r-mass - 'r-matrix >=1.4.0' + - r-matrixstats - 'r-pbkrtest >=0.4-4' - - r-progress - r-rdpack - - 'r-remacor >=0.0.11' + - 'r-remacor >=0.0.15' - r-reshape2 - r-rhpcblasctl - r-rlang diff --git a/recipes/bioconductor-variantannotation/meta.yaml b/recipes/bioconductor-variantannotation/meta.yaml index 9751715d5559b..77114340c26da 100644 --- a/recipes/bioconductor-variantannotation/meta.yaml +++ b/recipes/bioconductor-variantannotation/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.1" %} {% set name = "VariantAnnotation" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,55 +11,56 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d297f17e9369a4e04d41b1fa86535f4c + md5: 39b6f4907fe37495a903c338e6d4cc73 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle + run_exports: '{{ pin_subpackage("bioconductor-variantannotation", max_pin="x.x") }}' +# Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr # SystemRequirements: GNU make requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-dbi - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-matrixgenerics >=1.12.0,<1.13.0' - - 'bioconductor-rhtslib >=2.2.0,<2.3.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rhtslib >=2.4.0,<2.5.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-dbi build: diff --git a/recipes/bioconductor-variantexperiment/meta.yaml b/recipes/bioconductor-variantexperiment/meta.yaml index e0b33f5de1b02..d996d1d7f6948 100644 --- a/recipes/bioconductor-variantexperiment/meta.yaml +++ b/recipes/bioconductor-variantexperiment/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "VariantExperiment" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 307ba761619ec2eedb365f83b1e5950f + md5: cfa81c58331066ea4f23ce2ba29fa114 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-variantexperiment", max_pin="x.x") }}' noarch: generic # Suggests: testthat, knitr, rmarkdown, markdown, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayeddataframe >=1.16.0,<1.17.0' - - 'bioconductor-gdsarray >=1.20.0,<1.21.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayeddataframe >=1.18.0,<1.19.0' + - 'bioconductor-gdsarray >=1.22.0,<1.23.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayeddataframe >=1.16.0,<1.17.0' - - 'bioconductor-gdsarray >=1.20.0,<1.21.0' - - 'bioconductor-gdsfmt >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-seqarray >=1.40.0,<1.41.0' - - 'bioconductor-snprelate >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayeddataframe >=1.18.0,<1.19.0' + - 'bioconductor-gdsarray >=1.22.0,<1.23.0' + - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base test: commands: diff --git a/recipes/bioconductor-variantfiltering/meta.yaml b/recipes/bioconductor-variantfiltering/meta.yaml index 7d7cc657acfcc..339238b836f34 100644 --- a/recipes/bioconductor-variantfiltering/meta.yaml +++ b/recipes/bioconductor-variantfiltering/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.1" %} +{% set version = "1.38.0" %} {% set name = "VariantFiltering" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5b2f20003b47121950dfbb60c9e95a8 + md5: af4ddac4cfb857eea4db9309da6de07d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-variantfiltering", max_pin="x.x") }}' # Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dt - r-shiny @@ -48,25 +49,25 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-genomicscores >=2.12.0,<2.13.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.76.0,<1.77.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' - - 'bioconductor-xvector >=0.40.0,<0.41.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gviz >=1.46.0,<1.47.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.42.0,<0.43.0' - r-base - r-dt - r-shiny diff --git a/recipes/bioconductor-varianttools/meta.yaml b/recipes/bioconductor-varianttools/meta.yaml index 42cd6b757219b..6a504d7d03da0 100644 --- a/recipes/bioconductor-varianttools/meta.yaml +++ b/recipes/bioconductor-varianttools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "VariantTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,45 +11,46 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f6efd941310bd834bc9071454c65d5e + md5: 34afccb56ff143a33019bdd8f2e356ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-varianttools", max_pin="x.x") }}' noarch: generic -# Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3) +# Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrix run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-matrix test: diff --git a/recipes/bioconductor-varianttoolsdata/meta.yaml b/recipes/bioconductor-varianttoolsdata/meta.yaml index 26e84b603fd3e..a8a952360d6fc 100644 --- a/recipes/bioconductor-varianttoolsdata/meta.yaml +++ b/recipes/bioconductor-varianttoolsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "VariantToolsData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abaad839d98a3c855cac80bd443fa9b6 + md5: a85757ce237b03b0480f01488a78879b build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-varianttoolsdata", max_pin="x.x") }}' noarch: generic # Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-varianttoolsdata/post-link.sh b/recipes/bioconductor-varianttoolsdata/post-link.sh index 9ff9ab2726d17..7c1ae1c238049 100644 --- a/recipes/bioconductor-varianttoolsdata/post-link.sh +++ b/recipes/bioconductor-varianttoolsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "varianttoolsdata-1.24.0" +installBiocDataPackage.sh "varianttoolsdata-1.26.0" diff --git a/recipes/bioconductor-vasp/meta.yaml b/recipes/bioconductor-vasp/meta.yaml index 0d8a475a7222e..b3e673476385f 100644 --- a/recipes/bioconductor-vasp/meta.yaml +++ b/recipes/bioconductor-vasp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "VaSP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c9272543d5387f9619fee22096af873 + md5: 5fddc833bc7dd84dfb16e030fe966cd3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vasp", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-ballgown >=2.32.0,<2.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ballgown >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-matrixstats run: - - 'bioconductor-ballgown >=2.32.0,<2.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-ballgown >=2.34.0,<2.35.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cluster - r-matrixstats diff --git a/recipes/bioconductor-vbmp/meta.yaml b/recipes/bioconductor-vbmp/meta.yaml index d0ae8c93023a7..ce99b5aa8630f 100644 --- a/recipes/bioconductor-vbmp/meta.yaml +++ b/recipes/bioconductor-vbmp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.68.0" %} +{% set version = "1.70.0" %} {% set name = "vbmp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bbe85861887e0d02f6ab57203dfac89e + md5: b7d2a0a9950dd7ecdbcea5ffdfbd853c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vbmp", max_pin="x.x") }}' noarch: generic # Suggests: Biobase (>= 2.5.5), statmod requirements: diff --git a/recipes/bioconductor-vcfarray/meta.yaml b/recipes/bioconductor-vcfarray/meta.yaml index 5b3b0986decad..b97fe14953639 100644 --- a/recipes/bioconductor-vcfarray/meta.yaml +++ b/recipes/bioconductor-vcfarray/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "VCFArray" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,32 +11,33 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ed57985f5b6fcd3e8221e75ae29ca65 + md5: 0e101fbb3c6c6b57d792527a6c720654 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vcfarray", max_pin="x.x") }}' noarch: generic # Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicfiles >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base test: commands: diff --git a/recipes/bioconductor-vdjdive/meta.yaml b/recipes/bioconductor-vdjdive/meta.yaml index b0ff3da36ebdf..9f4d20bf8610f 100644 --- a/recipes/bioconductor-vdjdive/meta.yaml +++ b/recipes/bioconductor-vdjdive/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "VDJdive" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,43 +11,47 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4900fdc58bbcb9fd6d36bf12379f671a + md5: 938051376344953e02e510f65d156939 build: number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-vdjdive", max_pin="x.x") }}' # Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-ggplot2 - r-gridextra - r-matrix - r-rcolorbrewer - - r-reticulate + - r-rcpp + - libblas + - liblapack run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cowplot - r-ggplot2 - r-gridextra - r-matrix - r-rcolorbrewer - - r-reticulate + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-vectrapolarisdata/meta.yaml b/recipes/bioconductor-vectrapolarisdata/meta.yaml index 1a584263921ac..5c6b9f5915e33 100644 --- a/recipes/bioconductor-vectrapolarisdata/meta.yaml +++ b/recipes/bioconductor-vectrapolarisdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "VectraPolarisData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f427b5860f7e3498064deabff0328263 + md5: ea2006b85e374e76fbd70ca8b0819072 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vectrapolarisdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, dplyr requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-vectrapolarisdata/post-link.sh b/recipes/bioconductor-vectrapolarisdata/post-link.sh index 16113665d8f15..2f937fb860681 100644 --- a/recipes/bioconductor-vectrapolarisdata/post-link.sh +++ b/recipes/bioconductor-vectrapolarisdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "vectrapolarisdata-1.4.0" +installBiocDataPackage.sh "vectrapolarisdata-1.6.0" diff --git a/recipes/bioconductor-vegamc/meta.yaml b/recipes/bioconductor-vegamc/meta.yaml index 7c66f7ec08948..d21a2211e6724 100644 --- a/recipes/bioconductor-vegamc/meta.yaml +++ b/recipes/bioconductor-vegamc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.38.0" %} +{% set version = "3.40.0" %} {% set name = "VegaMC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 27fb05dee200093e81b0ad296ef9ce50 + md5: 0e02ae3375b7bed5ca1ed7011b60f180 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vegamc", max_pin="x.x") }}' requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-velociraptor/meta.yaml b/recipes/bioconductor-velociraptor/meta.yaml index 9cff79fb403b4..85b401a821df5 100644 --- a/recipes/bioconductor-velociraptor/meta.yaml +++ b/recipes/bioconductor-velociraptor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "velociraptor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,40 +11,41 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 725af79edbf1758273558a988c346605 + md5: d2c16e280b1957ef3989e5d02f4f0b5d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-velociraptor", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zellkonverter >=1.10.0,<1.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' - r-base - r-matrix - r-reticulate run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocsingular >=1.16.0,<1.17.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-scuttle >=1.10.0,<1.11.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-zellkonverter >=1.10.0,<1.11.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-biocsingular >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-scuttle >=1.12.0,<1.13.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' - r-base - r-matrix - r-reticulate diff --git a/recipes/bioconductor-veloviz/meta.yaml b/recipes/bioconductor-veloviz/meta.yaml index dc09829f4b3ff..8fa3402c305e9 100644 --- a/recipes/bioconductor-veloviz/meta.yaml +++ b/recipes/bioconductor-veloviz/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "veloviz" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7c3af954c6be66f853f9aaf1a2f03d97 + md5: 54c6f9e5fd6275be8b999a2c949cf6bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-veloviz", max_pin="x.x") }}' # Suggests: knitr, rmarkdown, testthat requirements: host: diff --git a/recipes/bioconductor-venndetail/meta.yaml b/recipes/bioconductor-venndetail/meta.yaml index 2b46196c5960f..42c138436e3dd 100644 --- a/recipes/bioconductor-venndetail/meta.yaml +++ b/recipes/bioconductor-venndetail/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "VennDetail" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2da7c3ccb316ab6914812bedd8f351a5 + md5: be9c3506e9707fe42642ea413c0873a6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-venndetail", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, markdown requirements: diff --git a/recipes/bioconductor-verso/meta.yaml b/recipes/bioconductor-verso/meta.yaml index 359162175c5a3..f142090d335ed 100644 --- a/recipes/bioconductor-verso/meta.yaml +++ b/recipes/bioconductor-verso/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "VERSO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7cc88c9858954443ebd083f066aac93 + md5: dcc0220c3f10bb1efaaa360448547771 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-verso", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics, BiocStyle, testthat, knitr requirements: diff --git a/recipes/bioconductor-vidger/meta.yaml b/recipes/bioconductor-vidger/meta.yaml index 00d83b649aa7e..6104b533f8e4e 100644 --- a/recipes/bioconductor-vidger/meta.yaml +++ b/recipes/bioconductor-vidger/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "vidger" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d2674cb15af21919dfd378d5fa4ad4aa + md5: 01029a545153064095a804a7e9093231 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vidger", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggally - r-ggplot2 @@ -35,10 +36,10 @@ requirements: - r-scales - r-tidyr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggally - r-ggplot2 diff --git a/recipes/bioconductor-viper/meta.yaml b/recipes/bioconductor-viper/meta.yaml index 1d91ca6cb6844..d7cc28cd92f69 100644 --- a/recipes/bioconductor-viper/meta.yaml +++ b/recipes/bioconductor-viper/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "viper" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 68e8e97c7b733610c09e2938f9c1ac42 + md5: 0d7f13a212bc6fc5d7cf2213a1bfbdb0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-viper", max_pin="x.x") }}' noarch: generic # Suggests: bcellViper requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-kernsmooth - r-mixtools run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - r-e1071 - r-kernsmooth diff --git a/recipes/bioconductor-viseago/meta.yaml b/recipes/bioconductor-viseago/meta.yaml index af9d0935c9c09..0ce17ff2718bd 100644 --- a/recipes/bioconductor-viseago/meta.yaml +++ b/recipes/bioconductor-viseago/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "ViSEAGO" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ef6ab35f2558111c341ddabf7d69b3d + md5: 90f43624392275cbfbcd026e323769b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-viseago", max_pin="x.x") }}' noarch: generic # Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-data.table - r-dendextend @@ -45,13 +46,13 @@ requirements: - r-scales - r-upsetr run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-annotationforge >=1.42.0,<1.43.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-go.db >=3.17.0,<3.18.0' - - 'bioconductor-gosemsim >=2.26.0,<2.27.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-annotationforge >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - 'bioconductor-go.db >=3.18.0,<3.19.0' + - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - 'bioconductor-topgo >=2.54.0,<2.55.0' - r-base - r-data.table - r-dendextend diff --git a/recipes/bioconductor-visse/meta.yaml b/recipes/bioconductor-visse/meta.yaml index 4d72ac521d56d..f9e749668920d 100644 --- a/recipes/bioconductor-visse/meta.yaml +++ b/recipes/bioconductor-visse/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "vissE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3b75cc7ccad5e8341533a72d2c5449a + md5: 1c5018fd43f416ebc2d035a143877154 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-visse", max_pin="x.x") }}' noarch: generic # Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr requirements: host: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-msigdb >=1.8.0,<1.9.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-msigdb >=1.10.0,<1.11.0' - r-base - r-ggforce - r-ggplot2 @@ -39,8 +40,8 @@ requirements: - r-tidygraph - r-tm run: - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-msigdb >=1.8.0,<1.9.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-msigdb >=1.10.0,<1.11.0' - r-base - r-ggforce - r-ggplot2 diff --git a/recipes/bioconductor-vitisviniferacdf/meta.yaml b/recipes/bioconductor-vitisviniferacdf/meta.yaml index 618b415f6dceb..700763f7b9e4a 100644 --- a/recipes/bioconductor-vitisviniferacdf/meta.yaml +++ b/recipes/bioconductor-vitisviniferacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "vitisviniferacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8eb491f3ffa3ff0814f5c155787ae160 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vitisviniferacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-vitisviniferaprobe/meta.yaml b/recipes/bioconductor-vitisviniferaprobe/meta.yaml index 78c017c3278e5..6c147fb71d4de 100644 --- a/recipes/bioconductor-vitisviniferaprobe/meta.yaml +++ b/recipes/bioconductor-vitisviniferaprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "vitisviniferaprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 386c0d5e37896d073ac20970e88b3160 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vitisviniferaprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-voyager/meta.yaml b/recipes/bioconductor-voyager/meta.yaml index f18eed13d0105..805d9605955ad 100644 --- a/recipes/bioconductor-voyager/meta.yaml +++ b/recipes/bioconductor-voyager/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.3" %} +{% set version = "1.4.0" %} {% set name = "Voyager" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,29 +11,30 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af8b62438ee17b2a3898ef9ee429a619 + md5: 1cc32e63cf1c410d82c2cd1a26f9f929 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-voyager", max_pin="x.x") }}' noarch: generic -# Suggests: adespatial, automap, BiocSingular, BiocStyle, cowplot, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, vroom +# Suggests: automap, BiocSingular, BiocStyle, cowplot, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, vroom requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spatialfeatureexperiment >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-spatialfeatureexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggnewscale - 'r-ggplot2 >=3.4.0' - r-lifecycle - r-matrix + - r-matrixstats - r-patchwork - r-rlang - r-rspectra @@ -43,19 +44,19 @@ requirements: - r-spdep - r-terra run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-bluster >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-sparsematrixstats >=1.12.0,<1.13.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' - - 'bioconductor-spatialfeatureexperiment >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-bluster >=1.12.0,<1.13.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - 'bioconductor-spatialfeatureexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-ggnewscale - 'r-ggplot2 >=3.4.0' - r-lifecycle - r-matrix + - r-matrixstats - r-patchwork - r-rlang - r-rspectra diff --git a/recipes/bioconductor-vplotr/meta.yaml b/recipes/bioconductor-vplotr/meta.yaml index c326702e06edc..60b10ff4e2b2e 100644 --- a/recipes/bioconductor-vplotr/meta.yaml +++ b/recipes/bioconductor-vplotr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.1" %} {% set name = "VplotR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a35b84246031a8a91934c6b0144d1c0d + md5: 91af0fd39cd72be94b7f5d674d9e494f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vplotr", max_pin="x.x") }}' noarch: generic # Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-ggplot2 @@ -35,12 +36,12 @@ requirements: - r-reshape2 - r-zoo run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-cowplot - r-ggplot2 diff --git a/recipes/bioconductor-vsclust/meta.yaml b/recipes/bioconductor-vsclust/meta.yaml index f256165c67c44..7ba0555dd39b9 100644 --- a/recipes/bioconductor-vsclust/meta.yaml +++ b/recipes/bioconductor-vsclust/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "vsclust" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa4f4df8fd8e0a96d3bce256e041f479 + md5: 0c492a6d65d0b230211a0f95706b51a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vsclust", max_pin="x.x") }}' # Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, clusterProfiler requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-matrixstats - r-rcpp @@ -30,9 +31,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' - r-base - r-matrixstats - r-rcpp diff --git a/recipes/bioconductor-vsn/meta.yaml b/recipes/bioconductor-vsn/meta.yaml index 289e82fa4ce0a..f9f993fd76b95 100644 --- a/recipes/bioconductor-vsn/meta.yaml +++ b/recipes/bioconductor-vsn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.68.0" %} +{% set version = "3.70.0" %} {% set name = "vsn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cc5c43447e41dc37b1132a6407ba298b + md5: 1c9484f361b22f76135af5567306f0c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vsn", max_pin="x.x") }}' # Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-lattice - libblas - liblapack run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-ggplot2 - r-lattice diff --git a/recipes/bioconductor-vtpnet/meta.yaml b/recipes/bioconductor-vtpnet/meta.yaml index 68ff7ed733dfe..5c0307387b96c 100644 --- a/recipes/bioconductor-vtpnet/meta.yaml +++ b/recipes/bioconductor-vtpnet/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.40.0" %} +{% set version = "0.42.0" %} {% set name = "vtpnet" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,26 +11,27 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cf95c0b39cbcd4f227c8b3e03c7d2906 + md5: a3a08b447e9ce26fafeed6fe2c515e10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vtpnet", max_pin="x.x") }}' noarch: generic # Suggests: MotifDb, VariantAnnotation, Rgraphviz requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gwascat >=2.32.0,<2.33.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gwascat >=2.34.0,<2.35.0' - r-base - r-doparallel - r-foreach run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-gwascat >=2.32.0,<2.33.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-gwascat >=2.34.0,<2.35.0' - r-base - r-doparallel - r-foreach diff --git a/recipes/bioconductor-vulcan/meta.yaml b/recipes/bioconductor-vulcan/meta.yaml index e0d4a0fa3f9f5..37d48d05d6a20 100644 --- a/recipes/bioconductor-vulcan/meta.yaml +++ b/recipes/bioconductor-vulcan/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "vulcan" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f526cacf3cf264b40ddb4f476a863e2c + md5: 0e0bf7a1e9b866d535489e7c37f2e19d build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vulcan", max_pin="x.x") }}' noarch: generic # Suggests: vulcandata requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-diffbind >=3.10.0,<3.11.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-diffbind >=3.12.0,<3.13.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-catools - r-gplots @@ -37,15 +38,15 @@ requirements: - r-wordcloud - r-zoo run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-chippeakanno >=3.34.0,<3.35.0' - - 'bioconductor-csaw >=1.34.0,<1.35.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-diffbind >=3.10.0,<3.11.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' + - 'bioconductor-csaw >=1.36.0,<1.37.0' + - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - 'bioconductor-diffbind >=3.12.0,<3.13.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-viper >=1.34.0,<1.35.0' + - 'bioconductor-viper >=1.36.0,<1.37.0' - r-base - r-catools - r-gplots diff --git a/recipes/bioconductor-vulcandata/meta.yaml b/recipes/bioconductor-vulcandata/meta.yaml index c83ee258ad24a..c63ea516eec1c 100644 --- a/recipes/bioconductor-vulcandata/meta.yaml +++ b/recipes/bioconductor-vulcandata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "vulcandata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e51d04a9825be5fdb9591377095a0da9 + md5: cd95ea7ac7f2b9edfd46c1ffccb7c3c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-vulcandata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-vulcandata/post-link.sh b/recipes/bioconductor-vulcandata/post-link.sh index 9bf717d9b7e82..29950d9bb1d51 100644 --- a/recipes/bioconductor-vulcandata/post-link.sh +++ b/recipes/bioconductor-vulcandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "vulcandata-1.22.0" +installBiocDataPackage.sh "vulcandata-1.24.0" diff --git a/recipes/bioconductor-waddr/meta.yaml b/recipes/bioconductor-waddr/meta.yaml index 9d0151af7f721..c7bc5ff14d5ed 100644 --- a/recipes/bioconductor-waddr/meta.yaml +++ b/recipes/bioconductor-waddr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "waddR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a4dd18e19d305d25e578016a82391c7 + md5: 97a692c918d531e3d872dc17141cd112 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-waddr", max_pin="x.x") }}' # Suggests: knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown, scater requirements: host: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - 'r-arm >=1.10-1' - r-base - r-eva @@ -31,9 +32,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.8.0,<2.9.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' + - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - 'r-arm >=1.10-1' - r-base - r-eva diff --git a/recipes/bioconductor-watermelon/meta.yaml b/recipes/bioconductor-watermelon/meta.yaml index c52d665c14f60..b6fb1b65082bf 100644 --- a/recipes/bioconductor-watermelon/meta.yaml +++ b/recipes/bioconductor-watermelon/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "wateRmelon" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4828a18835a1a56fde8a155a51452e7 + md5: dd08402958a5cc50170669a5f17e44f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-watermelon", max_pin="x.x") }}' noarch: generic # Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-matrixstats run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-lumi >=2.52.0,<2.53.0' - - 'bioconductor-methylumi >=2.46.0,<2.47.0' - - 'bioconductor-roc >=1.76.0,<1.77.0' + - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-lumi >=2.54.0,<2.55.0' + - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - 'bioconductor-roc >=1.78.0,<1.79.0' - r-base - r-matrixstats test: diff --git a/recipes/bioconductor-wavcluster/meta.yaml b/recipes/bioconductor-wavcluster/meta.yaml index 9b019e5241b76..db62a8f56c5cf 100644 --- a/recipes/bioconductor-wavcluster/meta.yaml +++ b/recipes/bioconductor-wavcluster/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.34.0" %} +{% set version = "2.36.0" %} {% set name = "wavClusteR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2894c6e0dbc3d6d968cf63dad83ab8e8 + md5: 9177c657b31b1abaac94079e658a9c18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wavcluster", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-foreach - r-ggplot2 @@ -37,14 +38,14 @@ requirements: - r-seqinr - r-stringr run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-genomicfeatures >=1.52.0,<1.53.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-foreach - r-ggplot2 diff --git a/recipes/bioconductor-weaver/meta.yaml b/recipes/bioconductor-weaver/meta.yaml index 735940fb2a99c..4eac9e85fb718 100644 --- a/recipes/bioconductor-weaver/meta.yaml +++ b/recipes/bioconductor-weaver/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.66.0" %} +{% set version = "1.68.0" %} {% set name = "weaver" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88b2dbb130fe48487b9f642f97475a3f + md5: 629d19681872923f14b50543d833c1ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-weaver", max_pin="x.x") }}' noarch: generic # Suggests: codetools requirements: diff --git a/recipes/bioconductor-webbioc/meta.yaml b/recipes/bioconductor-webbioc/meta.yaml index 652c70188c9c3..2186052bfbd19 100644 --- a/recipes/bioconductor-webbioc/meta.yaml +++ b/recipes/bioconductor-webbioc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "webbioc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,33 +11,34 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b1f539ec35de93f12f90c5432c7d30ea + md5: 59774accefb60098cdf15cfcd1cda508 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-webbioc", max_pin="x.x") }}' noarch: generic # SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annaffy >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annaffy >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-biocmanager run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-annaffy >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-gcrma >=2.72.0,<2.73.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-vsn >=3.68.0,<3.69.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' + - 'bioconductor-annaffy >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-gcrma >=2.74.0,<2.75.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - 'bioconductor-vsn >=3.70.0,<3.71.0' - r-base - r-biocmanager test: diff --git a/recipes/bioconductor-weberdivechalcdata/meta.yaml b/recipes/bioconductor-weberdivechalcdata/meta.yaml index 44c9361352f19..c4b66627150c2 100644 --- a/recipes/bioconductor-weberdivechalcdata/meta.yaml +++ b/recipes/bioconductor-weberdivechalcdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "WeberDivechaLCdata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7b4867dc3ce8463050bd897209d00c4 + md5: 3b75c693f86ed228e2b7816872cfe4b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-weberdivechalcdata", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-spatialexperiment >=1.10.0,<1.11.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-weberdivechalcdata/post-link.sh b/recipes/bioconductor-weberdivechalcdata/post-link.sh index cad6159f43b41..7776be0617620 100644 --- a/recipes/bioconductor-weberdivechalcdata/post-link.sh +++ b/recipes/bioconductor-weberdivechalcdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "weberdivechalcdata-1.2.0" +installBiocDataPackage.sh "weberdivechalcdata-1.4.0" diff --git a/recipes/bioconductor-weitrix/meta.yaml b/recipes/bioconductor-weitrix/meta.yaml index 9d4a0c43c50ef..eb99b763485c2 100644 --- a/recipes/bioconductor-weitrix/meta.yaml +++ b/recipes/bioconductor-weitrix/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "weitrix" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c32dce4e0730d66dd8757c78aadc44ad + md5: 101d61858d3d388a1396212f7ef5332e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-weitrix", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topconfects >=1.16.0,<1.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topconfects >=1.18.0,<1.19.0' - r-assertthat - r-base - r-ckmeans.1d.dp @@ -41,14 +42,14 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'bioconductor-topconfects >=1.16.0,<1.17.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'bioconductor-topconfects >=1.18.0,<1.19.0' - r-assertthat - r-base - r-ckmeans.1d.dp diff --git a/recipes/bioconductor-wes.1kg.wugsc/meta.yaml b/recipes/bioconductor-wes.1kg.wugsc/meta.yaml index 5f537e13c5d7b..755106b9959f2 100644 --- a/recipes/bioconductor-wes.1kg.wugsc/meta.yaml +++ b/recipes/bioconductor-wes.1kg.wugsc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "WES.1KG.WUGSC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4037de5e802a16f5aae76eca264b0be7 + md5: a0a3d230e27342090638ec4868756e5a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wes.1kg.wugsc", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-wes.1kg.wugsc/post-link.sh b/recipes/bioconductor-wes.1kg.wugsc/post-link.sh index ac9b442ef44fe..379916e93aea6 100644 --- a/recipes/bioconductor-wes.1kg.wugsc/post-link.sh +++ b/recipes/bioconductor-wes.1kg.wugsc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "wes.1kg.wugsc-1.32.0" +installBiocDataPackage.sh "wes.1kg.wugsc-1.34.0" diff --git a/recipes/bioconductor-wgsmapp/meta.yaml b/recipes/bioconductor-wgsmapp/meta.yaml index 5761c6cc97e9d..004433757f803 100644 --- a/recipes/bioconductor-wgsmapp/meta.yaml +++ b/recipes/bioconductor-wgsmapp/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "WGSmapp" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e4b497bab5e73445e19a84f86e40888 + md5: dfc3f5a82d532551e2d6c21b11c99566 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wgsmapp", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-wgsmapp/post-link.sh b/recipes/bioconductor-wgsmapp/post-link.sh index fa5f5b4d3d4ff..72a7d5958caa4 100644 --- a/recipes/bioconductor-wgsmapp/post-link.sh +++ b/recipes/bioconductor-wgsmapp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "wgsmapp-1.12.0" +installBiocDataPackage.sh "wgsmapp-1.14.0" diff --git a/recipes/bioconductor-wheatcdf/meta.yaml b/recipes/bioconductor-wheatcdf/meta.yaml index ce66b53e4ba95..e48303b1fdecd 100644 --- a/recipes/bioconductor-wheatcdf/meta.yaml +++ b/recipes/bioconductor-wheatcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "wheatcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0abeeeb9700b8d93a1a83769bdd8480f build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wheatcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-wheatprobe/meta.yaml b/recipes/bioconductor-wheatprobe/meta.yaml index f662ba5fe5d20..a8a7d02b42958 100644 --- a/recipes/bioconductor-wheatprobe/meta.yaml +++ b/recipes/bioconductor-wheatprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "wheatprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: b602d5050239850515be9dce12286360 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wheatprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-widgettools/meta.yaml b/recipes/bioconductor-widgettools/meta.yaml index a649ad5806073..9bd762908f52b 100644 --- a/recipes/bioconductor-widgettools/meta.yaml +++ b/recipes/bioconductor-widgettools/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.78.0" %} +{% set version = "1.80.0" %} {% set name = "widgetTools" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d5d6e9f2d028392979502b0b07d13cb7 + md5: bb5358a7e064436aa744ffb098a9c0ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-widgettools", max_pin="x.x") }}' noarch: generic # Suggests: Biobase requirements: diff --git a/recipes/bioconductor-wiggleplotr/meta.yaml b/recipes/bioconductor-wiggleplotr/meta.yaml index 21ba541310356..b8dcd748549bb 100644 --- a/recipes/bioconductor-wiggleplotr/meta.yaml +++ b/recipes/bioconductor-wiggleplotr/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "wiggleplotr" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,21 +11,22 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 15aa40f6d6b29b4f43f76f818daac0ec + md5: 9e05d485ba51bf035918d23e686e60ba build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wiggleplotr", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter requirements: host: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-cowplot @@ -33,11 +34,11 @@ requirements: - 'r-ggplot2 >=2.2.0' - r-purrr run: - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-assertthat - r-base - r-cowplot diff --git a/recipes/bioconductor-worm.db0/meta.yaml b/recipes/bioconductor-worm.db0/meta.yaml index 98bdfb084ad56..18bb7a5e84082 100644 --- a/recipes/bioconductor-worm.db0/meta.yaml +++ b/recipes/bioconductor-worm.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "worm.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5ab9b7c14dafa60945e528fe7b940d42 + md5: 67be1277b5ae184558259ac720a5741e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-worm.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-worm.db0/post-link.sh b/recipes/bioconductor-worm.db0/post-link.sh index bbbb7b1411a33..58e6b26a5f6a0 100644 --- a/recipes/bioconductor-worm.db0/post-link.sh +++ b/recipes/bioconductor-worm.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "worm.db0-3.17.0" +installBiocDataPackage.sh "worm.db0-3.18.0" diff --git a/recipes/bioconductor-wpm/meta.yaml b/recipes/bioconductor-wpm/meta.yaml index 9da297b9934f8..38ed8c9815556 100644 --- a/recipes/bioconductor-wpm/meta.yaml +++ b/recipes/bioconductor-wpm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "wpm" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,18 +11,19 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1c516e008e79b67ff826cf796f4eeced + md5: 44df6efb278049a19cefea84cb8a8b64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wpm", max_pin="x.x") }}' noarch: generic # Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-config @@ -39,8 +40,8 @@ requirements: - r-shinywidgets - r-stringr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-config diff --git a/recipes/bioconductor-wppi/meta.yaml b/recipes/bioconductor-wppi/meta.yaml index 7116847631e52..b3d8b9e3382a3 100644 --- a/recipes/bioconductor-wppi/meta.yaml +++ b/recipes/bioconductor-wppi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "wppi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6263659decef0f59841200d8558ec8a8 + md5: 1de428cfbb93be33d9e71b0415937cd9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wppi", max_pin="x.x") }}' noarch: generic # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-omnipathr >=3.8.0,<3.9.0' + - 'bioconductor-omnipathr >=3.10.0,<3.11.0' - r-base - r-dplyr - r-igraph @@ -35,7 +36,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-omnipathr >=3.8.0,<3.9.0' + - 'bioconductor-omnipathr >=3.10.0,<3.11.0' - r-base - r-dplyr - r-igraph @@ -57,4 +58,3 @@ about: summary: 'Weighting protein-protein interactions' description: 'Protein-protein interaction data is essential for omics data analysis and modeling. Database knowledge is general, not specific for cell type, physiological condition or any other context determining which connections are functional and contribute to the signaling. Functional annotations such as Gene Ontology and Human Phenotype Ontology might help to evaluate the relevance of interactions. This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.' license_file: LICENSE - diff --git a/recipes/bioconductor-wrench/meta.yaml b/recipes/bioconductor-wrench/meta.yaml index 6c7b3c52ded7b..8117dd068c109 100644 --- a/recipes/bioconductor-wrench/meta.yaml +++ b/recipes/bioconductor-wrench/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Wrench" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7e30debeed00e428d39c2b65fe51f8b + md5: 18e9fb2840f0002f41be3799688e2b1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-wrench", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR requirements: host: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit - r-matrixstats run: - - 'bioconductor-limma >=3.56.0,<3.57.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' - r-base - r-locfit - r-matrixstats diff --git a/recipes/bioconductor-xcms/meta.yaml b/recipes/bioconductor-xcms/meta.yaml index 8c2915782fe49..0db9d71304ea8 100644 --- a/recipes/bioconductor-xcms/meta.yaml +++ b/recipes/bioconductor-xcms/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.22.0" %} +{% set version = "4.0.0" %} {% set name = "xcms" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,53 +11,60 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 044ad9c66603d6d269746262f72ba146 + md5: 194314f3a5b94121a4007b58b17182b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat, pander, magrittr, rmarkdown, MALDIquant, pheatmap, Spectra (>= 1.1.17), MsBackendMgf, progress, signal + run_exports: '{{ pin_subpackage("bioconductor-xcms", max_pin="x.x") }}' +# Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat, pander, rmarkdown, MALDIquant, pheatmap, MsBackendMgf, MetaboCoreUtils, signal requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-massspecwavelet >=1.66.0,<1.67.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-msfeatures >=1.8.0,<1.9.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-msexperiment >=1.4.0,<1.5.0' + - 'bioconductor-msfeatures >=1.10.0,<1.11.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice - r-plyr + - r-progress - r-rann - r-rcolorbrewer - r-robustbase - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-massspecwavelet >=1.66.0,<1.67.0' - - 'bioconductor-mscoreutils >=1.12.0,<1.13.0' - - 'bioconductor-msfeatures >=1.8.0,<1.9.0' - - 'bioconductor-msnbase >=2.26.0,<2.27.0' - - 'bioconductor-multtest >=2.56.0,<2.57.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-protgenerics >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' + - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - 'bioconductor-msexperiment >=1.4.0,<1.5.0' + - 'bioconductor-msfeatures >=1.10.0,<1.11.0' + - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - 'bioconductor-multtest >=2.58.0,<2.59.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-spectra >=1.12.0,<1.13.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-lattice - r-plyr + - r-progress - r-rann - r-rcolorbrewer - r-robustbase diff --git a/recipes/bioconductor-xcore/meta.yaml b/recipes/bioconductor-xcore/meta.yaml index e84954b6e601d..f83edf02082ee 100644 --- a/recipes/bioconductor-xcore/meta.yaml +++ b/recipes/bioconductor-xcore/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "xcore" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5171f950290cc292a4878d982f241fa5 + md5: 4dd79b63bd7ff46aaa1b84dade889db2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xcore", max_pin="x.x") }}' noarch: generic # Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0), BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-foreach >=1.5.1' - 'r-glmnet >=4.1.2' @@ -34,12 +35,12 @@ requirements: - 'r-magrittr >=2.0.1' - 'r-matrix >=1.3.4' run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - 'r-foreach >=1.5.1' - 'r-glmnet >=4.1.2' diff --git a/recipes/bioconductor-xcoredata/meta.yaml b/recipes/bioconductor-xcoredata/meta.yaml index 121fd68bbdb97..d095f18812f83 100644 --- a/recipes/bioconductor-xcoredata/meta.yaml +++ b/recipes/bioconductor-xcoredata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "xcoredata" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 172e8208ccf23b03ead836908e84522a + md5: 214626bfcbb5d66445324f6e367142c7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xcoredata", max_pin="x.x") }}' noarch: generic # Suggests: BiocGenerics (>= 0.40.0), data.table (>= 1.14.2), GenomeInfoDb (>= 1.30.0), GenomicRanges (>= 1.46.1), IRanges (>= 2.28.0), knitr (>= 1.37), rmarkdown (>= 2.11), Matrix (>= 1.3.4), stringr (>= 1.4.0), S4Vectors (>= 0.32.3), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.14.0), xcore requirements: host: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base run: - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' + - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xcoredata/post-link.sh b/recipes/bioconductor-xcoredata/post-link.sh index e6dff1b4de2c8..fc698f3463f09 100644 --- a/recipes/bioconductor-xcoredata/post-link.sh +++ b/recipes/bioconductor-xcoredata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "xcoredata-1.4.0" +installBiocDataPackage.sh "xcoredata-1.6.0" diff --git a/recipes/bioconductor-xde/meta.yaml b/recipes/bioconductor-xde/meta.yaml index 12e69037dc1f4..925ec6e74d9ad 100644 --- a/recipes/bioconductor-xde/meta.yaml +++ b/recipes/bioconductor-xde/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "XDE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84d6c574373e0965f6bf5915f9771c11 + md5: aaf179de92edd3a7105c0fe20254f3d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xde", max_pin="x.x") }}' # Suggests: MASS, RUnit requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genemeta >=1.72.0,<1.73.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genemeta >=1.74.0,<1.75.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - r-gtools - r-mvtnorm @@ -32,11 +33,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-genemeta >=1.72.0,<1.73.0' - - 'bioconductor-siggenes >=1.74.0,<1.75.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-genemeta >=1.74.0,<1.75.0' + - 'bioconductor-siggenes >=1.76.0,<1.77.0' - r-base - r-gtools - r-mvtnorm diff --git a/recipes/bioconductor-xenopus.db0/meta.yaml b/recipes/bioconductor-xenopus.db0/meta.yaml index 9d6ae3a8ab3d1..43ceb31511611 100644 --- a/recipes/bioconductor-xenopus.db0/meta.yaml +++ b/recipes/bioconductor-xenopus.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "xenopus.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cbdcc91045acef0ea9998f965b24dc2e + md5: 67b245b456f21672e70fa0690d7e8410 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xenopus.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xenopus.db0/post-link.sh b/recipes/bioconductor-xenopus.db0/post-link.sh index bb5200ffd15a8..f0f7cb9144929 100644 --- a/recipes/bioconductor-xenopus.db0/post-link.sh +++ b/recipes/bioconductor-xenopus.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "xenopus.db0-3.17.0" +installBiocDataPackage.sh "xenopus.db0-3.18.0" diff --git a/recipes/bioconductor-xenopuslaeviscdf/meta.yaml b/recipes/bioconductor-xenopuslaeviscdf/meta.yaml index 7b4c9e53adb36..567de4b026944 100644 --- a/recipes/bioconductor-xenopuslaeviscdf/meta.yaml +++ b/recipes/bioconductor-xenopuslaeviscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xenopuslaeviscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9d09ff76471ae60faf71090e0638f240 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xenopuslaeviscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xenopuslaevisprobe/meta.yaml b/recipes/bioconductor-xenopuslaevisprobe/meta.yaml index 0853aa6c416f5..25b78155e0d34 100644 --- a/recipes/bioconductor-xenopuslaevisprobe/meta.yaml +++ b/recipes/bioconductor-xenopuslaevisprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xenopuslaevisprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 06a25268a5ab57bddf28bbb364ea977b build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xenopuslaevisprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xeva/meta.yaml b/recipes/bioconductor-xeva/meta.yaml index 6c08622a0c2a1..26be5b11abecf 100644 --- a/recipes/bioconductor-xeva/meta.yaml +++ b/recipes/bioconductor-xeva/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Xeva" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,19 +11,20 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b765aa8d8e7a153fb73707c5f95c805 + md5: 94733e069395be524fa2d7254f9c2c5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xeva", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-pharmacogx >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' - r-base - r-bbmisc - r-doparallel @@ -33,9 +34,9 @@ requirements: - r-rmisc - r-scales run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-pharmacogx >=3.4.0,<3.5.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' - r-base - r-bbmisc - r-doparallel diff --git a/recipes/bioconductor-xhybcasneuf/meta.yaml b/recipes/bioconductor-xhybcasneuf/meta.yaml index 487726e7771cb..82aa53006c4fa 100644 --- a/recipes/bioconductor-xhybcasneuf/meta.yaml +++ b/recipes/bioconductor-xhybcasneuf/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "XhybCasneuf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,28 +11,29 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9522270bba562cca4c2e5e2438294eca + md5: f3e6306b5c05fb026e36e4c60656e25a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xhybcasneuf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - 'bioconductor-ath1121501cdf >=2.18.0,<2.19.0' - - 'bioconductor-tinesath1cdf >=1.38.0,<1.39.0' + - 'bioconductor-tinesath1cdf >=1.40.0,<1.41.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-affy >=1.78.0,<1.79.0' + - 'bioconductor-affy >=1.80.0,<1.81.0' - 'bioconductor-ath1121501cdf >=2.18.0,<2.19.0' - - 'bioconductor-tinesath1cdf >=1.38.0,<1.39.0' + - 'bioconductor-tinesath1cdf >=1.40.0,<1.41.0' - r-base - r-rcolorbrewer - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xhybcasneuf/post-link.sh b/recipes/bioconductor-xhybcasneuf/post-link.sh index 67bc5c34fecf6..40faf39513b0d 100644 --- a/recipes/bioconductor-xhybcasneuf/post-link.sh +++ b/recipes/bioconductor-xhybcasneuf/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "xhybcasneuf-1.38.0" +installBiocDataPackage.sh "xhybcasneuf-1.40.0" diff --git a/recipes/bioconductor-xina/meta.yaml b/recipes/bioconductor-xina/meta.yaml index c33500c40dac5..727ba242c837e 100644 --- a/recipes/bioconductor-xina/meta.yaml +++ b/recipes/bioconductor-xina/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "XINA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,17 +11,18 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82af22019aa44d3dc2afb08123721e80 + md5: f6a090d9e94032485c8c42a6c985b223 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xina", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-alluvial - r-base - r-ggplot2 @@ -30,7 +31,7 @@ requirements: - r-mclust - r-plyr run: - - 'bioconductor-stringdb >=2.12.0,<2.13.0' + - 'bioconductor-stringdb >=2.14.0,<2.15.0' - r-alluvial - r-base - r-ggplot2 diff --git a/recipes/bioconductor-xlaevis.db/meta.yaml b/recipes/bioconductor-xlaevis.db/meta.yaml index 0cc840f89a298..cc34275d94283 100644 --- a/recipes/bioconductor-xlaevis.db/meta.yaml +++ b/recipes/bioconductor-xlaevis.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.2.3" %} {% set name = "xlaevis.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: deaffe47b4ee48a7edb159d8104dc241 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xlaevis.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.xl.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.xl.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.xl.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.xl.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xlaevis2cdf/meta.yaml b/recipes/bioconductor-xlaevis2cdf/meta.yaml index 8d60fc7d6bd5b..80adc6f158546 100644 --- a/recipes/bioconductor-xlaevis2cdf/meta.yaml +++ b/recipes/bioconductor-xlaevis2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xlaevis2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9e4a80d66397299b4e66a8d6715ca4aa build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xlaevis2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xlaevis2probe/meta.yaml b/recipes/bioconductor-xlaevis2probe/meta.yaml index 8f8442f4e7479..1cba9aafeeb01 100644 --- a/recipes/bioconductor-xlaevis2probe/meta.yaml +++ b/recipes/bioconductor-xlaevis2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xlaevis2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d86f8a05e106eb3123435da233ff851d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xlaevis2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xmapbridge/meta.yaml b/recipes/bioconductor-xmapbridge/meta.yaml index 880ef4a9d3fe4..8a8a6245590fd 100644 --- a/recipes/bioconductor-xmapbridge/meta.yaml +++ b/recipes/bioconductor-xmapbridge/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "xmapbridge" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 69bd426f8a70da8f291689f424ba0ed5 + md5: 8b07bc6daa0d9dad8943ef442076eb5e build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xmapbridge", max_pin="x.x") }}' noarch: generic # Suggests: RUnit, RColorBrewer requirements: diff --git a/recipes/bioconductor-xnastring/meta.yaml b/recipes/bioconductor-xnastring/meta.yaml index e0246413138d7..b489f8d737902 100644 --- a/recipes/bioconductor-xnastring/meta.yaml +++ b/recipes/bioconductor-xnastring/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "XNAString" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a510ae3de3d9ac6d5a9bcb22c06a954 + md5: d09bf1b8eba2843f2b6285d353fb51bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xnastring", max_pin="x.x") }}' # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-formattable @@ -35,11 +36,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - r-data.table - r-formattable diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml index d66daca16a817..ebe23beba3511 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.12" %} {% set name = "XtraSNPlocs.Hsapiens.dbSNP144.GRCh37" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 758d024c50d2349036dc27cc689b4e5a build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml index 1067bc0744ccc..ac390b39412d5 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.99.12" %} {% set name = "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,31 +13,32 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c617aa805c7ecf60ee9283eb3c51b1c7 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38", max_pin="x.x") }}' noarch: generic # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh38 requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-bsgenome >=1.68.0,<1.69.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xtropicaliscdf/meta.yaml b/recipes/bioconductor-xtropicaliscdf/meta.yaml index 2d5f6db6782db..117cb678fcdff 100644 --- a/recipes/bioconductor-xtropicaliscdf/meta.yaml +++ b/recipes/bioconductor-xtropicaliscdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xtropicaliscdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 253e3cde76a393789e124f395820e947 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xtropicaliscdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xtropicalisprobe/meta.yaml b/recipes/bioconductor-xtropicalisprobe/meta.yaml index d9e3ecbaf8a26..d9ebdd7601d4a 100644 --- a/recipes/bioconductor-xtropicalisprobe/meta.yaml +++ b/recipes/bioconductor-xtropicalisprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "xtropicalisprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 43d15a7e12edaec1bb5f24b87498b599 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xtropicalisprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-xvector/meta.yaml b/recipes/bioconductor-xvector/meta.yaml index f9ccd9271755f..35aa815312336 100644 --- a/recipes/bioconductor-xvector/meta.yaml +++ b/recipes/bioconductor-xvector/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.40.0" %} +{% set version = "0.42.0" %} {% set name = "XVector" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,27 +11,28 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5b392028689bd387623344c3edc457d + md5: f126998c6b563132e51ea31c3995c6b9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xvector", max_pin="x.x") }}' # Suggests: Biostrings, drosophila2probe, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-zlibbioc >=1.46.0,<1.47.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} diff --git a/recipes/bioconductor-yamss/meta.yaml b/recipes/bioconductor-yamss/meta.yaml index be366a95b73cb..7c64564193b38 100644 --- a/recipes/bioconductor-yamss/meta.yaml +++ b/recipes/bioconductor-yamss/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "yamss" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,34 +11,35 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b3a62f39c6f009aac9c61d866e163eca + md5: a60cfddcf6749fc165badbe9a0f8a311 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yamss", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrix run: - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-ebimage >=4.42.0,<4.43.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-mzr >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-mzr >=2.36.0,<2.37.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-data.table - r-matrix diff --git a/recipes/bioconductor-yapsa/meta.yaml b/recipes/bioconductor-yapsa/meta.yaml index 09e3ec2d5a308..ddef2c91d0bb8 100644 --- a/recipes/bioconductor-yapsa/meta.yaml +++ b/recipes/bioconductor-yapsa/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.25.0" %} +{% set version = "1.28.0" %} {% set name = "YAPSA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,25 +11,26 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46e58d6b25038c9f501d67e67e49eac4 + md5: 7da75a0c0eabc79012aeb87c9a6e9582 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yapsa", max_pin="x.x") }}' noarch: generic # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gtrellis >=1.32.0,<1.33.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-somaticsignatures >=2.36.0,<2.37.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gtrellis >=1.34.0,<1.35.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-somaticsignatures >=2.38.0,<2.39.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-circlize - r-corrplot @@ -46,15 +47,15 @@ requirements: - r-pracma - r-reshape2 run: - - 'bioconductor-biostrings >=2.68.0,<2.69.0' + - 'bioconductor-biostrings >=2.70.0,<2.71.0' - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gtrellis >=1.32.0,<1.33.0' - - 'bioconductor-keggrest >=1.40.0,<1.41.0' - - 'bioconductor-somaticsignatures >=2.36.0,<2.37.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-gtrellis >=1.34.0,<1.35.0' + - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - 'bioconductor-somaticsignatures >=2.38.0,<2.39.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-circlize - r-corrplot diff --git a/recipes/bioconductor-yarn/meta.yaml b/recipes/bioconductor-yarn/meta.yaml index 8253a3774aab2..2ac85ac689142 100644 --- a/recipes/bioconductor-yarn/meta.yaml +++ b/recipes/bioconductor-yarn/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "yarn" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 187cdd1c00ed2bad7d7378e1a14e10ca + md5: 90baa3de55a308d7deef0f913c6fdef8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yarn", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat (>= 0.8) requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-quantro >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-quantro >=1.36.0,<1.37.0' - r-base - r-downloader - r-gplots @@ -34,12 +35,12 @@ requirements: - r-rcolorbrewer - r-readr run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-quantro >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' + - 'bioconductor-biomart >=2.58.0,<2.59.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - 'bioconductor-quantro >=1.36.0,<1.37.0' - r-base - r-downloader - r-gplots diff --git a/recipes/bioconductor-ye6100subacdf/meta.yaml b/recipes/bioconductor-ye6100subacdf/meta.yaml index 3f2f1f1ecdd16..987121a33ff2b 100644 --- a/recipes/bioconductor-ye6100subacdf/meta.yaml +++ b/recipes/bioconductor-ye6100subacdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subacdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 27bd71410956bfe8bffc8de14b85bdb0 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ye6100subacdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ye6100subbcdf/meta.yaml b/recipes/bioconductor-ye6100subbcdf/meta.yaml index f854bb2a6c47e..e0bfba3fe6699 100644 --- a/recipes/bioconductor-ye6100subbcdf/meta.yaml +++ b/recipes/bioconductor-ye6100subbcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subbcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ee9ec4bd941940745bad538d79bfeab4 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ye6100subbcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ye6100subccdf/meta.yaml b/recipes/bioconductor-ye6100subccdf/meta.yaml index 782299ff2634b..ff6863fba3546 100644 --- a/recipes/bioconductor-ye6100subccdf/meta.yaml +++ b/recipes/bioconductor-ye6100subccdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subccdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: fcdfed29a695fe53b62bacfe13dfe0c1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ye6100subccdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ye6100subdcdf/meta.yaml b/recipes/bioconductor-ye6100subdcdf/meta.yaml index b9ffb737415e4..03e5320b76673 100644 --- a/recipes/bioconductor-ye6100subdcdf/meta.yaml +++ b/recipes/bioconductor-ye6100subdcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ye6100subdcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 521b501ddbcdc680c3d27b5b201029b1 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ye6100subdcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast.db0/meta.yaml b/recipes/bioconductor-yeast.db0/meta.yaml index 5f538d60bb615..b98f59b289457 100644 --- a/recipes/bioconductor-yeast.db0/meta.yaml +++ b/recipes/bioconductor-yeast.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "yeast.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ce5a6e6febb6565c3a382d188d7652c0 + md5: 483043596daee94866843e6a43dcf538 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeast.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast.db0/post-link.sh b/recipes/bioconductor-yeast.db0/post-link.sh index 3c67745d538b4..84300e3c77c28 100644 --- a/recipes/bioconductor-yeast.db0/post-link.sh +++ b/recipes/bioconductor-yeast.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeast.db0-3.17.0" +installBiocDataPackage.sh "yeast.db0-3.18.0" diff --git a/recipes/bioconductor-yeast2.db/meta.yaml b/recipes/bioconductor-yeast2.db/meta.yaml index ad899e25c4fd4..8a430b81ad727 100644 --- a/recipes/bioconductor-yeast2.db/meta.yaml +++ b/recipes/bioconductor-yeast2.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "yeast2.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: add5784349cde4d01b75ea4472d25597 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeast2.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast2cdf/meta.yaml b/recipes/bioconductor-yeast2cdf/meta.yaml index f7dfe00e0c340..af701c9f658c7 100644 --- a/recipes/bioconductor-yeast2cdf/meta.yaml +++ b/recipes/bioconductor-yeast2cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "yeast2cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 0a718d78ae56bef9bad8168123038ac8 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeast2cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeast2probe/meta.yaml b/recipes/bioconductor-yeast2probe/meta.yaml index 69700e2c68925..9e744a4c6cd0b 100644 --- a/recipes/bioconductor-yeast2probe/meta.yaml +++ b/recipes/bioconductor-yeast2probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "yeast2probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3f52a2b7bd379624bc2966ca28c9ddf9 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeast2probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastcc/meta.yaml b/recipes/bioconductor-yeastcc/meta.yaml index 20948f279f447..51737465e21ea 100644 --- a/recipes/bioconductor-yeastcc/meta.yaml +++ b/recipes/bioconductor-yeastcc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "yeastCC" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf769fb99f3c5b763cc44fb25947231a + md5: 847d9bba73cb25f458f608c2cd6bf0e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeastcc", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - 'bioconductor-biobase >=2.62.0,<2.63.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastcc/post-link.sh b/recipes/bioconductor-yeastcc/post-link.sh index de0088d2ddb2c..5cfa549de6683 100644 --- a/recipes/bioconductor-yeastcc/post-link.sh +++ b/recipes/bioconductor-yeastcc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastcc-1.40.0" +installBiocDataPackage.sh "yeastcc-1.42.0" diff --git a/recipes/bioconductor-yeastexpdata/meta.yaml b/recipes/bioconductor-yeastexpdata/meta.yaml index 41a56318dc5d8..e659778f8d1c3 100644 --- a/recipes/bioconductor-yeastexpdata/meta.yaml +++ b/recipes/bioconductor-yeastexpdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.46.0" %} +{% set version = "0.48.0" %} {% set name = "yeastExpData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,23 +11,24 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 57c3359351ed64d39e2d8d82abe2d852 + md5: 7cd63808a957defe831bf3e9d3ef4789 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeastexpdata", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db requirements: host: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base run: - - 'bioconductor-graph >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastexpdata/post-link.sh b/recipes/bioconductor-yeastexpdata/post-link.sh index 315ba75beea94..60ca33cf64171 100644 --- a/recipes/bioconductor-yeastexpdata/post-link.sh +++ b/recipes/bioconductor-yeastexpdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastexpdata-0.46.0" +installBiocDataPackage.sh "yeastexpdata-0.48.0" diff --git a/recipes/bioconductor-yeastgsdata/meta.yaml b/recipes/bioconductor-yeastgsdata/meta.yaml index 0d48dd94a2999..ae9c7079330f7 100644 --- a/recipes/bioconductor-yeastgsdata/meta.yaml +++ b/recipes/bioconductor-yeastgsdata/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "yeastGSData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09f1e0c194efae4d807ab0b3b14629a5 + md5: bc455a9ecd3eb2652f887026841b3c69 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeastgsdata", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastgsdata/post-link.sh b/recipes/bioconductor-yeastgsdata/post-link.sh index 412c2a9f44881..20a72ee7a6dc7 100644 --- a/recipes/bioconductor-yeastgsdata/post-link.sh +++ b/recipes/bioconductor-yeastgsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastgsdata-0.38.0" +installBiocDataPackage.sh "yeastgsdata-0.40.0" diff --git a/recipes/bioconductor-yeastnagalakshmi/meta.yaml b/recipes/bioconductor-yeastnagalakshmi/meta.yaml index 585074839b144..1fdc69c9ba943 100644 --- a/recipes/bioconductor-yeastnagalakshmi/meta.yaml +++ b/recipes/bioconductor-yeastnagalakshmi/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "yeastNagalakshmi" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9c196bfda6e0909a324d88a616dc992 + md5: ea5068bf2b4053452f416c56ab32736a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeastnagalakshmi", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastnagalakshmi/post-link.sh b/recipes/bioconductor-yeastnagalakshmi/post-link.sh index 21bc5072c30a3..38aeeac70d388 100644 --- a/recipes/bioconductor-yeastnagalakshmi/post-link.sh +++ b/recipes/bioconductor-yeastnagalakshmi/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastnagalakshmi-1.36.0" +installBiocDataPackage.sh "yeastnagalakshmi-1.38.0" diff --git a/recipes/bioconductor-yeastrnaseq/meta.yaml b/recipes/bioconductor-yeastrnaseq/meta.yaml index 7136e8f15b98f..267ad94c02c79 100644 --- a/recipes/bioconductor-yeastrnaseq/meta.yaml +++ b/recipes/bioconductor-yeastrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.38.0" %} +{% set version = "0.40.0" %} {% set name = "yeastRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f8a8b1a80312aeac4d1676bc8adcb0ee + md5: 2344deacf993b96e1709ad96b710471f build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-yeastrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: Biobase, ShortRead, IRanges requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-yeastrnaseq/post-link.sh b/recipes/bioconductor-yeastrnaseq/post-link.sh index a897a1a63c2fb..5e55679c515cb 100644 --- a/recipes/bioconductor-yeastrnaseq/post-link.sh +++ b/recipes/bioconductor-yeastrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastrnaseq-0.38.0" +installBiocDataPackage.sh "yeastrnaseq-0.40.0" diff --git a/recipes/bioconductor-ygs98.db/meta.yaml b/recipes/bioconductor-ygs98.db/meta.yaml index d4ae7caec47a2..a2127800e3fe5 100644 --- a/recipes/bioconductor-ygs98.db/meta.yaml +++ b/recipes/bioconductor-ygs98.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "ygs98.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d21c0dc1ee0f7512ae921a501b425fd3 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ygs98.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.sc.sgd.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ygs98cdf/meta.yaml b/recipes/bioconductor-ygs98cdf/meta.yaml index e4d5474142f4d..3fe615142da63 100644 --- a/recipes/bioconductor-ygs98cdf/meta.yaml +++ b/recipes/bioconductor-ygs98cdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ygs98cdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ec7df7564cf28e093646325ec55baf1e build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ygs98cdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ygs98frmavecs/meta.yaml b/recipes/bioconductor-ygs98frmavecs/meta.yaml index 52208c458cde6..aa59611da9db5 100644 --- a/recipes/bioconductor-ygs98frmavecs/meta.yaml +++ b/recipes/bioconductor-ygs98frmavecs/meta.yaml @@ -1,6 +1,6 @@ {% set version = "1.3.0" %} {% set name = "ygs98frmavecs" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,10 +13,11 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e78c8447eb381b91dafb2f9688da39dc build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ygs98frmavecs", max_pin="x.x") }}' noarch: generic requirements: host: @@ -24,7 +25,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-ygs98probe/meta.yaml b/recipes/bioconductor-ygs98probe/meta.yaml index 9c19a6f150513..727f6b9cb5c26 100644 --- a/recipes/bioconductor-ygs98probe/meta.yaml +++ b/recipes/bioconductor-ygs98probe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "ygs98probe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: f40f21d7074818a4ee74a45b5533e89d build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ygs98probe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafish.db/meta.yaml b/recipes/bioconductor-zebrafish.db/meta.yaml index 41da05b397de1..a67f14aba8f67 100644 --- a/recipes/bioconductor-zebrafish.db/meta.yaml +++ b/recipes/bioconductor-zebrafish.db/meta.yaml @@ -1,6 +1,6 @@ {% set version = "3.13.0" %} {% set name = "zebrafish.db" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,23 +13,24 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 64e40a61e81ac9397affb09880846559 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zebrafish.db", max_pin="x.x") }}' noarch: generic # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-org.dr.eg.db >=3.17.0,<3.18.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafish.db0/meta.yaml b/recipes/bioconductor-zebrafish.db0/meta.yaml index e61006f4c9cc7..47615e4211032 100644 --- a/recipes/bioconductor-zebrafish.db0/meta.yaml +++ b/recipes/bioconductor-zebrafish.db0/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.17.0" %} +{% set version = "3.18.0" %} {% set name = "zebrafish.db0" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf2c5c9a8aaee76228e865cab2901cd2 + md5: 5da71e369e2b538fe276cd58b511ebab build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zebrafish.db0", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafish.db0/post-link.sh b/recipes/bioconductor-zebrafish.db0/post-link.sh index df3ed7576fba4..9c2fee9d13f61 100644 --- a/recipes/bioconductor-zebrafish.db0/post-link.sh +++ b/recipes/bioconductor-zebrafish.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "zebrafish.db0-3.17.0" +installBiocDataPackage.sh "zebrafish.db0-3.18.0" diff --git a/recipes/bioconductor-zebrafishcdf/meta.yaml b/recipes/bioconductor-zebrafishcdf/meta.yaml index 228a47b0be6e1..fe5266cf6ca7e 100644 --- a/recipes/bioconductor-zebrafishcdf/meta.yaml +++ b/recipes/bioconductor-zebrafishcdf/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "zebrafishcdf" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 04edbb632600c97610b86423c2d850e7 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zebrafishcdf", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafishprobe/meta.yaml b/recipes/bioconductor-zebrafishprobe/meta.yaml index 07f967fbcbef9..a1f043e4c626b 100644 --- a/recipes/bioconductor-zebrafishprobe/meta.yaml +++ b/recipes/bioconductor-zebrafishprobe/meta.yaml @@ -1,6 +1,6 @@ {% set version = "2.18.0" %} {% set name = "zebrafishprobe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -13,20 +13,21 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: eea2747859afa763addc7313ab0a2452 build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zebrafishprobe", max_pin="x.x") }}' noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' + - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafishrnaseq/meta.yaml b/recipes/bioconductor-zebrafishrnaseq/meta.yaml index d3c760874b7b2..64a3e534df264 100644 --- a/recipes/bioconductor-zebrafishrnaseq/meta.yaml +++ b/recipes/bioconductor-zebrafishrnaseq/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "zebrafishRNASeq" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06390452c93fde30918ee5c5a3f6e5f2 + md5: c1fcbadec1b25e4b28483c015f7ab35c build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zebrafishrnaseq", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, knitr requirements: @@ -25,7 +26,7 @@ requirements: run: - r-base - curl - - bioconductor-data-packages>=20230706 + - 'bioconductor-data-packages >=20231203' test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-zebrafishrnaseq/post-link.sh b/recipes/bioconductor-zebrafishrnaseq/post-link.sh index f93e198eb9261..48e9432717478 100644 --- a/recipes/bioconductor-zebrafishrnaseq/post-link.sh +++ b/recipes/bioconductor-zebrafishrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "zebrafishrnaseq-1.20.0" +installBiocDataPackage.sh "zebrafishrnaseq-1.22.0" diff --git a/recipes/bioconductor-zellkonverter/meta.yaml b/recipes/bioconductor-zellkonverter/meta.yaml index 20a3cc49e9795..779bd0a947f9a 100644 --- a/recipes/bioconductor-zellkonverter/meta.yaml +++ b/recipes/bioconductor-zellkonverter/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.1" %} {% set name = "zellkonverter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,31 +11,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1163d42795ee3d22169a0d6212a95c17 + md5: 5ba05cd62d95057a39c194a5084c551a build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zellkonverter", max_pin="x.x") }}' noarch: generic -# Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rmarkdown, rhdf5, scRNAseq, spelling, testthat, withr +# Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rmarkdown, rhdf5 (>= 2.45.1), scRNAseq, spelling, testthat, withr requirements: host: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-matrix - r-reticulate run: - - 'bioconductor-basilisk >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-cli - r-matrix diff --git a/recipes/bioconductor-zenith/meta.yaml b/recipes/bioconductor-zenith/meta.yaml index 5df9b466a762e..20b3c23ba110d 100644 --- a/recipes/bioconductor-zenith/meta.yaml +++ b/recipes/bioconductor-zenith/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.2" %} {% set name = "zenith" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,20 +11,21 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 92aec1931e3466b18edd951d9f2f1866 + md5: 60c9729fb2407d62a1ea15b1aa5ee0eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zenith", max_pin="x.x") }}' noarch: generic # Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit requirements: host: - - 'bioconductor-enrichmentbrowser >=2.30.0,<2.31.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-variancepartition >=1.30.0,<1.31.0' + - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' - r-base - r-ggplot2 - 'r-msigdbr >=7.5.1' @@ -34,10 +35,10 @@ requirements: - r-rfast - r-tidyr run: - - 'bioconductor-enrichmentbrowser >=2.30.0,<2.31.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-variancepartition >=1.30.0,<1.31.0' + - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' + - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.58.0,<3.59.0' + - 'bioconductor-variancepartition >=1.32.0,<1.33.0' - r-base - r-ggplot2 - 'r-msigdbr >=7.5.1' diff --git a/recipes/bioconductor-zfpkm/meta.yaml b/recipes/bioconductor-zfpkm/meta.yaml index e3d521f2c1214..0624f38a002d1 100644 --- a/recipes/bioconductor-zfpkm/meta.yaml +++ b/recipes/bioconductor-zfpkm/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "zFPKM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,24 +11,25 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6819aae4b24e1a3ff09b47137e6e9a8f + md5: a167e99447d7fd6b5081152a7d4472a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zfpkm", max_pin="x.x") }}' noarch: generic # Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-dplyr - r-ggplot2 - r-tidyr run: - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-checkmate - r-dplyr diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml index 48a73518b7173..2dec8b8225d7f 100644 --- a/recipes/bioconductor-zinbwave/meta.yaml +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "zinbwave" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,30 +11,31 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eb568f3b13f70194dfbd6438d917b0d0 + md5: e909f5d76f0ce0b7d65358ee0f80b1f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zinbwave", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2 requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-softimpute run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-genefilter >=1.82.0,<1.83.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - 'bioconductor-edger >=4.0.0,<4.1.0' + - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - r-base - r-matrix - r-softimpute diff --git a/recipes/bioconductor-zlibbioc/meta.yaml b/recipes/bioconductor-zlibbioc/meta.yaml index bf2395a8350b9..2434de1bccde7 100644 --- a/recipes/bioconductor-zlibbioc/meta.yaml +++ b/recipes/bioconductor-zlibbioc/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "zlibbioc" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,12 +11,13 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1036b343d28d7fe87cd23543d6702425 + md5: babdaf77bc9e9e8218fa07d643f31730 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zlibbioc", max_pin="x.x") }}' # Suggests: BiocStyle requirements: host: diff --git a/recipes/bioconductor-zygositypredictor/meta.yaml b/recipes/bioconductor-zygositypredictor/meta.yaml index f304148a7bc32..6ed4225df0b9b 100644 --- a/recipes/bioconductor-zygositypredictor/meta.yaml +++ b/recipes/bioconductor-zygositypredictor/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.0.3" %} +{% set version = "1.2.0" %} {% set name = "ZygosityPredictor" %} -{% set bioc = "3.17" %} +{% set bioc = "3.18" %} package: name: 'bioconductor-{{ name|lower }}' @@ -11,22 +11,23 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 08898751473ecbad4c0b07367b5b8cfc + md5: c201664f307a2cf422119e2fa87759cf build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zygositypredictor", max_pin="x.x") }}' noarch: generic # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-igraph @@ -34,12 +35,12 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-genomicalignments >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.16.0,<2.17.0' - - 'bioconductor-variantannotation >=1.46.0,<1.47.0' + - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' + - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - 'bioconductor-iranges >=2.36.0,<2.37.0' + - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - r-base - r-dplyr - r-igraph diff --git a/recipes/expansionhunter/meta.yaml b/recipes/expansionhunter/meta.yaml index a0e856b6f9c2c..9e2552fbe11df 100644 --- a/recipes/expansionhunter/meta.yaml +++ b/recipes/expansionhunter/meta.yaml @@ -15,7 +15,7 @@ source: - 0004-add-fmt-formatters-for-classes.patch - 0005-apply-bioconda-4.0.2-patches.patch # [osx] build: - number: '0' + number: 1 run_exports: - {{ pin_subpackage('expansionhunter', max_pin="x") }} requirements: diff --git a/recipes/pxblat/build_failure.linux-64.yaml b/recipes/pxblat/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5b942524e2cd1 --- /dev/null +++ b/recipes/pxblat/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9910e8828c844b7213ab38c0600f3caa04cc87acd4497a3b3fbd44a337aefad8 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 169, in exc_logging_wrapper + status = run_func(*args) + ^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 248, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 377, in run + requirement_set = resolver.resolve( + ^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 73, in resolve + collected = self.factory.collect_root_requirements(root_reqs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 491, in collect_root_requirements + req = self._make_requirement_from_install_req( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 453, in _make_requirement_from_install_req + cand = self._make_candidate_from_link( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link + self._link_candidate_cache[link] = LinkCandidate( + ^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in __init__ + super().__init__( + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ + self.dist = self._prepare() + ^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare + dist = self._prepare_distribution() + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution + return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 516, in prepare_linked_requirement + return self._prepare_linked_requirement(req, parallel_builds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 631, in _prepare_linked_requirement + dist = _get_prepared_distribution( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 69, in _get_prepared_distribution + abstract_dist.prepare_distribution_metadata( + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/distributions/sdist.py", line 61, in prepare_distribution_metadata + self.req.prepare_metadata() + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/req/req_install.py", line 555, in prepare_metadata + self.metadata_directory = generate_metadata( + ^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata + distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_internal/utils/misc.py", line 713, in prepare_metadata_for_build_wheel + return super().prepare_metadata_for_build_wheel( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel + return self._call_hook('prepare_metadata_for_build_wheel', { + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 321, in _call_hook + raise BackendUnavailable(data.get('traceback', '')) + pip._vendor.pyproject_hooks._impl.BackendUnavailable: Traceback (most recent call last): + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 77, in _build_backend + obj = import_module(mod_path) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/pxblat_1688740629379/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.11/importlib/__init__.py", line 126, in import_module + return _bootstrap._gcd_import(name[level:], package, level) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1140, in _find_and_load_unlocked + ModuleNotFoundError: No module named 'poetry' + [0m[31m + [0mRemoved file://$SRC_DIR from build tracker '/tmp/pip-build-tracker-jl36fbnx' + Removed build tracker: '/tmp/pip-build-tracker-jl36fbnx' + Traceback (most recent call last): + File "/opt/conda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pxblat_1688740629379/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/pxblat/build_failure.osx-64.yaml b/recipes/pxblat/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7cf5a245e3926 --- /dev/null +++ b/recipes/pxblat/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9910e8828c844b7213ab38c0600f3caa04cc87acd4497a3b3fbd44a337aefad8 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 169, in exc_logging_wrapper + status = run_func(*args) + ^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 248, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 377, in run + requirement_set = resolver.resolve( + ^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 73, in resolve + collected = self.factory.collect_root_requirements(root_reqs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 491, in collect_root_requirements + req = self._make_requirement_from_install_req( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 453, in _make_requirement_from_install_req + cand = self._make_candidate_from_link( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link + self._link_candidate_cache[link] = LinkCandidate( + ^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in __init__ + super().__init__( + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ + self.dist = self._prepare() + ^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare + dist = self._prepare_distribution() + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution + return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 516, in prepare_linked_requirement + return self._prepare_linked_requirement(req, parallel_builds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 631, in _prepare_linked_requirement + dist = _get_prepared_distribution( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 69, in _get_prepared_distribution + abstract_dist.prepare_distribution_metadata( + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/distributions/sdist.py", line 61, in prepare_distribution_metadata + self.req.prepare_metadata() + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/req/req_install.py", line 555, in prepare_metadata + self.metadata_directory = generate_metadata( + ^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata + distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_internal/utils/misc.py", line 713, in prepare_metadata_for_build_wheel + return super().prepare_metadata_for_build_wheel( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel + return self._call_hook('prepare_metadata_for_build_wheel', { + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 321, in _call_hook + raise BackendUnavailable(data.get('traceback', '')) + pip._vendor.pyproject_hooks._impl.BackendUnavailable: Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 77, in _build_backend + obj = import_module(mod_path) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/importlib/__init__.py", line 126, in import_module + return _bootstrap._gcd_import(name[level:], package, level) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1126, in _find_and_load_unlocked + File "", line 241, in _call_with_frames_removed + File "", line 1204, in _gcd_import + File "", line 1176, in _find_and_load + File "", line 1140, in _find_and_load_unlocked + ModuleNotFoundError: No module named 'poetry' + + Removed file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-m00ixlfd' + Removed build tracker: '/private/tmp/pip-build-tracker-m00ixlfd' + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in + sys.exit(main()) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main + call_conda_build(action, config) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build + result = api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree + packages_from_this = build(metadata, stats, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build + utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/pxblat_1688740225962/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/r-acidbase/meta.yaml b/recipes/r-acidbase/meta.yaml index bf7918867c609..bd6a6b423c173 100644 --- a/recipes/r-acidbase/meta.yaml +++ b/recipes/r-acidbase/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 104b8c7907375ef5943217aa1565ef8fd01ac8bed4e4d9addc2aa489195b172d build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-acidbase', max_pin="x.x") }} diff --git a/recipes/r-basejump/meta.yaml b/recipes/r-basejump/meta.yaml index 8e6d80ca32c6f..6fe0a1493ed18 100644 --- a/recipes/r-basejump/meta.yaml +++ b/recipes/r-basejump/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 06b216c539d112468172d021ba9445b8d98918609319fb34c200093fa052cbb9 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-basejump', max_pin="x.x") }} diff --git a/recipes/r-biomartr/meta.yaml b/recipes/r-biomartr/meta.yaml index 350413e5b3959..a4fbd52da4fc5 100644 --- a/recipes/r-biomartr/meta.yaml +++ b/recipes/r-biomartr/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-chromium/meta.yaml b/recipes/r-chromium/meta.yaml index 323e18c9b526c..0c8141d3d61c6 100644 --- a/recipes/r-chromium/meta.yaml +++ b/recipes/r-chromium/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e2f58a6141ce55b73d631323360d86d3713bf7870476c2505f457c61f41a3d0b build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-chromium', max_pin="x.x") }} diff --git a/recipes/r-goalie/meta.yaml b/recipes/r-goalie/meta.yaml index ad0ccf22a5c52..166ff214cc367 100644 --- a/recipes/r-goalie/meta.yaml +++ b/recipes/r-goalie/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 58e751134e5b0431a3a8fee58eefdef2b169e782f1a6eea623c6c9e7fadcd937 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-goalie', max_pin="x.x") }} diff --git a/recipes/r-interpretmsspectrum/meta.yaml b/recipes/r-interpretmsspectrum/meta.yaml new file mode 100644 index 0000000000000..40d0de68aa104 --- /dev/null +++ b/recipes/r-interpretmsspectrum/meta.yaml @@ -0,0 +1,43 @@ +{% set version = '1.3.3' %} + +package: + name: r-interpretmsspectrum + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/InterpretMSSpectrum_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/InterpretMSSpectrum/InterpretMSSpectrum_{{ version }}.tar.gz + sha256: 306a1541504088a05636f49e71a12d806f32fcaaa2d0622a58288452012d71db + +build: + number: 1 + noarch: generic + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - bioconductor-rdisop + - r-envipat + - r-plyr + run: + - r-base + - bioconductor-rdisop + - r-envipat + - r-plyr + +test: + commands: + - $R -e "library('InterpretMSSpectrum')" + +about: + home: http://dx.doi.org/10.1021/acs.analchem.6b02743 + license: GPL-3.0-only + summary: Annotate and interpret deconvoluted mass spectra (mass*intensity pairs) from high + resolution mass spectrometry devices. + license_family: GPL3 + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/r-pipette/meta.yaml b/recipes/r-pipette/meta.yaml index 0a64d3387eaec..3c673788c57bd 100644 --- a/recipes/r-pipette/meta.yaml +++ b/recipes/r-pipette/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 80298775063372e1275191ff800ec00b7feb9cc33fdb9afb453826499e3b54c0 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-ramclustr/meta.yaml b/recipes/r-ramclustr/meta.yaml index bdaafa9cc6768..ac3e72aa6403e 100644 --- a/recipes/r-ramclustr/meta.yaml +++ b/recipes/r-ramclustr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: cd1154bb1411346a5426a919b2d374daedaabc08ce094b6ebed5a897c1fc9156 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-tinyarray/meta.yaml b/recipes/r-tinyarray/meta.yaml index dc511cf128aee..1a61d8ba0282c 100644 --- a/recipes/r-tinyarray/meta.yaml +++ b/recipes/r-tinyarray/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 68ea15eb8d726368919faa54c89e2d18806b94e73e21fdee365c350b7ee79eb3 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/ultraplex/meta.yaml b/recipes/ultraplex/meta.yaml index 68e00272ed7de..86c0708b1c4f0 100644 --- a/recipes/ultraplex/meta.yaml +++ b/recipes/ultraplex/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7b1efa09a421590907c7e5177eb9e4837deade89c237b961bcf2f7edfa9f2e90 build: - number: 0 + number: 1 skip: True # [py < 37 or py > 39] script: - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" From e0a007572db9ddbc80974e35c5d55d5cc4814be1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 15:49:02 -0500 Subject: [PATCH 1371/2173] Update deeplc to 2.2.26 (#44238) * Update deeplc to 2.2.23 * Update deeplc to 2.2.24 * add pyopenms * Update deeplc to 2.2.25 * Update deeplc to 2.2.26 * try extended base * revert extended base --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/deeplc/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/deeplc/meta.yaml b/recipes/deeplc/meta.yaml index ad2ebc4a427b0..51849c0d6507f 100644 --- a/recipes/deeplc/meta.yaml +++ b/recipes/deeplc/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DeepLC" %} -{% set version = "2.2.22" %} -{% set sha256 = "82049484d907a410ed8cdf27711af90a7a372adeb53fc8a2d2e0917109c4e611" %} +{% set version = "2.2.26" %} +{% set sha256 = "b4cbb3612a89fe82ddac6149a261f7440c721f4b87235ce534c4cbd95d424e1b" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ source: build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv run_exports: - {{ pin_subpackage("deeplc", max_pin="x") }} entry_points: @@ -40,6 +40,7 @@ requirements: - deeplcretrainer - psm-utils - hdf5plugin + - pyopenms test: imports: @@ -49,7 +50,8 @@ about: home: "https://compomics.github.io/projects/DeepLC" summary: 'DeepLC: Retention time prediction for (modified) peptides using Deep Learning.' dev_url: "https://github.com/compomics/DeepLC" - license: APACHE + license: Apache-2.0 + license_family: APACHE license_file: LICENSE extra: From 4dfed8028c3b2cca3124f54dff3f04aea2dba7c4 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 29 Dec 2023 15:57:53 -0600 Subject: [PATCH 1372/2173] Add recipe for CellBender v0.3.0 (#45024) * Add recipe for CellBender v0.3.0 * add run_exports --- recipes/cellbender/meta.yaml | 64 ++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 recipes/cellbender/meta.yaml diff --git a/recipes/cellbender/meta.yaml b/recipes/cellbender/meta.yaml new file mode 100644 index 0000000000000..68183da020015 --- /dev/null +++ b/recipes/cellbender/meta.yaml @@ -0,0 +1,64 @@ +{% set name = "cellbender" %} +{% set version = "0.3.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cellbender-{{ version }}.tar.gz + sha256: 94a46fb2b5921414ea86213cfdebca267b9ba6ba02df854cbd353980ab3aff42 + +build: + number: 0 + noarch: python + entry_points: + - cellbender = cellbender.base_cli:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('cellbender', max_pin="x.x") }} + +requirements: + host: + - python 3.7 + - setuptools >=61.2 + - pip + run: + - python 3.7 + - numpy + - scipy + - pytables + - pandas + - pyro-ppl >=1.8.4 + - pytorch + - matplotlib-base + - anndata >=0.7 + - loompy + - ipython + - jupyter + - jupyter_contrib_nbextensions + - notebook <7.0.0 + - nbconvert <7.0.0 + - psutil + +test: + imports: + - cellbender + commands: + - cellbender --help + +about: + home: https://github.com/broadinstitute/CellBender + summary: "A software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data" + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE + doc_url: https://cellbender.readthedocs.io/en/latest/ + dev_url: https://github.com/broadinstitute/CellBender + +extra: + recipe-maintainers: + - mencian + identifiers: + - biotools:CellBender + - doi:10.1038/s41592-023-01943-7 From d2899610ce579b55674b32a6049e27d7ec78a899 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 29 Dec 2023 18:46:16 -0600 Subject: [PATCH 1373/2173] Fix nrpys to build on python 3.8+ (#45025) --- recipes/nrpys/build.sh | 2 +- recipes/nrpys/cargo.patch | 9 +++++++++ recipes/nrpys/meta.yaml | 15 ++++++++------- recipes/nrpys/{patch => pyproject.patch} | 11 ++++++++--- 4 files changed, 26 insertions(+), 11 deletions(-) create mode 100644 recipes/nrpys/cargo.patch rename recipes/nrpys/{patch => pyproject.patch} (50%) diff --git a/recipes/nrpys/build.sh b/recipes/nrpys/build.sh index c08897288c011..6c41a389a5494 100644 --- a/recipes/nrpys/build.sh +++ b/recipes/nrpys/build.sh @@ -11,4 +11,4 @@ mkdir -p ${PREFIX}/bin # build shared Python module with Rust maturin build --release --strip -f -${PYTHON} -m pip install -vv . +${PYTHON} -m pip install -vvv --no-deps --no-build-isolation . diff --git a/recipes/nrpys/cargo.patch b/recipes/nrpys/cargo.patch new file mode 100644 index 0000000000000..71fb4191700c6 --- /dev/null +++ b/recipes/nrpys/cargo.patch @@ -0,0 +1,9 @@ +--- a/Cargo.toml ++++ b/Cargo.toml +@@ -14,5 +14,5 @@ crate-type = ["cdylib"] + + [dependencies] + nrps-rs = "0.2.1" +-pyo3 = { version = "0.18.0", features = ["extension-module"] } ++pyo3 = { version = "0.19.0", features = ["abi3-py38"] } + thiserror = "1.0.38" diff --git a/recipes/nrpys/meta.yaml b/recipes/nrpys/meta.yaml index 497aba8dd7f46..e1a1b94498112 100644 --- a/recipes/nrpys/meta.yaml +++ b/recipes/nrpys/meta.yaml @@ -7,26 +7,27 @@ package: version: {{ version }} build: - number: 2 - noarch: generic + number: 3 + noarch: python run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} source: url: https://github.com/kblin/nrpys/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} - patch: - - patch + patches: + - cargo.patch + - pyproject.patch requirements: host: - - python >=3.7 + - python >=3.8 - pip - rust - maturin - zlib run: - - python >=3.7 + - python >=3.8 test: imports: @@ -34,6 +35,6 @@ test: about: home: "https://github.com/kblin/nrpys" - license: GPL3 + license: AGPL-3.0-or-later license_file: LICENSE.txt summary: "Python language bindings for nrps-rs substrate specificity predictor." diff --git a/recipes/nrpys/patch b/recipes/nrpys/pyproject.patch similarity index 50% rename from recipes/nrpys/patch rename to recipes/nrpys/pyproject.patch index 99ab333ca033e..2a8640ef4169d 100644 --- a/recipes/nrpys/patch +++ b/recipes/nrpys/pyproject.patch @@ -1,15 +1,20 @@ --- a/pyproject.toml +++ b/pyproject.toml -@@ -1,5 +1,5 @@ +@@ -1,10 +1,10 @@ [build-system] -requires = ["maturin>=0.14,<0.15"] +requires = ["maturin>=1.0,<2.0"] build-backend = "maturin" [project] -@@ -13,3 +13,5 @@ classifiers = [ + name = "nrpys" +-requires-python = ">=3.7" ++requires-python = ">=3.8" + classifiers = [ + "Programming Language :: Rust", + "Programming Language :: Python :: Implementation :: CPython", +@@ -13,3 +13,4 @@ classifiers = [ [tool.maturin] python-source = "python" +features = ["pyo3/extension-module"] -+cargo-extra-args = "--features extension-module" From 97765cce7a94dd3b3fd62d0a5491dc21ca0f5344 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 19:46:30 -0500 Subject: [PATCH 1374/2173] Update oakvar to 2.9.83 (#45026) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index f4b045bd05e12..3980d2f261a57 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.82" %} -{% set sha256 = "77865978a9b646ce02a6e728f3f74f203a801bb4cf3df816badaca46d71ab4d2" %} +{% set version = "2.9.83" %} +{% set sha256 = "b7157f768ee6b631a202ac50a05a6b69c233320c036437f484ebeb2660422f77" %} package: name: {{ name|lower }} From 7c2849152e12a55d475a4ad533997ffd2f5389a1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 29 Dec 2023 21:08:55 -0500 Subject: [PATCH 1375/2173] Update foldcomp to 0.0.6 (#45018) * Update foldcomp to 0.0.6 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/foldcomp/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/foldcomp/meta.yaml b/recipes/foldcomp/meta.yaml index e27989971aa76..f645e6e9482ca 100644 --- a/recipes/foldcomp/meta.yaml +++ b/recipes/foldcomp/meta.yaml @@ -1,12 +1,14 @@ -{% set version = "0.0.5" %} -{% set sha256 = "f4997c67023946287a3958866a75a9776978d533ec8cbcb1b6ccc8b2c081d0b2" %} +{% set version = "0.0.6" %} +{% set sha256 = "7f77fded798ea711f816220e4ca20fe4a9fed9917b9b2d3f7eba22ad5e1aa7f5" %} package: name: foldcomp version: {{ version }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('foldcomp', max_pin="x.x") }} source: url: https://github.com/steineggerlab/foldcomp/archive/v{{ version }}.tar.gz @@ -31,10 +33,11 @@ test: about: home: https://github.com/steineggerlab/foldcomp - license: GPLv3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE.txt summary: "Foldcomp: a library and format for compressing and indexing large protein structure sets" extra: identifiers: - - doi:10.1101/2022.12.09.519715 + - doi:10.1093/bioinformatics/btad153 From 204bfaa53f2666542fe1a6ac273bdb22b8addf41 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 29 Dec 2023 21:35:58 -0600 Subject: [PATCH 1376/2173] Update antismash-lite to 7.1.0 (#45027) --- recipes/antismash-lite/build.sh | 4 +-- recipes/antismash-lite/meta.yaml | 55 ++++++++++++++++++-------------- 2 files changed, 33 insertions(+), 26 deletions(-) diff --git a/recipes/antismash-lite/build.sh b/recipes/antismash-lite/build.sh index 9b87424be5101..3ad1536ca047f 100644 --- a/recipes/antismash-lite/build.sh +++ b/recipes/antismash-lite/build.sh @@ -1,5 +1,5 @@ #!/bin/bash echo "include antismash/detection/genefinding/data/train_crypto" >> MANIFEST.in -df -h -$PYTHON -m pip install . --ignore-installed --no-deps -vv \ No newline at end of file +df -h +$PYTHON -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv diff --git a/recipes/antismash-lite/meta.yaml b/recipes/antismash-lite/meta.yaml index 2e3d43924775c..a41431b1a3b3f 100644 --- a/recipes/antismash-lite/meta.yaml +++ b/recipes/antismash-lite/meta.yaml @@ -1,59 +1,65 @@ -{% set name = "antiSMASH-lite" %} -{% set version = "6.1.1" %} -{% set sha256 = "38c9fa8d34dea2552d3b21e3cb2ca293864f2f53d381764de9dd3d5f0b40139e" %} +{% set name = "antismash-lite" %} +{% set version = "7.1.0" %} +{% set sha256 = "5c01cce48ef5cc2bc60bfd2e185a5937e731e86a711c4c822a336640984e9b48" %} package: name: {{ name|lower }} version: {{ version }} -build: - number: 1 - noarch: python - source: url: https://dl.secondarymetabolites.org/releases/{{ version }}/antismash-{{ version }}.tar.gz sha256: {{ sha256 }} +build: + number: 0 + noarch: python + entry_points: + - download-antismash-databases=antismash.download_databases:_main + - antismash=antismash.__main__:entrypoint + run_exports: + - {{ pin_subpackage('antismash-lite', max_pin="x") }} + requirements: host: - - python >=3.7 + - python >=3.9 - pip run: - - python >=3.7 + - python >=3.9 + - brawn >=1.0.1 - numpy - - biopython 1.78 - - helperlibs >=0.2.0 + - biopython 1.78.* + - helperlibs >=0.2.1 - jinja2 - joblib - jsonschema - - markupsafe >=2.0 + - markupsafe >=2.1.0 + - nrpys >=0.1.1 - pysvg-py3 - bcbio-gff - - pyscss + - libsass - matplotlib-base - scipy - - openjdk - - scikit-learn >=0.19 - - diamond >=0.9,<=2.0.15 + - scikit-learn >=1.3.2 + - moods >=1.9.4 + - diamond - fasttree 2.1.* - - glimmerhmm ==3.0.* + - glimmerhmm 3.0.* - hmmer2 - hmmer >=3.1b2 - - meme <=4.11.2 - - muscle 3.8.* + - meme 4.11.2 - blast - prodigal test: + imports: + - antismash commands: - - antismash -h - - blastp -help - - fasttree -help - - diamond --help 2>&1 > /dev/null + - antismash --help + - download-antismash-databases --help about: home: https://docs.antismash.secondarymetabolites.org/intro/ - license: AGPL-3.0 + license: AGPL-3.0-or-later license_family: AGPL license_file: LICENSE.txt summary: antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell @@ -72,4 +78,5 @@ extra: - doi:10.1093/nar/gkx319 - doi:10.1093/nar/gkz310 - doi:10.1093/nar/gkab335 + - doi:10.1093/nar/gkad344 - usegalaxy-eu:antismash From 7d07a0d2e5d83197afd0fab090655dffc7056c48 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 30 Dec 2023 09:10:50 -0500 Subject: [PATCH 1377/2173] Update jcvi to 1.3.9 (#45029) * Update jcvi to 1.3.9 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/jcvi/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/jcvi/meta.yaml b/recipes/jcvi/meta.yaml index d563589238e5b..fff106f59101f 100644 --- a/recipes/jcvi/meta.yaml +++ b/recipes/jcvi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "jcvi" %} -{% set version = "1.3.8" %} +{% set version = "1.3.9" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: f193f93b0a967ab6b6e940645f68e7ab640f2838973d270a0aa8662fe3f774ae + sha256: 495940ed40e419a32c8b9dc9582fe64e233edf8d796fca71422223c3494ceaa8 build: skip: True # [py2k or osx] @@ -77,5 +77,6 @@ about: home: http://github.com/tanghaibao/jcvi license: BSD-2-Clause license_family: BSD + license_file: LICENSE summary: Python utility libraries on genome assembly, annotation and comparative genomics description: "JCVI utility libraries" From 98e7bfb178de3614e39f6ba82609193d6ca6e25e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 30 Dec 2023 12:34:04 -0500 Subject: [PATCH 1378/2173] Update recognizer to 1.10.1 (#45031) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: João Sequeira --- recipes/recognizer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/recognizer/meta.yaml b/recipes/recognizer/meta.yaml index c8acd63dc115b..efcc7fb27632f 100644 --- a/recipes/recognizer/meta.yaml +++ b/recipes/recognizer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "recognizer" %} -{% set version = "1.10.0" %} -{% set sha256 = "7f001a4fb888777a7b14707f76458f25fc98fe14299d1bdcbf2452eba7cab75f" %} +{% set version = "1.10.1" %} +{% set sha256 = "1d97b521a5b8660e5dd1726c95b885bcdce53654d01a001d8e6522a9c76d81c2" %} package: name: {{ name|lower }} From 8aa9e9e18f20a5c07ec16ffaac829b79d4c24d9a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 31 Dec 2023 11:51:27 -0500 Subject: [PATCH 1379/2173] Update midsv to 0.11.0 (#45028) * Update midsv to 0.11.0 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/midsv/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/midsv/meta.yaml b/recipes/midsv/meta.yaml index 653a9df45db78..7193ae74b64af 100644 --- a/recipes/midsv/meta.yaml +++ b/recipes/midsv/meta.yaml @@ -1,5 +1,5 @@ {% set name = "midsv" %} -{% set version = "0.10.2" %} +{% set version = "0.11.0" %} package: name: {{ name|lower }} @@ -7,12 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/midsv-{{ version }}.tar.gz - sha256: 5ead1213b3f34f3a4a676ddb5e88cf7bc63ae2aac1226afe735bc46a7602e559 + sha256: 713a164c4bce68f1caa72d50f7b7eef7a62b869bd65f2aebf8024d33ba6cc5b8 build: noarch: python script: {{ PYTHON }} -m pip install . -vv number: 0 + run_exports: + - {{ pin_subpackage('midsv', max_pin="x") }} requirements: host: From 686bc582d4600feed182646489ce39d9966360cb Mon Sep 17 00:00:00 2001 From: Carl Mathias Kobel Date: Wed, 3 Jan 2024 10:05:07 +0100 Subject: [PATCH 1380/2173] Update meta.yaml (#45041) Snakemake refactored in newer version. --- recipes/assemblycomparator2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index 350463aca94b1..f0d50c8973c9b 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.14" %} +{% set version = "2.5.15" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: d95f39d996330ab72ceffc5e8aa17b9348b39478fd2a4bfd01ca960adff2d20e + sha256: 9605f4021710e975365090fba1c13c2005c46978cec48c6cabe678167c86d33e build: @@ -17,7 +17,7 @@ build: requirements: run: - - snakemake >=7.32.3 + - snakemake =7.32.4 - mamba >=1.4.9 # Necessary for snakemake to install child environments during development. From e60c1e91f288303aa10c63e1b68586dec0e5be2b Mon Sep 17 00:00:00 2001 From: John Lees Date: Wed, 3 Jan 2024 09:05:40 +0000 Subject: [PATCH 1381/2173] Rebuild unitig caller for new bifrost version (#45035) * Rebuild unitig caller for new bifrost version * Add run_exports * Fix string interpolation in pinning --- recipes/unitig-caller/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/unitig-caller/meta.yaml b/recipes/unitig-caller/meta.yaml index 66a861b27b3ad..67bcd0abf6cb4 100644 --- a/recipes/unitig-caller/meta.yaml +++ b/recipes/unitig-caller/meta.yaml @@ -12,10 +12,12 @@ source: - 0001-No-experimental.patch build: - number: 2 + number: 3 skip: True # [py27] entry_points: - unitig-caller = unitig_caller.__main__:main + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: @@ -29,12 +31,12 @@ requirements: - pybind11 - zlib - bzip2 - - bifrost >=1.2.0 + - bifrost >=1.3.0 - libgomp # [linux64] - llvm-openmp # [osx] run: - python - - bifrost >=1.2.0 + - bifrost >=1.3.0 test: imports: From 13c6a96b0ea97609dbcf79de3f27ac383ed34b0b Mon Sep 17 00:00:00 2001 From: Ray <851836818@qq.com> Date: Wed, 3 Jan 2024 17:09:09 +0800 Subject: [PATCH 1382/2173] Update annosine2 build (#45033) * Update meta.yaml * Update meta.yaml --- recipes/annosine2/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/annosine2/meta.yaml b/recipes/annosine2/meta.yaml index 9c474c8c73b80..98c711f9ab79d 100644 --- a/recipes/annosine2/meta.yaml +++ b/recipes/annosine2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c9d12adec9875c4a429c6e9da5b76d31c760ef7474635caf742d25592378f34c build: - number: 0 + number: 1 entry_points: - annosine2 = AnnoSINE.AnnoSINE_v2:main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " @@ -27,6 +27,7 @@ requirements: - kiwisolver - matplotlib-base - numpy + - pandas - pillow - pyparsing - python From b1b7d184ba500f7978947a35fb7bbf33b5d5a886 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Jan 2024 04:09:55 -0500 Subject: [PATCH 1383/2173] Update rasusa to 0.8.0 (#45042) * Update rasusa to 0.8.0 * add run_export * bump msrv --------- Co-authored-by: Michael Hall --- recipes/rasusa/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/rasusa/meta.yaml b/recipes/rasusa/meta.yaml index 0bd1e57489918..b61dc1feb6422 100644 --- a/recipes/rasusa/meta.yaml +++ b/recipes/rasusa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.1" %} +{% set version = "0.8.0" %} {% set name = "rasusa" %} package: @@ -7,14 +7,16 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz - sha256: 7a7e3f2f2038b3fd3ce112fa7264ef8cbd91c2aa14fe60d8be1be1bb13416a56 + sha256: 903fa09fd7f7cc92880953131487186c3fbf539a127dc82f502559f9c1e9c11a build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('rasusa', max_pin="x.x") }} requirements: build: - - rust >=1.53 + - rust >=1.70 - {{ compiler('c') }} # [not win] test: From f5e01912c3aab299bd87a31466d7147e55340a1e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Jan 2024 07:52:25 -0500 Subject: [PATCH 1384/2173] Update annonars to 0.33.0 (#45043) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 7cd859e346249..d7d44551f9f50 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.32.0" %} +{% set version = "0.33.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 467ebd15737c4a6451f5993fa1e93f52c5ecb4a1cdf0b0cd754b414261730f37 + sha256: 258cfc2aee680718fc1acc8bccddb571416e425198ca258ee295cdc42cc19f71 requirements: build: From 3b158a4bc23d19f3d1386e2052d01182491ae253 Mon Sep 17 00:00:00 2001 From: Florian Zwagemaker <49153065+florianzwagemaker@users.noreply.github.com> Date: Wed, 3 Jan 2024 14:33:27 +0100 Subject: [PATCH 1385/2173] patch viroconstrictor snakemake requirements to not use version 8.x (#45036) --- recipes/viroconstrictor/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/viroconstrictor/meta.yaml b/recipes/viroconstrictor/meta.yaml index aed7470960f98..a1f44a2d6cd3d 100644 --- a/recipes/viroconstrictor/meta.yaml +++ b/recipes/viroconstrictor/meta.yaml @@ -17,7 +17,7 @@ build: - viroConstrictor = ViroConstrictor.__main__:main - Viroconstrictor = ViroConstrictor.__main__:main script: {{ PYTHON }} -m pip install . --no-deps -vvv - number: 0 + number: 1 run_exports: - {{ pin_subpackage('viroconstrictor', max_pin="x") }} @@ -25,7 +25,7 @@ requirements: host: - python >=3.10 - pip - - snakemake >=7.15.2 + - snakemake >=7.15.2, < 8 - conda run: - python >=3.10 @@ -37,7 +37,7 @@ requirements: - openpyxl - pyyaml ==6.0 - rich ==13.* - - snakemake >=7.15.2 + - snakemake >=7.15.2, < 8 - aminoextract ==0.3.1 - conda - mamba From 69ef94e6ab6b5eba9076ae39fecef35d63511983 Mon Sep 17 00:00:00 2001 From: Kanglu123 <64641114+Kanglu123@users.noreply.github.com> Date: Wed, 3 Jan 2024 21:35:21 +0800 Subject: [PATCH 1386/2173] Add Deepmei version 1.0.0 recipes (#45005) --- recipes/deepmei/build.sh | 4 + recipes/deepmei/license.txt | 674 ++++++++++++++++++++++++++++++++++++ recipes/deepmei/meta.yaml | 35 ++ 3 files changed, 713 insertions(+) create mode 100644 recipes/deepmei/build.sh create mode 100644 recipes/deepmei/license.txt create mode 100644 recipes/deepmei/meta.yaml diff --git a/recipes/deepmei/build.sh b/recipes/deepmei/build.sh new file mode 100644 index 0000000000000..1b8b9158061ef --- /dev/null +++ b/recipes/deepmei/build.sh @@ -0,0 +1,4 @@ +mkdir -p $PREFIX/bin +ls $PREFIX/bin/ +cp -r * $PREFIX/bin/ +chmod +x $PREFIX/bin/* diff --git a/recipes/deepmei/license.txt b/recipes/deepmei/license.txt new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/deepmei/license.txt @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/deepmei/meta.yaml b/recipes/deepmei/meta.yaml new file mode 100644 index 0000000000000..ab40e3175008d --- /dev/null +++ b/recipes/deepmei/meta.yaml @@ -0,0 +1,35 @@ +package: + name: deepmei + version: 1.0.0 + +source: + url: https://raw.githubusercontent.com/kanglu123/deepmei_v1.0.0/master/DeepMEI.without_models_and_files.tar.gz + sha256: 6af31abb690b3ba209d719a1e924baaab725760deb47a69319c171308d095269 +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('deepmei', max_pin="x.x") }} + +requirements: + run: + # List dependencies here. e.g.: + # ... any other dependencies + - bedtools =2.30.0 + - bwa + - pysam =0.17.0 + - repeatmasker + - tensorflow =2.7.0 + - python >=3.8,<=3.9 + - perl =5.32.1 + - samtools + +test: + commands: + - deepmeiv1 + +about: + home: https://github.com/Kanglu123/deepmei + license: GPL-3.0 + license_file: license.txt + summary: A pipeline to detect mobile elements insertion in human genome From de353c877a169165cd7db4cdb71c22410cf8866a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 3 Jan 2024 14:27:42 -0500 Subject: [PATCH 1387/2173] Update keggcharter to 1.1.0 (#45046) --- recipes/keggcharter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/keggcharter/meta.yaml b/recipes/keggcharter/meta.yaml index b4284f829e7c1..a77bcf562f63d 100644 --- a/recipes/keggcharter/meta.yaml +++ b/recipes/keggcharter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "keggcharter" %} -{% set version = "1.0.2" %} -{% set sha256 = "605795641af04a7045cc92b6f37ee0b0c0b8e508b85fb70bcc6c00234b9d5d89" %} +{% set version = "1.1.0" %} +{% set sha256 = "092622dd992432e18d650be0f36572a3285ebb4f18703fca21d2161af9e272ff" %} package: name: {{ name|lower }} From 2199755eee978005de9d02248309ba1147d5863e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 06:53:23 -0500 Subject: [PATCH 1388/2173] Update mosca to 2.2.0 (#45054) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update mosca to 2.2.0 * Update meta.yaml Added run_exports Added pandas as dependency Fixed python version to <3.12 Fixed snakemake version to <8 --------- Co-authored-by: João Sequeira --- recipes/mosca/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/mosca/meta.yaml b/recipes/mosca/meta.yaml index 11788ab31187e..eec8c3b69c882 100644 --- a/recipes/mosca/meta.yaml +++ b/recipes/mosca/meta.yaml @@ -1,6 +1,6 @@ {% set name = "mosca" %} -{% set version = "2.1.0" %} -{% set sha256 = "823bffe56b298505136d7cbad3ab0cca526736edeba4458bc3dbb0b4450ab132" %} +{% set version = "2.2.0" %} +{% set sha256 = "575d17f70b7ff1860789bc352055d32af06b6c5fbe16e2169d762ae3d49a7ca2" %} package: name: {{ name|lower }} @@ -13,11 +13,14 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage("mosca", max_pin="x.x") }} requirements: run: - - python >=3.9 - - snakemake + - python >=3.9, <3.12 + - pandas + - snakemake <8 test: commands: @@ -47,4 +50,4 @@ about: extra: recipe-maintainers: - - iquasere \ No newline at end of file + - iquasere From a2b77cb8358df2b7eef081b0401c86d981953c66 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 06:55:33 -0500 Subject: [PATCH 1389/2173] Update fgbio to 2.2.1 (#45050) --- recipes/fgbio/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fgbio/meta.yaml b/recipes/fgbio/meta.yaml index e48a484303a73..ee2047de82028 100644 --- a/recipes/fgbio/meta.yaml +++ b/recipes/fgbio/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.2.0" %} +{% set version = "2.2.1" %} package: name: fgbio @@ -6,7 +6,7 @@ package: source: url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar - sha256: e3907b0edf525f9becc69472f843fa3bf5a5fd6e2e03b88532d6622aa264ed3d + sha256: bb875e9a9218b841f39bdd007492b56be25b4d112ef7c22311c554b7b60fcd2c build: noarch: generic From 85f70f6ff6f61306b9747a12e6b764d5997e27cd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 06:56:00 -0500 Subject: [PATCH 1390/2173] Update fgbio-minimal to 2.2.1 (#45051) --- recipes/fgbio-minimal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fgbio-minimal/meta.yaml b/recipes/fgbio-minimal/meta.yaml index c1588facf506d..23242dc27e036 100644 --- a/recipes/fgbio-minimal/meta.yaml +++ b/recipes/fgbio-minimal/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.2.0" %} +{% set version = "2.2.1" %} package: name: fgbio-minimal @@ -6,7 +6,7 @@ package: source: url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar - sha256: e3907b0edf525f9becc69472f843fa3bf5a5fd6e2e03b88532d6622aa264ed3d + sha256: bb875e9a9218b841f39bdd007492b56be25b4d112ef7c22311c554b7b60fcd2c build: noarch: generic From 70e88ab8d2792eb3386263c7ed4833979d67ebe9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:22:25 -0500 Subject: [PATCH 1391/2173] Update viralmsa to 1.1.41 (#45047) --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index 1a41b2d896121..78d60f0913045 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.40" %} +{% set version = "1.1.41" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: eb61ebad514448b5eebb675a19bfe91b622c7d825fb11528c8331aa9d3d7222d + sha256: 1475eb3497823fd85febd5bb983c919b830b1e367aa7cf21af19fb33d437404b requirements: run: From 99c7a32baf563db718d1aa197fab9ef408689c1b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:22:48 -0500 Subject: [PATCH 1392/2173] Update ndex2 to 3.7.0 (#45049) --- recipes/ndex2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ndex2/meta.yaml b/recipes/ndex2/meta.yaml index de8e93c6e67c0..223be915ae200 100644 --- a/recipes/ndex2/meta.yaml +++ b/recipes/ndex2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ndex2" %} -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} package: @@ -8,7 +8,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ndex2-{{ version }}.tar.gz" - sha256: "d6e95ba33747c59ae47d32ebce55837f17d001f776ea811a70b9e716592d2d1e" + sha256: "5fed3b6c204275fd75724f7d609823f9f6e249b3d468fdd8b0a1f7a9be7a294f" build: noarch: python From e24ae98aa24a1a39819258f1dc2a271f3a24a976 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:22:59 -0500 Subject: [PATCH 1393/2173] Update expam to 1.2.2.5 (#45053) --- recipes/expam/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/expam/meta.yaml b/recipes/expam/meta.yaml index 01df06215fcbd..6ca6b72a1a13b 100644 --- a/recipes/expam/meta.yaml +++ b/recipes/expam/meta.yaml @@ -1,5 +1,5 @@ {% set name = "expam" %} -{% set version = "1.2.2.4" %} +{% set version = "1.2.2.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c33b249351c13fd3cfcbd0b2411a9d61e5e1e6239d5b841c2d980dcb9a88debc + sha256: 4a102a67da23c37598c0a0778d0caf99d4c6c0ea4286aff7ca0ab360dc5cda09 build: number: 0 From 41e755bbf0e8791faec3d9631bf49658628c3b95 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:23:11 -0500 Subject: [PATCH 1394/2173] Update bustools to 0.43.2 (#45055) --- recipes/bustools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bustools/meta.yaml b/recipes/bustools/meta.yaml index 331adae0b3b1a..1e1cf6991bd0f 100644 --- a/recipes/bustools/meta.yaml +++ b/recipes/bustools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.43.1" %} +{% set version = "0.43.2" %} package: name: bustools @@ -6,7 +6,7 @@ package: source: url: https://github.com/BUStools/bustools/archive/v{{ version }}.tar.gz - sha256: ac94a33ca459de81c5756825a7a7f8daeae357fc6bf0ef88d4900e77b70f2b90 + sha256: ad5816152644ee615316daecf5883183994bd7cc96e6c008439123f4cd750b1f build: number: 0 From b041a80c1e599e4b00199eb9a7d3cbbd1862acd2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:23:38 -0500 Subject: [PATCH 1395/2173] Update kb-python to 0.28.1 (#45056) --- recipes/kb-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kb-python/meta.yaml b/recipes/kb-python/meta.yaml index 9cc58afa65d9a..9838dbed1aff6 100644 --- a/recipes/kb-python/meta.yaml +++ b/recipes/kb-python/meta.yaml @@ -1,5 +1,5 @@ {% set name = "kb-python" %} -{% set version = "0.28.0" %} +{% set version = "0.28.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/pachterlab/kb_python/archive/v{{ version }}.tar.gz - sha256: ed3d655f6e60d87be5b5b013ffc54e68a943f2997b70ba4f7b3e8a1c83bd2b8a + sha256: a45f396046f544326089c0c25deabcca254989eebab040b12e07114e6d87a09d patches: config.py.patch build: From 2bb52279cb4be1f7d7af03386a874dea28ce4126 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:24:41 -0500 Subject: [PATCH 1396/2173] Update xengsort to 2.0.5 (#44888) * Update xengsort to 2.0.4 * pin python to 3.11 * Update xengsort to 2.0.5 --------- Co-authored-by: joshuazhuang7 --- recipes/xengsort/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/xengsort/meta.yaml b/recipes/xengsort/meta.yaml index 0c8ea25b50318..64fbad850f790 100644 --- a/recipes/xengsort/meta.yaml +++ b/recipes/xengsort/meta.yaml @@ -1,5 +1,5 @@ {% set name = "xengsort" %} -{% set version = "2.0.3" %} +{% set version = "2.0.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 4783b53d4641b053f928994c9c316962b6cb1604ed7de0853aa3aa3e339e7e76 + sha256: 243567ee3bdb7111ca7294c5979c2cd9ab5e76fdeefd30b7e27a177c839b33c9 build: number: 0 @@ -16,14 +16,14 @@ build: run_exports: - {{ pin_subpackage(name, max_pin="x") }} noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" requirements: host: - pip - - python >=3.10 + - python ==3.11 run: - - python >=3.10 + - python ==3.11 - numpy >=1.22 - numba >=0.56 - zarr @@ -48,6 +48,6 @@ about: extra: identifiers: - - doi:10.4230/LIPIcs.WABI.2020.4 + - doi:10.4230/LIPIcs.WABI.2020.4 recipe-maintainers: - JZentgraf From df038adfb106b67c8cd31f9d991439f3015e07e1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 10:49:40 -0500 Subject: [PATCH 1397/2173] Update ena-webin-cli to 6.8.0 (#45059) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index 249da97616a98..582fa0f98d569 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.7.2" %} -{% set sha256 = "f45f9e54813711b6ea57130efae83a3381b2a3c66debd6d941fc1d9a85c69c6e" %} +{% set version = "6.8.0" %} +{% set sha256 = "08d39ed646f00d2e682ea83849c04e0665106af9f7ae25ca04c07bdd086c91ef" %} package: name: ena-webin-cli From 39f62e83de4be861be7b19b983209a69a5adf797 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 16:26:04 -0500 Subject: [PATCH 1398/2173] Update zol to 1.3.17 (#45067) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index c1af50a0bcea9..ce26b14a3821b 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.16" %} +{% set version = "1.3.17" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 1b881771eac51bfcf0b58ea13b090514e3f0ed1e1d4d0a252709881ffc46730f + sha256: 71205d5144d4489d863d63dd0e4eb5b4341e66b71bf4bc7fc186e9bed98fa17b build: number: 0 From 00fc676a6a823ca181f3497eb29e230874d4379e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 17:49:39 -0500 Subject: [PATCH 1399/2173] Update pybiolib to 1.1.1673 (#45057) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index d1e5bb09bb712..92e71dea5060c 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1666" %} +{% set version = "1.1.1673" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 71888c84f4ad3cf97f461d2fc5e9955560d131e0c74d9a453e378d5d80262442 + sha256: cb62441a9fabcab0a8cb1d1a541936ee90e39599a51e55ddd87d963a0499ff02 build: noarch: python From 117bc945aebdd7d330402eb98937737c2bb3bc9c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jan 2024 18:39:40 -0500 Subject: [PATCH 1400/2173] Update pybiolib to 1.1.1682 (#45072) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 92e71dea5060c..135ea9c49e89f 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1673" %} +{% set version = "1.1.1682" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: cb62441a9fabcab0a8cb1d1a541936ee90e39599a51e55ddd87d963a0499ff02 + sha256: 3bb0789aea5e55cf7fc33f41e898e6d3abb05adbafd870ba6be1c761e762c105 build: noarch: python From 8adcfa9e9dc9f0e228bd3b10bd4571884062f2e1 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 5 Jan 2024 03:30:49 -0600 Subject: [PATCH 1401/2173] Update adam to 1.0.1 (#45069) * Update adam to 1.0.1 * add pin_subpackage --- recipes/adam/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/adam/meta.yaml b/recipes/adam/meta.yaml index c29df2abaf583..51700f7519ec5 100644 --- a/recipes/adam/meta.yaml +++ b/recipes/adam/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.0" %} +{% set version="1.0.1" %} package: name: adam @@ -6,7 +6,7 @@ package: source: url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/adam/adam-distribution-spark3_2.12/{{ version }}/adam-distribution-spark3_2.12-{{ version }}-bin.tar.gz - sha256: 1c1d91ccb42d2faaefb075f93a11bfb5a8c6dd575c7f01d21842a8957204f705 + sha256: cd6259148a2d9d8bf10549cedd09fe5b12d9f34a25e80a4025f96d60e50be807 patches: - adam-shell.patch - adam-submit.patch @@ -14,6 +14,8 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('adam', max_pin="1") }} requirements: run: From fb76c615539e4ffef9697da577d42d6c440182a5 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 5 Jan 2024 03:31:25 -0600 Subject: [PATCH 1402/2173] Update cannoli to 1.0.1 (#45070) * Update cannoli to 1.0.1. * add pin_subpackage --- recipes/cannoli/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/cannoli/meta.yaml b/recipes/cannoli/meta.yaml index 37e73896b7434..e4b3a7739a686 100644 --- a/recipes/cannoli/meta.yaml +++ b/recipes/cannoli/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.0" %} +{% set version="1.0.1" %} package: name: cannoli @@ -6,11 +6,13 @@ package: source: url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/{{ version }}/cannoli-distribution-spark3_2.12-{{ version }}-bin.tar.gz - sha256: 28c076ebd64278c07e9169e5b5de13ea5fd30a1f68daffbe551518092089ef6a + sha256: 4cfbbe1d2085298e62d4143116f8776ef2c91854f36a0803c27164c51b541e12 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('cannoli', max_pin="1") }} requirements: run: From 02b5b023bc33bad1c8218579acae97cbfc9a34c3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 09:36:41 -0500 Subject: [PATCH 1403/2173] Update keggcharter to 1.1.1 (#45079) --- recipes/keggcharter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/keggcharter/meta.yaml b/recipes/keggcharter/meta.yaml index a77bcf562f63d..aa9fb12f6ef41 100644 --- a/recipes/keggcharter/meta.yaml +++ b/recipes/keggcharter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "keggcharter" %} -{% set version = "1.1.0" %} -{% set sha256 = "092622dd992432e18d650be0f36572a3285ebb4f18703fca21d2161af9e272ff" %} +{% set version = "1.1.1" %} +{% set sha256 = "66e33b222572eaa38b37ce0e04f844550b505c78e05533cbcaead31053c3fc69" %} package: name: {{ name|lower }} From 349d130cc071cf995e7f8d040000ac9c741342c8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:11:31 -0500 Subject: [PATCH 1404/2173] Update galaxy-objectstore to 23.1.4 (#45061) --- recipes/galaxy-objectstore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml index ac332bc820da2..148329751bff0 100644 --- a/recipes/galaxy-objectstore/meta.yaml +++ b/recipes/galaxy-objectstore/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.1.3" %} -{% set sha256 = "52b9b213e15f1e219a25304f616e44f29f0ac52b61c753a6e89fac9d5c2a0fa2" %} +{% set version = "23.1.4" %} +{% set sha256 = "548af50412cac61a38299b5ab6a7e9b787afc51db43370e058e4e58f2d10706b" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From 2577efa6b3c0e41d562444afef775d78cfb89db8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:11:40 -0500 Subject: [PATCH 1405/2173] Update galaxy-files to 23.1.4 (#45062) --- recipes/galaxy-files/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml index 0a61489a554ce..ffe4ded18d97d 100644 --- a/recipes/galaxy-files/meta.yaml +++ b/recipes/galaxy-files/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.1.3" %} -{% set sha256 = "0facf5bfe8573a6e1a576d4e4b7f0ad7fa7924a1291111b9dfc1714520e1d559" %} +{% set version = "23.1.4" %} +{% set sha256 = "9d36250e580a29c8982904e90b1ad89b1712de0743750e72bea3f740960a6524" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From 35a75a53d174c57e9d3912122727615865375a2f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:43:05 -0500 Subject: [PATCH 1406/2173] Update mashmap to 3.1.3 (#45064) --- recipes/mashmap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mashmap/meta.yaml b/recipes/mashmap/meta.yaml index 672f557d6afef..86acff531bec5 100644 --- a/recipes/mashmap/meta.yaml +++ b/recipes/mashmap/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.1.2" %} +{% set version = "3.1.3" %} {% set github = "https://github.com/marbl/MashMap" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: cf9bb085cc85b0f1b91f4fc45a907cff536099a4a82031f1e112259e24ba5976 + sha256: 7719dd6b3c25e650e16218252eaae7dbf424a10890d717ec3ad0920b102fd05a build: number: 0 From b364f44358cd9ffe3c2a84d585ffcf1c76e26656 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:46:31 -0500 Subject: [PATCH 1407/2173] Update rosella to 0.5.3 (#45075) --- recipes/rosella/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/rosella/meta.yaml b/recipes/rosella/meta.yaml index bcc70f4e4c7a5..090fd11d0e2ac 100644 --- a/recipes/rosella/meta.yaml +++ b/recipes/rosella/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.5.2" %} +{% set version = "0.5.3" %} {% set name = "rosella" %} -{% set hash = "7f0851bbeef7e694983b3002a06c4cc1346544818a532373ca63dab14fa0245a" %} +{% set hash = "a7a07f3217c40bc0308eb2fb964092662d6c99f4093e68e96c9575bce208d214" %} package: name: rosella From df5d13b901d9b8c58ce80d0dfff84d9753d74584 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:55:48 -0500 Subject: [PATCH 1408/2173] Update snakemake-executor-plugin-googlebatch to 0.2.0 (#45039) * Update snakemake-executor-plugin-googlebatch to 0.2.0 * add summary --------- Co-authored-by: mencian --- .../snakemake-executor-plugin-googlebatch/meta.yaml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml index 06a457c3e614b..2b428cb274a58 100644 --- a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml +++ b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-googlebatch" %} -{% set version = "0.1.1" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_googlebatch-{{ version }}.tar.gz - sha256: 12a25a51f4471d6fb774ed0e837a49c8f3cebbe5a6494a5b2daf96146df87925 + sha256: 3cccef6db07f47d53c0863db960c36d24c6336caabbea2b7fd3f2fc42c95edc4 build: noarch: python @@ -35,15 +35,12 @@ requirements: test: imports: - snakemake_executor_plugin_googlebatch - commands: - - pip check - requires: - - pip about: home: https://github.com/snakemake/snakemake-executor-plugin-googlebatch - summary: '' + summary: 'Snakemake executor plugin for Google Batch' license: MIT + license_family: MIT license_file: LICENSE extra: From 74859b13be262c96723db90c5b46b95d7b6a7fb9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:56:34 -0500 Subject: [PATCH 1409/2173] Update hifihla to 0.2.3 (#45066) --- recipes/hifihla/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hifihla/meta.yaml b/recipes/hifihla/meta.yaml index c0eedd01c0050..df508026a76a4 100644 --- a/recipes/hifihla/meta.yaml +++ b/recipes/hifihla/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hifihla" %} -{% set version = "0.2.2" %} -{% set hifihla_sha256 = "3de4f6166f7a253571a6feeeed17fc38a53f274881757c883204c7c3963de5cc" %} +{% set version = "0.2.3" %} +{% set hifihla_sha256 = "f2c3cf24ca12b1bf1bec88dae6a30089c702077e683eb01451f216b3ee93bbe0" %} package: name: {{ name }} From 628cbc6060cec450e34e9658903b854600e23ca0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:56:45 -0500 Subject: [PATCH 1410/2173] Update micom to 0.33.1 (#45071) --- recipes/micom/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/micom/meta.yaml b/recipes/micom/meta.yaml index 2e740c6af928e..cd53b1a6dd737 100644 --- a/recipes/micom/meta.yaml +++ b/recipes/micom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "micom" %} -{% set version = "0.33.0" %} +{% set version = "0.33.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 489d15dd2b7aa14db6c2c2887069f3ef5588df95c06a2b397bd81bb8b8970604 + sha256: 75e8a1fe8f1535d12a466a028cd4e3caa7c199788b02c18d1bff9f03ae1d92ec build: number: 0 From 63950f8441eb4f09ecb1c6dc3840eabc6d32d552 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:57:08 -0500 Subject: [PATCH 1411/2173] Update flight-genome to 1.6.3 (#45073) --- recipes/flight-genome/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/flight-genome/meta.yaml b/recipes/flight-genome/meta.yaml index 98ec30f242755..cbad38fef8043 100644 --- a/recipes/flight-genome/meta.yaml +++ b/recipes/flight-genome/meta.yaml @@ -1,5 +1,5 @@ {% set name = "flight-genome" %} -{% set version = "1.6.2" %} +{% set version = "1.6.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d07b920f3a6bfabb6190d27eb2cbe8ad8a1ddb40b0cbf62104d3adbb71c484a2 + sha256: 48a450da686d634aaed5d223d79481876836929892a5b730e42610d9b741dc6e build: number: 0 From 64237a019f064b5680995784189a35fb4b87dea9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 10:57:32 -0500 Subject: [PATCH 1412/2173] Update bioframe to 0.6.0 (#45076) --- recipes/bioframe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioframe/meta.yaml b/recipes/bioframe/meta.yaml index 3dd3614557adf..0cd0bbd8b9c45 100644 --- a/recipes/bioframe/meta.yaml +++ b/recipes/bioframe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioframe" %} -{% set version = "0.5.1" %} +{% set version = "0.6.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 416132f14334f3921d700a692bf94ea21161ca608e5e3b9a119f97c01012d578 + sha256: 7998f6aa072ab9655354b64c511a093c9f1a181f2d994f0e884b9c48c4d0c313 build: noarch: python From 13f6f3b89543406f12e7e4caf1aca3702b937fe8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 11:32:38 -0500 Subject: [PATCH 1413/2173] Update metdatamodel to 0.5.5 (#45082) --- recipes/metdatamodel/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metdatamodel/meta.yaml b/recipes/metdatamodel/meta.yaml index bfd1858956799..e83742363e601 100644 --- a/recipes/metdatamodel/meta.yaml +++ b/recipes/metdatamodel/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metdatamodel" %} -{% set version = "0.4.14" %} +{% set version = "0.5.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metDataModel-{{ version }}.tar.gz - sha256: 49583289a596934204f458c4464579d3b58e18765ae97d283b32b58028de0fbc + sha256: 8ed0c978ffe4e1a75d169ae58687cb86f15c991d05529748791c554c9f1103a9 build: noarch: python From eac0bed596320e0104e9b3bdfc79ca3f61b7e7aa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 12:25:23 -0500 Subject: [PATCH 1414/2173] Update odgi to 0.8.4 (#45077) * Update odgi to 0.8.4 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/odgi/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/odgi/meta.yaml b/recipes/odgi/meta.yaml index 43c3c89859e29..44d9dfd0ea1b0 100644 --- a/recipes/odgi/meta.yaml +++ b/recipes/odgi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "odgi" %} -{% set version = "0.8.3" %} +{% set version = "0.8.4" %} package: name: "{{ name }}" @@ -7,11 +7,13 @@ package: source: url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 13a63b8ada79851fd8ce5e7638dda1a8b75ef0346a5d93552ee2179256eb81bf + sha256: bc656e541a42c890f71e748e4420215e1efba5b7b890d8c009bfef114c811f47 build: skip: True # [osx or py27] number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: From 501904abe6afa80e521bc788b2b3da355715ee4b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 12:59:33 -0500 Subject: [PATCH 1415/2173] Update nanovar to 1.5.1 (#45084) --- recipes/nanovar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanovar/meta.yaml b/recipes/nanovar/meta.yaml index d0b873ee9c1ff..9d412711b5581 100644 --- a/recipes/nanovar/meta.yaml +++ b/recipes/nanovar/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.5.0" %} +{% set version = "1.5.1" %} package: name: nanovar @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nanovar/nanovar-{{ version }}.tar.gz - sha256: cca25fde5da27bd5497e80c3a2bfd5eb6bffa46d348d30682bbe4cca20ed767f + sha256: 5b189ff18958be0e7406752f7700e0c70d464ae64b70ed278fd32a2fe61280a4 build: skip: True # [py2k or osx or py > 39] From b2774f29d57d3768fcb0e2edb4bdf81bc642a233 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 15:59:45 -0500 Subject: [PATCH 1416/2173] Update r-ldweaver to 1.4 (#45058) * Update r-ldweaver to 1.4 * drop genbankr dependency * it seems genbankr is still needed --------- Co-authored-by: mencian --- recipes/r-ldweaver/meta.yaml | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/recipes/r-ldweaver/meta.yaml b/recipes/r-ldweaver/meta.yaml index f5c10cbc6684e..26d05b5b7316e 100644 --- a/recipes/r-ldweaver/meta.yaml +++ b/recipes/r-ldweaver/meta.yaml @@ -1,6 +1,6 @@ {% set name = "r-ldweaver" %} -{% set version = "1.3.1" %} -{% set sha256 = "a926d946b4fea6abdc2e7fdcc3ac8a55865da0403d45180eeb60cda0b92d3de0" %} +{% set version = "1.4" %} +{% set sha256 = "8fca169dbf073a280cb47d1352fbb1a49b7f0b4daeba146928705def61650608" %} package: name: {{ name }} @@ -23,10 +23,10 @@ requirements: build: - {{ compiler('c') }} # [not win] - {{ compiler('cxx') }} # [not win] - host: - r-base 4.* - bioconductor-genomicranges + - bioconductor-genbankr - r-matrix - r-matrixextra - r-rcolorbrewer @@ -37,7 +37,6 @@ requirements: - r-data.table - r-dplyr - r-fitdistrplus - - bioconductor-genbankr - r-ggnewscale - r-ggplot2 - r-ggraph @@ -47,12 +46,12 @@ requirements: - r-igraph - r-phytools - r-plyr - - r-stringi + - r-stringi - openjdk - run: - r-base 4.* - bioconductor-genomicranges + - bioconductor-genbankr - r-matrix - r-matrixextra - r-rcolorbrewer @@ -63,7 +62,6 @@ requirements: - r-data.table - r-dplyr - r-fitdistrplus - - bioconductor-genbankr - r-ggnewscale - r-ggplot2 - r-ggraph @@ -73,7 +71,7 @@ requirements: - r-igraph - r-phytools - r-plyr - - r-stringi + - r-stringi - openjdk test: @@ -86,5 +84,4 @@ about: license: GPL-3.0-or-later summary: Perform genomewide epistasis analysis by evaluating the LD structure in bacteria. license_family: GPL3 - license_file: - - LICENSE + license_file: LICENSE From 53b8d0d50fa4c15a90613f1e0d7cddfce2348909 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 5 Jan 2024 16:00:03 -0500 Subject: [PATCH 1417/2173] Update ncbi-datasets-pylib to 16.1.1 (#45090) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 2712a35e55419..8e24d691bd6a8 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.0.0" %} -{% set sha256 = "499f5664b768ae4c6e2e5ab2965e0b6e150de2f81c667ba89eb5f29a2e67ce1d" %} +{% set version = "16.1.1" %} +{% set sha256 = "cddfde551d1a5948d0f3b87660968887a0e22d31db2f2810384393192c112eaf" %} package: name: {{ name|lower }} From a2df0facbc0a119a0b12de3fe12e03aaee3a5753 Mon Sep 17 00:00:00 2001 From: "Le (Lena) Huang" Date: Fri, 5 Jan 2024 18:10:15 -0500 Subject: [PATCH 1418/2173] Update dbcan to 4.1.0 (#45088) * Update dbcan to 4.1.0 * fix bug * add hatchling and other fixes * edit sha256 --------- Co-authored-by: mencian --- recipes/dbcan/meta.yaml | 45 +++++++++++++++++++++++++++++------------ 1 file changed, 32 insertions(+), 13 deletions(-) diff --git a/recipes/dbcan/meta.yaml b/recipes/dbcan/meta.yaml index e9856eac10155..b4c30e8cb658f 100644 --- a/recipes/dbcan/meta.yaml +++ b/recipes/dbcan/meta.yaml @@ -1,29 +1,38 @@ {% set name = "dbcan" %} -{% set version = "4.0.0" %} +{% set version = "4.1.0" %} package: name: "{{ name|lower }}" version: {{ version }} source: + # the sha256 sum is generated by doing + # wget -0- [URL] | shasum -a 256 url: https://github.com/linnabrown/run_dbcan/releases/download/{{ version }}/dbcan-{{ version }}.tar.gz - sha256: c90e99168fa3414696575b8f5a6c2862173151d1f0d7246ebd5713704b597435 + sha256: cb0907eb10eb916bcf676c58f54e67a67dd4ed559152e5547bb44d071f063b8f + build: number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + entry_points: + - run_dbcan = dbcan.cli.run_dbcan:cli_main + - cgc_standard2json = dbcan.cli.cgc_process_json:main + - syntenic_plot = dbcan.cli.syntenic_plot:main + - dbcan_utils = dbcan.utils.utils:main + - dbcan_plot = dbcan.utils.plots:main + - dbcan_asmfree = dbcan.utils.diamond_unassembly:main + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: - - natsort - pip - - python - - setuptools - - setuptools_scm_git_archive - + - python >=3.6 + - hatchling run: - natsort - - python + - python >=3.6 - diamond - hmmer - prodigal @@ -32,18 +41,28 @@ requirements: - numpy >1.19 - biopython - pandas + - session-info test: imports: - dbcan + commands: + - run_dbcan --help about: - home: http://bcb.unl.edu/dbCAN2/ + home: https://bcb.unl.edu/dbCAN2/ dev_url: https://github.com/linnabrown/run_dbcan - license: GPLv3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE - summary: Standalone version of dbCAN annotation tool for automated CAZyme annotation + summary: "Standalone version of dbCAN annotation tool for automated CAZyme annotation" + doc_url: https://dbcan.readthedocs.io/en/latest/ extra: recipe-maintainers: - - Le Huang + - linnabrown + identifiers: + - doi:10.1093/nar/gkx894 + - doi:10.1093/nar/gky418 + - doi:10.1093/nar/gkad328 + - biotools:dbcan2 From 2a2b5a8d25f32e1a1dd85d171c7db3a7ec347ebb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 07:17:10 -0500 Subject: [PATCH 1419/2173] Update perl-math-bigint to 2.003002 (#45096) --- recipes/perl-math-bigint/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/perl-math-bigint/meta.yaml b/recipes/perl-math-bigint/meta.yaml index ac043f49bd2c9..f72bad5acfaaf 100644 --- a/recipes/perl-math-bigint/meta.yaml +++ b/recipes/perl-math-bigint/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-math-bigint" %} -{% set version = "2.003001" %} -{% set sha256 = "9e14c5b0b7eecd1dca6d7c1eca680befccf212f7e6683f0b874348375a0333fc" %} +{% set version = "2.003002" %} +{% set sha256 = "5ac1fd255cca29d7cf5cb9283e6bb8177cdb07c5bb97502a58084b1c6eace35c" %} package: name: {{ name }} From 346e96b576ddd894d11dd55a2c74b84d933f1fdf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 12:38:27 -0500 Subject: [PATCH 1420/2173] Update nf-test to 0.8.3 (#45098) --- recipes/nf-test/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-test/meta.yaml b/recipes/nf-test/meta.yaml index 1ad10e7398e1e..21bcaf9fe3c08 100644 --- a/recipes/nf-test/meta.yaml +++ b/recipes/nf-test/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.2" %} +{% set version = "0.8.3" %} package: @@ -13,7 +13,7 @@ build: source: url: https://github.com/askimed/nf-test/releases/download/v{{version}}/nf-test-{{version}}.tar.gz - sha256: 5d640cea4339da4de50ce3687e9a61bd10488f2cac342eb1f11743414c6a27cd + sha256: af48883e8d0cd2d65b0846b3f60a476a5ec28a3799ba9374e0cb307a2a2d634d requirements: host: From 37c691730e813e253168fad3ddbfbcfcf45d181d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 12:38:41 -0500 Subject: [PATCH 1421/2173] Update foldcomp to 0.0.7 (#45097) --- recipes/foldcomp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/foldcomp/meta.yaml b/recipes/foldcomp/meta.yaml index f645e6e9482ca..96977ef6197a7 100644 --- a/recipes/foldcomp/meta.yaml +++ b/recipes/foldcomp/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.0.6" %} -{% set sha256 = "7f77fded798ea711f816220e4ca20fe4a9fed9917b9b2d3f7eba22ad5e1aa7f5" %} +{% set version = "0.0.7" %} +{% set sha256 = "34cf6df7bb48f6bdd5c94337ddb1e1f16eafead841da8afed62dac1b5b8a9467" %} package: name: foldcomp From 03024e0ce53fa727962d68450ba17c572dac89e7 Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Sun, 7 Jan 2024 09:40:47 -0800 Subject: [PATCH 1422/2173] Update meta.yaml (#45086) --- recipes/ampliconsuite/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml index 84c00115d5bdf..24da7d68a4da9 100644 --- a/recipes/ampliconsuite/meta.yaml +++ b/recipes/ampliconsuite/meta.yaml @@ -1,7 +1,7 @@ {% set name="ampliconsuite" %} -{% set AS_version="1.2.0" %} +{% set AS_version="1.2.1" %} {% set AA_version="1.3.r7" %} -{% set AC_version="1.1.0" %} +{% set AC_version="1.1.1" %} package: name: {{ name }} @@ -11,12 +11,12 @@ source: # the sha256 sum is generated by doing # $ wget -O- [URL] | shasum -a 256 - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz - sha256: 749aa74579aa19d400078fc045d1f1d943159b2ebdcd43a449ee7d5ab2d8ca6d + sha256: 79515b2c1a57a8ea22905737f3c02047a4319d7ab91554dff1a058ead653c720 - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz sha256: be65a0293da9ced3f6f744657db475c16dd4dcaf9f037e17ee1a19f4ceaa7430 folder: ampliconarchitectlib - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz - sha256: e656b557fd8e1c598dd8df9b29e25d4208cb0e1c66e97235c27104751654b7f6 + sha256: 040400d2eb0b4c847245666a481de927eb0c9a368088c1e97f117e7a228c8c5d build: noarch: python From 9e43a5bb0e019034925f792bf87afafff3d214de Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 12:41:34 -0500 Subject: [PATCH 1423/2173] Update ltr_retriever to 2.9.8 (#45006) * Update ltr_retriever to 2.9.8 * add run_exports * revert channel specifications * remove channels section --------- Co-authored-by: joshuazhuang7 --- recipes/ltr_retriever/meta.yaml | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/recipes/ltr_retriever/meta.yaml b/recipes/ltr_retriever/meta.yaml index 64ee4402ab215..0945912461b47 100644 --- a/recipes/ltr_retriever/meta.yaml +++ b/recipes/ltr_retriever/meta.yaml @@ -1,6 +1,6 @@ {% set name = "LTR_retriever" %} -{% set version = "2.9.5" %} -{% set sha256 = "f50812e6342a1d427a69e11e7ccbf21d7d72acf52c373fbd4ffdbe8a96dd62b7" %} +{% set version = "2.9.8" %} +{% set sha256 = "c5723c69c8897e717f03a7a0690a8f9b4a6c56991d947eddb224066ddf2d1448" %} package: name: "{{ name|lower }}" @@ -13,21 +13,17 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('ltr_retriever', max_pin="x") }} -channels: - - bioconda - - anaconda - - conda-forge - - defaults - requirements: run: - perl-text-soundex - perl - cd-hit - repeatmasker <4.1.5 - - rmblast <2.11 - - libstdcxx-ng <13 + - rmblast + - libstdcxx-ng - tesorter test: @@ -36,8 +32,13 @@ test: about: home: https://github.com/oushujun/LTR_retriever - license: GPLv3 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Sensitive and accurate identification of LTR retrotransposons dev_url: https://github.com/oushujun/LTR_retriever + +extra: + identifiers: + - doi:10.1104/pp.17.01310 + - biotools:ltr_retriever From 6ed403b6ce3fd7e51bb34be2b565343901c33e42 Mon Sep 17 00:00:00 2001 From: Afif Elghraoui Date: Sun, 7 Jan 2024 09:42:55 -0800 Subject: [PATCH 1424/2173] prodigal: include upstream patches fixing critical bugs (#45091) * prodigal: freshen up * prodigal: include patches for critical bugs fixed upstream but unreleased The developer has accepted these changes, but no new release has been made in over a year. --- recipes/prodigal/meta.yaml | 11 +++++- recipes/prodigal/score_nodes.patch | 32 ++++++++++++++++++ recipes/prodigal/sd_motif_A.patch | 32 ++++++++++++++++++ recipes/prodigal/sd_motif_B.patch | 54 ++++++++++++++++++++++++++++++ 4 files changed, 128 insertions(+), 1 deletion(-) create mode 100644 recipes/prodigal/score_nodes.patch create mode 100644 recipes/prodigal/sd_motif_A.patch create mode 100644 recipes/prodigal/sd_motif_B.patch diff --git a/recipes/prodigal/meta.yaml b/recipes/prodigal/meta.yaml index f8c5bcbcff963..abb4fd87c74b2 100644 --- a/recipes/prodigal/meta.yaml +++ b/recipes/prodigal/meta.yaml @@ -5,9 +5,17 @@ package: source: url: https://github.com/hyattpd/Prodigal/archive/v2.6.3.zip sha256: 4f73f64ea09be8421e08afabdc641db7775632210f5ef896f5fab4604c9dfcd9 + patches: + # accepted PR https://github.com/hyattpd/Prodigal/pull/88 + - score_nodes.patch + # accepted PR https://github.com/hyattpd/Prodigal/pull/100 + - sd_motif_A.patch + - sd_motif_B.patch build: - number: 6 + number: 7 + run_exports: + - {{ pin_subpackage('prodigal', max_pin=None) }} requirements: build: @@ -22,5 +30,6 @@ test: about: home: http://prodigal.ornl.gov/ + dev_url: https://github.com/hyattpd/Prodigal license: GPL v3 summary: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program diff --git a/recipes/prodigal/score_nodes.patch b/recipes/prodigal/score_nodes.patch new file mode 100644 index 0000000000000..890a7ef773286 --- /dev/null +++ b/recipes/prodigal/score_nodes.patch @@ -0,0 +1,32 @@ +From b34b63b17f712aedb371a70eccf6660c3e524808 Mon Sep 17 00:00:00 2001 +From: Martin Larralde +Date: Sun, 12 Sep 2021 14:30:12 +0200 +Subject: [PATCH] Fix typo in `score_nodes` function of `node.c` +URL: https://github.com/hyattpd/Prodigal/pull/88 + +--- + node.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/node.c b/node.c +index 5f7ccc4..7438dfb 100644 +--- a/node.c ++++ b/node.c +@@ -487,7 +487,7 @@ void score_nodes(unsigned char *seq, unsigned char *rseq, int slen, + /* genes are also penalized. */ + /**************************************************************/ + if(is_meta == 1 && slen < 3000 && edge_gene == 0 && +- (nod[i].cscore < 5.0 || abs(nod[i].ndx-nod[i].stop_val < 120))) { ++ (nod[i].cscore < 5.0 || abs(nod[i].ndx-nod[i].stop_val) < 120)) { + nod[i].cscore -= META_PEN*dmax(0, (3000-slen)/2700.0); + } + +@@ -515,7 +515,7 @@ void score_nodes(unsigned char *seq, unsigned char *rseq, int slen, + else nod[i].sscore -= 0.5; + } + else if(nod[i].cscore < 5.0 && is_meta == 1 && abs(nod[i].ndx- +- nod[i].stop_val < 120) && nod[i].sscore < 0.0) ++ nod[i].stop_val) < 120 && nod[i].sscore < 0.0) + nod[i].sscore -= tinf->st_wt; + } + } diff --git a/recipes/prodigal/sd_motif_A.patch b/recipes/prodigal/sd_motif_A.patch new file mode 100644 index 0000000000000..972921686fcc4 --- /dev/null +++ b/recipes/prodigal/sd_motif_A.patch @@ -0,0 +1,32 @@ +From 7b8614dced6b431d872b6e8c8d5d62566caa0214 Mon Sep 17 00:00:00 2001 +From: Martin Larralde +Date: Fri, 27 Jan 2023 17:54:59 +0100 +Subject: [PATCH] Fix buffer initialization in SD motif detection code +URL: https://github.com/hyattpd/Prodigal/pull/100 + +--- + sequence.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/sequence.c b/sequence.c +index d5c8436..b2be997 100644 +--- a/sequence.c ++++ b/sequence.c +@@ -663,7 +663,7 @@ int shine_dalgarno_exact(unsigned char *seq, int pos, int start, double *rwt) { + double match[6], cur_ctr, dis_flag; + + limit = imin(6, start-4-pos); +- for(i = limit; i < 6; i++) match[i] = -10.0; ++ for(i = 0; i < 6; i++) match[i] = -10.0; + + /* Compare the 6-base region to AGGAGG */ + for(i = 0; i < limit; i++) { +@@ -739,7 +739,7 @@ int shine_dalgarno_mm(unsigned char *seq, int pos, int start, double *rwt) { + double match[6], cur_ctr, dis_flag; + + limit = imin(6, start-4-pos); +- for(i = limit; i < 6; i++) match[i] = -10.0; ++ for(i = 0; i < 6; i++) match[i] = -10.0; + + /* Compare the 6-base region to AGGAGG */ + for(i = 0; i < limit; i++) { diff --git a/recipes/prodigal/sd_motif_B.patch b/recipes/prodigal/sd_motif_B.patch new file mode 100644 index 0000000000000..91d2e519519aa --- /dev/null +++ b/recipes/prodigal/sd_motif_B.patch @@ -0,0 +1,54 @@ +From 7cb28c92f50e910d3cc14fc92bf6b9c197c8c6bf Mon Sep 17 00:00:00 2001 +From: Martin Larralde +Date: Fri, 27 Jan 2023 20:52:51 +0100 +Subject: [PATCH] Slightly refactor comparison code in `shine_dalgarno` + functions +URL: https://github.com/hyattpd/Prodigal/pull/100 + +--- + sequence.c | 25 +++++++++++++------------ + 1 file changed, 13 insertions(+), 12 deletions(-) + +diff --git a/sequence.c b/sequence.c +index b2be997..515c8b1 100644 +--- a/sequence.c ++++ b/sequence.c +@@ -667,10 +667,10 @@ int shine_dalgarno_exact(unsigned char *seq, int pos, int start, double *rwt) { + + /* Compare the 6-base region to AGGAGG */ + for(i = 0; i < limit; i++) { +- if(pos+i < 0) continue; +- if(i%3 == 0 && is_a(seq, pos+i) == 1) match[i] = 2.0; +- else if(i%3 != 0 && is_g(seq, pos+i) == 1) match[i] = 3.0; +- else match[i] = -10.0; ++ if(pos + i >= 0) { ++ if(i%3 == 0 && is_a(seq, pos+i) == 1) match[i] = 2.0; ++ else if(i%3 != 0 && is_g(seq, pos+i) == 1) match[i] = 3.0; ++ } + } + + /* Find the maximally scoring motif */ +@@ -743,14 +743,15 @@ int shine_dalgarno_mm(unsigned char *seq, int pos, int start, double *rwt) { + + /* Compare the 6-base region to AGGAGG */ + for(i = 0; i < limit; i++) { +- if(pos+i < 0) continue; +- if(i % 3 == 0) { +- if(is_a(seq, pos+i) == 1) match[i] = 2.0; +- else match[i] = -3.0; +- } +- else { +- if(is_g(seq, pos+i) == 1) match[i] = 3.0; +- else match[i] = -2.0; ++ if(pos+i >= 0) { ++ if(i % 3 == 0) { ++ if(is_a(seq, pos+i) == 1) match[i] = 2.0; ++ else match[i] = -3.0; ++ } ++ else { ++ if(is_g(seq, pos+i) == 1) match[i] = 3.0; ++ else match[i] = -2.0; ++ } + } + } + From a4d027bbd05c48d35e6bb1d533fda216ab4d113e Mon Sep 17 00:00:00 2001 From: Mark Santcroos Date: Sun, 7 Jan 2024 18:53:57 +0100 Subject: [PATCH 1425/2173] Add vcfphasesets (#45092) * Add vcfphasesets. * Change meta.yaml for run exports. --- recipes/vcfphasesets/meta.yaml | 40 ++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 recipes/vcfphasesets/meta.yaml diff --git a/recipes/vcfphasesets/meta.yaml b/recipes/vcfphasesets/meta.yaml new file mode 100644 index 0000000000000..a7e53659eb6f4 --- /dev/null +++ b/recipes/vcfphasesets/meta.yaml @@ -0,0 +1,40 @@ +{% set name = "vcfphasesets" %} +{% set version = "0.3" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: 2a6b8fc061d42bb4fa0d2c717978f90137a55a956928b535d6ea55c2dbd1be81 + +build: + number: 0 + script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + noarch: python + run_exports: + - {{ pin_subpackage('vcfphasesets', max_pin="x") }} + + +requirements: + host: + - python >=3.7 + - pip + run: + - python >=3.7 + - pysam + +test: + imports: + - vcfphasesets + +about: + home: https://github.com/LUMC/vcfphasesets + license: MIT + license_family: MIT + summary: Get variants as phase sets from a VCF file using pysam. + +extra: + recipe-maintainers: + - marksantcroos From adecd1f09445436bee7df5aa486f478aae8592e1 Mon Sep 17 00:00:00 2001 From: Koke <49822617+jorgeavilacartes@users.noreply.github.com> Date: Sun, 7 Jan 2024 19:05:05 +0100 Subject: [PATCH 1426/2173] Complexcgr (#45089) * Add complexcgr v0.8.0 * Add complexcgr v0.8.0 * Add complexcgr v0.8.0 --- recipes/complexcgr/meta.yaml | 49 ++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/complexcgr/meta.yaml diff --git a/recipes/complexcgr/meta.yaml b/recipes/complexcgr/meta.yaml new file mode 100644 index 0000000000000..0dd7c0b71a5f1 --- /dev/null +++ b/recipes/complexcgr/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "complexcgr" %} +{% set version = "0.8.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/complexcgr-{{ version }}.tar.gz + sha256: 800085b4f2187a0acc4c2cb09d4c8459d9192f6d91a502101393e012978960dd + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + build: + run_exports: + - {{ pin_subpackage('complexcgr', max_pin="x.x") }} + +requirements: + host: + - python >=3.9,<4.0 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.9.0,<4.0.0 + - tqdm >=4.61.2,<5.0.0 + - matplotlib-base >=3.4.2,<4.0.0 + - pillow >=10.0.0,<11.0.0 + - numpy >=1.22.3,<2.0.0 + - biopython >=1.79.0,<2.0.0 + +test: + imports: + - complexcgr + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/AlgoLab/complexCGR + summary: Encoders and Image representation of DNA/RNA sequences based on the Chaos Game Representation of DNA + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - jorgeavilacartes From 3169721faf72863f8b0b9e8603dd37df90de57ac Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 13:20:19 -0500 Subject: [PATCH 1427/2173] Update ribowaltz to 2.0 (#45065) * Update ribowaltz to 2.0 * add run_exports --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ribowaltz/meta.yaml | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/recipes/ribowaltz/meta.yaml b/recipes/ribowaltz/meta.yaml index 1d3b50dd02917..1725593a487e9 100755 --- a/recipes/ribowaltz/meta.yaml +++ b/recipes/ribowaltz/meta.yaml @@ -1,21 +1,23 @@ {% set name = "riboWaltz" %} -{% set version = "1.2.0" %} -{% set sha256 = "1a915eccd23fd122eca470320b8f17762687350fdeb642aef01fb7990e98938b" %} +{% set version = "2.0" %} +{% set sha256 = "55f2f4e44709f1b41f788351b64cce4615194062775f5e0dc714320e01d6f65c" %} package: - name: {{ name|lower }} - version: {{ version }} + name: {{ name|lower }} + version: {{ version }} source: - url: https://github.com/LabTranslationalArchitectomics/{{ name }}/archive/v{{ version }}.tar.gz - sha256: {{ sha256 }} + url: https://github.com/LabTranslationalArchitectomics/{{ name }}/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('ribowaltz', max_pin="x") }} requirements: host: @@ -47,5 +49,6 @@ test: about: home: https://github.com/LabTranslationalArchitectomics/riboWaltz license: MIT + license_family: MIT license_file: LICENSE summary: Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. From 6e288e17788675388e60b051d5061b6ce84cc06a Mon Sep 17 00:00:00 2001 From: Mark Santcroos Date: Sun, 7 Jan 2024 20:24:58 +0100 Subject: [PATCH 1428/2173] Update vcf2variants (#45083) * Update to version 1.0. * Add run_exports. * Extra dependency. * Bump version. * Bump version and test import. * Fix import test. * Add additional requirement. --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/vcf2variants/meta.yaml | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/recipes/vcf2variants/meta.yaml b/recipes/vcf2variants/meta.yaml index 06461f2201e7e..ce21048d701da 100644 --- a/recipes/vcf2variants/meta.yaml +++ b/recipes/vcf2variants/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcf2variants" %} -{% set version = "0.3" %} +{% set version = "1.2" %} package: name: '{{ name|lower }}' @@ -7,12 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8780f3cf331e76dde7add454dbf346b38a69eb0b398b8b751f07413824f1b9a4 + sha256: 7830202ec67de08e7b223649365eed4a4a66d1339c985123d21c65cca7283728 build: number: 0 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv noarch: python + run_exports: + - {{ pin_subpackage('vcf2variants', max_pin="x") }} requirements: host: @@ -20,11 +22,15 @@ requirements: - pip run: - python >=3.6 - - cyvcf2 + - natsort + - pysam + - vcfphasesets test: commands: - vcf2variants -h + imports: + - vcf2variants about: home: https://github.com/varda/varda2_preprocessing From 4037bcdd31c450a7e8ee2cbc1d30db9ec5071472 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 18:16:37 -0500 Subject: [PATCH 1429/2173] Update snapatac2 to 2.5.2 (#45078) * Update snapatac2 to 2.5.2 * add typing_extensions to run section --------- Co-authored-by: joshuazhuang7 --- recipes/snapatac2/meta.yaml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/recipes/snapatac2/meta.yaml b/recipes/snapatac2/meta.yaml index 52674eddb1726..725e76a0f899f 100644 --- a/recipes/snapatac2/meta.yaml +++ b/recipes/snapatac2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "snapatac2" %} -{% set version = "2.5.1" %} -{% set sha256 = "c60fff185fb502d03518b440b63e24b794f8c6f9592df06cd94d85e156721fa6" %} +{% set version = "2.5.2" %} +{% set sha256 = "7d851340005b72881311ab712a435c2ac3864155be305ff24ccdcd7972c3d2c7" %} package: name: {{ name }} @@ -12,10 +12,9 @@ source: build: number: 0 - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . -vvv --no-build-isolation --no-deps run_exports: - - {{ pin_subpackage('snapatac2', max_pin="x.x.x") }} - + - {{ pin_subpackage('snapatac2', max_pin="x") }} requirements: build: @@ -23,12 +22,10 @@ requirements: - cmake - rust - {{ compiler('c') }} - host: - python - pip - setuptools-rust - run: - python - anndata @@ -45,6 +42,7 @@ requirements: - packaging - rustworkx - pooch + - typing_extensions test: imports: @@ -52,9 +50,12 @@ test: about: home: https://github.com/kaizhang/SnapATAC2 - summary: Python/Rust package for single-cell epigenomics analysis + summary: "Python/Rust package for single-cell epigenomics analysis" license: MIT + license_family: MIT license_file: LICENSE + doc_url: https://kzhang.org/SnapATAC2/ + dev_url: https://github.com/kaizhang/SnapATAC2 extra: identifiers: From 585d826bbaf83aec9216cde60f0b20afddebb65e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 19:30:08 -0500 Subject: [PATCH 1430/2173] Update breseq to 0.38.2 (#45103) * Update breseq to 0.38.2 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/breseq/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/breseq/meta.yaml b/recipes/breseq/meta.yaml index ee573da392da4..2b9c00862c815 100644 --- a/recipes/breseq/meta.yaml +++ b/recipes/breseq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.38.1" %} +{% set version = "0.38.2" %} package: name: breseq @@ -6,10 +6,12 @@ package: source: url: https://github.com/barricklab/breseq/releases/download/v{{ version }}/breseq-{{ version }}-Source.tar.gz - sha256: "92af34f7248f7c8cf65951e1b86ffc0d6f7446dbe9d3323aa43c577ea1ff48b3" + sha256: "d451670b9e7e3c87b76d3107efe7f1a9a94904011a32e5d407f4cce7ee3b2892" build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('breseq', max_pin="x.x") }} requirements: build: @@ -31,8 +33,9 @@ test: about: home: https://github.com/barricklab/breseq - license: GPL-3.0 + license: GPL-2.0-or-later license_family: GPL license_file: COPYING summary: A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data. + doc_url: "https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/" From 42e390eb8e0817c06632c8731e6607ea500a9b19 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 19:30:24 -0500 Subject: [PATCH 1431/2173] Update mitos to 2.1.6 (#45104) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/mitos/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mitos/meta.yaml b/recipes/mitos/meta.yaml index ee2cddc84aeb1..eec1dc7b5f508 100644 --- a/recipes/mitos/meta.yaml +++ b/recipes/mitos/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "2.1.5" %} +{% set version = "2.1.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: c82a48eeaf63f7733c3439047154c1869842ba0106e95bb4ab556131d161b428 + sha256: 66d6ca1138bdda459d4ed6271a946ff86ea6298dcf7e3bb6f63c283213f77284 build: number: 0 From 6906b5f16910ecd1415f1778e797ceadee86cbd4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 7 Jan 2024 19:30:53 -0500 Subject: [PATCH 1432/2173] Update harmony-pytorch to 0.1.8 (#45106) * Update harmony-pytorch to 0.1.8 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/harmony-pytorch/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/harmony-pytorch/meta.yaml b/recipes/harmony-pytorch/meta.yaml index e29cb986fdae9..ac40e479722ae 100644 --- a/recipes/harmony-pytorch/meta.yaml +++ b/recipes/harmony-pytorch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "harmony-pytorch" %} -{% set version = "0.1.7" %} +{% set version = "0.1.8" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "90b6d6d7a9ae0a20584840828cff415d503be5449a7328b0c76fc45ed3f8c4df" + sha256: "1b097906d49c6ed9dde6cf234f7d987fb49a3b649b8a1323d99e6ea71b5b7df2" build: - number: 1 + number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('harmony-pytorch', max_pin="x.x") }} requirements: host: @@ -35,7 +37,8 @@ test: about: home: "https://github.com/lilab-bcb/harmony-pytorch" - license: BSD + license: BSD-3-Clause + license_family: BSD license_file: LICENSE summary: "This is a Pytorch implementation of Harmony algorithm on single-cell sequencing data integration." From 98d7cfba45c541bd61cd97ed897991f606107039 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 06:45:25 -0500 Subject: [PATCH 1433/2173] Update snakemake to 8.1.0 (#45108) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 66d8213406374..ec9cb7290f522 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.0.1" %} +{% set version = "8.1.0" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 72f1158a345e8c53f73a14b3480bdfd6c1605f7c1c4a8a46f96fac489133ab80 + sha256: 3aeb95197ced3f50d89eabaa95ad93414db64bda7683283bdec6690810d598e9 build: number: 0 From 05530c32a1edc95c95d16532ba822924d6d76297 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 10:14:12 -0500 Subject: [PATCH 1434/2173] Update ltr_retriever to 2.9.9 (#45107) --- recipes/ltr_retriever/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ltr_retriever/meta.yaml b/recipes/ltr_retriever/meta.yaml index 0945912461b47..fab51c19ad426 100644 --- a/recipes/ltr_retriever/meta.yaml +++ b/recipes/ltr_retriever/meta.yaml @@ -1,6 +1,6 @@ {% set name = "LTR_retriever" %} -{% set version = "2.9.8" %} -{% set sha256 = "c5723c69c8897e717f03a7a0690a8f9b4a6c56991d947eddb224066ddf2d1448" %} +{% set version = "2.9.9" %} +{% set sha256 = "ef7d59349c0cbb3c819a102e68488b85cb116c099a4512d72d8a70293f13c7c8" %} package: name: "{{ name|lower }}" From 84308caff764d3ffaa4a64a16398d7860b82d74e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 10:16:40 -0500 Subject: [PATCH 1435/2173] Update tn93 to 1.0.13 (#45109) --- recipes/tn93/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tn93/meta.yaml b/recipes/tn93/meta.yaml index dd24eb3675cba..37df7d1f5e9e2 100644 --- a/recipes/tn93/meta.yaml +++ b/recipes/tn93/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.12" %} +{% set version = "1.0.13" %} package: name: tn93 @@ -6,7 +6,7 @@ package: source: url: https://github.com/veg/tn93/archive/v{{ version }}.tar.gz - sha256: d60281b1b4375bff585bcfae57be6938606500a656682249da3e10ce222b889d + sha256: 58f26807cd762cfc5cb6f088b57dfb26c69e8dd8e59a3e3db42a51ddea03bb3c build: number: 0 From 98b445f7df8a23016997d65c1f6ccc185c97dad9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 11:41:42 -0500 Subject: [PATCH 1436/2173] Update hyphy to 2.5.59 (#45111) --- recipes/hyphy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hyphy/meta.yaml b/recipes/hyphy/meta.yaml index 66f4c7839bcdf..7e05e89fcba7a 100644 --- a/recipes/hyphy/meta.yaml +++ b/recipes/hyphy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.5.58" %} -{% set sha256 = "f448d4a95bdb356eb6b1384b0c507a79f152511ad76bb67170ab5b8eb2798231" %} +{% set version = "2.5.59" %} +{% set sha256 = "18d7fc1569ca9fa5cbd7df0517ccb3e03de118fb42ab339073dbf3a7d82c8546" %} package: name: hyphy From 827cd8ce371015c71c8566a139d550d7c15f9bdd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 12:46:59 -0500 Subject: [PATCH 1437/2173] Update pyfaidx to 0.8.0 (#45113) --- recipes/pyfaidx/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pyfaidx/meta.yaml b/recipes/pyfaidx/meta.yaml index d39bacf8ec44f..9209e777f8e00 100644 --- a/recipes/pyfaidx/meta.yaml +++ b/recipes/pyfaidx/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.7.2.2" %} +{% set version = "0.8.0" %} package: name: pyfaidx version: {{ version }} source: - url: https://files.pythonhosted.org/packages/19/ec/929a2ab2247105210ccc6ea61ab1af0bd9316eb6b3412123cfbd88a0bc60/pyfaidx-0.7.2.2.tar.gz - sha256: 3b7693c052c82691000fe4a92475db82ffc3b5a721a12b10dfbc87119c4b4d30 + url: https://files.pythonhosted.org/packages/ef/95/aa7e6d1c1b68e64234d5ed985a761edbbce124baea17c2056935626958d2/pyfaidx-0.8.0.tar.gz + sha256: 1eed70f4eafb4ba9c4cf7022cd748947b8ebe0f4c86cb56f42f587ab7f2da027 build: number: 0 From f11e39e4f6a911464ec249014fec96f554085fee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 16:29:03 -0500 Subject: [PATCH 1438/2173] Update mitgard to 1.1 (#45101) * Update mitgard to 1.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/mitgard/meta.yaml | 32 ++++++++++++++++++-------------- 1 file changed, 18 insertions(+), 14 deletions(-) diff --git a/recipes/mitgard/meta.yaml b/recipes/mitgard/meta.yaml index 2f83790b1ea71..7c3341012ee75 100644 --- a/recipes/mitgard/meta.yaml +++ b/recipes/mitgard/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0" %} +{% set version = "1.1" %} package: name: mitgard @@ -6,32 +6,36 @@ package: source: url: https://github.com/pedronachtigall/MITGARD/archive/refs/tags/v{{ version }}.tar.gz - sha256: 97bf3299242c573e744ded016f70f7e0d3a07c3f4b62ce88d084b9a2c3a9dabd + sha256: f00bf3d7795e6d320416cb1fb856d8dee936d95055f77b19ac74e1d42e88ed5f build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('mitgard', max_pin="x") }} requirements: - host: - - python>=3.6 - run: - - samtools=1.9 - - bowtie2=2.3 - - minimap2=2.17 - - trinity=2.8.5 - - spades=3.13.1 - - python>=3.6 - - biopython=1.69 + - samtools + - bowtie2 + - minimap2 + - trinity =2.8.5 + - spades =3.13.1 + - python >=3.6 + - biopython + - hifiasm + - canu + - blast test: commands: - "MITGARD.py -h" + - "MITGARD-LR.py -h" about: home: https://github.com/pedronachtigall/MITGARD - license: GPLv3 + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE.txt summary: "Mitochondrial Genome Assembly from RNA-seq Data." doc_url: https://github.com/pedronachtigall/MITGARD From 3e12337c1296bcf2500841b63f8ff1211b5c48ea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 19:00:37 -0500 Subject: [PATCH 1439/2173] Update bioframe to 0.6.1 (#45120) --- recipes/bioframe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioframe/meta.yaml b/recipes/bioframe/meta.yaml index 0cd0bbd8b9c45..81590d40e0556 100644 --- a/recipes/bioframe/meta.yaml +++ b/recipes/bioframe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioframe" %} -{% set version = "0.6.0" %} +{% set version = "0.6.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7998f6aa072ab9655354b64c511a093c9f1a181f2d994f0e884b9c48c4d0c313 + sha256: 63aec69ac37aebcdc8298ed41154a875ba99652cc7ef081dd1458bc90537f73b build: noarch: python From 0a248bbce6ad8cba8df5cfac4214490d02e75eb2 Mon Sep 17 00:00:00 2001 From: Zhou ZJ <43747306+ZhijianZhou01@users.noreply.github.com> Date: Tue, 9 Jan 2024 08:01:01 +0800 Subject: [PATCH 1440/2173] Add virusrecom (#45099) * add virusrecom recipes * add virusrecom recipes xx * Update meta.yaml * add python to run section and use SPDX identifier --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/virusrecom/build.sh | 4 +++ recipes/virusrecom/meta.yaml | 47 ++++++++++++++++++++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 recipes/virusrecom/build.sh create mode 100644 recipes/virusrecom/meta.yaml diff --git a/recipes/virusrecom/build.sh b/recipes/virusrecom/build.sh new file mode 100644 index 0000000000000..c65b9bb44d4b1 --- /dev/null +++ b/recipes/virusrecom/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +# build +$PYTHON setup.py install --single-version-externally-managed --record=record.txt \ No newline at end of file diff --git a/recipes/virusrecom/meta.yaml b/recipes/virusrecom/meta.yaml new file mode 100644 index 0000000000000..7c76abee9b068 --- /dev/null +++ b/recipes/virusrecom/meta.yaml @@ -0,0 +1,47 @@ +{% set name = "virusrecom" %} +{% set version = "1.1.2.2" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: d06eb57299eb38b3fbf2341af3ede2265a400962c2d147d84d19993ed496d024 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('virusrecom', max_pin="x") }} + + +requirements: + host: + - python >=3.5,<3.8 + - pip + - setuptools + + run: + - matplotlib-base + - numpy >=1.19.3 + - pandas >=1.1.5 + - scipy >=1.5.4 + - psutil >=5.9.1 + - python >=3.5,<3.8 + - openpyxl >=3.0.5 + +test: + commands: + - virusrecom --help + +about: + home: "https://github.com/ZhijianZhou01/virusrecom" + license: "LGPL-2.1-or-later" + license_family: "LGPL" + license_file: LICENSE + summary: "An information-theory-based method for recombination detection of viral lineages." + +extra: + identifiers: + - doi:10.1093/bib/bbac513 From feacfc47b323e7dde44e5b4fbfcabf2398459218 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 9 Jan 2024 01:01:24 +0100 Subject: [PATCH 1441/2173] bump mitos1 (#45112) * bump mitos1 * repin blast-legacy .. add tests first --- recipes/mitos/mitos1/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/mitos/mitos1/meta.yaml b/recipes/mitos/mitos1/meta.yaml index 9ce262fca6fec..c1a015275ecc6 100644 --- a/recipes/mitos/mitos1/meta.yaml +++ b/recipes/mitos/mitos1/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 0e750ada0f69626407e81bd953c83717a917c6b96f49d0f154bbe740a4b5fe12 + sha256: 4f541044977dd3b33628ff780f6435094f1d633a031a88b5bda80342efa05bae build: number: 0 @@ -25,8 +25,7 @@ requirements: - python >=3 - blast-legacy =2.2 - infernal =1.0 - - viennarna <2 - - r-base >=4 + - viennarna - r-ggplot2 - r-reshape2 - openjdk >8 @@ -61,6 +60,8 @@ test: - mitos.webserver commands: - runmitos.py -h + - 'R -e "library(''reshape2'')"' + - 'R -e "library(''ggplot2'')"' about: home: http://mitos.bioinf.uni-leipzig.de From 2dffe96866e4fb05a6f0c3804242f4f36944c96b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 19:28:19 -0500 Subject: [PATCH 1442/2173] Update pybiolib to 1.1.1685 (#45119) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 135ea9c49e89f..d7727d223aa67 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1682" %} +{% set version = "1.1.1685" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 3bb0789aea5e55cf7fc33f41e898e6d3abb05adbafd870ba6be1c761e762c105 + sha256: 44921a3ec42de028d164b048374691906edeaa59b8fb7b9366e82dabee1aba8c build: noarch: python From e29b84a7835fc1c2188a9fc99213acd2d09d2e79 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 21:18:23 -0500 Subject: [PATCH 1443/2173] Update ncbi-datasets-pylib to 16.1.2 (#45124) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 8e24d691bd6a8..42d3681568ee5 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.1.1" %} -{% set sha256 = "cddfde551d1a5948d0f3b87660968887a0e22d31db2f2810384393192c112eaf" %} +{% set version = "16.1.2" %} +{% set sha256 = "4bee7893737320c5b63887b513ad92712db3c2a3eb306b3ba26ac5590088cba7" %} package: name: {{ name|lower }} From 85857654571c45e414d2c03e050b183a94279cef Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 21:18:32 -0500 Subject: [PATCH 1444/2173] Update das_tool to 1.1.7 (#45123) * Update das_tool to 1.1.7 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/das_tool/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/das_tool/meta.yaml b/recipes/das_tool/meta.yaml index 2fdb95251dd2e..6aab0c2d4911b 100644 --- a/recipes/das_tool/meta.yaml +++ b/recipes/das_tool/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DAS_Tool" %} -{% set version = "1.1.6" %} -{% set sha256 = "a4c02f6789e7f6ca61e0b563261d5f17f12e1b931157a4ae0f413ffdea6eacfb" %} +{% set version = "1.1.7" %} +{% set sha256 = "3633b69242209ceee9cd523e3458adbe89da9c52ecd8724afef2e2099923c56c" %} package: name: {{ name|lower }} @@ -16,6 +16,8 @@ build: rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('das_tool', max_pin="x") }} requirements: host: @@ -30,7 +32,6 @@ requirements: - prodigal >=2.6.3 - blast >=2.7.1 - diamond >=0.9.14 - run: - codeutils # [osx] - unzip From 86be51d9f3c352e50e02290f99cbe4147dcdb281 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 8 Jan 2024 21:18:44 -0500 Subject: [PATCH 1445/2173] Update virusrecom to 1.1.3 (#45122) --- recipes/virusrecom/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/virusrecom/meta.yaml b/recipes/virusrecom/meta.yaml index 7c76abee9b068..84f3000fefdb9 100644 --- a/recipes/virusrecom/meta.yaml +++ b/recipes/virusrecom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "virusrecom" %} -{% set version = "1.1.2.2" %} +{% set version = "1.1.3" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d06eb57299eb38b3fbf2341af3ede2265a400962c2d147d84d19993ed496d024 + sha256: 1950537ea6f2cf83dcfc44dd31b5c524a8e5b6988ca284c1ed291a2234d692c7 build: number: 0 From 35b10553079583a2a46690aeef34fedfa0824579 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:20:35 -0500 Subject: [PATCH 1446/2173] Update severus to 0.1.2 (#45135) --- recipes/severus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/severus/meta.yaml b/recipes/severus/meta.yaml index 51de9dbeecbb8..6fbcfbe6a28f5 100644 --- a/recipes/severus/meta.yaml +++ b/recipes/severus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: severus @@ -6,7 +6,7 @@ package: source: url: https://github.com/KolmogorovLab/Severus/archive/refs/tags/{{ version }}.tar.gz - sha256: aa9cf7bfc78234b770e5b67a38e6ee98ee94c1e45e11d61429d8e02df8793570 + sha256: 6fd60f673aea6e6ff930a207311be3c533a944c8875e9a677235b99dc18e5135 build: number: 0 From 0536992bb8fbbb77426ac681116a3b6eac05db3d Mon Sep 17 00:00:00 2001 From: Zhou ZJ <43747306+ZhijianZhou01@users.noreply.github.com> Date: Tue, 9 Jan 2024 23:42:25 +0800 Subject: [PATCH 1447/2173] Update virusrecom (#45130) * add virusrecom recipes * Update meta.yaml * edit recipe-maintainer --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/virusrecom/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/virusrecom/meta.yaml b/recipes/virusrecom/meta.yaml index 84f3000fefdb9..bafd8ea722121 100644 --- a/recipes/virusrecom/meta.yaml +++ b/recipes/virusrecom/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1950537ea6f2cf83dcfc44dd31b5c524a8e5b6988ca284c1ed291a2234d692c7 build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage('virusrecom', max_pin="x") }} @@ -18,7 +18,7 @@ build: requirements: host: - - python >=3.5,<3.8 + - python >=3.5,!=3.8 - pip - setuptools @@ -28,7 +28,7 @@ requirements: - pandas >=1.1.5 - scipy >=1.5.4 - psutil >=5.9.1 - - python >=3.5,<3.8 + - python >=3.5,!=3.8 - openpyxl >=3.0.5 test: @@ -45,3 +45,5 @@ about: extra: identifiers: - doi:10.1093/bib/bbac513 + recipe-maintainers: + - ZhijianZhou01 From e8cc25806f9fb803ac45da2956ba72e12a5fe3c1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:42:41 -0500 Subject: [PATCH 1448/2173] Update hybracter to 0.5.0 (#45128) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index 4fd336ec8d85d..8e85a27f1af6e 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.4.1" %} +{% set version = "0.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 934eb7cc5024a4aac40e6f239a371cd2f1c987361d0c423f27cb24cc65b39217 + sha256: 6bdc2376e0000556622b957e765f27014972784700f306943b345956739d4592 build: number: 0 From 29d5b86c77f3afc7d5bc9adb3b4edc3d3cfaf0dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:42:49 -0500 Subject: [PATCH 1449/2173] Update dnaapler to 0.5.1 (#45129) --- recipes/dnaapler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnaapler/meta.yaml b/recipes/dnaapler/meta.yaml index e483b65cb9b96..5737d45fcec6a 100644 --- a/recipes/dnaapler/meta.yaml +++ b/recipes/dnaapler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dnaapler" %} -{% set version = "0.5.0" %} +{% set version = "0.5.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 19bc7c140b9047be5a094ad65c71f042b438cc1bb1a9c03a2c11ea8b54c3d506 + sha256: 9bc6289ebefaa2e9725709cae2dbfa2723ad0d4e7f073f781a23e9b799bac8a8 build: number: 0 From 56e928cc768523d806a249994367341d2453c116 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:43:01 -0500 Subject: [PATCH 1450/2173] Update recentrifuge to 1.13.1 (#45132) --- recipes/recentrifuge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/recentrifuge/meta.yaml b/recipes/recentrifuge/meta.yaml index 76f4032164e44..2490ce7708084 100644 --- a/recipes/recentrifuge/meta.yaml +++ b/recipes/recentrifuge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "recentrifuge" %} -{% set version = "1.13.0" %} +{% set version = "1.13.1" %} package: name: {{ name }} @@ -14,7 +14,7 @@ build: source: url: https://github.com/khyox/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 6b7c4d80ad53115bca363d72352ee4d9074aa3385ed2556840ce4e3f24855e17 + sha256: a8c3826302c7a39fe0735176b49fc635964b83d5cc110fc3139c83783c27984d requirements: host: From def0e003ca28cfa06579a7577cc4558bdb2b40aa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:44:18 -0500 Subject: [PATCH 1451/2173] Update tissuumaps to 3.2.0.3 (#45137) --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index a8cc66ef61471..8555dcfae9eba 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.0.2" %} +{% set version = "3.2.0.3" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: d47443e5cda7c1f8dd63879feeb799a1874638026d15c7ce1f190004d87fd384 + sha256: 372a92e7aa8fb5f6149bac1133aae6d04653c87ba3048af9ed95da84a64f2592 build: number: 0 From e81047dead4ae2053927ae9be15ca0550a88a851 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Tue, 9 Jan 2024 16:45:08 +0100 Subject: [PATCH 1452/2173] mitos: add tests for R packages (#44971) * mitos: add tests for R packages In test with the container I got: Exception: b"Warning message:\npackage \xe2\x80\x98ggplot2\xe2\x80\x99 was built under R version 3.6.3 \nError: package or namespace load failed for \xe2\x80\x98reshape2\xe2\x80\x99 in dyn.load(file, DLLpath = DLLpath, ...):\n unable to load shared object '/usr/local/lib/R/library/stringi/libs/stringi.so':\n libicui18n.so.64: cannot open shared object file: No such file or directory\nIn addition: Warning message:\npackage \xe2\x80\x98reshape2\xe2\x80\x99 was built under R version 3.6.3 \nExecution halted\n" * try to use R directly in tests * try R > 3 * bump and unpin vienna * retry R>3 * another try * try to pin r-stringi * bump * cnt * unpin some more requirements * remove stringi * repin infernal * repin hmmer * repin blast * Revert "repin blast" This reverts commit 6a5717a86f8231c1ced5ca58e21f97f01c264e2f. --- recipes/mitos/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/mitos/meta.yaml b/recipes/mitos/meta.yaml index eec1dc7b5f508..7523ada0fc540 100644 --- a/recipes/mitos/meta.yaml +++ b/recipes/mitos/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 66d6ca1138bdda459d4ed6271a946ff86ea6298dcf7e3bb6f63c283213f77284 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " noarch: python run_exports: @@ -23,11 +23,11 @@ requirements: run: - biopython <1.82 - python >=3 - - blast =2.9 + - blast >=2.9 - hmmer =3.2 - infernal =1.1 - - viennarna <2 - - r-base >=3 + - viennarna + - r-base - r-ggplot2 - r-reshape2 - openjdk >8 @@ -61,6 +61,8 @@ test: - mitos.webserver commands: - runmitos.py -h + - 'R -e "library(''reshape2'')"' + - 'R -e "library(''ggplot2'')"' about: home: http://mitos.bioinf.uni-leipzig.de From 1bf0463e6c451ed4bdb44f4308d85493b413af65 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 11:47:42 -0500 Subject: [PATCH 1453/2173] Update kb-python to 0.28.2 (#45138) --- recipes/kb-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/kb-python/meta.yaml b/recipes/kb-python/meta.yaml index 9838dbed1aff6..23a0ad79fcaaa 100644 --- a/recipes/kb-python/meta.yaml +++ b/recipes/kb-python/meta.yaml @@ -1,5 +1,5 @@ {% set name = "kb-python" %} -{% set version = "0.28.1" %} +{% set version = "0.28.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/pachterlab/kb_python/archive/v{{ version }}.tar.gz - sha256: a45f396046f544326089c0c25deabcca254989eebab040b12e07114e6d87a09d + sha256: e8c910865fd5196b1b3163e18a565ef96c8518b2cf34f87f288dfdc85b339078 patches: config.py.patch build: From 9b4978740d702446c1a3c198fd73017e60675e21 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 11:47:49 -0500 Subject: [PATCH 1454/2173] Update ena-webin-cli to 6.9.0 (#45139) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index 582fa0f98d569..98bc27a785056 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.8.0" %} -{% set sha256 = "08d39ed646f00d2e682ea83849c04e0665106af9f7ae25ca04c07bdd086c91ef" %} +{% set version = "6.9.0" %} +{% set sha256 = "13218491e3d0dce8b28360606e23ffd54bd491452449c996e7f05944bf352217" %} package: name: ena-webin-cli From b295045c5f541f1fdc701fc002030e393990482f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 11:49:50 -0500 Subject: [PATCH 1455/2173] Update r-seqmagick to 0.1.7 (#45131) * Update r-seqmagick to 0.1.7 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-seqmagick/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/r-seqmagick/meta.yaml b/recipes/r-seqmagick/meta.yaml index dd1ab5449d137..72e09c9aa4e16 100644 --- a/recipes/r-seqmagick/meta.yaml +++ b/recipes/r-seqmagick/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.1.6' %} +{% set version = '0.1.7' %} package: name: r-seqmagick @@ -8,24 +8,28 @@ source: url: - {{ cran_mirror }}/src/contrib/seqmagick_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/seqmagick/seqmagick_{{ version }}.tar.gz - sha256: 4f872c7b3f39e5b21a5820478102e0b39ecf5d7e2a12dfba263568ab250ab1f5 + sha256: 95cf80c9c0a266e07cf7b124de105818c58f8f843f70ab25e0877a910211b8e5 build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-seqmagick', max_pin="x.x") }} requirements: host: - r-base - bioconductor-biostrings - r-magrittr + - r-yulab.utils >0.1.1 run: - r-base - bioconductor-biostrings - r-magrittr + - r-yulab.utils >0.1.1 test: commands: From 1e6263e997b095dbb49615f8b45e2404e485fbc0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 12:17:47 -0500 Subject: [PATCH 1456/2173] Update snakefmt to 0.9.0 (#45134) --- recipes/snakefmt/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakefmt/meta.yaml b/recipes/snakefmt/meta.yaml index 49a1189437a9a..9ef41f71bddc2 100644 --- a/recipes/snakefmt/meta.yaml +++ b/recipes/snakefmt/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.5" %} +{% set version = "0.9.0" %} package: name: snakefmt @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakefmt/snakefmt-{{ version }}.tar.gz - sha256: 5aa5182dbbbeb84d477dd0f5a9eeeba41bac1f185cfd4897a0b005d4af59ba71 + sha256: 54c78050edead20cea5f87a6c9674ee1b5e4e38faac2852b45d0650faf9cb319 build: number: 0 From f13fe4d3116d7b4a5b1e310bf87cc79944cce062 Mon Sep 17 00:00:00 2001 From: boukn Date: Tue, 9 Jan 2024 15:37:26 -0500 Subject: [PATCH 1457/2173] remove static compilation (#45141) --- recipes/ncbi-fcs-gx/meta.yaml | 2 +- recipes/ncbi-fcs-gx/no_static.patch | 19 ++++++++----------- 2 files changed, 9 insertions(+), 12 deletions(-) diff --git a/recipes/ncbi-fcs-gx/meta.yaml b/recipes/ncbi-fcs-gx/meta.yaml index 2ed106374b726..e1f67d2619dea 100644 --- a/recipes/ncbi-fcs-gx/meta.yaml +++ b/recipes/ncbi-fcs-gx/meta.yaml @@ -26,7 +26,7 @@ requirements: - grep >=3.4 build: - number: 2 + number: 3 skip: True # [not linux or not x86_64] run_exports: - {{ pin_compatible('ncbi-fcs-gx', max_pin="0.5") }} diff --git a/recipes/ncbi-fcs-gx/no_static.patch b/recipes/ncbi-fcs-gx/no_static.patch index 3d09172fa9770..8d8e22f22579e 100644 --- a/recipes/ncbi-fcs-gx/no_static.patch +++ b/recipes/ncbi-fcs-gx/no_static.patch @@ -1,13 +1,10 @@ -diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt -index b2d24ff..007a3ac 100644 ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -32,7 +32,7 @@ include_directories(${PROJECT_SOURCE_DIR}/include/) +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -5,6 +5,6 @@ + set(gx_VERSION_MINOR 0) - set_source_files_properties(main.cpp PROPERTIES COMPILE_FLAGS "-DGIT_REVISION=`../../build-support/git_describe.sh`") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS} -O0 -ggdb3 -DDEBUG") +-set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS} -static -O2 -DNDEBUG") # TODO: investigate whether can/should enable -march=x86-64-v4 ++set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS} -O2 -DNDEBUG") # TODO: investigate whether can/should enable -march=x86-64-v4 --link_libraries("-flto -pthread -Wl,--format=binary -Wl,../../LICENSE -Wl,--format=default") # see show-license command in main.cpp -+link_libraries("-flto -Wl,--whole-archive -lrt -lpthread -Wl,--no-whole-archive -Wl,--format=binary -Wl,../../LICENSE -Wl,--format=default") # see show-license command in main.cpp - - #add_compile_options(-fsanitize=address) - #add_link_options(-fsanitize=address) + add_subdirectory(src) From 05387ea5e55549d3ddc36a9a98291f51895839ad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 21:56:33 -0500 Subject: [PATCH 1458/2173] Update dajin2 to 0.3.6 (#45143) --- recipes/dajin2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index ec633abd38945..eca8b4b9afad9 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "DAJIN2" %} -{% set version = "0.3.5" %} +{% set version = "0.3.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: f6a6c20eda88b3b1a86ccde2e3ac1a63d934c503eda0f44604f4d83ca77441d5 + sha256: cf9e686f78041682589c8e90bcac8eb2ad6473987c96bd574faf36e0b461613c build: entry_points: From a38fa1affeda383ae9bd8881ce1beb16ecaa1e0e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 21:56:46 -0500 Subject: [PATCH 1459/2173] Update jbrowse2 to 2.10.1 (#45145) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 05698606f2fc5..48774c686d68b 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.10.0" %} +{% set version = "2.10.1" %} package: name: jbrowse2 version: {{ version }} source: - sha256: c1dcb2c3e4edd544dcdd566d9f96ca51f93587c444ad6d16d5deff7d3e271862 + sha256: 9495e73d98e4eb287c8a48d8d4a61f2523755a4582681ce4e8e09b9e0fbef291 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From 1a22da5786f5f707d2d67328db39c3c36aec207d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 9 Jan 2024 21:56:56 -0500 Subject: [PATCH 1460/2173] Update ncbi-datasets-pylib to 16.2.0 (#45144) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 42d3681568ee5..6327205797c4f 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.1.2" %} -{% set sha256 = "4bee7893737320c5b63887b513ad92712db3c2a3eb306b3ba26ac5590088cba7" %} +{% set version = "16.2.0" %} +{% set sha256 = "2be4cc1b4bf42dabf0c9a4eabfa2db66bc4eb740b844f87b371da861bc995891" %} package: name: {{ name|lower }} From 28ae119be5a1e36370a27fe6a76505e54e9da76b Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 9 Jan 2024 19:58:31 -0700 Subject: [PATCH 1461/2173] Add ACI (#45121) * adding aci recipe * fixed entry point typo * fix typo * matplotlib-base * url * revert url * underscore * version --------- Co-authored-by: Thanh Lee --- recipes/aci/meta.yaml | 49 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/aci/meta.yaml diff --git a/recipes/aci/meta.yaml b/recipes/aci/meta.yaml new file mode 100644 index 0000000000000..92a18bd603fcd --- /dev/null +++ b/recipes/aci/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "aci" %} +{% set repo = "amplicon_coverage_inspector" %} +{% set version = "1.2.20231229" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ repo[0] }}/{{ repo }}/{{ repo }}-{{ version }}.tar.gz + sha256: f54b1829a8eb1972751fce0b5d6a7d48a62d9cc80935a609302779a9966f104d + +build: + number: 0 + noarch: python + entry_points: + - aci=aci.aci:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('aci', max_pin='x') }} + +requirements: + host: + - python >=3.7,<4.0 + - pip + run: + - python >=3.7,<4.0 + - matplotlib-base >=3.8.2 + - numpy >=1.26.2 + - pandas >=2.1.4 + - pysam >=0.22.0 + +test: + imports: + - aci + commands: + - aci --help + +about: + home: https://github.com/erinyoung/ACI + license: MIT + license_family: MIT + license_file: LICENSE + summary: Visualizes coverage for amplicons + doc_url: https://github.com/erinyoung/ACI/blob/main/README.md + +extra: + recipe-maintainers: + - erinyoung From 7e17503b1af5071bad6bf644a3e9ed19d647372d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Jan 2024 03:26:52 -0500 Subject: [PATCH 1462/2173] Update ngs-chew to 0.9.0 (#45140) --- recipes/ngs-chew/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/ngs-chew/meta.yaml b/recipes/ngs-chew/meta.yaml index bf1055c64d5b6..70a556610a8a9 100644 --- a/recipes/ngs-chew/meta.yaml +++ b/recipes/ngs-chew/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.1" %} -{% set sha256 = "28b27061a6f418ef8dd805ce3135d4f8210521bab8c65a44b5c61092f2a999e8" %} +{% set version = "0.9.2" %} +{% set sha256 = "5220182a9b2e6d2c2adf8ca6053c5a8ebf917942c6486eeee19aa2ccc6bea561" %} package: name: ngs-chew @@ -14,15 +14,18 @@ build: noarch: python entry_points: - ngs-chew = chew.cli:cli - script: python -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('ngs-chew', max_pin="x.x") }} requirements: host: - - python >=3.7 + - python >=3.8 - pip run: - - python >=3.7 + - python >=3.8 - attrs + - cattrs - click - logzero - numpy From 3378fcaa66157a7f3894d6fbd51fff0ae0eb3a78 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Jan 2024 03:27:39 -0500 Subject: [PATCH 1463/2173] Update vcfpy to 0.13.7 (#45150) --- recipes/vcfpy/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/vcfpy/meta.yaml b/recipes/vcfpy/meta.yaml index fff3b36cc93c2..a16833b549124 100644 --- a/recipes/vcfpy/meta.yaml +++ b/recipes/vcfpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.13.6" %} -{% set sha256 = "778afe1dfec387206ddac754186e0777c326e0c300496b7631ade532532ce0bb" %} +{% set version = "0.13.8" %} +{% set sha256 = "e7d00965105e7ca9567299f073ad60c6bbfc78d685d25ba33353988af9b33160" %} package: name: vcfpy @@ -10,16 +10,18 @@ source: sha256: {{ sha256 }} build: - script: python -m pip install --no-deps --ignore-installed . noarch: python number: 0 + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('vcfpy', max_pin="x.x") }} requirements: host: - - python >=3 + - python >=3.8 - pip run: - - python >=3 + - python >=3.8 - pysam >=0.10.0 test: From be0c8305ab78601801a1542798c43b0ba7a8e65b Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Wed, 10 Jan 2024 11:03:32 +0100 Subject: [PATCH 1464/2173] Update dependencies for vcf2db (#45151) * Update dependencies for vcf2db The older versions caused some issues in genotype parsing * Add run exports --- recipes/vcf2db/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/vcf2db/meta.yaml b/recipes/vcf2db/meta.yaml index 2e3d15adaf1ec..720a0de40e411 100644 --- a/recipes/vcf2db/meta.yaml +++ b/recipes/vcf2db/meta.yaml @@ -4,7 +4,9 @@ package: build: noarch: generic - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage("vcf2db", max_pin="x") }} source: url: https://github.com/quinlan-lab/vcf2db/archive/89f3a30d14550763488fdd1eec121f5b2dbf4f7e.tar.gz @@ -19,10 +21,10 @@ requirements: - snappy - python-snappy - sqlalchemy - - cyvcf2 + - cyvcf2 >=0.30 - numpy - peddy >=0.2.9 - - geneimpacts >0.2.0 + - geneimpacts >=0.3 test: commands: From 12115312d363891920d8beaf2db395ae01abb687 Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Wed, 10 Jan 2024 21:37:44 +1000 Subject: [PATCH 1465/2173] Update snakefmt dependencies (#45148) --- recipes/snakefmt/meta.yaml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/recipes/snakefmt/meta.yaml b/recipes/snakefmt/meta.yaml index 9ef41f71bddc2..399a36ceda420 100644 --- a/recipes/snakefmt/meta.yaml +++ b/recipes/snakefmt/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 54c78050edead20cea5f87a6c9674ee1b5e4e38faac2852b45d0650faf9cb319 build: - number: 0 + number: 1 noarch: python entry_points: - snakefmt = snakefmt.snakefmt:main @@ -19,18 +19,17 @@ build: requirements: host: - - black >=23.1.0,<24.0 + - black >=23.12.1,<24.0 - click >=8.0.0,<9.0.0 - pip - - python >=3.7 + - python >=3.8 - toml >=0.10.2,<0.11.0 - poetry >=1.3,<2.0 run: - - black >=23.1.0,<24.0 + - black >=23.12.1,<24.0 - click >=8.0.0,<9.0.0 - - python >=3.7 + - python >=3.8 - toml >=0.10.2,<0.11.0 - - importlib_metadata >=1.7,<5.0.0 # [py<3.8] test: imports: From 5bb686f1f0fb5d495ad09a1581b59b2a9799e713 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Jan 2024 06:39:24 -0500 Subject: [PATCH 1466/2173] Update hisat2-pipeline to 1.0.7 (#45146) --- recipes/hisat2-pipeline/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hisat2-pipeline/meta.yaml b/recipes/hisat2-pipeline/meta.yaml index 6941c76f0c96a..dfa4a265057f7 100644 --- a/recipes/hisat2-pipeline/meta.yaml +++ b/recipes/hisat2-pipeline/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hisat2-pipeline" %} -{% set version = "1.0.6" %} -{% set sha256 = "cc218d21ba1443a6581a2934afef2434d26aaac4bdc974b9747341fd1bac9fd7" %} +{% set version = "1.0.7" %} +{% set sha256 = "4c21e62b8cf1e326b398eafb78e09d2b90843c852198bedb164ac5f1cfc7d33f" %} {% set DOI = "https://doi.org/10.5281/zenodo.10389729" %} package: From 0703a1c4e1af755162e3a24ac5a8246914baaeb5 Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Thu, 11 Jan 2024 00:25:26 +1100 Subject: [PATCH 1467/2173] orthofinder seems to use the old muscle syntax (#45149) see https://github.com/davidemms/OrthoFinder/blob/04455a31c12f361b34ae2791253a546338678cec/scripts_of/config.json#L13 --- recipes/orthofinder/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/orthofinder/meta.yaml b/recipes/orthofinder/meta.yaml index f3613f21558b7..d55ffefa16324 100644 --- a/recipes/orthofinder/meta.yaml +++ b/recipes/orthofinder/meta.yaml @@ -7,7 +7,9 @@ package: build: noarch: generic - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage('orthofinder', max_pin="x") }} source: url: https://github.com/davidemms/OrthoFinder/releases/download/{{ version }}/OrthoFinder_source.tar.gz @@ -24,7 +26,7 @@ requirements: - fastme - mafft - fasttree - - muscle + - muscle <5 - raxml - raxml-ng - iqtree From 69ce2ba17474b7320b508fa531387d7a4ef79d79 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Wed, 10 Jan 2024 15:41:46 +0100 Subject: [PATCH 1468/2173] Fix even more dependencies in vcf2db (#45157) --- recipes/vcf2db/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vcf2db/meta.yaml b/recipes/vcf2db/meta.yaml index 720a0de40e411..7be4b6ebd145b 100644 --- a/recipes/vcf2db/meta.yaml +++ b/recipes/vcf2db/meta.yaml @@ -4,7 +4,7 @@ package: build: noarch: generic - number: 2 + number: 3 run_exports: - {{ pin_subpackage("vcf2db", max_pin="x") }} @@ -20,7 +20,7 @@ requirements: - nomkl # [unix] - snappy - python-snappy - - sqlalchemy + - sqlalchemy <2.0 - cyvcf2 >=0.30 - numpy - peddy >=0.2.9 From d0150efafc64c0c22e4054c2cfdc38abbf49b5f7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Jan 2024 10:51:58 -0500 Subject: [PATCH 1469/2173] Update query_phenomizer to 1.2.1 (#45136) * Update query_phenomizer to 1.2.1 * add run_exports --------- Co-authored-by: mencian --- recipes/query_phenomizer/meta.yaml | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/recipes/query_phenomizer/meta.yaml b/recipes/query_phenomizer/meta.yaml index a0d364e9a2741..b547aaff23c4b 100644 --- a/recipes/query_phenomizer/meta.yaml +++ b/recipes/query_phenomizer/meta.yaml @@ -1,25 +1,23 @@ package: name: query_phenomizer - version: "1.2" + version: "1.2.1" source: - url: https://files.pythonhosted.org/packages/f8/a7/af989c9a672e267ef38009c32206f53c752cc7bac13b29b586c0b93a3da8/query_phenomizer-1.2.tar.gz - sha256: ae6f85331bfa7947fd0edf245780559581a7c728e563093d4b4dc44415517cc7 + url: https://files.pythonhosted.org/packages/02/21/0e62f38dcf337727a4d3b7d18dc55b090296f43ac95a070c2dbe3e5ef24f/query_phenomizer-1.2.1.tar.gz + sha256: fe673970e435bf49fd4d7f14283d8f4e11546fca597a39abf8ca87158da9ca20 build: number: 0 noarch: python entry_points: - query_phenomizer = query_phenomizer.__main__:cli - + run_exports: + - {{ pin_subpackage('query_phenomizer', max_pin="x") }} requirements: host: - python - - setuptools - - click - - requests - - pytest + - pip run: - python - click @@ -30,14 +28,15 @@ test: # Python imports imports: - query_phenomizer - commands: # click requires a unicode locale - query_phenomizer --help about: home: https://www.github.com/moonso/query_phenomizer - license: MIT License + license: MIT + license_family: MIT + license_file: LICENSE summary: 'Tool for query and parsing the phenomizer tool' extra: From 61c6cfe256620065c8f5b9a077ab6a29251cd0ed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Jan 2024 10:52:14 -0500 Subject: [PATCH 1470/2173] Update customtkinter to 5.2.2 (#45147) --- recipes/customtkinter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/customtkinter/meta.yaml b/recipes/customtkinter/meta.yaml index 0dbc3d2ed778d..31b733fbe6f28 100644 --- a/recipes/customtkinter/meta.yaml +++ b/recipes/customtkinter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "customtkinter" %} -{% set version = "5.2.1" %} +{% set version = "5.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/customtkinter-{{ version }}.tar.gz - sha256: eddc1c416063e1ce1aa2793959b0814e95e22d3de3f2a940bd84828f7301f555 + sha256: fd8db3bafa961c982ee6030dba80b4c2e25858630756b513986db19113d8d207 build: script: "{{ PYTHON }} -m pip install . --no-deps -vvv" From c67e9aea129c2df90bd085248e0f50838bc5682c Mon Sep 17 00:00:00 2001 From: "Le (Lena) Huang" Date: Wed, 10 Jan 2024 16:22:24 -0500 Subject: [PATCH 1471/2173] Update dbcan to 4.1.1 (#45160) --- recipes/dbcan/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/dbcan/meta.yaml b/recipes/dbcan/meta.yaml index b4c30e8cb658f..64a233372b504 100644 --- a/recipes/dbcan/meta.yaml +++ b/recipes/dbcan/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dbcan" %} -{% set version = "4.1.0" %} +{% set version = "4.1.1" %} package: name: "{{ name|lower }}" @@ -9,7 +9,7 @@ source: # the sha256 sum is generated by doing # wget -0- [URL] | shasum -a 256 url: https://github.com/linnabrown/run_dbcan/releases/download/{{ version }}/dbcan-{{ version }}.tar.gz - sha256: cb0907eb10eb916bcf676c58f54e67a67dd4ed559152e5547bb44d071f063b8f + sha256: 500fe10463f8a8034e89aa47eba349119575afc25d18c3649ec8aef86f7fe4d5 build: number: 0 @@ -22,6 +22,7 @@ build: - dbcan_utils = dbcan.utils.utils:main - dbcan_plot = dbcan.utils.plots:main - dbcan_asmfree = dbcan.utils.diamond_unassembly:main + - dbcan_build = dbcan.utils.dbcan_build:main run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -41,6 +42,7 @@ requirements: - numpy >1.19 - biopython - pandas + - tqdm - session-info test: @@ -65,4 +67,4 @@ extra: - doi:10.1093/nar/gkx894 - doi:10.1093/nar/gky418 - doi:10.1093/nar/gkad328 - - biotools:dbcan2 + - biotools:dbcan2 \ No newline at end of file From a714b391133f110eb84eec15d0ac584e99a9cec6 Mon Sep 17 00:00:00 2001 From: arihueb Date: Wed, 10 Jan 2024 21:24:02 +0000 Subject: [PATCH 1472/2173] Update conipher version 2.2.0 (#45155) * Updated version and associated doi * added run_exports --- recipes/conipher/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/conipher/meta.yaml b/recipes/conipher/meta.yaml index 99b2e50c63268..27ec14933e8da 100644 --- a/recipes/conipher/meta.yaml +++ b/recipes/conipher/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.1.0" %} -{% set sha256 = "5b5d988dbf79288e6dca09c2c41d65ad89c9186e40a31c2bfdb4504a43d3919f" %} +{% set version = "2.2.0" %} +{% set sha256 = "d985126f31ce71141e031e6431ee0c0baaad0b42a65492f46de06456638ee151" %} package: name: conipher @@ -10,11 +10,13 @@ source: sha256: '{{ sha256 }}' build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib - lib/ + run_exports: + - {{ pin_subpackage('conipher', max_pin="x.x") }} requirements: host: @@ -81,4 +83,4 @@ extra: recipe-maintainers: - arihueb identifiers: - - doi:10.21203/rs.3.pex-2158/v1 \ No newline at end of file + - doi:10.1038/s41596-023-00913-9 \ No newline at end of file From 81bafa1883886ce16aecb94022759c705c7cf097 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Jan 2024 16:24:53 -0500 Subject: [PATCH 1473/2173] Update snakemake-executor-plugin-slurm to 0.1.5 (#45159) --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 3f6877dafc3b2..91f1fb8d28a72 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.1.4" %} +{% set version = "0.1.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 924cdeca812bc2e38478c120f0143d5113170e20204a2911a1e104cf4c2daace + sha256: 3179bba49f8f56982cde26bcb7432cdd720569701d49eb4f2f406149fa559742 build: noarch: python From 12b2d28465be3d25273359b8689565260537fd48 Mon Sep 17 00:00:00 2001 From: Oliver Cheng Date: Thu, 11 Jan 2024 05:26:16 +0800 Subject: [PATCH 1474/2173] Update Flexiplex to v1.01 (#45110) * Update Flexiplex to v1.01 * Fix build number issue --- recipes/flexiplex/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/flexiplex/meta.yaml b/recipes/flexiplex/meta.yaml index c0fdf2351e711..1f9b10908a891 100644 --- a/recipes/flexiplex/meta.yaml +++ b/recipes/flexiplex/meta.yaml @@ -1,15 +1,15 @@ -{% set version = "0.97.1" %} +{% set version = "1.01" %} package: name: flexiplex version: {{ version }} source: - url: https://github.com/DavidsonGroup/flexiplex/releases/download/Version-{{ version }}/flexiplex-Version-{{ version }}.tar.gz - sha256: bb773f195d5a06ab65965c5a63f572cf3cd31cecbc0434d6b17f0c115e2f4b0c + url: https://github.com/DavidsonGroup/flexiplex/releases/download/v{{ version }}/flexiplex-{{ version }}.tar.gz + sha256: a5b3391aded069e15422a0c201d94ca1fdc02e9fec488608b082ff2f43ca3ec7 build: - number: 1 + number: 0 entry_points: - flexiplex-filter = flexiplex_filter.main:cli run_exports: From e7206ccfa9172f742c0c83e9093a6664decdd7c8 Mon Sep 17 00:00:00 2001 From: Rob Edwards Date: Thu, 11 Jan 2024 07:28:05 +1000 Subject: [PATCH 1475/2173] Add pygenetic code (#45034) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * adding pygenetic code repo * run_exports * bumping to version 0.20 with better functionality * bumping version * adding scikit-build-core * adding cmake * adding compilers and make ... whats next? * adding build.sh * removing noarch * host-> build * removing unncessary build.sh * cleaning tests * running and hosting * adding scikit, again * making changes suggested by Björn Grüning * Build failed. Adding python back to run: --------- Co-authored-by: Thanh Lee --- recipes/pygenetic_code/meta.yaml | 49 ++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/pygenetic_code/meta.yaml diff --git a/recipes/pygenetic_code/meta.yaml b/recipes/pygenetic_code/meta.yaml new file mode 100644 index 0000000000000..f09a44c1ff4fb --- /dev/null +++ b/recipes/pygenetic_code/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "pygenetic_code" %} +{% set version = "0.20.0" %} +{% set sha256 = "2d4773e4e8a8b994e604b986ce831b12bbf68b41780e24377bfc14639e017423" %} + +package: + name: "{{ name|lower }}" + version: '{{ version }}' + +source: + url: "https://files.pythonhosted.org/packages/b6/6f/034dc48dd7768cb5aecabb4c2b68e5ff48d7fea6ee3fc51fed7a068e7c11/{{ name }}-{{ version }}.tar.gz" + sha256: '{{ sha256 }}' + +build: + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps -vv " + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - make + - cmake >=3.15 + host: + - python >=3 + - pip + - scikit-build-core + - zlib + run: + - python >=3 + +test: + commands: + - pygenetic_code --help + - pygenetic_code --version + +about: + home: https://github.com/linsalrob/genetic_codes + license: MIT + license_family: MIT + summary: 'Python code for translating sequences using different NCBI translation tables and genetic codes' + dev_url: https://github.com/linsalrob/genetic_codes + +extra: + recipe-maintainers: + - linsalrob + identifiers: + - doi:10.5281/zenodo.10450718 + From 760674765422e1656f8c0196423e9d005a25143f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Jan 2024 17:34:28 -0500 Subject: [PATCH 1476/2173] Update pbstarphase to 0.8.0 (#45165) --- recipes/pbstarphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbstarphase/meta.yaml b/recipes/pbstarphase/meta.yaml index 977430f8b9081..9b43d0bc72b8f 100644 --- a/recipes/pbstarphase/meta.yaml +++ b/recipes/pbstarphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbstarphase" %} -{% set version = "0.7.3" %} -{% set sha256 = "b5dd73ba2e67d7adc0036d34371c596df0caeb900033043efed045f82a9c8c2f" %} +{% set version = "0.8.0" %} +{% set sha256 = "df207d5aa29f0e0088dff838403664ca624f71d1f6c176374f2354234b74850e" %} package: name: {{ name }} From d3b01a5555b5e58e0df8bfe64d0ed74677f6df0f Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Thu, 11 Jan 2024 00:56:16 +0100 Subject: [PATCH 1477/2173] Remove r-interpretmsspectrum, it was readded through the bulk branch yet again (#45169) See #41896 and #42070 --- recipes/r-interpretmsspectrum/meta.yaml | 43 ------------------------- 1 file changed, 43 deletions(-) delete mode 100644 recipes/r-interpretmsspectrum/meta.yaml diff --git a/recipes/r-interpretmsspectrum/meta.yaml b/recipes/r-interpretmsspectrum/meta.yaml deleted file mode 100644 index 40d0de68aa104..0000000000000 --- a/recipes/r-interpretmsspectrum/meta.yaml +++ /dev/null @@ -1,43 +0,0 @@ -{% set version = '1.3.3' %} - -package: - name: r-interpretmsspectrum - version: {{ version|replace("-", "_") }} - -source: - url: - - {{ cran_mirror }}/src/contrib/InterpretMSSpectrum_{{ version }}.tar.gz - - {{ cran_mirror }}/src/contrib/Archive/InterpretMSSpectrum/InterpretMSSpectrum_{{ version }}.tar.gz - sha256: 306a1541504088a05636f49e71a12d806f32fcaaa2d0622a58288452012d71db - -build: - number: 1 - noarch: generic - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - host: - - r-base - - bioconductor-rdisop - - r-envipat - - r-plyr - run: - - r-base - - bioconductor-rdisop - - r-envipat - - r-plyr - -test: - commands: - - $R -e "library('InterpretMSSpectrum')" - -about: - home: http://dx.doi.org/10.1021/acs.analchem.6b02743 - license: GPL-3.0-only - summary: Annotate and interpret deconvoluted mass spectra (mass*intensity pairs) from high - resolution mass spectrometry devices. - license_family: GPL3 - license_file: - - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' From 52babdcb6e6ca4246586b788443689248df8fd6a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 10 Jan 2024 21:54:48 -0500 Subject: [PATCH 1478/2173] Update fibertools-rs to 0.3.7 (#43555) --- recipes/fibertools-rs/build.sh | 38 +++++++++------------------- recipes/fibertools-rs/meta.yaml | 44 +++++++++++++++++++-------------- 2 files changed, 38 insertions(+), 44 deletions(-) diff --git a/recipes/fibertools-rs/build.sh b/recipes/fibertools-rs/build.sh index 1d66b9cf26634..6a4023caabe45 100644 --- a/recipes/fibertools-rs/build.sh +++ b/recipes/fibertools-rs/build.sh @@ -1,5 +1,4 @@ #!/bin/bash -e - # # Set the desitnation for the libtorch files # @@ -17,6 +16,8 @@ export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${LIBTORCH}/lib # # download pytorch libraries # +if [[ "x" == "y" ]]; then + export TORCH_VERSION="2.0.1" export INSTALL_TYPE="cu118" # "cu117" or "cu118" or "cpu" export INSTALL_TYPE="cpu" @@ -41,6 +42,8 @@ rm libtorch.zip # patchelf --set-soname $SONAME $F popd +echo "Done downloading libtorch" 1>&2 + # # move libtorch to OUTDIR # @@ -53,6 +56,8 @@ else mv ${PREFIX}/libtorch/share/* ${OUTDIR}/share/. fi +echo "Done setting up libtorch" 1>&2 + # # fix conflict with libgomp # @@ -65,6 +70,8 @@ if [[ ${target_platform} =~ linux.* ]]; then echo "Using the included libgomp" fi +fi + # # TODO: Remove the following export when pinning is updated and we use # {{ compiler('rust') }} in the recipe. @@ -78,10 +85,13 @@ export BINDGEN_EXTRA_CLANG_ARGS="${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" # HOME=$(pwd) pushd ${PREFIX} -cargo install --all-features --no-track --verbose \ +# --all-features +cargo install --no-track --verbose \ --root "${PREFIX}" --path "${HOME}" popd +echo "Done building ft" 1>&2 + # # clean up the include files since they are not needed and there is a lot of them ~8,000 # @@ -96,30 +106,6 @@ fi # ft --help -# -# try patchelf -# -if [[ ${target_platform} =~ linux.* ]]; then - ldd "$(which ft)" - patchelf --print-needed $(which ft) - #for OLD in ${PREFIX}/lib/libgomp.so*; do - # NEW=${OUTDIR}/lib/libgomp-a34b3233.so.1 - # patchelf --debug --replace-needed $OLD $NEW ${PREFIX}/bin/ft - # patchelf --debug --replace-needed $(basename $OLD) $NEW ${PREFIX}/bin/ft - #done - #echo "after patchelf" - #patchelf --print-needed $(which ft) - #OLD=${OUTDIR}/lib/libtorch_cpu.so - #NEW=${OUTDIR}/lib/libmine.so.1 - #mv $OLD $NEW - #patchelf --replace-needed $OLD $NEW ${PREFIX}/bin/ft - #patchelf --replace-needed $(basename $OLD) $NEW ${PREFIX}/bin/ft - #patchelf --set-rpath \$ORIGIN/../lib ${PREFIX}/bin/ft - #ft --help - #ldd "$(which ft)" - #patchelf --print-needed $(which ft) -fi - # # test install on data # diff --git a/recipes/fibertools-rs/meta.yaml b/recipes/fibertools-rs/meta.yaml index b885ea2f594a4..078fd91c3b47d 100644 --- a/recipes/fibertools-rs/meta.yaml +++ b/recipes/fibertools-rs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.2" %} +{% set version = "0.3.7" %} {% set name = "fibertools-rs" %} {% set build_number = "0" %} @@ -6,28 +6,26 @@ package: name: {{ name }} version: {{ version }} + +source: + url: https://github.com/fiberseq/fibertools-rs/archive/v{{ version }}.tar.gz + sha256: 395615d051a322fa08b1d1453691c7d8ece8ca7cc77b91e5c78d3274e1d15498 + + build: run_exports: - {{ pin_subpackage('fibertools-rs', max_pin="x") }} number: {{ build_number }} - detect_binary_files_with_prefix: False - # skip: True # [osx] rpaths: - lib/ - share/{{ name }}-{{ version }}-{{ build_number }}/lib/ - missing_dso_whitelist: - - share/{{ name }}-{{ version }}-{{ build_number }}/lib/* - - "$RPATH/libgomp-a34b3233.so.1" - - "$RPATH/libcudart-d0da41ae.so.11.0" - #runpath_whitelist: + #detect_binary_files_with_prefix: False + #missing_dso_whitelist: # - share/{{ name }}-{{ version }}-{{ build_number }}/lib/* - # overlinking_ignore_patterns: - # - share/{{ name }}-{{ version }}-{{ build_number }}/lib/* - + # - "$RPATH/libgomp-a34b3233.so.1" + # - "$RPATH/libcudart-d0da41ae.so.11.0" + # skip: True # [osx] -source: - url: https://github.com/fiberseq/fibertools-rs/archive/v{{ version }}.tar.gz - sha256: 3607996fce7fe009e31b80b2f7d6fd6ddd152537428aa6506c24190c6f89d329 requirements: build: @@ -38,12 +36,21 @@ requirements: - cmake - unzip - curl + # all the host and run requirements match those needed for htslib host: + - libcurl + - bzip2 + - xz + - zlib + - libdeflate + - openssl # [not osx] run: - -# libz -# $RPATH/libcuda.so.1 -# Needed DSO lib/libgomp.so.1 + - libcurl + - bzip2 + - xz + - zlib + - libdeflate + - openssl # [not osx] test: commands: @@ -59,3 +66,4 @@ about: extra: recipe-maintainers: - mrvollger + From d0176da0f520a4458d0387341d138372584e2c66 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 10:16:32 -0500 Subject: [PATCH 1479/2173] Update ribodetector to 0.3.1 (#45166) --- recipes/ribodetector/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ribodetector/meta.yaml b/recipes/ribodetector/meta.yaml index e0e1f6562be2f..98111d9b655b4 100644 --- a/recipes/ribodetector/meta.yaml +++ b/recipes/ribodetector/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: ribodetector version: {{ version }} source: - url: https://files.pythonhosted.org/packages/e3/92/be698538c8ca7f1929295f87f080352d56c20749e92ef3f9f97bed953058/ribodetector-0.3.0.tar.gz - sha256: 42922dfde736c8fb1b83a0fd2c3b77864a5e9a4b8b3a0b31f0bf3764556bf1f9 + url: https://files.pythonhosted.org/packages/7a/83/da07dc151cea39c3f6edb55ac41581f5d6eb248464ac8fcdedc70b52cf5f/ribodetector-0.3.1.tar.gz + sha256: a520a411879a193f813ba5f7ad530e57aed31c0519c622de47490bb5144f0595 build: number: 0 From 4d26f05752fc3475a7ab3867e34f4980a4ee9915 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 10:16:41 -0500 Subject: [PATCH 1480/2173] Update pyensembl to 2.3.0 (#45167) --- recipes/pyensembl/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyensembl/meta.yaml b/recipes/pyensembl/meta.yaml index 7a0be0abda1ae..f883f99562491 100644 --- a/recipes/pyensembl/meta.yaml +++ b/recipes/pyensembl/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PyEnsembl" %} -{% set version = "2.2.9" %} -{% set sha256 = "f570073181130855be0bfd813c605546cbd97aa3017aa82998ddbc0595ddf24d" %} +{% set version = "2.3.0" %} +{% set sha256 = "4bb78314049d5255e7057ff7a174cc1b363adff0632920f0cdb299edd251e8df" %} package: name: {{ name|lower }} From 7aca7a4ec6fcbfc483c58de420e52d424a07ec0b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 10:17:01 -0500 Subject: [PATCH 1481/2173] Update hmftools-amber to 3.9.1 (#45170) * Update hmftools-amber to 3.9.1 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/hmftools-amber/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/hmftools-amber/meta.yaml b/recipes/hmftools-amber/meta.yaml index c3defd0a479d2..0b7a3cc9085f9 100644 --- a/recipes/hmftools-amber/meta.yaml +++ b/recipes/hmftools-amber/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.9" %} -{% set sha256 = "a1f249d691c1d45f41e4b844d0f9e91dadf3920e340bc8d80c9130c4b7d2522b" %} +{% set version = "3.9.1" %} +{% set sha256 = "47d2dba76b56252bd0f3a21f535096a97e2d51bc66c087f4f975272c4aaf92ef" %} package: name: hmftools-amber @@ -11,7 +11,9 @@ source: build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage("hmftools-amber", max_pin="x.x") }} requirements: run: From a65c468e071d0e6b29d4256c94159369346ffa06 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 10:19:03 -0500 Subject: [PATCH 1482/2173] Update snakemake to 8.1.1 (#45176) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index ec9cb7290f522..dbfec93ae150a 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.1.0" %} +{% set version = "8.1.1" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 3aeb95197ced3f50d89eabaa95ad93414db64bda7683283bdec6690810d598e9 + sha256: 767e165b9803a3eb91d50e5f7d4410f537f3f1db102c99fcc97a9b40371cd46a build: number: 0 From eabd98eeab1fcd06a07f7d0e60b5c0cba82d2972 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 10:45:15 -0500 Subject: [PATCH 1483/2173] Update pharokka to 1.6.0 (#45171) * Update pharokka to 1.6.0 * Update meta.yaml force bio python <1.82 --------- Co-authored-by: George Bouras <84495559+gbouras13@users.noreply.github.com> --- recipes/pharokka/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pharokka/meta.yaml b/recipes/pharokka/meta.yaml index 329ca37487d77..f4cc32edee438 100644 --- a/recipes/pharokka/meta.yaml +++ b/recipes/pharokka/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.5.1" %} +{% set version = "1.6.0" %} {% set name = "pharokka" %} -{% set sha256 = "b862e2d44021e6a767dec317d78a12afcf2cd918bab2c0cb629413398923fb28" %} +{% set sha256 = "67a6459e1d7a3e22801a3eba0149056fcf9b3e61ea614d55893fdaa0cca7f5be" %} {% set user = "gbouras13" %} package: @@ -25,7 +25,7 @@ requirements: run: - python >=3.5 - bcbio-gff >=0.7.0 - - biopython >=1.78 + - biopython >=1.78,<1.82 - phanotate >=1.5.0 - mmseqs2 ==13.45111 - trnascan-se >=2.0.9 From 5367ec131e651eef43b67595002878a033582906 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 12:18:16 -0500 Subject: [PATCH 1484/2173] Update abpoa to 1.5.0 (#45179) --- recipes/abpoa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abpoa/meta.yaml b/recipes/abpoa/meta.yaml index 40d2677da1ceb..5490da5c89b38 100644 --- a/recipes/abpoa/meta.yaml +++ b/recipes/abpoa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.3" %} +{% set version = "1.5.0" %} {% set program = "abpoa" %} {% set PROGRAM = "abPOA" %} @@ -8,7 +8,7 @@ package: source: url: https://github.com/yangao07/{{ PROGRAM }}/releases/download/v{{ version }}/{{ PROGRAM }}-v{{ version }}.tar.gz - sha256: c6e9f6e1e8938f5ecb47ef41c2571f3563fd7fdf5eb32e9500099cbd29e72612 + sha256: 221e62c68e4cd728b85ab5f9864f7711f2102ff58c800c1477368cc83fee42d8 build: number: 0 From 41e88d2e858ad642c892fb1cb4e665bdebd78a08 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 12:19:20 -0500 Subject: [PATCH 1485/2173] Update pyabpoa to 1.5.0 (#44883) * Update pyabpoa to 1.4.3 * Update pyabpoa to 1.5.0 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pyabpoa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyabpoa/meta.yaml b/recipes/pyabpoa/meta.yaml index 11bab9a30140e..1a1872e3a6f85 100644 --- a/recipes/pyabpoa/meta.yaml +++ b/recipes/pyabpoa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyabpoa" %} -{% set version = "1.4.2" %} +{% set version = "1.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/yangao07/abPOA/releases/download/v{{ version }}/abPOA-v{{ version }}.tar.gz - sha256: 955109ee28ccdef60c371f7ad113e380d1a6d42b658243eafc00239b9e58a087 + sha256: 221e62c68e4cd728b85ab5f9864f7711f2102ff58c800c1477368cc83fee42d8 build: number: 0 From e937b6aeb7a4b72669b1cc379dc8dc6e925e6da6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 12:39:58 -0500 Subject: [PATCH 1486/2173] Update keggcharter to 1.1.2 (#45181) --- recipes/keggcharter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/keggcharter/meta.yaml b/recipes/keggcharter/meta.yaml index aa9fb12f6ef41..36e89a4a7cab3 100644 --- a/recipes/keggcharter/meta.yaml +++ b/recipes/keggcharter/meta.yaml @@ -1,6 +1,6 @@ {% set name = "keggcharter" %} -{% set version = "1.1.1" %} -{% set sha256 = "66e33b222572eaa38b37ce0e04f844550b505c78e05533cbcaead31053c3fc69" %} +{% set version = "1.1.2" %} +{% set sha256 = "53735598428a7a2eb75c763f2eba04efecd9c8fae3d69ea7a29747ffc60396cd" %} package: name: {{ name|lower }} From e0062ca8547dff8341955451672d7031efb25a15 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karel=20B=C5=99inda?= Date: Thu, 11 Jan 2024 19:32:59 +0100 Subject: [PATCH 1487/2173] Add meta.yaml for attotree (#45182) --- recipes/attotree/meta.yaml | 42 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 recipes/attotree/meta.yaml diff --git a/recipes/attotree/meta.yaml b/recipes/attotree/meta.yaml new file mode 100644 index 0000000000000..6fa340d6d68ba --- /dev/null +++ b/recipes/attotree/meta.yaml @@ -0,0 +1,42 @@ +{% set name = "attotree" %} +{% set version = "0.1.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: e604555bcbff83384d3266048af7dcec026773a0aaf6945582994ad9c8af69e3 + +build: + number: 0 + noarch: python + entry_points: + - attotree=attotree.attotree:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('attotree', max_pin="x") }} + +requirements: + host: + - pip + - python >=3 + run: + - python >=3 + - mash + - quicktree + +test: + imports: + - attotree + +about: + home: https://github.com/karel-brinda/attotree + license: MIT + license_family: MIT + license_file: LICENSE.txt + doc_url: https://github.com/karel-brinda/attotree + summary: 'rapid estimation of phylogenetic trees using sketching' + + From bfb335f5c3cd841700187422e91655ba0089c9b0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 16:48:21 -0500 Subject: [PATCH 1488/2173] Update pyensembl to 2.3.4 (#45184) --- recipes/pyensembl/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyensembl/meta.yaml b/recipes/pyensembl/meta.yaml index f883f99562491..1b7955c7189c3 100644 --- a/recipes/pyensembl/meta.yaml +++ b/recipes/pyensembl/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PyEnsembl" %} -{% set version = "2.3.0" %} -{% set sha256 = "4bb78314049d5255e7057ff7a174cc1b363adff0632920f0cdb299edd251e8df" %} +{% set version = "2.3.4" %} +{% set sha256 = "e0052ab1f769d451cbc71b0d5be5d0443be2bd0d7e41efb802dd4357462bf09c" %} package: name: {{ name|lower }} From e0e44171476fd98b60b122b50162972386656628 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 16:48:40 -0500 Subject: [PATCH 1489/2173] Update pybiolib to 1.1.1689 (#45175) * Update pybiolib to 1.1.1687 * Update pybiolib to 1.1.1689 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index d7727d223aa67..b4b1f16fe1b7d 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1685" %} +{% set version = "1.1.1689" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 44921a3ec42de028d164b048374691906edeaa59b8fb7b9366e82dabee1aba8c + sha256: f33b444bdbde72a8b93f236777544de8d2a5fc0633f7cdb4c1e73f392eae0040 build: noarch: python From 2e1f6704a083db8dd76d4b12daa91458d94a5076 Mon Sep 17 00:00:00 2001 From: Mike Tisza Date: Thu, 11 Jan 2024 15:55:19 -0600 Subject: [PATCH 1490/2173] Add Cenote-Taker3 v3.2.0 (#45180) --- recipes/cenote-taker3/meta.yaml | 62 +++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 recipes/cenote-taker3/meta.yaml diff --git a/recipes/cenote-taker3/meta.yaml b/recipes/cenote-taker3/meta.yaml new file mode 100644 index 0000000000000..6717368a52f63 --- /dev/null +++ b/recipes/cenote-taker3/meta.yaml @@ -0,0 +1,62 @@ +{% set name = "cenote-taker3" %} +{% set version = "3.2.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://github.com/mtisza1/{{ name }}/archive/v{{ version }}.tar.gz" + sha256: fe28c66009a4b1ee6755fbabcfbe5a8d0cba985977818155d6aefd0324ea9f95 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage("cenote-taker3", max_pin="x") }} + entry_points: + - cenotetaker3 = cenote.cenotetaker3:cenotetaker3 + - get_ct3_dbs = cenote.get_ct3_databases:get_ct3_dbs + script: + - {{ PYTHON }} -m pip install . --no-deps -vv + +requirements: + host: + - pip + - python >=3.10 + run: + - python >=3.10 + - seqkit + - prodigal + - pyrodigal-gv >=0.3.1 + - hhsuite + - mmseqs2 + - trnascan-se + - minimap2 + - tbl2asn-forever + - biopython + - bedtools + - phanotate + - pyhmmer + - findutils + - coreutils + - sed + - grep + - samtools + + +test: + commands: + - cenotetaker3 --version + - get_ct3_dbs -h + +about: + home: "https://github.com/mtisza1/Cenote-Taker3" + license: MIT + license_file: LICENSE + summary: "Cenote-Taker 3: Discover and annotate the virome" + dev_url: "https://github.com/mtisza1/Cenote-Taker3" + +extra: + recipe-maintainers: + - mtisza1 \ No newline at end of file From 2ee650057cd3f9954fead0672b22c31566a61cf4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 17:27:03 -0500 Subject: [PATCH 1491/2173] Update gtfparse to 2.3.0 (#45183) * Update gtfparse to 2.2.0 * Update gtfparse to 2.3.0 * edit polars version --------- Co-authored-by: mencian --- recipes/gtfparse/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/gtfparse/meta.yaml b/recipes/gtfparse/meta.yaml index 2a89b763b912d..410ae0b32eafa 100644 --- a/recipes/gtfparse/meta.yaml +++ b/recipes/gtfparse/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gtfparse" %} -{% set version = "2.1.0" %} -{% set sha256 = "d1e94897f159a6cc89984fe4eb8b614fbd57b57ce6432ca00c15672eec7e7956" %} +{% set version = "2.3.0" %} +{% set sha256 = "c2d74d6964d54d710e2d6264d47ca9e0a5288a781d47d3db08b4f6a5ee7e15f1" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ source: build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . --no-deps -vvv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv run_exports: - {{ pin_subpackage('gtfparse', max_pin="x.x") }} @@ -23,9 +23,10 @@ requirements: - pip run: - python - - polars <0.17 + - polars >=0.20.2,<0.21.0 - numpy >=1.7 - pandas >=0.15 + - pyarrow >=14.0.2 test: imports: From 3a4459922a3e5c995376b4152bb8e5460530c49e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 18:42:40 -0500 Subject: [PATCH 1492/2173] Update annosine2 to 1.0.5 (#45173) * Update annosine2 to 1.0.5 * Update meta.yaml (#45174) --------- Co-authored-by: Ray <851836818@qq.com> Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- recipes/annosine2/meta.yaml | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/recipes/annosine2/meta.yaml b/recipes/annosine2/meta.yaml index 98c711f9ab79d..8e3f769b95e18 100644 --- a/recipes/annosine2/meta.yaml +++ b/recipes/annosine2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "annosine2" %} -{% set version = "1.0.4" %} +{% set version = "1.0.5" %} package: name: "{{ name|lower }}" @@ -7,12 +7,12 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: c9d12adec9875c4a429c6e9da5b76d31c760ef7474635caf742d25592378f34c + sha256: 4b51d569f064657d31ad70893723ce1809e0be22d9be0fa23bb4c9924645a423 build: - number: 1 + number: 0 entry_points: - - annosine2 = AnnoSINE.AnnoSINE_v2:main + - AnnoSINE_v2 = AnnoSINE.AnnoSINE_v2:main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " run_exports: - {{ pin_subpackage('annosine2', max_pin="x") }} @@ -23,7 +23,7 @@ requirements: - pip - python run: - - cycler ==0.10.0 + - cycler - kiwisolver - matplotlib-base - numpy @@ -33,27 +33,27 @@ requirements: - python - python-dateutil - six - - hmmer ==3.3.1 - - minimap2 ==2.26 - - nodejs ==18.12.1 - - trf ==4.09 - - irf ==3.08 - - cd-hit ==4.8.1 - - repeatmasker ==4.1.2.p1 - - seqtk ==1.4 + - hmmer + - minimap2 + - nodejs + - trf + - irf + - cd-hit + - repeatmasker + - seqtk test: imports: - AnnoSINE commands: - - annosine2 --help + - AnnoSINE_v2 --help about: - home: https://github.com/liaoherui/AnnoSINE + home: https://github.com/liaoherui/AnnoSINE_v2 license: MIT license_family: MIT - summary: AnnoSINE2 - SINE Annotation Tool for Plant and Animal Genomes + summary: AnnoSINE_v2 - SINE Annotation Tool for Plant and Animal Genomes extra: recipe-maintainers: From 28ebdfaf5d73be2893a5b6e4aa00262e9312773d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 19:52:45 -0500 Subject: [PATCH 1493/2173] Update crispector2 to 2.0.7 (#45178) * Update crispector2 to 2.0.7 * add mpmath --------- Co-authored-by: joshuazhuang7 --- recipes/crispector2/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/crispector2/meta.yaml b/recipes/crispector2/meta.yaml index 43f209d4a9b36..8b47e82f104df 100644 --- a/recipes/crispector2/meta.yaml +++ b/recipes/crispector2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.6" %} +{% set version = "2.0.7" %} package: name: crispector2 @@ -15,13 +15,12 @@ build: source: url: https://github.com/theAguy/crispector2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 4cb9a6d5b6ca5e697448613d22eae1c4791bb403200e8bced7d1dc948915dbd2 + sha256: 3531fd5cad957c046a54355a18552453bf1dac7141b3e7b7c13b40ccf5599a86 requirements: host: - python 3.7 - pip - - setuptools run: - python 3.7 - biopython >=1.74 @@ -38,6 +37,7 @@ requirements: - statsmodels - jinja2 - tqdm >=4.66.0 + - mpmath test: commands: From 2daaa41af99d53c23c1298a28007f799a8a09360 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 20:35:54 -0500 Subject: [PATCH 1494/2173] Update hictk to 0.0.6 (#45187) --- recipes/hictk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index 02e7110847842..aaa53c1d48491 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.5" %} -{% set sha256 = "12a784bfb83e64c99c2fb36839bdcb2c4a579688dced1e342df8eb6da7c8506d" %} +{% set version = "0.0.6" %} +{% set sha256 = "5913792f858304ff82996c9e9720442736b443d56c53aa8eb2a1ac2ae8ccc88f" %} package: name: {{ name|lower }} From 1daf6fe8757a7fdae46e21e626e30026d210b20c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 11 Jan 2024 21:41:25 -0500 Subject: [PATCH 1495/2173] Update cyvcf2 to 0.30.26 (#45154) * Update cyvcf2 to 0.30.26 * edit setup.py.patch * add autoconf * add automake * add make --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cyvcf2/meta.yaml | 17 +++++++---- recipes/cyvcf2/patches/setup.py.patch | 43 ++++++++------------------- 2 files changed, 24 insertions(+), 36 deletions(-) diff --git a/recipes/cyvcf2/meta.yaml b/recipes/cyvcf2/meta.yaml index c90af45fe4553..b959105c2467d 100644 --- a/recipes/cyvcf2/meta.yaml +++ b/recipes/cyvcf2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cyvcf2" %} -{% set version = "0.30.25" %} -{% set sha256 = "40f1fda66e3bad9873bba08fe3c0839f590089137b2aa7070247561e77ce0d8d" %} +{% set version = "0.30.26" %} +{% set sha256 = "e8473957181ef7b037213d110217046d107cd6a0eb4671f13c47a7a24412db05" %} package: name: {{ name }} @@ -16,7 +16,7 @@ source: build: number: 0 skip: True # [py < 37] - script: {{ PYTHON }} -m pip install . --use-pep517 -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - cyvcf2 = cyvcf2.__main__:cli run_exports: @@ -25,6 +25,9 @@ build: requirements: build: - {{ compiler('c') }} + - autoconf + - automake + - make host: - python - cython @@ -40,18 +43,22 @@ requirements: - python - coloredlogs - click - - numpy + - {{ pin_compatible('numpy') }} test: imports: - cyvcf2 + commands: + - cyvcf2 --help about: home: "https://github.com/brentp/cyvcf2/" - summary: A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files + summary: "A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files" license: MIT + license_family: MIT license_file: LICENSE doc_url: "https://brentp.github.io/cyvcf2/" + dev_url: "https://github.com/brentp/cyvcf2/" extra: identifiers: diff --git a/recipes/cyvcf2/patches/setup.py.patch b/recipes/cyvcf2/patches/setup.py.patch index 8d9ff3497ea6c..c0454bda7a141 100644 --- a/recipes/cyvcf2/patches/setup.py.patch +++ b/recipes/cyvcf2/patches/setup.py.patch @@ -1,43 +1,24 @@ --- a/setup.py +++ b/setup.py -@@ -7,10 +7,6 @@ import platform - import pkg_resources - from setuptools import setup, Extension +@@ -10,13 +10,6 @@ from setuptools import setup, Extension, Command + from setuptools.command.build_ext import build_ext + from setuptools.command.sdist import sdist -if sys.version_info.major == 2 and sys.version_info.minor != 7: -- sys.stderr.write("ERROR: cyvcf2 is only for python 2.7 or greater you are running %d.%d\n", (sys.version_info.major, sys.version_info.minor)) +- sys.stderr.write( +- "ERROR: cyvcf2 is only for python 2.7 or greater you are running %d.%d\n", +- (sys.version_info.major, sys.version_info.minor), +- ) - sys.exit(1) - import numpy as np -@@ -42,18 +38,8 @@ def no_cythonize(extensions, **_ignore): - return extensions +@@ -236,6 +229,7 @@ htslib_include_dirs = ["htslib", "htslib/htslib"] - --# Build the Cython extension by statically linking to the bundled htslib --sources = [ -- x for x in glob.glob('htslib/*.c') -- if not any(e in x for e in ['irods', 'plugin']) --] --sources += glob.glob('htslib/cram/*.c') --sources += glob.glob('htslib/htscodecs/htscodecs/*.c') --# Exclude the htslib sources containing main()'s --sources = [x for x in sources if not x.endswith(('htsfile.c', 'tabix.c', 'bgzip.c'))] --sources.append('cyvcf2/helpers.c') -- --extra_libs = [] -+sources = ['cyvcf2/helpers.c'] + # Build the Cython extension by statically linking to the bundled htslib + sources = ["cyvcf2/cyvcf2.pyx", "cyvcf2/helpers.c"] +extra_libs = ['hts'] - if platform.system() != 'Darwin': - extra_libs.append('crypt') - if bool(int(os.getenv("LIBDEFLATE", 0))): -@@ -65,7 +51,7 @@ extensions = [Extension("cyvcf2.cyvcf2", - extra_compile_args=["-Wno-sign-compare", "-Wno-unused-function", - "-Wno-strict-prototypes", - "-Wno-unused-result", "-Wno-discarded-qualifiers"], -- include_dirs=['htslib', 'cyvcf2', np.get_include()])] -+ include_dirs=['cyvcf2', np.get_include()])] - - CYTHONIZE = bool(int(os.getenv("CYTHONIZE", 0))) + extensions = [ + Extension( From bb34be519ccf37b3be8a9a8571dee4274e53bea2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Jan 2024 09:23:42 -0500 Subject: [PATCH 1496/2173] Update snakemake-executor-plugin-slurm to 0.2.0 (#45194) --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 91f1fb8d28a72..38b2c9922ffa1 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.1.5" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 3179bba49f8f56982cde26bcb7432cdd720569701d49eb4f2f406149fa559742 + sha256: 161e965a79151274c3835866070bd48483655c4c2efda4e56a54f60af61fddbb build: noarch: python From aec8a21498a4c8c1d4082043ebabf327ea01ee65 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Jan 2024 10:01:06 -0500 Subject: [PATCH 1497/2173] Update r-corncob to 0.4.1 (#45168) * Update r-corncob to 0.4.1 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-corncob/meta.yaml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/recipes/r-corncob/meta.yaml b/recipes/r-corncob/meta.yaml index ae07dcf364081..59804c6fc189d 100644 --- a/recipes/r-corncob/meta.yaml +++ b/recipes/r-corncob/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.3.2' %} +{% set version = '0.4.1' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -10,7 +10,7 @@ source: url: - {{ cran_mirror }}/src/contrib/corncob_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/corncob/corncob_{{ version }}.tar.gz - sha256: fa0e1df242f88b2f8c88cc46b673271b8ade1b0ae32089fb0b71539e59d2ec46 + sha256: 9658ee516843ed7e229e24e77df3f7c0e361c428f1700818209c21e3d24f5089 build: merge_build_host: True # [win] @@ -34,8 +34,7 @@ requirements: - r-ggplot2 - r-magrittr - r-numderiv - - r-optimr - - bioconductor-phyloseq + - r-rlang - r-scales - r-trust run: @@ -46,8 +45,7 @@ requirements: - r-ggplot2 - r-magrittr - r-numderiv - - r-optimr - - bioconductor-phyloseq + - r-rlang - r-scales - r-trust From f5debaf24812fffcf7139042742abc58615c5dbf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Jan 2024 10:49:48 -0500 Subject: [PATCH 1498/2173] Update peaks2utr to 1.2.2 (#45199) --- recipes/peaks2utr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/peaks2utr/meta.yaml b/recipes/peaks2utr/meta.yaml index fde63cc700b3b..b95b6a98d6d21 100644 --- a/recipes/peaks2utr/meta.yaml +++ b/recipes/peaks2utr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "peaks2utr" %} -{% set version = "1.2.0" %} +{% set version = "1.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/peaks2utr-{{ version }}.tar.gz - sha256: 9b7058f96455fb00c595759a92ab1c16bbaab4ec81658c89f37977cc1f4bb7c5 + sha256: 9bd1fcd1683a342b240639bd99c9e2c24f74021698e7537b981c4ce3e43ca030 build: number: 0 From be550aa74a3447530c8c0c6954a5510dd3edbbf8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Jan 2024 11:04:48 -0500 Subject: [PATCH 1499/2173] Update crossmap to 0.7.0 (#45192) * Update crossmap to 0.7.0 * add run_exports * edit tests --------- Co-authored-by: mencian --- recipes/crossmap/build.sh | 2 +- recipes/crossmap/meta.yaml | 36 ++++++++++++++++++------------------ 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/recipes/crossmap/build.sh b/recipes/crossmap/build.sh index 2dbf7cf108167..b634892e50b82 100644 --- a/recipes/crossmap/build.sh +++ b/recipes/crossmap/build.sh @@ -3,4 +3,4 @@ rm -f lib/psyco_full.py rm -rf data test -$PYTHON setup.py install --single-version-externally-managed --record=record.txt +${PYTHON} -m pip install . -vvv --no-deps --no-build-isolation diff --git a/recipes/crossmap/meta.yaml b/recipes/crossmap/meta.yaml index d283a3ca926c7..d1809d5385aa7 100644 --- a/recipes/crossmap/meta.yaml +++ b/recipes/crossmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "CrossMap" %} -{% set version = "0.6.5" %} -{% set sha256hash = "b16a942b38bf7f26e9b53bc6cddd5cfa7dee98e97f7ee8bb0dc699a4340aafbf" %} +{% set version = "0.7.0" %} +{% set sha256 = "fec5bc7537c6f767e39f7b8a176ceb522e10de4a79ebdd0d645ea0af948c4bd4" %} package: name: {{ name|lower }} @@ -8,23 +8,22 @@ package: source: url: https://github.com/liguowang/CrossMap/archive/v{{ version }}.tar.gz - sha256: {{ sha256hash }} + sha256: {{ sha256 }} build: number: 0 noarch: python + entry_points: + - CrossMap = cmmodule:crossmap + run_exports: + - {{ pin_subpackage('crossmap', max_pin="x.x") }} requirements: host: - - python >=3 - - cython >=0.17 - - numpy - - nose >=0.10.4 - - pysam >=0.15 - - bx-python + - python >=3.8 + - pip run: - - python >=3 - - cython >=0.17 + - python >=3.8 - numpy - pysam >=0.15 - bx-python @@ -33,23 +32,24 @@ requirements: test: commands: - - CrossMap.py bed -h - - CrossMap.py vcf -h + - CrossMap bed -h + - CrossMap vcf -h about: - home: http://crossmap.sourceforge.net + home: https://crossmap.sourceforge.net license: GPL-3.0-or-later - license_family: GPL + license_family: GPL3 license_file: LICENSE.txt summary: "CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies." + dev_url: https://github.com/liguowang/CrossMap + doc_url: https://crossmap.readthedocs.io/en/latest/ extra: - skip-lints: - - cython_needs_compiler - - cython_must_be_in_host identifiers: - usegalaxy-eu:crossmap_bam - usegalaxy-eu:crossmap_bed - usegalaxy-eu:crossmap_vcf - usegalaxy-eu:crossmap_wig - usegalaxy-eu:crossmap_gff + - doi:10.1093/bioinformatics/btt730 + - biotools:crossmap From e0ccfdcc3c4a50f794d19410272eb21a436bd179 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Sat, 13 Jan 2024 05:44:59 +1300 Subject: [PATCH 1500/2173] Added evigene (#45191) * Added evigene * Added desc, lic and version pin * Updated test * edit perl shebang in tr2aacds.pl --------- Co-authored-by: mencian --- recipes/evigene/build.sh | 19 +++++++++++++++++ recipes/evigene/meta.yaml | 45 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 recipes/evigene/build.sh create mode 100644 recipes/evigene/meta.yaml diff --git a/recipes/evigene/build.sh b/recipes/evigene/build.sh new file mode 100644 index 0000000000000..3675e01e7a23a --- /dev/null +++ b/recipes/evigene/build.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +readonly EVIGENEHOME=${PREFIX}/opt/${PKG_NAME}-${PKG_VERSION} + +mkdir -p ${EVIGENEHOME} + +cd ${SRC_DIR} + +cp -Rp config lib scripts ${EVIGENEHOME} + + +mkdir -p ${PREFIX}/etc/conda/activate.d/ +echo "export EVIGENEHOME=${EVIGENEHOME}" > ${PREFIX}/etc/conda/activate.d/${PKG_NAME}-${PKG_VERSION}.sh + +mkdir -p ${PREFIX}/etc/conda/deactivate.d/ +echo "unset EVIGENEHOME" > ${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}-${PKG_VERSION}.sh + +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${EVIGENEHOME}/scripts/prot/tr2aacds.pl +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${EVIGENEHOME}/scripts/prot/tr2aacds4.pl diff --git a/recipes/evigene/meta.yaml b/recipes/evigene/meta.yaml new file mode 100644 index 0000000000000..1bbf7e8dcae8e --- /dev/null +++ b/recipes/evigene/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "evigene" %} +{% set raw_version = "23jul15" %} +{% set version = "23.7.15" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/{{ name }}{{ raw_version }}.tar + sha256: 8fe8e5c21ac3f8b7134d8e26593fe66647eb8b7ba2c1cd1c158fc811769b9539 + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('evigene', max_pin='x') }} + +requirements: + run: + - perl + - exonerate + - cd-hit + - blast + +test: + commands: + - capture_die=$(bash -c "perl $EVIGENEHOME/scripts/prot/tr2aacds.pl || true" 2>&1) + - echo "$capture_die" | grep "VERSION 2022.04.05" + +about: + home: http://arthropods.eugenes.org/EvidentialGene/ + summary: 'A genome informatics project for Evidence Directed Gene Construction for Eukaryotes' + description: | + EvidentialGene is a genome informatics project for "Evidence Directed Gene Construction for Eukaryotes", + for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed + by Don Gilbert at Indiana University, gilbertd at indiana edu. The perl scripts are nested inside the + 'scripts' folder and, therefor can only be used by providing the full path + such as '$EVIGENEHOME/scripts/prot/tr2aacds.pl -h' + license: Don Gilbert, gilbertd At indiana edu, 2018 + +extra: + recipe-maintainers: + - gallvp + From 684688735ace1eead791107882f62c40e2f409fe Mon Sep 17 00:00:00 2001 From: balajtimate <51365402+balajtimate@users.noreply.github.com> Date: Fri, 12 Jan 2024 18:02:38 +0100 Subject: [PATCH 1501/2173] Add HTSinfer (#45197) * Add HTSinfer * remove pip from run dependencies and add recipe-maintainer --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/htsinfer/meta.yaml | 57 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 recipes/htsinfer/meta.yaml diff --git a/recipes/htsinfer/meta.yaml b/recipes/htsinfer/meta.yaml new file mode 100644 index 0000000000000..a88775a875d23 --- /dev/null +++ b/recipes/htsinfer/meta.yaml @@ -0,0 +1,57 @@ +{% set name = "HTSinfer" %} +{% set version = "0.9.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/zavolanlab/htsinfer/archive/refs/tags/v0.9.0.tar.gz + sha256: f4708d43e56389240752e45ac3f4cdcb620ab3783b57ff068599eec0adbd91f3 + +build: + number: 0 + noarch: python + entry_points: + - htsinfer = htsinfer.cli:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} + +requirements: + host: + - python >=3.8, <=3.10 + - pip >=20.2.3 + - setuptools-git >=1.2 + - numpy >=1.22, <1.25 + - pandas >=1.3.5, <1.4.0 + - biopython >=1.78 + - pydantic >=1.8.1, <2 + - pysam >=0.16.0 + - pyahocorasick >=1.4.0 + run: + - biopython >=1.78 + - cutadapt >=3.5, <=4.2 + - kallisto >=0.46.1, <= 0.48.0 + - numpy >=1.22, <1.25 + - pandas >=1.3.5, <1.4.0 + - pyahocorasick >=1.4.0 + - pydantic >=1.8.1, <2 + - pysam >=0.16.0 + - python >=3.8, <=3.10 + - star >=2.7.6 + +test: + commands: + - htsinfer --version + +about: + home: https://github.com/zavolanlab/htsinfer + license: Apache-2.0 + license_family: APACHE + license_file: LICENSE + summary: HTSinfer infers metadata from Illumina high throughput sequencing (HTS) data + +extra: + recipe-maintainers: + - balajtimate \ No newline at end of file From 1a4a98e79acd24b9bbb606684ef24a1407cc5ffd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Jan 2024 12:07:55 -0500 Subject: [PATCH 1502/2173] Update egglib to 3.3.1 (#45200) * Update egglib to 3.3.1 * edit meta.yaml --------- Co-authored-by: mencian --- recipes/egglib/meta.yaml | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/recipes/egglib/meta.yaml b/recipes/egglib/meta.yaml index d79bb0ab1732f..00a8af2197238 100644 --- a/recipes/egglib/meta.yaml +++ b/recipes/egglib/meta.yaml @@ -1,18 +1,21 @@ {% set name = "egglib" %} -{% set version = "3.3.0" %} +{% set version = "3.3.1" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: "https://files.pythonhosted.org/packages/a7/f2/8840daacb59c75d7bf216a8dba18ea38311126925d91d46718426503103d/EggLib-3.3.0.tar.gz" - sha256: 781b8e01d16762026b18514687be40acf68f97cdd975ea670854d74d2f8bd5c5 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/EggLib-{{ version }}.zip + sha256: ef918149243b7a6c3007629b3bb8df59a49af53910300bc3a07c698ac84bec55 build: number: 0 - skip: True # [py2k or osx] - script: {{ PYTHON }} -m pip install . -vv + skip: True # [py < 38 or osx] + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + entry_points: + - egglib-config = egglib.cli.config:main + - egglib-test = egglib.cli.test:main run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -27,6 +30,7 @@ requirements: run: - python - platformdirs + - click test: imports: @@ -39,7 +43,7 @@ test: about: home: "https://egglib.org/" - license: "GNU General Public v3 or later (GPLv3+)" + license: "GPL-3.0-or-later" license_family: GPL3 license_file: LICENSE summary: "Evolutionary Genetics and Genomics Library. EggLib is a C++/Python library and program package for evolutionary genetics and genomics. Main features are sequence data management, sequence polymorphism analysis, and coalescent simulations. EggLib is a flexible Python module with a performant underlying C++ library and allows fast and intuitive development of Python programs and scripts." @@ -50,4 +54,5 @@ extra: recipe-maintainers: - ranwez identifiers: - - https://doi.org/10.1111/1755-0998.13672 + - doi:10.1111/1755-0998.13672 + - biotools:egglib From a0a2430d09ee13accfb6c11a7e8687e1efcb982a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Jan 2024 12:33:53 -0500 Subject: [PATCH 1503/2173] Update psims to 1.3.3 (#45201) --- recipes/psims/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/psims/meta.yaml b/recipes/psims/meta.yaml index 92f026d771450..fbab7ed9f4c18 100644 --- a/recipes/psims/meta.yaml +++ b/recipes/psims/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.3.2" %} -{% set sha256 = "53efaa9cbd8ae8eec263f39d69e4fcd02cbf2f25b359badf7c38e81fa812a273" %} +{% set version = "1.3.3" %} +{% set sha256 = "d956fb6d2a42087fe35595ad452802fe115a7952c8bcb63951d19b99530b1358" %} package: name: "psims" From e1f1ad83dfc1f3a30e7203ae7a2680ebcc857247 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Jan 2024 12:46:01 -0500 Subject: [PATCH 1504/2173] Update ensembl-vep to 111.0 (#45195) * Update ensembl-vep to 111.0 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/ensembl-vep/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ensembl-vep/meta.yaml b/recipes/ensembl-vep/meta.yaml index 85160b5f607d6..53df662c2a172 100644 --- a/recipes/ensembl-vep/meta.yaml +++ b/recipes/ensembl-vep/meta.yaml @@ -1,4 +1,4 @@ -{% set version="110.1" %} +{% set version="111.0" %} package: name: ensembl-vep @@ -6,11 +6,13 @@ package: source: url: https://github.com/Ensembl/ensembl-vep/archive/release/{{ version }}.tar.gz - sha256: 95b2238209bc9acfa01d4eff202dfbc22e8935abc64b750ea93d1c354a438bae + sha256: 4a2688e91bc31df52909657a1785d5a613f1f858450b7fab7b369ccb4b48e466 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('ensembl-vep', max_pin="x.x") }} requirements: build: From 684e5e8933a11d13813e2a72f95baec28a6412f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Fri, 12 Jan 2024 20:39:04 +0100 Subject: [PATCH 1505/2173] pin max version of pulp to <2.8.0 for Snakemake <8.1.2 (#45203) * pin max version of pulp in Snakemake <2.8.2 * update version --- recipes/bioconda-repodata-patches/gen_patch_json.py | 7 +++++++ recipes/bioconda-repodata-patches/meta.yaml | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/recipes/bioconda-repodata-patches/gen_patch_json.py b/recipes/bioconda-repodata-patches/gen_patch_json.py index d6a8e38c8d273..7c729627c9df0 100755 --- a/recipes/bioconda-repodata-patches/gen_patch_json.py +++ b/recipes/bioconda-repodata-patches/gen_patch_json.py @@ -184,6 +184,13 @@ def _gen_new_index(repodata, subdir): deps[i] += ",<=0.22.1" # append an upper bound break + # snakemake <8.1.2 requires pulp <2.8.0 + if record_name == 'snakemake-minimal' and has_dep(record, "pulp") and version < "8.1.2": + for i, dep in enumerate(deps): + if dep.startswith("pulp") and has_no_upper_bound(dep): + deps[i] = "pulp >=2.0,<2.8.0" + + return index diff --git a/recipes/bioconda-repodata-patches/meta.yaml b/recipes/bioconda-repodata-patches/meta.yaml index fba5666b40699..71e65ad66f5eb 100644 --- a/recipes/bioconda-repodata-patches/meta.yaml +++ b/recipes/bioconda-repodata-patches/meta.yaml @@ -1,6 +1,6 @@ package: name: bioconda-repodata-patches - version: 20231213 # ensure that this is the "current" date, and always higher than the latest version in master + version: 20240112 # ensure that this is the "current" date, and always higher than the latest version in master source: path: . From a835a8e7374c2241879c850b34bb114e18218a0b Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Fri, 12 Jan 2024 16:24:15 -0500 Subject: [PATCH 1506/2173] Update piscem to 0.7.0 (#44884) * Update meta.yaml Bump piscem to v0.7.0 * Update meta.yaml * Update meta.yaml * Update build.sh Try to reduce the number of threads to make the build take less memory. * Update build.sh * Update conda_build_config.yaml * Update meta.yaml update with added -lrt to KMC linker flags * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml Rust 1.75 isn't available upstream yet * Update build.sh * Update build.sh no spaces when setting env variables * Update build.sh More verbose output * Update build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update meta.yaml --- recipes/piscem/build.sh | 8 ++++++-- recipes/piscem/conda_build_config.yaml | 4 ++++ recipes/piscem/meta.yaml | 8 ++++---- 3 files changed, 14 insertions(+), 6 deletions(-) diff --git a/recipes/piscem/build.sh b/recipes/piscem/build.sh index acd3d77c823be..4f3eb6f967819 100644 --- a/recipes/piscem/build.sh +++ b/recipes/piscem/build.sh @@ -19,16 +19,20 @@ fi # We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. export CARGO_NET_GIT_FETCH_WITH_CLI=true export CARGO_HOME="$(pwd)/.cargo" +export NUM_JOBS=1 +export CARGO_BUILD_JOBS=1 if [ "$unamestr" == 'Darwin' ]; then # build statically linked binary with Rust -RUSTFLAGS="-C link-args=-Wl,-undefined,dynamic_lookup" RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . +RUSTFLAGS="-C link-args=-Wl,-undefined,dynamic_lookup" RUST_BACKTRACE=1 cargo install -v -v -j 1 --verbose --root $PREFIX --path . else +export CFLAGS="${CFLAGS} --param ggc-min-expand=20 --param ggc-min-heapsize=8192" +export CXXFLAGS="${CXXFLAGS} --param ggc-min-expand=20 --param ggc-min-heapsize=8192" # build statically linked binary with Rust -RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . +RUST_BACKTRACE=1 cargo install -v -v -j 1 --verbose --root $PREFIX --path . fi diff --git a/recipes/piscem/conda_build_config.yaml b/recipes/piscem/conda_build_config.yaml index 90ff7dab2c6f3..ca927c3a82db0 100644 --- a/recipes/piscem/conda_build_config.yaml +++ b/recipes/piscem/conda_build_config.yaml @@ -2,3 +2,7 @@ MACOSX_DEPLOYMENT_TARGET: # [osx and x86_64] - "10.15" # [osx and x86_64] MACOSX_SDK_VERSION: # [osx and x86_64] - "10.15" # [osx and x86_64] +c_compiler_version: # [linux] + - 11.4 # [linux] +cxx_compiler_version: # [linux] + - 11.4 # [linux] diff --git a/recipes/piscem/meta.yaml b/recipes/piscem/meta.yaml index ded5982191439..c8a3c44e6338e 100644 --- a/recipes/piscem/meta.yaml +++ b/recipes/piscem/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.6.3" %} -{% set git_commit = "3ed9e23b91d6d21a1d7cb17cc9a8c374a1843dfb" %} -{% set sha256 = "ce2f9a3cc6f3c5c214468f6d3c82759c0272792b41d04c7049101e8fb7fe3a03" %} +{% set version = "0.7.0" %} +{% set git_commit = "c2b7489018f5b146d7206b3f080ca949cc6427fc" %} +{% set sha256 = "a72af2ab728e95aa6766a3bb4520af6273a9ea3be44a6a8dc260cd97615877df" %} package: name: piscem @@ -19,7 +19,7 @@ source: requirements: build: - - rust >=1.70 + - rust >=1.74.1 - cmake - autoconf - make From ad9016852e0658af0457ba70383ec2973848a9c5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 12 Jan 2024 16:53:21 -0500 Subject: [PATCH 1507/2173] Update busco to 5.6.0 (#45196) * Update busco to 5.6.0 * update meta.yaml * add name variable * Update patch line numbers * edit patch * fix spacing in patch * Fix patch * edit patch again * edit patch again --------- Co-authored-by: Matthew Berkeley <42berkeley@cua.edu> Co-authored-by: mencian --- ...default-config-path-within-prefix-updated.patch | 9 +++++---- ...001-Add-default-config-path-within-prefix.patch | 14 -------------- recipes/busco/meta.yaml | 13 ++++++++++--- 3 files changed, 15 insertions(+), 21 deletions(-) delete mode 100644 recipes/busco/0001-Add-default-config-path-within-prefix.patch diff --git a/recipes/busco/0001-Add-default-config-path-within-prefix-updated.patch b/recipes/busco/0001-Add-default-config-path-within-prefix-updated.patch index 46f2d39e219fc..3d375e51e4c16 100644 --- a/recipes/busco/0001-Add-default-config-path-within-prefix-updated.patch +++ b/recipes/busco/0001-Add-default-config-path-within-prefix-updated.patch @@ -1,6 +1,6 @@ --- a/src/busco/ConfigManager.py +++ b/src/busco/ConfigManager.py -@@ -42,10 +42,12 @@ class BuscoConfigManager: +@@ -44,11 +44,13 @@ class BuscoConfigManager: return except KeyError: pass @@ -8,13 +8,14 @@ - os.environ.get("BUSCO_CONFIG_FILE"), os.R_OK - ): - self.config_file = os.environ.get("BUSCO_CONFIG_FILE") +- self.run_stats["config_file"] = "BUSCO_CONFIG_FILE environment variable" + config_file = ( + os.environ.get("BUSCO_CONFIG_FILE") + or "/opt/anaconda1anaconda2anaconda3/share/busco/config.ini" + ) + if config_file and os.access(config_file, os.R_OK): -+ self.config_file = config_file ++ self.config_file = config_file ++ self.run_stats["config_file"] = "BUSCO_CONFIG_FILE environment variable" else: self.config_file = "local environment" - return self.config_file - + self.run_stats["config_file"] = "local environment" diff --git a/recipes/busco/0001-Add-default-config-path-within-prefix.patch b/recipes/busco/0001-Add-default-config-path-within-prefix.patch deleted file mode 100644 index 32b151b252be4..0000000000000 --- a/recipes/busco/0001-Add-default-config-path-within-prefix.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- src/busco/ConfigManager.py -+++ src/busco/ConfigManager.py -@@ -32,8 +32,9 @@ - return - except KeyError: - pass -- if os.environ.get("BUSCO_CONFIG_FILE") and os.access(os.environ.get("BUSCO_CONFIG_FILE"), os.R_OK): -- self.config_file = os.environ.get("BUSCO_CONFIG_FILE") -+ config_file = os.environ.get("BUSCO_CONFIG_FILE") or "/opt/anaconda1anaconda2anaconda3/share/busco/config.ini" -+ if config_file and os.access(config_file, os.R_OK): -+ self.config_file = config_file - else: - raise SystemExit("Please specify a BUSCO config file using either " - "(i) an environment variable by entering 'export BUSCO_CONFIG_FILE=/path/to/config.ini' " diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml index dfa64a4b84a80..bc859a09bf67c 100644 --- a/recipes/busco/meta.yaml +++ b/recipes/busco/meta.yaml @@ -1,5 +1,6 @@ -{% set version = "5.5.0" %} -{% set sha256 = "07ca32892ddd6016e5610c34f830cc8445dbcade3f7b460c3d898e27c9650cc7" %} +{% set name = "busco" %} +{% set version = "5.6.0" %} +{% set sha256 = "dcf864b23d97d6f25e09dd7682d5f51b1adf94191dc9c5814984d15fe2057e59" %} package: name: busco @@ -8,6 +9,8 @@ package: build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} source: url: https://gitlab.com/ezlab/busco/-/archive/{{ version }}/busco-{{ version }}.tar.gz @@ -31,6 +34,7 @@ requirements: - pandas - bbmap - miniprot + - requests run: - python >=3.3 - wget @@ -47,6 +51,7 @@ requirements: - pandas - bbmap - miniprot + - requests - fonts-conda-ecosystem test: @@ -58,14 +63,16 @@ test: - test_data about: - home: http://busco.ezlab.org/ + home: https://busco.ezlab.org/ license: MIT + license_family: MIT license_file: LICENSE summary: Assessment of assembly completeness using Universal Single Copy Orthologs description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. + dev_url: https://gitlab.com/ezlab/busco extra: container: From 23d4033b67d2b3ebe1f7bdf4a4f846a817a903b0 Mon Sep 17 00:00:00 2001 From: pirovc <4673375+pirovc@users.noreply.github.com> Date: Fri, 12 Jan 2024 23:21:52 +0100 Subject: [PATCH 1508/2173] ganon v2.0.1 (#45205) --- recipes/ganon/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ganon/meta.yaml b/recipes/ganon/meta.yaml index a2aa06fab08cb..3f42b377f4284 100755 --- a/recipes/ganon/meta.yaml +++ b/recipes/ganon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ganon" %} -{% set version = "2.0.0" %} +{% set version = "2.0.1" %} package: name: "{{ name|lower }}" @@ -8,7 +8,7 @@ package: source: - folder: ganon url: https://github.com/pirovc/{{ name }}/archive/{{ version }}.tar.gz - sha256: 065013bbc4d8817c1895793fcf41c9f68c9f36cae590ded005b389e3cc8941d6 + sha256: e8050f9522e35fe41abd5425ebe35a292081ff179a6a42cd285002ba0ef89f5f - folder: robin-hood-hashing url: https://github.com/martinus/robin-hood-hashing/archive/refs/tags/3.11.3.tar.gz sha256: dcf2b7fa9ef9dd0c67102d94c28e8df3effbe1845e0ed1f31f4772ca5e857fc4 From 6ba5705432e607dbfbe0339080998f86acdeed28 Mon Sep 17 00:00:00 2001 From: John Lees Date: Sat, 13 Jan 2024 09:08:34 +0000 Subject: [PATCH 1509/2173] Update fastlin to v0.2.3 (#45198) * Bump fastlin to v0.2.3 * Release has typo missing v --- recipes/fastlin/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/fastlin/meta.yaml b/recipes/fastlin/meta.yaml index adfd8a2ba286c..48e37b8638cb2 100644 --- a/recipes/fastlin/meta.yaml +++ b/recipes/fastlin/meta.yaml @@ -1,13 +1,13 @@ {% set name = "fastlin" %} -{% set version = "0.2.2.1" %} +{% set version = "0.2.3" %} package: name: {{ name|lower}} version: {{ version }} source: - url: https://github.com/rderelle/fastlin/archive/v{{ version }}.tar.gz - sha256: 0e2773ead72ae17fdd0a41965f97bb6282170cead24cfe3d80ab1c46317777fc + url: https://github.com/rderelle/fastlin/archive/{{ version }}.tar.gz + sha256: 07c427740b520756d25e435e784e3b3d1cca0d08bcce07c5e213a35c4694ccaf build: number: 0 From 90fe0175f205bfee7a95eac6a0d941ca51a592dc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Jan 2024 11:18:23 -0500 Subject: [PATCH 1510/2173] Update snakemake-executor-plugin-slurm-jobstep to 0.1.9 (#45210) --- recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml b/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml index dd3cfeedd0a26..f9e5feae2616e 100644 --- a/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm-jobstep" %} -{% set version = "0.1.8" %} +{% set version = "0.1.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm_jobstep-{{ version }}.tar.gz - sha256: 60e28ceae224107bc415a06ebeeca6b5216765f62622bcbf8ef5ecbc28cd4695 + sha256: 98580067acb9a90ac1cfafda88237155f128d52774e6aa0f41adbd93440c9746 build: noarch: python From 45bba03b5b8ce15b132f6ad6f9172c33349fb34d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Jan 2024 11:18:44 -0500 Subject: [PATCH 1511/2173] Update snakemake to 8.1.2 (#45211) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index dbfec93ae150a..615b4e6918d56 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.1.1" %} +{% set version = "8.1.2" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 767e165b9803a3eb91d50e5f7d4410f537f3f1db102c99fcc97a9b40371cd46a + sha256: 594b73269a3b1903929f07f055609c42f166abc3a6bd1f0b06403bd83e7ff9c8 build: number: 0 From 428e9216f2f8fe5a29f6a450046d522fe06cf18a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Jan 2024 11:19:07 -0500 Subject: [PATCH 1512/2173] Update nextflow to 23.10.1 (#45207) --- recipes/nextflow/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nextflow/meta.yaml b/recipes/nextflow/meta.yaml index ccb24e6cfbb15..067f640311e94 100644 --- a/recipes/nextflow/meta.yaml +++ b/recipes/nextflow/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.10.0" %} -{% set sha256 = "4b7fba61ecc6d53a6850390bb435455a54ae4d0c3108199f88b16b49e555afdd" %} +{% set version = "23.10.1" %} +{% set sha256 = "9abc54f1ffb2b834a8135d44300404552d1e27719659cbb635199898677b660a" %} package: name: nextflow From cf01f8b61edfb71e7fbf736aa0f4d73ddfa8b7d8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Jan 2024 16:56:33 -0500 Subject: [PATCH 1513/2173] Update ncbi-datasets-pylib to 16.3.0 (#45208) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 6327205797c4f..150d6075f3184 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.2.0" %} -{% set sha256 = "2be4cc1b4bf42dabf0c9a4eabfa2db66bc4eb740b844f87b371da861bc995891" %} +{% set version = "16.3.0" %} +{% set sha256 = "9dafbff2b355d0b28f3621cdab580e5cadc8299d2ceeb845bb474d8413d14b85" %} package: name: {{ name|lower }} From 64632d6f323c69be2ce785002c68537b5167e356 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Jan 2024 17:31:46 -0500 Subject: [PATCH 1514/2173] Update compleasm to 0.2.5 (#45206) --- recipes/compleasm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/compleasm/meta.yaml b/recipes/compleasm/meta.yaml index 7c5b0fa3c27f9..db6a28c2c338e 100644 --- a/recipes/compleasm/meta.yaml +++ b/recipes/compleasm/meta.yaml @@ -1,6 +1,6 @@ {% set name = "compleasm" %} -{% set version = "0.2.4" %} -{% set hash = "3658a8104716d2d9345b1d71215fdc200798f5d366ae7f450eca0431ed8b2976" %} +{% set version = "0.2.5" %} +{% set hash = "d2da3f30cf6850daf8328f78986e6bfb6fac1baf2b4b207a14f2180a659a04c7" %} package: name: "{{ name|lower }}" From cb77e1b4faed1719c40d342663e13b9915c9ce0d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 13 Jan 2024 18:53:12 -0500 Subject: [PATCH 1515/2173] Update bellmans-gapc to 2024.01.12 (#45209) * Update bellmans-gapc to 2024.01.12 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/bellmans-gapc/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/bellmans-gapc/meta.yaml b/recipes/bellmans-gapc/meta.yaml index f929e5c91ba7e..aeeba10b347fc 100644 --- a/recipes/bellmans-gapc/meta.yaml +++ b/recipes/bellmans-gapc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2023.07.05" %} +{% set version = "2024.01.12" %} package: name: bellmans-gapc @@ -6,10 +6,12 @@ package: source: url: https://github.com/jlab/gapc/archive/{{ version }}.tar.gz - sha256: 05ebe0707c767dc80f0f9a67d5387a098bcf6bf2e26408c5f2059f373410df69 + sha256: 590b62d5fc39b1deb45855b0586d7ca3674ef17c59fc84ef445d2760a480f7ba build: number: 0 + run_exports: + - {{ pin_subpackage('bellmans-gapc', max_pin=None) }} requirements: build: @@ -38,6 +40,7 @@ test: about: home: https://bibiserv.cebitec.uni-bielefeld.de/gapc - license: 'GPLv3+' + license: 'GPL-3.0-or-later' + license_family: GPL3 license_file: LICENSE summary: 'A language and compiler for algebraic dynamic programming.' From b1d487d85ba69ff24a12b080c6425062873ce02f Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 13 Jan 2024 18:31:37 -0600 Subject: [PATCH 1516/2173] Update braker3 to 3.0.7 (#45212) * Update braker3 to 3.0.7 * add compleasm --- recipes/braker3/build.sh | 8 +------- recipes/braker3/meta.yaml | 11 +++++------ 2 files changed, 6 insertions(+), 13 deletions(-) diff --git a/recipes/braker3/build.sh b/recipes/braker3/build.sh index d84e45e0d2e7f..36cee98375ec7 100644 --- a/recipes/braker3/build.sh +++ b/recipes/braker3/build.sh @@ -1,4 +1,5 @@ #!/bin/bash + # Copy scripts mkdir -p ${PREFIX}/bin chmod +x scripts/*.pl @@ -6,10 +7,3 @@ cp scripts/*.pl ${PREFIX}/bin/ cp scripts/*.pm ${PREFIX}/bin/ cp scripts/*.py ${PREFIX}/bin/ cp -r scripts/cfg/ ${PREFIX}/bin/ - -# install TSEBRA -cp tsebra/bin/* ${PREFIX}/bin -mkdir -p ${SP_DIR}/tsebra_mod -mv tsebra/bin/* ${SP_DIR}/tsebra_mod -mkdir ${PREFIX}/config -mv tsebra/config/* ${PREFIX}/config diff --git a/recipes/braker3/meta.yaml b/recipes/braker3/meta.yaml index 963a2bf73bdde..cbf46b0d20506 100644 --- a/recipes/braker3/meta.yaml +++ b/recipes/braker3/meta.yaml @@ -1,16 +1,13 @@ {% set name = "BRAKER3" %} -{% set version = "3.0.6" %} -{% set sha256 = "2609410c597a95017966c88bdc1787c44494caf9a2b2242a7a849fee6484282b" %} +{% set version = "3.0.7" %} +{% set sha256 = "578b51538e9d18c6f4d8892452d05d59b9126dcfbb6a32a1fe6f70c210370c96" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: -- url: https://github.com/Gaius-Augustus/BRAKER/archive/refs/tags/v3.06.tar.gz +- url: https://github.com/Gaius-Augustus/BRAKER/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} -- url: https://github.com/Gaius-Augustus/TSEBRA/archive/refs/tags/v.1.1.1.tar.gz - sha256: 0426c243888135ee3fd6ea0ca9f37eb4af03dd117498165257fa756f59d49ce9 - folder: tsebra build: number: 0 @@ -52,6 +49,8 @@ requirements: - cdbtools >=0.99 - genomethreader >=1.7.0 - diamond >=2.1.6 + - tsebra + - compleasm # - GeneMark-ES/ET/EP+ >=4.64 # - prothint >=2.6.0 From 19b7e3d569df6a1dcee04f6d0a90d28d2da593ea Mon Sep 17 00:00:00 2001 From: "Dr. K. D. Murray" <1560490+kdm9@users.noreply.github.com> Date: Sun, 14 Jan 2024 13:20:35 +0100 Subject: [PATCH 1517/2173] Update deepvariant dependency versions (#45214) * Update deepvariant dependency versions * Add run exports --- recipes/deepvariant/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/deepvariant/meta.yaml b/recipes/deepvariant/meta.yaml index d89ae1cc5fb84..27b668f7cb492 100644 --- a/recipes/deepvariant/meta.yaml +++ b/recipes/deepvariant/meta.yaml @@ -19,8 +19,10 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 skip: true # [osx or not py36] + run_exports: + - {{ pin_subpackage("deepvariant", max_pin="x") }} requirements: host: @@ -33,8 +35,9 @@ requirements: # - google-cloud-sdk # - bazel run: + # NB: maintainers, check versions with upstream's settings.sh - openjdk >=8,<9 - - python 3.6.* + - python 3.8.* # TF slim is difficult because there is an existing tf-slim package in conda-forge # https://github.com/conda-forge/tf-slim-feedstock # which is different than the google one: https://github.com/google-research/tf-slim @@ -48,14 +51,14 @@ requirements: - htslib - numpy - curl - - tensorflow-gpu 2.0.* - - tensorflow-estimator 2.0.* + - tensorflow-gpu 2.11.* + - tensorflow-estimator 2.11.* - protobuf - contextlib2 - enum34 - intervaltree - mock - - numpy 1.16.* + - numpy 1.19.* - psutil - requests - scipy From bc442b2583a0efb3cdc36d4e114f3afa8e5bfa0e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 14 Jan 2024 13:02:32 -0500 Subject: [PATCH 1518/2173] Update busco to 5.6.1 (#45215) --- recipes/busco/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml index bc859a09bf67c..515c990c241e1 100644 --- a/recipes/busco/meta.yaml +++ b/recipes/busco/meta.yaml @@ -1,6 +1,6 @@ {% set name = "busco" %} -{% set version = "5.6.0" %} -{% set sha256 = "dcf864b23d97d6f25e09dd7682d5f51b1adf94191dc9c5814984d15fe2057e59" %} +{% set version = "5.6.1" %} +{% set sha256 = "1129d8dd1779455b77c47a926650e1974aaca58eeb9e6b3b6e4a706154ab2da8" %} package: name: busco From 9ce8d58d76a7911b59cf2229cfed9c0771e558d3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 14 Jan 2024 15:19:02 -0500 Subject: [PATCH 1519/2173] Update edta to 2.2.0 (#45172) * Update edta to 2.2.0 * add run_export * replace tool name * re-order tools alphabeticaly + add missing tools * remove tool pins excepted python set to >=3.8 * edit matplotlib to matplotlib-base * add annosine2 * Update edta to 2.2.0 * edit tests * edit tests * softlink EDTA_processI.pl * I not J --------- Co-authored-by: Jacques Dainat Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/edta/build.sh | 4 ++- recipes/edta/meta.yaml | 61 +++++++++++++++++++++++++++--------------- 2 files changed, 43 insertions(+), 22 deletions(-) diff --git a/recipes/edta/build.sh b/recipes/edta/build.sh index 6f788aca9f249..729d94a5a9379 100644 --- a/recipes/edta/build.sh +++ b/recipes/edta/build.sh @@ -16,5 +16,7 @@ END chmod a+x ${PREFIX}/bin/EDTA.pl for name in ${EDTA_OTHER_PROGRAMS} ; do - ln -s ${PREFIX}/bin/EDTA.pl ${PREFIX}/bin/$(basename $name) + ln -sf ${PREFIX}/bin/EDTA.pl ${PREFIX}/bin/$(basename $name) done + +ln -sf ${EDTA_DIR}/development/EDTA_processI.pl ${PREFIX}/bin/ diff --git a/recipes/edta/meta.yaml b/recipes/edta/meta.yaml index e9f32040263c3..3e5f7651efd27 100644 --- a/recipes/edta/meta.yaml +++ b/recipes/edta/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EDTA" %} -{% set version = "2.1.0" %} -{% set sha256 = "d62425df133d7021db57b5b0ecdd38b21ac837c45a8237c0a1ec2da0bd21e6b6" %} +{% set version = "2.2.0" %} +{% set sha256 = "3515667804437f749f0bb934812ca83b23ec5472c221786f6e5a0d4b613a1a7a" %} package: name: "{{ name|lower }}" @@ -11,35 +11,46 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('edta', max_pin='x') }} requirements: run: - - perl + - annosine2 + - bedtools + - biopython + - blast - cd-hit + - coreutils + - genericrepeatfinder + - genometools-genometools + - glob2 + - h5py + - hmmer + - irfinder + - keras + - ltr_finder + - ltr_retriever - repeatmodeler - - muscle + - matplotlib-base - mdust - - blast + - minimap2 + - multiprocess + - muscle + - nodejs - openjdk + - pandas + - perl - perl-text-soundex - - multiprocess + - python >=3.8 - regex - - tensorflow ==1.14 - - keras >=2.2.4 - - scikit-learn >=0.19.0 - - biopython - - pandas - - glob2 - - h5py <3 - - python <3.7 + - scikit-learn + - seqtk + - swifter + - tensorflow - tesorter - - genericrepeatfinder - - genometools-genometools - - ltr_retriever - - ltr_finder - - coreutils test: commands: @@ -52,7 +63,15 @@ test: about: home: https://github.com/oushujun/EDTA license: GPL-3.0-only - license_family: GPL + license_family: GPL3 license_file: LICENSE summary: Extensive de-novo TE Annotator dev_url: https://github.com/oushujun/EDTA + doc_url: https://github.com/oushujun/EDTA/wiki + +extra: + identifiers: + - doi:10.1186/s13059-019-1905-y + - doi:10.1101/2022.10.09.511471 + - biotools:EDTA + - usegalaxy-eu:edta From f23a4859123f52c5ee50372ab1fc38cbe42b9ca4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 04:04:44 -0500 Subject: [PATCH 1520/2173] Update binchicken to 0.10.3 (#45222) --- recipes/binchicken/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/binchicken/meta.yaml b/recipes/binchicken/meta.yaml index caebd6ed54297..ec1cc96708dbd 100644 --- a/recipes/binchicken/meta.yaml +++ b/recipes/binchicken/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.10.0" %} +{% set version = "0.10.3" %} {% set name = "binchicken" %} -{% set sha256 = "32d47924d8f137c0b5a142c8e8abc4a1632da9537a6e1f30d69bfe2377c3b6ab" %} +{% set sha256 = "da3a5a7e88c29e5470111e6011eb4395e7597c1ed50927b0cef16997d6484545" %} package: name: binchicken From 69d5a9a708b47a9e65e5113bd678a97f30db56b4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 09:14:12 -0500 Subject: [PATCH 1521/2173] Update mosca to 2.2.1 (#45227) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update mosca to 2.2.1 * Update build.sh --------- Co-authored-by: João Sequeira --- recipes/mosca/build.sh | 4 ++-- recipes/mosca/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/mosca/build.sh b/recipes/mosca/build.sh index 09ffed14a0a72..4582f8c0c8704 100644 --- a/recipes/mosca/build.sh +++ b/recipes/mosca/build.sh @@ -1,5 +1,5 @@ echo "Storing MOSCA's files in the Conda environment at: ${PREFIX}" mkdir -p "${PREFIX}/share/MOSCA" "${PREFIX}/bin" -cp -r workflow/* "${PREFIX}/share/MOSCA" +cp -r workflow/* resources/*.json "${PREFIX}/share/MOSCA" chmod +x "${PREFIX}/share/MOSCA/mosca.py" -ln -s "${PREFIX}/share/MOSCA/mosca.py" "${PREFIX}/bin/mosca" \ No newline at end of file +ln -s "${PREFIX}/share/MOSCA/mosca.py" "${PREFIX}/bin/mosca" diff --git a/recipes/mosca/meta.yaml b/recipes/mosca/meta.yaml index eec8c3b69c882..d4ec74195aabd 100644 --- a/recipes/mosca/meta.yaml +++ b/recipes/mosca/meta.yaml @@ -1,6 +1,6 @@ {% set name = "mosca" %} -{% set version = "2.2.0" %} -{% set sha256 = "575d17f70b7ff1860789bc352055d32af06b6c5fbe16e2169d762ae3d49a7ca2" %} +{% set version = "2.2.1" %} +{% set sha256 = "c2b66c9cb0d55edf1c452fd23e31965ce9fb45793007521b372a1229ab5ed254" %} package: name: {{ name|lower }} From c57b689159b13602893d9f530e0f11ab5f897461 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 09:35:38 -0500 Subject: [PATCH 1522/2173] Update peaks2utr to 1.2.3 (#45228) --- recipes/peaks2utr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/peaks2utr/meta.yaml b/recipes/peaks2utr/meta.yaml index b95b6a98d6d21..0e80fb16b8bd0 100644 --- a/recipes/peaks2utr/meta.yaml +++ b/recipes/peaks2utr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "peaks2utr" %} -{% set version = "1.2.2" %} +{% set version = "1.2.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/peaks2utr-{{ version }}.tar.gz - sha256: 9bd1fcd1683a342b240639bd99c9e2c24f74021698e7537b981c4ce3e43ca030 + sha256: 328e23a64f2304177bfff07e9da59692f9fde2cf6207da425a58c67bc189b588 build: number: 0 From 9e7f5303d77940248ba270759587ee6f738330a3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 09:36:07 -0500 Subject: [PATCH 1523/2173] Update attotree to 0.1.1 (#45229) --- recipes/attotree/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/attotree/meta.yaml b/recipes/attotree/meta.yaml index 6fa340d6d68ba..3cd8f4c661f08 100644 --- a/recipes/attotree/meta.yaml +++ b/recipes/attotree/meta.yaml @@ -1,5 +1,5 @@ {% set name = "attotree" %} -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: e604555bcbff83384d3266048af7dcec026773a0aaf6945582994ad9c8af69e3 + sha256: ada454ac2a9392667476816c466c005935d5ffe73f87b2b7bc7960a0ec0753a4 build: number: 0 From 7fbb5e610a7c6beec70bba2b49f9d12772fa5bfa Mon Sep 17 00:00:00 2001 From: Arya Massarat <23412689+aryarm@users.noreply.github.com> Date: Mon, 15 Jan 2024 06:37:56 -0800 Subject: [PATCH 1524/2173] Update haptools to 0.4.0 (#45223) add back pip check, include pgenlib dependency, and add support for python 3.11 --- recipes/haptools/meta.yaml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/haptools/meta.yaml b/recipes/haptools/meta.yaml index 17c43e75a5d19..402565706e9c1 100644 --- a/recipes/haptools/meta.yaml +++ b/recipes/haptools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "haptools" %} -{% set version = "0.3.0" %} +{% set version = "0.4.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/haptools-{{ version }}.tar.gz - sha256: 9ecb9891ce01bb91c460426e1f94d4e939a0465e13529f3ec3d122f9b2c3ee77 + sha256: 85dba0bde58e33ac71c298eb37e1272ca83276d06714d6516f8bc722c3455fe0 build: number: 0 @@ -22,21 +22,25 @@ requirements: host: - pip >=19.0.3 - poetry-core >=1.0.0 - - python >=3.7,<3.11 + - python >=3.7,<4.0 run: - click >=8.0.3 - cyvcf2 >=0.30.14 - matplotlib-base >=3.5.1 - numpy >=1.20.0 + - pgenlib >=0.90.1 - pysam >=0.19.0 - - python >=3.7,<3.11 + - python >=3.7,<4.0 test: imports: - haptools - haptools.data commands: + - pip check - haptools --help + requires: + - pip about: home: https://github.com/cast-genomics/haptools From e2edfb65b4c91a8efe084bac0b0df7aeae72aaf0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 09:39:13 -0500 Subject: [PATCH 1525/2173] Update metaphor to 1.7.10 (#45219) --- recipes/metaphor/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/metaphor/meta.yaml b/recipes/metaphor/meta.yaml index 53267b80f5cc6..a5d1801709fb8 100644 --- a/recipes/metaphor/meta.yaml +++ b/recipes/metaphor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metaphor" %} -{% set version = "1.7.9" %} +{% set version = "1.7.10" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: https://github.com/vinisalazar/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 36c089a427a4fba0ed8768b2bbfc8312bd53d0f51b357b715ab1fe7a2b33dfe1 + sha256: f8b49aac85fd16b78210cbacc34e615baeb8551e3aa11eed36748385333c9f49 build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage(name, max_pin="x") }} From 5b99f809b83b1b096727b9c906f5f7c5f71e4bbc Mon Sep 17 00:00:00 2001 From: "Le (Lena) Huang" Date: Mon, 15 Jan 2024 09:40:03 -0500 Subject: [PATCH 1526/2173] dbCAN2 update to 4.1.2 (#45218) * dbCAN2 update * change matplotlib into matplotlib-base --- recipes/dbcan/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/dbcan/meta.yaml b/recipes/dbcan/meta.yaml index 64a233372b504..7be1bbfbd0487 100644 --- a/recipes/dbcan/meta.yaml +++ b/recipes/dbcan/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dbcan" %} -{% set version = "4.1.1" %} +{% set version = "4.1.2" %} package: name: "{{ name|lower }}" @@ -9,7 +9,7 @@ source: # the sha256 sum is generated by doing # wget -0- [URL] | shasum -a 256 url: https://github.com/linnabrown/run_dbcan/releases/download/{{ version }}/dbcan-{{ version }}.tar.gz - sha256: 500fe10463f8a8034e89aa47eba349119575afc25d18c3649ec8aef86f7fe4d5 + sha256: 3a675683379d1afc9f3444fc9894272f1485956df266a6ee4fc11a8f628e6d51 build: number: 0 @@ -43,6 +43,8 @@ requirements: - biopython - pandas - tqdm + - openpyxl + - matplotlib-base - session-info test: From 951e2b8c4430d991bfa67d44e390ade46adab04f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 09:41:05 -0500 Subject: [PATCH 1527/2173] Update pyfamsa to 0.3.1 (#45216) * Update pyfamsa to 0.3.1 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/pyfamsa/meta.yaml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/recipes/pyfamsa/meta.yaml b/recipes/pyfamsa/meta.yaml index bfd3445e2a511..14d799d24909a 100644 --- a/recipes/pyfamsa/meta.yaml +++ b/recipes/pyfamsa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyfamsa" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b00e6fdf87975d9e256ef493cc82880308bd66b4fd29b5185b5337f0709cd28f + sha256: 1122a8b06bbbe1045a185d7671e87be0030e3db8e2dd0cb885ff21744c9d24a6 build: number: 0 - skip: True #[py2k] - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + skip: True # [py2k] + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" + run_exports: + - {{ pin_subpackage('pyfamsa', max_pin="x.x") }} requirements: build: @@ -22,11 +24,9 @@ requirements: - python - pip - cython - - setuptools - semantic_version run: - python - - setuptools test: imports: @@ -36,11 +36,12 @@ test: about: home: https://github.com/althonos/pyfamsa - license: GPL-3 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 license_file: COPYING summary: Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments. doc_url: https://pyfamsa.readthedocs.org/ + dev_url: https://github.com/althonos/pyfamsa extra: recipe-maintainers: From 271d6679a8e54aa895a2acc3fb86289680d0478d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 12:11:04 -0500 Subject: [PATCH 1528/2173] Update snakemake to 8.1.3 (#45226) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 615b4e6918d56..24f6f8ff38fb9 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.1.2" %} +{% set version = "8.1.3" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 594b73269a3b1903929f07f055609c42f166abc3a6bd1f0b06403bd83e7ff9c8 + sha256: 58bccaa64f80f9332891d19aaa6544e6d11e508bb5c57d3512159888787a16a2 build: number: 0 From 3339b62ec3ab43f4ec378275bd3198c3f8371890 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 12:11:22 -0500 Subject: [PATCH 1529/2173] Update peaks2utr to 1.2.4 (#45230) --- recipes/peaks2utr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/peaks2utr/meta.yaml b/recipes/peaks2utr/meta.yaml index 0e80fb16b8bd0..b0f5d08d094ca 100644 --- a/recipes/peaks2utr/meta.yaml +++ b/recipes/peaks2utr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "peaks2utr" %} -{% set version = "1.2.3" %} +{% set version = "1.2.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/peaks2utr-{{ version }}.tar.gz - sha256: 328e23a64f2304177bfff07e9da59692f9fde2cf6207da425a58c67bc189b588 + sha256: 9fb91c2361e8de95994f1de7bf8414710777ecd52b23d35628270f0bb2e2412e build: number: 0 From 6aa1ee77d0fc46bfd9e9a4bfa50a28e8d32ac8db Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 12:11:39 -0500 Subject: [PATCH 1530/2173] Update annotsv to 3.3.9 (#45231) --- recipes/annotsv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annotsv/meta.yaml b/recipes/annotsv/meta.yaml index e7d2ab3035882..c729ada9c6038 100644 --- a/recipes/annotsv/meta.yaml +++ b/recipes/annotsv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "annotsv" %} -{% set version = "3.3.8" %} -{% set sha256 = "e06f016fcbf16fe13e839adb4979a626dfeb4753a8ca5dc348d2581531cfeecd" %} +{% set version = "3.3.9" %} +{% set sha256 = "698db38f70aaf7e839fbe090fc647b5dd7584c71a9b6397e38bf5af83a4e4c44" %} package: name: {{ name }} From ed7f91ed2cd400cd18d85cb1005b3f08dc560eb4 Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Mon, 15 Jan 2024 12:13:10 -0500 Subject: [PATCH 1531/2173] Update bindash v2.0 (#45220) * Update bindash v2.0 * Update bindash v2.0 * Update bindash v2.0 --- recipes/bindash/meta.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/bindash/meta.yaml b/recipes/bindash/meta.yaml index deac0b5e9f345..a7667087921b2 100644 --- a/recipes/bindash/meta.yaml +++ b/recipes/bindash/meta.yaml @@ -1,17 +1,18 @@ -{% set name = "bindash" %} -{% set version = "1.0" %} +{% set version = "2.0" %} package: - name: {{ name|lower }} + name: bindash version: {{ version }} source: - url: https://github.com/zhaoxiaofei/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 6f7c68fec2ad5e2d869fbe52c324010de2ed61c3a5d5800cf6ab8f9c5deaaa1a + url: https://github.com/jianshu93/bindash/archive/v{{ version }}.tar.gz + sha256: 300fd4709df1d000470feb5af1a7d1ecd95c15f9c35f7535ae9c40dce4a540a8 build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage('bindash', max_pin="x.x") }} requirements: build: From 865fb21dc4911db79e3cad6189fffc69aef58ea0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 14:53:05 -0500 Subject: [PATCH 1532/2173] Update capcruncher to 0.3.11 (#45232) --- recipes/capcruncher/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/capcruncher/meta.yaml b/recipes/capcruncher/meta.yaml index da3b10db17215..39a98b445fdb9 100644 --- a/recipes/capcruncher/meta.yaml +++ b/recipes/capcruncher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "capcruncher" %} -{% set version = "0.3.10" %} +{% set version = "0.3.11" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/capcruncher-{{ version }}.tar.gz - sha256: 3c81d6228ff7a2f7a84301cbcc5e9cd1988952c5d670b0eaf0903d2cfa3e3ac1 + sha256: 1baee46dc9eaab97125796292bc7d6a24821c69538d43f205a344f550db14a7a build: number: 0 From 0aaf0f92d57d56a40fa1707afa11188635a38e9f Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 16 Jan 2024 09:26:34 +1300 Subject: [PATCH 1533/2173] Repalced bin_perl with env_perl in all perl files (#45225) --- recipes/evigene/build.sh | 4 ++-- recipes/evigene/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/evigene/build.sh b/recipes/evigene/build.sh index 3675e01e7a23a..d55e09fafd6b1 100644 --- a/recipes/evigene/build.sh +++ b/recipes/evigene/build.sh @@ -15,5 +15,5 @@ echo "export EVIGENEHOME=${EVIGENEHOME}" > ${PREFIX}/etc/conda/activate.d/${PKG_ mkdir -p ${PREFIX}/etc/conda/deactivate.d/ echo "unset EVIGENEHOME" > ${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}-${PKG_VERSION}.sh -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${EVIGENEHOME}/scripts/prot/tr2aacds.pl -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${EVIGENEHOME}/scripts/prot/tr2aacds4.pl +find $EVIGENEHOME -name *.pl | xargs -I {} sed -i.bak '1 s|#!/usr/bin/perl|#!/usr/bin/env perl|g' {} +find $EVIGENEHOME -name *.perl | xargs -I {} sed -i.bak '1 s|#!/usr/bin/perl|#!/usr/bin/env perl|g' {} diff --git a/recipes/evigene/meta.yaml b/recipes/evigene/meta.yaml index 1bbf7e8dcae8e..a4c43d0e8aa4e 100644 --- a/recipes/evigene/meta.yaml +++ b/recipes/evigene/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('evigene', max_pin='x') }} @@ -25,7 +25,7 @@ requirements: test: commands: - - capture_die=$(bash -c "perl $EVIGENEHOME/scripts/prot/tr2aacds.pl || true" 2>&1) + - capture_die=$(bash -c "$EVIGENEHOME/scripts/prot/tr2aacds.pl || true" 2>&1) - echo "$capture_die" | grep "VERSION 2022.04.05" about: From 99142eb8d60ba73beffc333ef582ca40670726ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 17:05:18 -0500 Subject: [PATCH 1534/2173] Update phigaro to 2.4.0 (#45117) * Update phigaro to 2.4.0 * add run_exports * remove singleton * Phigaro: remove argparse, python <=3.7.11 (#45237) Removed argparse requierement, since it's a part of the Python Standard Library. Restricted Python <=3.7.11 to prevent from trying to use 2.12.0_pr3 --------- Co-authored-by: joshuazhuang7 Co-authored-by: Polina --- recipes/phigaro/meta.yaml | 34 +++++++++++----------------------- 1 file changed, 11 insertions(+), 23 deletions(-) diff --git a/recipes/phigaro/meta.yaml b/recipes/phigaro/meta.yaml index c7575e658cfa7..02183858fef6a 100644 --- a/recipes/phigaro/meta.yaml +++ b/recipes/phigaro/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phigaro" %} -{% set version = "2.3.0" %} +{% set version = "2.4.0" %} package: name: "{{ name|lower }}" @@ -7,36 +7,23 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 758012cabec53841f6c18f90ef5a1dc0819e72c9b765b2c86bc0401afd7c5e8a + sha256: fd764d792a37984bcabaea0da39185dc6c864b8ecfbd8a806553a68ac876d800 build: - number: 1 - noarch: python + number: 0 + noarch: python entry_points: - phigaro = phigaro.cli.batch:main - phigaro-setup = phigaro.cli.helper:main - script: "{{ PYTHON }} -m pip install . -vv; echo https://files.pythonhosted.org/packages/51/d3/0271413b3b9d1ed2a532e2575287bec9481d2183e445ecc0ebc1df8f1ddc/singleton-0.1.0.tar.gz > requirements.txt; {{ PYTHON }} -m pip install -r requirements.txt" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv; echo https://files.pythonhosted.org/packages/51/d3/0271413b3b9d1ed2a532e2575287bec9481d2183e445ecc0ebc1df8f1ddc/singleton-0.1.0.tar.gz > requirements.txt; {{ PYTHON }} -m pip install -r requirements.txt" + run_exports: + - {{ pin_subpackage('phigaro', max_pin="x") }} requirements: host: - - argparse - - beautifulsoup4 >=4.4.0 - - biopython - - bs4 - - future - - lxml - - numpy - - pandas >=0.23.4 - pip - - plotly - - python >=3.6 - - pyyaml >=5.1 - - sh - - six >=1.7.0 - - prodigal - - hmmer + - python >=3.6,<=3.11.7 run: - - argparse - beautifulsoup4 >=4.4.0 - biopython - bs4 @@ -45,7 +32,7 @@ requirements: - numpy - pandas >=0.23.4 - plotly - - python >=3.6 + - python >=3.6,<=3.11.7 - pyyaml >=5.1 - sh - six >=1.7.0 @@ -67,7 +54,8 @@ test: - phigaro-setup --help about: - home: "https://phigaro.readthedocs.io/" + home: https://github.com/bobeobibo/phigaro + doc_url: "https://phigaro.readthedocs.io/" license: MIT license_family: MIT license_file: "LICENSE.md" From f7e3c8fd22a8c1327d8fa3c94531813f6fde2c34 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 15 Jan 2024 23:32:00 +0100 Subject: [PATCH 1535/2173] pulp dependency changes (#45234) See https://github.com/snakemake/snakemake/pull/2610/files Since v8.1.2 actually --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 24f6f8ff38fb9..3a6dd2c52e5ce 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 58bccaa64f80f9332891d19aaa6544e6d11e508bb5c57d3512159888787a16a2 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage("snakemake", max_pin="x") }} @@ -96,7 +96,7 @@ outputs: - nbformat - packaging - psutil - - pulp >=2.0 + - pulp >=2.3.1,<2.9 - pyyaml - requests >=2.8.1 - reretry From 5a30d94c9a83435f1a7b9f7a032f8b3d9b55f867 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 18:34:11 -0500 Subject: [PATCH 1536/2173] Update neofox to 1.1.0 (#43902) * Update neofox to 1.1.0 * add run_exports * upgrade dependencies * add cython to host as lint complains * remove cython version as linter still complains * change cython to the beggining of requirements * try adding skip-lint * loosen blast and pysam version dependencies * explicitly set R dependencies to conda-forge * remove old reference to neoag from recipe * try R dependencies only in run section --------- Co-authored-by: joshuazhuang7 Co-authored-by: Thanh Lee Co-authored-by: Pablo Riesgo-Ferreiro --- recipes/neofox/meta.yaml | 59 +++++++++++++++++++--------------------- 1 file changed, 28 insertions(+), 31 deletions(-) diff --git a/recipes/neofox/meta.yaml b/recipes/neofox/meta.yaml index 8851aa1e1e53e..1440752000709 100644 --- a/recipes/neofox/meta.yaml +++ b/recipes/neofox/meta.yaml @@ -1,5 +1,5 @@ {% set name = "neofox" %} -{% set version = "1.0.2" %} +{% set version = "1.1.0" %} package: name: "{{ name|lower }}" @@ -7,62 +7,58 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e93ea0c146fe4fbf9e477ecef8d973b0b84121733135702b581a1ff0b565edb8 + sha256: c09b8b3df49b290ee239301626edfd9057c354ab6e8bd344aa1cae2765f4b105 build: number: 0 noarch: python entry_points: - neofox=neofox.command_line:neofox_cli + - neofox-epitope=neofox.command_line:neofox_epitope_cli - neofox-configure=neofox.command_line:neofox_configure - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('neofox', max_pin="x") }} requirements: host: + - cython - betterproto >=1.2.5,<1.3.0 - biopython ==1.76 - - dask[complete] >=2021.10.0 - - distributed >=2021.10.0 - - faker >=6.6.2,<7.0.0 + - dask[complete] >=2022.2.0,<2023.0.0 + - distributed >=2022.2.0,<2023.0.0 + - faker >=13.13.0,<13.14.0 - logzero >=1.5.0 - mock >=4.0.3,<5.0.0 - - numpy >=1.21 + - numpy >=1.21,<1.22 - orjson >=3.5.2,<4.0.0 - - pandas >=1.1.5 + - pandas >=1.3.5,<1.4 - pip - - pysam >=0.19.1,<0.20.0 + - pysam - python >=3.7,<=3.8 - python-dotenv >=0.12.0,<0.13.0 - - scikit-learn >=0.22.1,<0.23.0 - - scipy >=1.5.4 + - scikit-learn ==0.22.1 + - scipy >=1.7.3,<1.8 - xmltodict >=0.12.0,<0.13.0 - - blast ==2.10.1 - - r-base - - r-lattice - - r-ggplot2 - - r-caret - - r-peptides - - r-doparallel - - r-gbm - - bioconductor-biostrings + - blast run: - betterproto >=1.2.5,<1.3.0 - biopython ==1.76 - - dask[complete] >=2021.10.0 - - distributed >=2021.10.0 - - faker >=6.6.2,<7.0.0 + - dask[complete] >=2022.2.0,<2023.0.0 + - distributed >=2022.2.0,<2023.0.0 + - faker >=13.13.0,<13.14.0 - logzero >=1.5.0 - mock >=4.0.3,<5.0.0 - - numpy >=1.21 + - numpy >=1.21,<1.22 - orjson >=3.5.2,<4.0.0 - - pandas >=1.1.5 - - pysam >=0.19.1,<0.20.0 + - pandas >=1.3.5,<1.4 + - pysam - python >=3.7,<=3.8 - python-dotenv >=0.12.0,<0.13.0 - - scikit-learn >=0.22.1,<0.23.0 - - scipy >=1.5.4 + - scikit-learn ==0.22.1 + - scipy >=1.7.3,<1.8 - xmltodict >=0.12.0,<0.13.0 - - blast ==2.10.1 + - blast - r-base - r-lattice - r-ggplot2 @@ -89,7 +85,6 @@ test: - neofox.published_features.dissimilarity_garnish - neofox.published_features.hex - neofox.published_features.iedb_immunogenicity - - neofox.published_features.neoag - neofox.published_features.neoantigen_fitness - neofox.published_features.self_similarity - neofox.published_features.vaxrank @@ -104,13 +99,15 @@ test: about: home: "https://github.com/tron-bioinformatics/neofox" - license: "GNU General Public v3 (GPLv3)" + license: "GPL-3.0-or-later" license_family: GPL3 license_file: LICENSE summary: "Annotation of mutated peptide sequences (mps) with published or novel potential neo-epitope descriptors" doc_url: "https://neofox.readthedocs.io/" extra: + skip-lints: + - cython_must_be_in_host recipe-maintainers: - priesgo - franla23 From 4205d465a6e926d4d7de22aa1e8c5545da43b1c9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 19:07:48 -0500 Subject: [PATCH 1537/2173] Update polypolish to 0.6.0 (#45221) * Update polypolish to 0.6.0 * add run_exports * edit build.sh * edit tests --------- Co-authored-by: joshuazhuang7 --- recipes/polypolish/build.sh | 4 +--- recipes/polypolish/meta.yaml | 22 +++++++++++++++------- 2 files changed, 16 insertions(+), 10 deletions(-) diff --git a/recipes/polypolish/build.sh b/recipes/polypolish/build.sh index 8a376961d49d2..d70db500fe871 100644 --- a/recipes/polypolish/build.sh +++ b/recipes/polypolish/build.sh @@ -6,6 +6,4 @@ export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" # build statically linked binary with Rust RUST_BACKTRACE=1 -cargo install --verbose --path . --root $PREFIX -# Copy python scripts into bin dir -cp scripts/*.{py,pxd} $PREFIX/bin +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/polypolish/meta.yaml b/recipes/polypolish/meta.yaml index 112816c703f71..1fb18422206e1 100644 --- a/recipes/polypolish/meta.yaml +++ b/recipes/polypolish/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.0" %} +{% set version = "0.6.0" %} package: name: polypolish @@ -6,10 +6,12 @@ package: source: url: https://github.com/rrwick/Polypolish/archive/refs/tags/v{{ version }}.tar.gz - sha256: 183156093c03094290951f140010b3aef6222a672bf538e9136914178775fb1f + sha256: 99ea799352cecf6723b73fb4c5c64dd2091ff1cdab6eef10309e06c642e56855 build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage('polypolish', max_pin="x.x") }} requirements: build: @@ -25,12 +27,18 @@ requirements: test: commands: - - polypolish -h - - polypolish_insert_filter.py --help + - polypolish polish --help + - polypolish filter --help about: home: https://github.com/rrwick/Polypolish - license: GPLv3 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Polishing genome assemblies with short reads. + doc_url: https://github.com/rrwick/Polypolish/wiki + +extra: + identifiers: + - doi:10.1371/journal.pcbi.1009802 + - biotools:polypolish From af6b092800ae052c6d726e0dcc3bdd1b8eb1542d Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 15 Jan 2024 19:31:48 -0600 Subject: [PATCH 1538/2173] Update meme to 5.5.5 (#45238) * Update meme to 5.5.5 * add automake --- recipes/meme/build.sh | 9 ++++----- recipes/meme/meta.yaml | 6 ++++-- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/recipes/meme/build.sh b/recipes/meme/build.sh index 58e05134d1b50..d421c84749228 100644 --- a/recipes/meme/build.sh +++ b/recipes/meme/build.sh @@ -5,19 +5,17 @@ export MEME_ETC_DIR=${PREFIX}/etc #HOME=/tmp cpanm CGI::Application #HOME=/tmp cpanm XML::Parser::Expat --configure-args "EXPATLIBPATH=$PREFIX/lib" --configure-args "EXPATHINCPATH=$PREFIX/include" -autoconf -autoheader +autoreconf -i perl scripts/dependencies.pl ./configure CC="${CC}" \ - CFLAGS="-O3 -I${PREFIX}/include" \ + CFLAGS="${CFLAGS} -O3 -I${PREFIX}/include" \ LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \ --prefix="${PREFIX}" \ --enable-build-libxml2 \ --enable-build-libxslt -make clean make AM_CFLAGS='-DNAN="(0.0/0.0)"' -j4 # tests will only work inside the build dir, but @@ -27,8 +25,9 @@ make AM_CFLAGS='-DNAN="(0.0/0.0)"' -j4 # make test make install +make clean -ln -s ${PREFIX}/libexec/${PKG_NAME}-${PKG_VERSION}/* ${PREFIX}/bin/ +ln -sf ${PREFIX}/libexec/${PKG_NAME}-${PKG_VERSION}/* ${PREFIX}/bin/ # if building with python3, # modify meme-chip script to use python3 version of DREME diff --git a/recipes/meme/meta.yaml b/recipes/meme/meta.yaml index 11ef8b60c8a80..c2f07609794e0 100644 --- a/recipes/meme/meta.yaml +++ b/recipes/meme/meta.yaml @@ -1,6 +1,6 @@ {% set name = "MEME" %} -{% set version = "5.5.4" %} -{% set sha256 = "cda6011c2b855bf2563c4e7a2c255e11e99b5b6e5e73736ff008942507580153" %} +{% set version = "5.5.5" %} +{% set sha256 = "bebb4a176e72d62e3a2d5ba5f22439185bbc4bbf4769604fbca12dff8e1f739f" %} package: name: {{ name|lower }} @@ -21,6 +21,8 @@ requirements: - {{ compiler('c') }} - make - autoconf + - automake + - libtool host: - nodejs >=16.4.1 - openmpi From 8921bcccdd8077681ec75cc5e6af797b9fd00d58 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 15 Jan 2024 22:10:17 -0500 Subject: [PATCH 1539/2173] Update abpoa to 1.5.1 (#45241) --- recipes/abpoa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abpoa/meta.yaml b/recipes/abpoa/meta.yaml index 5490da5c89b38..a4fdf9234fc98 100644 --- a/recipes/abpoa/meta.yaml +++ b/recipes/abpoa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.5.0" %} +{% set version = "1.5.1" %} {% set program = "abpoa" %} {% set PROGRAM = "abPOA" %} @@ -8,7 +8,7 @@ package: source: url: https://github.com/yangao07/{{ PROGRAM }}/releases/download/v{{ version }}/{{ PROGRAM }}-v{{ version }}.tar.gz - sha256: 221e62c68e4cd728b85ab5f9864f7711f2102ff58c800c1477368cc83fee42d8 + sha256: f0e1b41b1c9e18ecd2096df9b60ad053260ec773d70eecb307b02cca0efab89d build: number: 0 From 3e82e8ccb46681e0b676264010f74103364a17ac Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 06:42:22 -0500 Subject: [PATCH 1540/2173] Update snakemake-interface-executor-plugins to 8.2.0 (#45244) --- recipes/snakemake-interface-executor-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-executor-plugins/meta.yaml b/recipes/snakemake-interface-executor-plugins/meta.yaml index 7972cf75a5c94..a52840165b3ea 100644 --- a/recipes/snakemake-interface-executor-plugins/meta.yaml +++ b/recipes/snakemake-interface-executor-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-executor-plugins" %} -{% set version = "8.1.3" %} +{% set version = "8.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_executor_plugins-{{ version }}.tar.gz - sha256: 1bafb4de9ab4bcbfb71de5ed66c6e3d2367d6e551426be21b0d293f15411ec1d + sha256: 4c74e3e1751bab6b266baf8688e854b8b4c5c5e10f5e34c581f42d69af4ff13b build: noarch: python From 15e6f032ad67d58ea5f5710996a6e621a6638cec Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 06:44:13 -0500 Subject: [PATCH 1541/2173] Update snakemake to 8.2.0 (#45243) --- recipes/snakemake/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 3a6dd2c52e5ce..cedec7fc176f7 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.1.3" %} +{% set version = "8.2.0" %} package: name: snakemake @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 58bccaa64f80f9332891d19aaa6544e6d11e508bb5c57d3512159888787a16a2 + sha256: 4226179d344152e046d5ceaa589f4a77c2b19af99976322ca2ede58a57942a63 build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_subpackage("snakemake", max_pin="x") }} From 82ba7d9ed04da2ad49a21aaffdfd539946649eee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 07:36:23 -0500 Subject: [PATCH 1542/2173] Update snakemake-interface-common to 1.15.1 (#45249) --- recipes/snakemake-interface-common/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 6e68562e29c2e..c5e119044e696 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.15.0" %} +{% set version = "1.15.1" %} package: name: {{ name|lower }} @@ -7,12 +7,12 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 58eb3c02d0e34fa1fd28c87218964d3ab65df6de3a0dab0f51fdce2c9179d8d0 + sha256: 5a779c7a0f27412bce26e1dfe4ccc712d04e0c0b9ceaa1640335a35d02509732 build: noarch: python script: {{ PYTHON }} -m pip install . -vvv - number: 1 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x") }} From ca0191803cae901a5747749ccf96d033a48c61cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 09:01:13 -0500 Subject: [PATCH 1543/2173] Update versionix to 0.2.4 (#45242) --- recipes/versionix/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/versionix/meta.yaml b/recipes/versionix/meta.yaml index eac216c2f4759..6e3ae36edb194 100644 --- a/recipes/versionix/meta.yaml +++ b/recipes/versionix/meta.yaml @@ -1,5 +1,5 @@ {% set name = "versionix" %} -{% set version = "0.2.3" %} +{% set version = "0.2.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/versionix-{{ version }}.tar.gz - sha256: b8a83f09615ffb233115d64cbb42a193a187f62ce9f8769d3900cfbcc2e085c1 + sha256: f78960fff3863d5bf02fa8b6e841a4350b5fa2f5ffff409a94083b66f729cf75 build: entry_points: From 6692856f8722809531f746b81673c610fc99387b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 10:33:49 -0500 Subject: [PATCH 1544/2173] Update chewbbaca to 3.3.2 (#45250) --- recipes/chewbbaca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index c54514c5a1e82..fae78e05f24ed 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -1,5 +1,5 @@ {% set name = 'chewBBACA' %} -{% set version = '3.3.1' %} +{% set version = '3.3.2' %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: e8abae869c60763670b2d53515188cd06ab4b48ef05e7387ba9849511c695f18 + sha256: 4e282320ce8b6b3b6e71d2db8961911c523d970f8b06e16c7c42b2aff0ae5f03 build: number: 0 From cff877061c98eb1bf2c453f921c2403ed85020bf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 13:14:36 -0500 Subject: [PATCH 1545/2173] Update lotus2 to 2.32 (#45254) * Update lotus2 to 2.32 * Fix lambda3 path in lOTUs.cfg --------- Co-authored-by: Nicola Soranzo --- recipes/lotus2/build.sh | 4 ++-- recipes/lotus2/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/lotus2/build.sh b/recipes/lotus2/build.sh index bd60e65cb0fa8..5b4edbec842fd 100644 --- a/recipes/lotus2/build.sh +++ b/recipes/lotus2/build.sh @@ -4,10 +4,10 @@ SHARE_DIR=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM rm -rf bin/installs/ bin/LCA bin/rtk bin/sdm bin/vsearch configs/sdm_src/ # Configure LotuS2 cp configs/LotuS.cfg.def lOTUs.cfg -for binary in blastn clustalo lambda LCA mafft minimap2 rtk sdm swarm vsearch; do +for binary in blastn clustalo lambda3 LCA mafft minimap2 rtk sdm swarm vsearch; do sed -i.bak -e "s|^$binary[[:space:]].*|$binary $PREFIX/bin/$binary|" lOTUs.cfg done -for binary in cd-hit fasttree hmmsearch iqtree itsx lambda_index makeBlastDB RDPjar; do +for binary in cd-hit fasttree hmmsearch iqtree itsx makeBlastDB RDPjar; do sed -i.bak -e "s|^$binary[[:space:]]\(.*\)|$binary $PREFIX/bin/\1|" lOTUs.cfg done # Install diff --git a/recipes/lotus2/meta.yaml b/recipes/lotus2/meta.yaml index 1b9451722cb34..5bf44952a4f59 100644 --- a/recipes/lotus2/meta.yaml +++ b/recipes/lotus2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "lotus2" %} -{% set version = "2.31" %} -{% set sha256 = "ee6eb9d31249077e5c0f9a5386b340d511a3a6826b5de8dcfad93c9980392970" %} +{% set version = "2.32" %} +{% set sha256 = "5c1c4e6e0cb6cd7277be6a163d184ea4dd30eac3b03b171deede8ce85509fb4e" %} package: name: {{ name }} From 2168dacfa4c6a8b6a95bf11ae03aa23a9cdafdda Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 13:21:11 -0500 Subject: [PATCH 1546/2173] Update snapatac2 to 2.5.3 (#45251) --- recipes/snapatac2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snapatac2/meta.yaml b/recipes/snapatac2/meta.yaml index 725e76a0f899f..26323292e6ebe 100644 --- a/recipes/snapatac2/meta.yaml +++ b/recipes/snapatac2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "snapatac2" %} -{% set version = "2.5.2" %} -{% set sha256 = "7d851340005b72881311ab712a435c2ac3864155be305ff24ccdcd7972c3d2c7" %} +{% set version = "2.5.3" %} +{% set sha256 = "14c4083a42fe79869528045dbbf84e4d997357907b51713620f9b63c11e20331" %} package: name: {{ name }} From 167eaae4d7ffcd853bd216e67c94600fc2139254 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 16:28:03 -0500 Subject: [PATCH 1547/2173] Update gtfparse to 2.4.0 (#45255) --- recipes/gtfparse/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gtfparse/meta.yaml b/recipes/gtfparse/meta.yaml index 410ae0b32eafa..585cf8ab8bc26 100644 --- a/recipes/gtfparse/meta.yaml +++ b/recipes/gtfparse/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gtfparse" %} -{% set version = "2.3.0" %} -{% set sha256 = "c2d74d6964d54d710e2d6264d47ca9e0a5288a781d47d3db08b4f6a5ee7e15f1" %} +{% set version = "2.4.0" %} +{% set sha256 = "607edb2b4fc37afa460e0575825a0ae54dc7d5808dd86b2196f6f27d77c4b47a" %} package: name: {{ name|lower }} From 05ec9bc35239a2bf10a1ad0dd7bcd08450997120 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 16:28:29 -0500 Subject: [PATCH 1548/2173] Update influx-si-data-manager to 1.0.0 (#45253) --- recipes/influx-si-data-manager/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/influx-si-data-manager/meta.yaml b/recipes/influx-si-data-manager/meta.yaml index ca2b9010333ef..dade7d4fe4c17 100644 --- a/recipes/influx-si-data-manager/meta.yaml +++ b/recipes/influx-si-data-manager/meta.yaml @@ -1,5 +1,5 @@ {% set name = "influx-si-data-manager" %} -{% set version = "0.1.4" %} +{% set version = "1.0.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/influx_si_data_manager-{{ version }}.tar.gz - sha256: 3d5e224166d4c85995a56e1f906548630e54066413f59651c9c6874800999c38 + sha256: 0cea604084022f74b0886a7ce088cd1966f29cc35b2854b33b62545bafe84eb9 build: entry_points: From 4344b045092c8e68aaba8c7cf5e7c2b1bfc8e5f1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 16:51:52 -0500 Subject: [PATCH 1549/2173] Update snakemake-executor-plugin-slurm-jobstep to 0.1.10 (#45246) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake-executor-plugin-slurm-jobstep to 0.1.10 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml b/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml index f9e5feae2616e..0674423f6262c 100644 --- a/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm-jobstep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm-jobstep" %} -{% set version = "0.1.9" %} +{% set version = "0.1.10" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm_jobstep-{{ version }}.tar.gz - sha256: 98580067acb9a90ac1cfafda88237155f128d52774e6aa0f41adbd93440c9746 + sha256: 321b6bdf7883a8fb40ff4aeeb88633502e4db8394e40b6628db41a430c2eae2b build: noarch: python @@ -24,7 +24,7 @@ requirements: run: - python >=3.11.0,<4.0.0 - snakemake-interface-common >=1.13.0,<2.0.0 - - snakemake-interface-executor-plugins >=8.0.2,<9.0.0 + - snakemake-interface-executor-plugins >=8.2.0,<9.0.0 test: imports: From 437c82475da8e786a5ec5edb9cf3d30186286fcb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 16:52:12 -0500 Subject: [PATCH 1550/2173] Update snakemake-storage-plugin-ftp to 0.1.2 (#45247) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake-storage-plugin-ftp to 0.1.2 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake-storage-plugin-ftp/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-storage-plugin-ftp/meta.yaml b/recipes/snakemake-storage-plugin-ftp/meta.yaml index 48183cbe50141..2cb90d57b7c10 100644 --- a/recipes/snakemake-storage-plugin-ftp/meta.yaml +++ b/recipes/snakemake-storage-plugin-ftp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-ftp" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_ftp-{{ version }}.tar.gz - sha256: 9daf4d0eee152f776848b4787dcaf1a3bc34785caabafe2273b3d13e5bd2119c + sha256: e3097e19dbe9ed4c8cf794e1d4594c3032ee7f7a9f7797dfb0d2556f0aafe07c build: noarch: python @@ -23,7 +23,7 @@ requirements: - pip run: - python >=3.11.0,<4.0.0 - - snakemake-interface-common >=1.15.0,<2.0.0 + - snakemake-interface-common >=1.15.1,<2.0.0 - snakemake-interface-storage-plugins >=3.0.0,<4.0.0 - ftputil >=5.0.4,<6.0.0 From 51dafd1074e425657bfd3c1849dd2481d73cef0d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 17:43:53 -0500 Subject: [PATCH 1551/2173] Update pyensembl to 2.3.6 (#45257) --- recipes/pyensembl/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyensembl/meta.yaml b/recipes/pyensembl/meta.yaml index 1b7955c7189c3..9693ad2d94240 100644 --- a/recipes/pyensembl/meta.yaml +++ b/recipes/pyensembl/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PyEnsembl" %} -{% set version = "2.3.4" %} -{% set sha256 = "e0052ab1f769d451cbc71b0d5be5d0443be2bd0d7e41efb802dd4357462bf09c" %} +{% set version = "2.3.6" %} +{% set sha256 = "206981651d926d455ee85fa813fefb0d6e8bd29983821aef1136df28337b8597" %} package: name: {{ name|lower }} From d80159fb950edbbd92aba9ce96f61e492d8d42eb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 18:08:00 -0500 Subject: [PATCH 1552/2173] Update gtfparse to 2.4.1 (#45258) --- recipes/gtfparse/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gtfparse/meta.yaml b/recipes/gtfparse/meta.yaml index 585cf8ab8bc26..e67367f8fe766 100644 --- a/recipes/gtfparse/meta.yaml +++ b/recipes/gtfparse/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gtfparse" %} -{% set version = "2.4.0" %} -{% set sha256 = "607edb2b4fc37afa460e0575825a0ae54dc7d5808dd86b2196f6f27d77c4b47a" %} +{% set version = "2.4.1" %} +{% set sha256 = "dbb6dd88bc5535b1d6ca8fab3154f3408c9b67d7215bbc1762d8f855919cc8a5" %} package: name: {{ name|lower }} From f10eb4b6164e3b59be32683e48b22f6392c13c28 Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Wed, 17 Jan 2024 00:11:37 +0100 Subject: [PATCH 1553/2173] Update nextclade to 3.0.0 (#45259) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index 9b1edcb0d60bf..1a01d3d0d15c5 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "2.14.0" %} +{% set version = "3.0.0" %} package: name: "{{ name|lower }}" @@ -7,14 +7,14 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: 1a9a82655830243ffd01937ebb895744ff46ec49f725ef6feff9a3f0e37d90d1 # [linux64] + sha256: b5f40f1ef809ad17bdb1fe31661b965c861115325ea2d73beadc86550ffccf16 # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: 432f56d2152edda49b8c4a2c3f81d9a5da7419a6cc7c4a3d5205d17d5f834cf6 # [osx and x86_64] + sha256: a5763a28d4b1da627aac358156923650b3ea21dae1b1c3bbfb5f5e617c2ed3a4 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: aaac669618d953381428eac3674fe6cb22bef66e7c1ae55552f6a1567f3d3030 # [arm64] + sha256: ce156efb5f5a9ead01ac140d6f701f4b780b224cc64c27cb15a4dcfd13dbdc7a # [arm64] build: - number: 2 + number: 0 binary_relocation: False run_exports: - {{ pin_compatible(name, max_pin='x') }} From 85804cc3d959eca638fec0bcff2bc0ec97175359 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 23:55:35 -0500 Subject: [PATCH 1554/2173] Update dxpy to 0.368.1 (#45256) * Update dxpy to 0.368.1 * bump python requirement * pin python to <=3.11.7 * bump websocket-client version * edit meta.yaml --------- Co-authored-by: mencian --- recipes/dxpy/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index cd113ae146441..2f93229ada451 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.367.0" %} +{% set version = "0.368.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 21491f943b3cd1aeb5d0ad33b8f5e269653c43f23ce796b129c93599204d7caa + sha256: e8fd366edfbe7c9ffd86be14e89d1a0086843442807bea3c404146ca7e96de62 build: number: 0 @@ -17,9 +17,9 @@ build: - dx-build-app = dxpy.scripts.dx_build_app:main - dx = dxpy.scripts.dx:main - dx-app-wizard = dxpy.scripts.dx_app_wizard:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" run_exports: - - {{ pin_subpackage('dxpy', max_pin="x") }} + - {{ pin_subpackage('dxpy', max_pin="x.x") }} requirements: host: @@ -27,12 +27,14 @@ requirements: - pip run: - argcomplete >=1.9.4 + - certifi - cryptography >=3.4.2,<37 - psutil >=3.3.0 - python - python-dateutil >=2.5 - requests >=2.8.0,<2.27.1 - - websocket-client ==0.53.0 + - urllib3 >=1.25,<2.2 + - websocket-client ==0.54.0 - pandas >=1.3.5 test: From eecc0a73303b7307e6a50536366032ce07a97d8d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 16 Jan 2024 23:55:45 -0500 Subject: [PATCH 1555/2173] Update aci to 1.4.20240116 (#45260) * Update aci to 1.4.20240116 * bump python requirement --------- Co-authored-by: mencian --- recipes/aci/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/aci/meta.yaml b/recipes/aci/meta.yaml index 92a18bd603fcd..8e8f688c489d8 100644 --- a/recipes/aci/meta.yaml +++ b/recipes/aci/meta.yaml @@ -1,6 +1,6 @@ {% set name = "aci" %} {% set repo = "amplicon_coverage_inspector" %} -{% set version = "1.2.20231229" %} +{% set version = "1.4.20240116" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ repo[0] }}/{{ repo }}/{{ repo }}-{{ version }}.tar.gz - sha256: f54b1829a8eb1972751fce0b5d6a7d48a62d9cc80935a609302779a9966f104d + sha256: 06cf71bde19ecb8ac760c14548b3cdb24f99755da36d53daeea62cf053f5b12c build: number: 0 @@ -21,10 +21,10 @@ build: requirements: host: - - python >=3.7,<4.0 + - python >=3.8,<4.0 - pip run: - - python >=3.7,<4.0 + - python >=3.8,<4.0 - matplotlib-base >=3.8.2 - numpy >=1.26.2 - pandas >=2.1.4 From f45c4e00b40c5b7fbb588b37201dc8d16553ae06 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 03:04:27 -0500 Subject: [PATCH 1556/2173] Update snakemake-executor-plugin-slurm to 0.2.1 (#45248) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake-executor-plugin-slurm to 0.2.1 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 38b2c9922ffa1..a7cdccccdb508 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 161e965a79151274c3835866070bd48483655c4c2efda4e56a54f60af61fddbb + sha256: dd484fcb136612a3f2bdcccf15ca4ebffc2f5fcdfa7f1fcc14416dd272812999 build: noarch: python @@ -24,8 +24,8 @@ requirements: run: - python >=3.11.0,<4.0.0 - snakemake-interface-common >=1.13.0,<2.0.0 - - snakemake-interface-executor-plugins >=8.0.2,<9.0.0 - - snakemake-executor-plugin-slurm-jobstep >=0.1.5,<0.2.0 + - snakemake-interface-executor-plugins >=8.2.0,<9.0.0 + - snakemake-executor-plugin-slurm-jobstep >=0.1.10,<0.2.0 - throttler >=1.2.2,<2.0.0 test: From 2b687c2caa071f7437b30dab1c96b407784ceed5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 17 Jan 2024 09:51:11 +0100 Subject: [PATCH 1557/2173] Update meta.yaml From 9c548161c39aa9992f84458c189ad352b6a99f79 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 09:08:22 -0500 Subject: [PATCH 1558/2173] Update bowtie2 to 2.5.3 (#45261) --- recipes/bowtie2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bowtie2/meta.yaml b/recipes/bowtie2/meta.yaml index 0d332684fac38..ece3f06a3d3f0 100644 --- a/recipes/bowtie2/meta.yaml +++ b/recipes/bowtie2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.2" %} +{% set version = "2.5.3" %} package: name: bowtie2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/BenLangmead/bowtie2/archive/v{{ version }}.tar.gz - sha256: 2f86dbfbf3dcb8521d559f830594fe28ac6e4c40d81313a8c2bfb17c82a501e0 + sha256: 4ac3ece3db011322caab14678b9d80cfc7f75208cdaf0c58b24a6ea0f1a0a60e build: number: 0 From 7ae0e89fb071469848d31193e1a2723f43d68528 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Wed, 17 Jan 2024 17:16:32 +0100 Subject: [PATCH 1559/2173] Update raptor (#45270) --- recipes/raptor/meta.yaml | 2 +- recipes/raptor/raptor | 11 ++++++----- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/raptor/meta.yaml b/recipes/raptor/meta.yaml index 0b38ef4ed151c..cf815b6a65db9 100644 --- a/recipes/raptor/meta.yaml +++ b/recipes/raptor/meta.yaml @@ -10,7 +10,7 @@ source: sha256: be44e7b2635e110c940cf40ff132956200551a2e25765d9f057e844f7a3ccebb build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/raptor/raptor b/recipes/raptor/raptor index 180b5b084c99f..107b82cc749f2 100644 --- a/recipes/raptor/raptor +++ b/recipes/raptor/raptor @@ -6,11 +6,12 @@ set -eu # -m 1 : stop after first match, i.e. count is either 0 or 1 # -E : use extended regular expressions # \b : matches any non alphanumeric character, i.e. space, tab, newline, etc. -HAS_SSE2=$(grep -c -m 1 -E '\bsse2\b' /proc/cpuinfo) -HAS_SSE4_2=$(grep -c -m 1 -E '\bsse4_2\b' /proc/cpuinfo) -HAS_AVX2=$(grep -c -m 1 -E '\bavx2\b' /proc/cpuinfo) -HAS_AVX512F=$(grep -c -m 1 -E '\bavx512f\b' /proc/cpuinfo) -HAS_AVX512BW=$(grep -c -m 1 -E '\bavx512bw\b' /proc/cpuinfo) +# || true: ignore `grep -c` returning a non-zero exit code (behavior depends on OS) +HAS_SSE2=$(grep -c -m 1 -E '\bsse2\b' /proc/cpuinfo || true) +HAS_SSE4_2=$(grep -c -m 1 -E '\bsse4_2\b' /proc/cpuinfo || true) +HAS_AVX2=$(grep -c -m 1 -E '\bavx2\b' /proc/cpuinfo || true) +HAS_AVX512F=$(grep -c -m 1 -E '\bavx512f\b' /proc/cpuinfo || true) +HAS_AVX512BW=$(grep -c -m 1 -E '\bavx512bw\b' /proc/cpuinfo || true) if [ ${HAS_AVX512F} -eq 1 ] && [ ${HAS_AVX512BW} -eq 1 ]; then HAS_AVX512=1 else From 0aba0f31071c93cb5c8165687aa91ec3b9865647 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 17 Jan 2024 10:31:28 -0600 Subject: [PATCH 1560/2173] Add recipe for MAEGATK v0.2.0 (#45272) * Add recipe for MAEGATK v0.2.0 * edit entry_points and tests --- recipes/maegatk/meta.yaml | 63 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 recipes/maegatk/meta.yaml diff --git a/recipes/maegatk/meta.yaml b/recipes/maegatk/meta.yaml new file mode 100644 index 0000000000000..6e622c1497f78 --- /dev/null +++ b/recipes/maegatk/meta.yaml @@ -0,0 +1,63 @@ +{% set name = "maegatk" %} +{% set version = "0.2.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/maegatk-{{ version }}.tar.gz + sha256: fce1ec287914e03ce2b317a4f6a338f1806cd82e5c77f4e4cb1efbd48c87bdda + +build: + number: 0 + noarch: python + entry_points: + - maegatk = maegatk.cli:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('maegatk', max_pin="x.x") }} + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - click + - pysam + - pytest + - snakemake-minimal + - biopython + - optparse-pretty + - regex + - ruamel.yaml + - openjdk + - fgbio + - bwa + - samtools + - freebayes + - r-base + - r-dplyr + - r-data.table + - r-matrix + - bioconductor-genomicranges + - bioconductor-summarizedexperiment + +test: + imports: + - maegatk + commands: + - maegatk --help + +about: + home: https://github.com/caleblareau/maegatk + summary: Mitochondrial Alteration Enrichment and Genome Analysis Toolkit + license: MIT + license_family: MIT + license_file: LICENSE.txt + description: Processing and quality control of mitochondrial genome variants from MAESTER data. + +extra: + recipe-maintainers: + - mencian From d309b9e949e2a47387109e8b9a31409fa98494bd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 11:31:40 -0500 Subject: [PATCH 1561/2173] Update matchms to 0.24.1 (#45267) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/matchms/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 20b110efe079c..9cb15af6297b8 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.24.0" %} +{% set version = "0.24.1" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e62b1591782b01c3ef83850245609d85e3d612a7f7c350b4fc2ad067d8bc9d15 + sha256: 8cb7098f0e5149c3ab5ad7b39789472b35e12f7668a79c12a3c58e51b50c255c build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps -vvv" noarch: python run_exports: From 55e4eeed1eb4a297acf1516a5467ea7bc1e9afc9 Mon Sep 17 00:00:00 2001 From: Jacob Morrison Date: Wed, 17 Jan 2024 12:44:22 -0500 Subject: [PATCH 1562/2173] Update to biscuit version 1.4.0 (#45118) * remove unused file * patch file no longer needed * update to biscuit v1.4.0 * correct pthread requirement name * modify sgsl and utils Makefiles in build * add CC to make call * try finding zlib * try C_INCLUDE_PATH * edit build.sh * revert to CPATH * try make * edit tests * try adding perl to host for testing * add shebang via sed for asset builder --------- Co-authored-by: mencian --- recipes/biscuit/build.sh | 21 ++++++++----- recipes/biscuit/meta.yaml | 24 +++++++-------- recipes/biscuit/patch | 64 --------------------------------------- recipes/biscuit/script.sh | 1 - 4 files changed, 26 insertions(+), 84 deletions(-) delete mode 100644 recipes/biscuit/patch delete mode 100644 recipes/biscuit/script.sh diff --git a/recipes/biscuit/build.sh b/recipes/biscuit/build.sh index b69c7a1e293f1..f19d32dd1e12f 100644 --- a/recipes/biscuit/build.sh +++ b/recipes/biscuit/build.sh @@ -1,9 +1,16 @@ #!/bin/bash -BIN=$PREFIX/bin -mkdir -p $BIN -make CC="$CC $LDFLAGS" CFLAGS="$CFLAGS" -cp biscuit $BIN -cp QC.sh $BIN -cp build_biscuit_QC_assets.pl $BIN -sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $BIN/build_biscuit_QC_assets.pl +# Needed for building utils dependency +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -pthread -L${PREFIX}/lib" + +mkdir -p "${PREFIX}/bin" +mkdir -p build +cd build || exit 1 +cmake -DCMAKE_INSTALL_PREFIX:PATH="${PREFIX}" .. +make CC="${CC} ${LDFLAGS}" CFLAGS="${CFLAGS} -O3" +make install + +# Needed to run asset builder +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/build_biscuit_QC_assets.pl diff --git a/recipes/biscuit/meta.yaml b/recipes/biscuit/meta.yaml index 380b874c46af9..39e7a090e8671 100644 --- a/recipes/biscuit/meta.yaml +++ b/recipes/biscuit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.0.20231027" %} +{% set version = "1.4.0.20240108" %} package: name: biscuit @@ -11,36 +11,36 @@ build: source: - url: https://github.com/huishenlab/biscuit/releases/download/v{{ version }}/release-source.zip - sha256: 027d4343a49fde7c497f4a0292a2cb5bb475b4bcacedb17f251680dbf4f56995 - patches: - - patch - - url: https://github.com/huishenlab/biscuit/releases/download/v{{ version }}/QC.sh - sha256: f2b9237f1166681a5f4e2cb0b297b2c2a086ea4975948a292b4871e391244b13 - - url: https://github.com/huishenlab/biscuit/releases/download/v{{ version }}/build_biscuit_QC_assets.pl - sha256: 7967240b63c8f816e7da79c3c0eb890933ec47df1114f6893b9e9736c8e564a8 + sha256: 58625f286a4bda4a3884feb10be575e4cb205f09b9ddb1075d099ca2259c1c17 requirements: build: - make + - cmake - {{ compiler('c') }} host: - zlib - ncurses + - pthread-stubs - libcurl run: - zlib - ncurses + - pthread-stubs - libcurl - perl test: commands: - - biscuit 2>&1 || true - - QC.sh -h 2>&1 | grep Usage - - build_biscuit_QC_assets.pl -h 2>&1 | grep Usage + - biscuit 2>&1 | grep "Usage" + - QC.sh -h 2>&1 | grep "Usage" + - build_biscuit_QC_assets.pl -h 2>&1 | grep "Usage" about: home: https://github.com/huishenlab/biscuit license: MIT + license_family: MIT + license_file: LICENSE summary: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data - + dev_url: https://github.com/huishenlab/biscuit + doc_url: https://huishenlab.github.io/biscuit/ diff --git a/recipes/biscuit/patch b/recipes/biscuit/patch deleted file mode 100644 index 2ef00a4400ab0..0000000000000 --- a/recipes/biscuit/patch +++ /dev/null @@ -1,64 +0,0 @@ -diff --git a/Makefile b/Makefile -index d54b6c2..8ee48a2 100644 ---- a/Makefile -+++ b/Makefile -@@ -1,5 +1,5 @@ --CC = gcc --CFLAGS = -W -Wall -finline-functions -fPIC -std=gnu99 -Wno-unused-result -O3 -+CC ?= gcc -+CFLAGS ?= -W -Wall -finline-functions -fPIC -std=gnu99 -Wno-unused-result -O3 - CLIB = -lncurses -lpthread -lz -lm - CF_OPTIMIZE = 1 - -diff --git a/lib/htslib/Makefile b/lib/htslib/Makefile -index 9c4ce60..c6722fd 100644 ---- a/lib/htslib/Makefile -+++ b/lib/htslib/Makefile -@@ -22,7 +22,7 @@ - # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - # DEALINGS IN THE SOFTWARE. - --CC = gcc -+CC ?= gcc - AR = ar - RANLIB = ranlib - -diff --git a/lib/klib/Makefile b/lib/klib/Makefile -index 15ad2fc..aebbf64 100644 ---- a/lib/klib/Makefile -+++ b/lib/klib/Makefile -@@ -1,4 +1,4 @@ --CC = gcc -+CC ?= gcc - AR = ar - CFLAGS = -g -Wall - -diff --git a/lib/sgsl/Makefile b/lib/sgsl/Makefile -index c939453..bc5fd6e 100644 ---- a/lib/sgsl/Makefile -+++ b/lib/sgsl/Makefile -@@ -1,4 +1,4 @@ --CC = gcc -+CC ?= gcc - AR = ar - CFLAGS = -g -Wall - # -std=gnu11 travis complains about this -@@ -25,7 +25,7 @@ libgsl.a: $(OBJECTS) - $(AR) -csr $@ $^ - - test: libgsl.a -- gcc -I. test/test.c libgsl.a -std=c99 -lm -o test-main -+ $(CC) -I. test/test.c libgsl.a -std=c99 -lm -o test-main - - clean: - rm -f $(OBJECTS) -diff --git a/lib/utils/Makefile b/lib/utils/Makefile -index 9c7f457..3b0cfef 100644 ---- a/lib/utils/Makefile -+++ b/lib/utils/Makefile -@@ -1,4 +1,4 @@ --CC = gcc -+CC ?= gcc - AR = ar - CFLAGS = -g -Wall - diff --git a/recipes/biscuit/script.sh b/recipes/biscuit/script.sh deleted file mode 100644 index 80e0ff397a83b..0000000000000 --- a/recipes/biscuit/script.sh +++ /dev/null @@ -1 +0,0 @@ -echo efrat From 963d9980f499f23bf4fabc6c7703863ae132db43 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 12:44:54 -0500 Subject: [PATCH 1563/2173] Update gtfparse to 2.5.0 (#45262) --- recipes/gtfparse/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gtfparse/meta.yaml b/recipes/gtfparse/meta.yaml index e67367f8fe766..41e4bd86031e9 100644 --- a/recipes/gtfparse/meta.yaml +++ b/recipes/gtfparse/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gtfparse" %} -{% set version = "2.4.1" %} -{% set sha256 = "dbb6dd88bc5535b1d6ca8fab3154f3408c9b67d7215bbc1762d8f855919cc8a5" %} +{% set version = "2.5.0" %} +{% set sha256 = "9fea54811cd87f597a110a49dc1b1b6a3325ffb7d1f36ecc62c32d14d3eb9493" %} package: name: {{ name|lower }} From 8ee63047ac14c58e09aeed615db4f0939b2638b4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 12:45:03 -0500 Subject: [PATCH 1564/2173] Update pyensembl to 2.3.9 (#45263) * Update pyensembl to 2.3.7 * Update pyensembl to 2.3.9 --- recipes/pyensembl/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyensembl/meta.yaml b/recipes/pyensembl/meta.yaml index 9693ad2d94240..cb30778055db9 100644 --- a/recipes/pyensembl/meta.yaml +++ b/recipes/pyensembl/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PyEnsembl" %} -{% set version = "2.3.6" %} -{% set sha256 = "206981651d926d455ee85fa813fefb0d6e8bd29983821aef1136df28337b8597" %} +{% set version = "2.3.9" %} +{% set sha256 = "444c4f489818fd639c34a631a9527cd6bb6586bf20b58daffe1b79d1d1ef86f4" %} package: name: {{ name|lower }} From ee7e7a08f48155bc99613d5065b2dc851c26a26e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 12:45:34 -0500 Subject: [PATCH 1565/2173] Update peaks2utr to 1.2.5 (#45271) --- recipes/peaks2utr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/peaks2utr/meta.yaml b/recipes/peaks2utr/meta.yaml index b0f5d08d094ca..03cb588cdd03b 100644 --- a/recipes/peaks2utr/meta.yaml +++ b/recipes/peaks2utr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "peaks2utr" %} -{% set version = "1.2.4" %} +{% set version = "1.2.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/peaks2utr-{{ version }}.tar.gz - sha256: 9fb91c2361e8de95994f1de7bf8414710777ecd52b23d35628270f0bb2e2412e + sha256: d24ed841692059e237800cceca00adb4f17638c6751b214d4146ca0fe26cf97e build: number: 0 From b163ae6db10e35befe281a5bc624acfea4be4a1e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 15:51:41 -0500 Subject: [PATCH 1566/2173] Update pbstarphase to 0.8.1 (#45278) --- recipes/pbstarphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbstarphase/meta.yaml b/recipes/pbstarphase/meta.yaml index 9b43d0bc72b8f..1416f4902aaa7 100644 --- a/recipes/pbstarphase/meta.yaml +++ b/recipes/pbstarphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbstarphase" %} -{% set version = "0.8.0" %} -{% set sha256 = "df207d5aa29f0e0088dff838403664ca624f71d1f6c176374f2354234b74850e" %} +{% set version = "0.8.1" %} +{% set sha256 = "cea59d70ebefe3660e90b566944e5c2928ce5a1107916199f5700b1117cc85ee" %} package: name: {{ name }} From d6475487b27f855e3d043a3bfff8d3a465c9a4eb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 15:52:14 -0500 Subject: [PATCH 1567/2173] Update snakemake to 8.2.1 (#45279) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index cedec7fc176f7..1904589e0671a 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.2.0" %} +{% set version = "8.2.1" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 4226179d344152e046d5ceaa589f4a77c2b19af99976322ca2ede58a57942a63 + sha256: f177ada98188a10602aa2ed758fc9b7ff13e7107c5e582463ae681c525c28f0c build: number: 0 From 48ca251538038b946244aa5c93b5cdf386ab6e7d Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Wed, 17 Jan 2024 16:18:09 -0600 Subject: [PATCH 1568/2173] Update HTSeq version (#45273) * Update HTSeq version * Change url for osx build * Remove extra url line * Add wheel * Try pypi link for osx * Update url --------- Co-authored-by: Natasha Pavlovikj --- recipes/htseq/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/htseq/meta.yaml b/recipes/htseq/meta.yaml index a68cff9aff26b..2d524cc2a529a 100644 --- a/recipes/htseq/meta.yaml +++ b/recipes/htseq/meta.yaml @@ -1,17 +1,18 @@ -{% set version = '2.0.4' %} +{% set name = "HTSeq" %} +{% set version = "2.0.5" %} +{% set sha256 = "2519675246dd1639115a76c9aacf19ab5bc5bed2f3598bf89cd97be5c0d066b3" %} package: - name: htseq + name: {{ name|lower }} version: {{ version }} source: - url: https://files.pythonhosted.org/packages/ed/ca/6f1e2f556cb2aad34ea8481f41a5a16dc52bef2e4fa55e7107b0b8e6bfe5/HTSeq-{{ version }}.tar.gz - sha256: 5510d855617d61efff2287af4cdc60a73e94bd735e44c15b57f189ea0634e6e0 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: {{ sha256 }} build: number: 0 - skip: True # [py2k or py == 36] - script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation run_exports: - {{ pin_subpackage('htseq', max_pin="x") }} @@ -25,6 +26,7 @@ requirements: - pip - cython - numpy + - wheel - pysam >=0.15.1 - swig >=3.0.8 run: @@ -32,6 +34,8 @@ requirements: - {{ pin_compatible('numpy') }} - matplotlib-base >=1.4 - pysam >=0.15.1 + - scipy >=1.5.0 + - pandas >=1.1.0 test: # Python imports From 0a08aacff22fc0c77448d781ffbf03d654e02eb4 Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Wed, 17 Jan 2024 14:32:52 -0800 Subject: [PATCH 1569/2173] Add tntblast (thermonucleotideBLAST) (#45186) * Add tntblast * Add run_exports * move run_exports to correct location * Remove extra url * Add openmp, use g++ * use CXX_FOR_BUILD * Filter out USE_MPI flag * Add zlib * unsed BLAST_DIR * Add LIBS when compiling cpp files * Revert adding LIBS * zlib check * adjust variables * Try CXX instead of CC * Add true to test, to force exit code 0 * Add quotes to test definition * Try removing quotes from grep cmd in test * Add dummy test * Create bin dir before copying * Remove dummy test * Limit openmp to linux --------- Co-authored-by: Thanh Lee Co-authored-by: Robert A. Petit III --- recipes/tntblast/build.sh | 16 +++++++++++++ recipes/tntblast/meta.yaml | 48 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 recipes/tntblast/build.sh create mode 100644 recipes/tntblast/meta.yaml diff --git a/recipes/tntblast/build.sh b/recipes/tntblast/build.sh new file mode 100644 index 0000000000000..9faf1b0cc953d --- /dev/null +++ b/recipes/tntblast/build.sh @@ -0,0 +1,16 @@ +#!/bin/bash + +sed -i.bak 's/-DUSE_MPI//g' Makefile +sed -i.bak '/BLAST_DIR =/d' Makefile + +export INCLUDE_PATH="${BUILD_PREFIX}/include" +export LIBRARY_PATH="${BUILD_PREFIX}/lib" +export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BUILD_PREFIX}/lib" + +export LDFLAGS="-lm -lz -L${BUILD_PREFIX}/lib" +export CPPFLAGS="-I${BUILD_PREFIX}/include" + +make CC="${CXX}" INC="${CPPFLAGS}" LIBS="${LDFLAGS}" all + +mkdir -p $PREFIX/bin +cp tntblast $PREFIX/bin diff --git a/recipes/tntblast/meta.yaml b/recipes/tntblast/meta.yaml new file mode 100644 index 0000000000000..1879071879028 --- /dev/null +++ b/recipes/tntblast/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "tntblast" %} +{% set version = "2.61" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage( name|lower, max_pin="x") }} + +source: + url: https://github.com/jgans/thermonucleotideBLAST/archive/refs/tags/v{{ version }}.tar.gz + sha256: c2c8862ea772e7a655183b037995d02f319a04e3b359b447069b5f8fc0d11ec4 + +requirements: + build: + - make + - {{ compiler('cxx') }} + - openmp #[linux] + - llvm-openmp #[osx] + - zlib + host: + - openmp #[linux] + - llvm-openmp #[osx] + - zlib + run: + - openmp #[linux] + - llvm-openmp #[osx] + - zlib + +test: + commands: + - '{ tntblast 2>&1 || true; } | grep v.{{ version }}' + +about: + home: https://github.com/jgans/thermonucleotideBLAST + license: BSD License + license_file: LICENSE + license_family: BSD + summary: Searching DNA/RNA sequence databases with PCR and/or probe queries + dev_url: https://github.com/jgans/thermonucleotideBLAST + doc_url: https://github.com/jgans/thermonucleotideBLAST#readme + +extra: + identifiers: + - doi:10.1093/nar/gkn301 From 6612961bd3965cbe138b0244068cbb2c36aba8ad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 18:53:17 -0500 Subject: [PATCH 1570/2173] Update pypolca to 0.3.0 (#45268) --- recipes/pypolca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pypolca/meta.yaml b/recipes/pypolca/meta.yaml index 6981ef124abde..84b6e54e58dca 100644 --- a/recipes/pypolca/meta.yaml +++ b/recipes/pypolca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pypolca" %} -{% set version = "0.2.1" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 104f9a794d21f36454eb8e89ef317bd086d452a7fc1d4e2433b1afaa8d649c5c + sha256: 8f65a6f010a65ced2f0e470d6f1ae9703236fece666674afe76cfb4475bfa440 build: number: 0 From 7b180ba5d1ea088ac15d62ff9b29b10df37642e7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 17 Jan 2024 18:53:40 -0500 Subject: [PATCH 1571/2173] Update pharokka to 1.6.1 (#45264) --- recipes/pharokka/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pharokka/meta.yaml b/recipes/pharokka/meta.yaml index f4cc32edee438..fad8abba9cbc1 100644 --- a/recipes/pharokka/meta.yaml +++ b/recipes/pharokka/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.6.0" %} +{% set version = "1.6.1" %} {% set name = "pharokka" %} -{% set sha256 = "67a6459e1d7a3e22801a3eba0149056fcf9b3e61ea614d55893fdaa0cca7f5be" %} +{% set sha256 = "b172d91d182bc0d25610bd6241c489e3efd947c2f4bdc4204cc5bf2b07a55afd" %} {% set user = "gbouras13" %} package: From 4b7350d0f6830136955520d64afc5488ada26820 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:14:39 -0500 Subject: [PATCH 1572/2173] Update itolapi to 4.1.3 (#45265) --- recipes/itolapi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/itolapi/meta.yaml b/recipes/itolapi/meta.yaml index 89d85e715441f..14938580238b2 100644 --- a/recipes/itolapi/meta.yaml +++ b/recipes/itolapi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "itolapi" %} -{% set version = "4.1.2" %} +{% set version = "4.1.3" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 37a866a117a80d3d72a6eb6b2cba30444751c644cc6bc4242f050750375a8397 + sha256: b4f683630e4c816529b79a326de515809ad6174e473b6a25bc3954aaadd16778 build: noarch: python From c2d7a8a3172a3537cf9633be30cb4d6007a9fe89 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:15:24 -0500 Subject: [PATCH 1573/2173] Update recentrifuge to 1.13.2 (#45269) --- recipes/recentrifuge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/recentrifuge/meta.yaml b/recipes/recentrifuge/meta.yaml index 2490ce7708084..8f89c36bb4498 100644 --- a/recipes/recentrifuge/meta.yaml +++ b/recipes/recentrifuge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "recentrifuge" %} -{% set version = "1.13.1" %} +{% set version = "1.13.2" %} package: name: {{ name }} @@ -14,7 +14,7 @@ build: source: url: https://github.com/khyox/{{ name }}/archive/v{{ version }}.tar.gz - sha256: a8c3826302c7a39fe0735176b49fc635964b83d5cc110fc3139c83783c27984d + sha256: 548cfe12d075e3d9e9c01e380891acc5278eae20e075818d7863136e7cf20b81 requirements: host: From 73bf15d31d2733b3db33a63b7c66d315d604765b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:16:15 -0500 Subject: [PATCH 1574/2173] Update synapseclient to 4.0.0 (#45275) --- recipes/synapseclient/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/synapseclient/meta.yaml b/recipes/synapseclient/meta.yaml index 3b475ae73277e..58be08dcd1ec8 100644 --- a/recipes/synapseclient/meta.yaml +++ b/recipes/synapseclient/meta.yaml @@ -1,5 +1,5 @@ {% set name = "synapseclient" %} -{% set version = "3.2.0" %} +{% set version = "4.0.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/synapseclient-{{ version }}.tar.gz - sha256: 87c91f03dbca7074efd18144325df07db24e07ea92e0b7c8691aaec46c28329a + sha256: 9b1acfa4fc9d76c3d69fab3a362e80a4f3cb8dbd60cea0dd6ab34fbb120a9b34 build: noarch: python From 64cc14d8319e962e7099b45da01d6c9ab3f28bb2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:20:31 -0500 Subject: [PATCH 1575/2173] Update hybracter to 0.6.0 (#45286) --- recipes/hybracter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml index 8e85a27f1af6e..aca31cdfc5401 100644 --- a/recipes/hybracter/meta.yaml +++ b/recipes/hybracter/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybracter" %} -{% set version = "0.5.0" %} +{% set version = "0.6.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz - sha256: 6bdc2376e0000556622b957e765f27014972784700f306943b345956739d4592 + sha256: 2d7d79818f6b896e47c0ad4c4e4583d2028019a2d43c5aa502762c4a22cbacd1 build: number: 0 From 194def659dbea86b8e076bc0e6cbf07c3dee7e20 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:29:58 -0500 Subject: [PATCH 1576/2173] Update abromics_galaxy_json_extractor to 0.8.3.4 (#45288) --- recipes/abromics_galaxy_json_extractor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/abromics_galaxy_json_extractor/meta.yaml b/recipes/abromics_galaxy_json_extractor/meta.yaml index 9b20f38f812b2..ab4d067298934 100644 --- a/recipes/abromics_galaxy_json_extractor/meta.yaml +++ b/recipes/abromics_galaxy_json_extractor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.3" %} +{% set version = "0.8.3.4" %} context: {} @@ -8,7 +8,7 @@ package: source: url: https://gitlab.com/ifb-elixirfr/abromics/abromics-galaxy-json-extractor/-/archive/{{ version }}/abromics-galaxy-json-extractor-{{ version }}.tar.gz - sha256: '81fc614902567dfe83d57fc978bf98cc22e26a58f0e25e359c9d647df6f05bb9' + sha256: '4106ed76eb759f3bd3fcb866d18fdafce64f4ef6d364967f7ccee29b6af06d19' build: noarch: python From d7bb90a459cc41e70c7a7ada1a9bd0c7f4cbc559 Mon Sep 17 00:00:00 2001 From: "Le (Lena) Huang" Date: Thu, 18 Jan 2024 10:31:36 -0500 Subject: [PATCH 1577/2173] update (#45283) --- recipes/dbcan/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/dbcan/meta.yaml b/recipes/dbcan/meta.yaml index 7be1bbfbd0487..34d2f399cac8b 100644 --- a/recipes/dbcan/meta.yaml +++ b/recipes/dbcan/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dbcan" %} -{% set version = "4.1.2" %} +{% set version = "4.1.3" %} package: name: "{{ name|lower }}" @@ -9,7 +9,7 @@ source: # the sha256 sum is generated by doing # wget -0- [URL] | shasum -a 256 url: https://github.com/linnabrown/run_dbcan/releases/download/{{ version }}/dbcan-{{ version }}.tar.gz - sha256: 3a675683379d1afc9f3444fc9894272f1485956df266a6ee4fc11a8f628e6d51 + sha256: 6346e0b6b2c810e2f808bc0bc901643c16f3eda2652d50b8f8470eb722fb419b build: number: 0 @@ -46,6 +46,7 @@ requirements: - openpyxl - matplotlib-base - session-info + - blast test: imports: From dbf9d0bc7ef212f8456d3e460396b78b18877f53 Mon Sep 17 00:00:00 2001 From: hjulienne Date: Thu, 18 Jan 2024 16:38:08 +0100 Subject: [PATCH 1578/2173] Raiss 4.0 (#45162) * added new tag for RAISS * corrected raiss recipe * formatted version constraints * added run export * updated dependancies * corrected sha sum * fixed version issue with scipy * update version number --------- Co-authored-by: hjulienn --- recipes/raiss/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/raiss/meta.yaml b/recipes/raiss/meta.yaml index 07f2b3b1215de..6ba190e766b4d 100644 --- a/recipes/raiss/meta.yaml +++ b/recipes/raiss/meta.yaml @@ -1,5 +1,6 @@ {% set name = "raiss" %} -{% set version = "4.0" %} + +{% set version = "4.0.1" %} package: name: {{ name }} @@ -7,7 +8,8 @@ package: source: url: https://gitlab.pasteur.fr/statistical-genetics/{{ name }}/-/archive/{{ version }}/{{ name }}-{{ version }}.tar.gz - sha256: 771a4ec126967daa367daa599178909cd182ed5d564c169b64e0491f1bb19714 + sha256: eb5cc6b67b395fbf5c2678a253dd7fd2c30c5f62a7358253778b1c6c1161a89f + build: noarch: python @@ -29,7 +31,7 @@ requirements: - pandas - python-dateutil - pytz - - scipy + - scipy >=1.7.0 - six - tzdata From 0d5a0f44b01a879a122b07e15ec4bfdc1394c611 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 11:00:27 -0500 Subject: [PATCH 1579/2173] Update wgd to 2.0.25 (#45282) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index c67fb54a19082..aabbc58070e0f 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.24" %} +{% set version = "2.0.25" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: 60c986d848cacff15037567e02931c908d7644306e201ba48952810c1ff0545a + sha256: d43295772471abbade56b343f8e2152682594ed16fc8ca779a2a0ec642a784f5 build: number: 0 From 4456ccc1f13e9d0cd11da2298ad4337d09694c0a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 13:00:39 -0500 Subject: [PATCH 1580/2173] Update nanometa-live to 0.4.2 (#45293) --- recipes/nanometa-live/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanometa-live/meta.yaml b/recipes/nanometa-live/meta.yaml index ab801d6964c57..8c98e0ee36a38 100644 --- a/recipes/nanometa-live/meta.yaml +++ b/recipes/nanometa-live/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanometa-live" %} -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/FOI-Bioinformatics/nanometa_live/archive/{{ version }}.tar.gz - sha256: bc241b82277b641df9d419cb014a80a223a5f2db47a596925663589d8dbda5c2 + sha256: 82bbb858a17468c481837bd17a32ec7b9e09789ce32a0dd9ec01dcc4e7dbdbe5 build: number: 0 From b123745ab87e2ae8b67e85e477d868f829d8f909 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 16:09:34 -0500 Subject: [PATCH 1581/2173] Update annonars to 0.34.0 (#45290) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index d7d44551f9f50..61ae02aad9578 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.33.0" %} +{% set version = "0.34.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 258cfc2aee680718fc1acc8bccddb571416e425198ca258ee295cdc42cc19f71 + sha256: 8b0725fc8d7e861bc08c96882f6e9e489b5079c10eb723295b26d2100e6e86f9 requirements: build: From 9558382575c418b6057065cadad2c3b51cf66c16 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 18 Jan 2024 16:31:11 -0600 Subject: [PATCH 1582/2173] Add recipe for MGATK v0.7.0 (#45297) * Add recipe for MGATK v0.7.0 * add additional dependencies --- recipes/mgatk/meta.yaml | 66 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 recipes/mgatk/meta.yaml diff --git a/recipes/mgatk/meta.yaml b/recipes/mgatk/meta.yaml new file mode 100644 index 0000000000000..dcc431be31cd5 --- /dev/null +++ b/recipes/mgatk/meta.yaml @@ -0,0 +1,66 @@ +{% set name = "mgatk" %} +{% set version = "0.7.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgatk-{{ version }}.tar.gz + sha256: f42f5eb8fcfd38dd6ef3db853764071311cb70d841a73ff2f40f0a0c9e9d7de9 + +build: + number: 0 + noarch: python + entry_points: + - mgatk = mgatk.cli:main + - mgatk-del-find = mgatk.deletioncalling.clifind:main + - mgatk-del = mgatk.deletioncalling.clidel:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('mgatk', max_pin="x.x") }} + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - click + - pysam + - pytest + - snakemake-minimal + - biopython + - numpy + - pandas + - optparse-pretty + - regex + - ruamel.yaml + - openjdk + - picard-slim + - r-base + - r-dplyr + - r-data.table + - r-matrix + - bioconductor-genomicranges + - bioconductor-summarizedexperiment + +test: + imports: + - mgatk + commands: + - mgatk --help + - mgatk-del-find --help + - mgatk-del --help + +about: + home: https://github.com/caleblareau/mgatk + summary: Mitochondrial genome analysis toolkit. + license: MIT + license_family: MIT + license_file: LICENSE.txt + doc_url: https://github.com/caleblareau/mgatk/wiki + +extra: + recipe-maintainers: + - mencian From 045bc031cb8b7a4da5ae7e3d5d83e3c46149b6da Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 18 Jan 2024 18:04:20 -0500 Subject: [PATCH 1583/2173] Update nextstrain-cli to 8.0.0 (#45298) --- recipes/nextstrain-cli/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml index cdd7f714d9895..ea7189f07bb13 100644 --- a/recipes/nextstrain-cli/meta.yaml +++ b/recipes/nextstrain-cli/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "7.4.0" %} +{% set version = "8.0.0" %} package: name: nextstrain-cli @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain-cli-{{ version }}.tar.gz - sha256: bc678d817dac6351466728122dff1ce37d7e8f3f8b8402fd2cef5822287b7de4 + sha256: 515fb4be3c013a9a30ef8cc28d8e7430d20e2edd840a9a3aa3419764b57e8268 build: - number: 1 + number: 0 noarch: python entry_points: - nextstrain = nextstrain.cli.__main__:main From 873d5ddb495e814285e05e1ed881461eecea5b59 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 19 Jan 2024 20:41:47 +1300 Subject: [PATCH 1584/2173] LTR_FINDER_parallel is now also exposed to /usr/local/bin (#45280) --- recipes/edta/build.sh | 9 +++++++++ recipes/edta/meta.yaml | 3 ++- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/recipes/edta/build.sh b/recipes/edta/build.sh index 729d94a5a9379..e47cfd13c7302 100644 --- a/recipes/edta/build.sh +++ b/recipes/edta/build.sh @@ -20,3 +20,12 @@ for name in ${EDTA_OTHER_PROGRAMS} ; do done ln -sf ${EDTA_DIR}/development/EDTA_processI.pl ${PREFIX}/bin/ + +LTR_FINDER_PARALLEL_DIR=${EDTA_DIR}/bin/LTR_FINDER_parallel + +cat <>${PREFIX}/bin/LTR_FINDER_parallel +#!/bin/bash +perl ${LTR_FINDER_PARALLEL_DIR}/LTR_FINDER_parallel \$@ +END + +chmod a+x ${PREFIX}/bin/LTR_FINDER_parallel \ No newline at end of file diff --git a/recipes/edta/meta.yaml b/recipes/edta/meta.yaml index 3e5f7651efd27..eb2e7f1763bc2 100644 --- a/recipes/edta/meta.yaml +++ b/recipes/edta/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('edta', max_pin='x') }} @@ -59,6 +59,7 @@ test: - EDTA_processI.pl -h 2>&1 | grep -i "Perform EDTA" - EDTA_raw.pl -h 2>&1 | grep -i "Obtain raw" - lib-test.pl -h 2>&1 | grep -i "To test" + - LTR_FINDER_parallel -check_dependencies > /dev/null about: home: https://github.com/oushujun/EDTA From f3c281504987421da7297e11c8c69cbe140fe5ab Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:43:19 -0500 Subject: [PATCH 1585/2173] Update ppanggolin to 2.0.1 (#45245) * Update ppanggolin to 2.0.0 * update with new requirements of 2.0.0 * add run_exports and relax version of mafft and mmseq2 * fix run_exports location * Fix name variable * test with cython <3 to solve os fail * move to v2.0.1 with patches to let the recipe compile on macOS --------- Co-authored-by: JeanMainguy --- recipes/ppanggolin/meta.yaml | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/recipes/ppanggolin/meta.yaml b/recipes/ppanggolin/meta.yaml index 4e0712795ef53..fe77191e7d636 100644 --- a/recipes/ppanggolin/meta.yaml +++ b/recipes/ppanggolin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.105" %} +{% set version = "2.0.1" %} package: name: ppanggolin @@ -6,36 +6,39 @@ package: source: url: https://github.com/labgem/PPanGGOLiN/archive/{{ version }}.tar.gz - sha256: 410a51029302d9aae534846fc5dde9c01c17aa63ae91c9d48db47e399d2d2a47 + sha256: 0e13410a03f825894ceccb7c7a85f8acee060cd98c720486fbb90df71cbd5275 build: - number: 1 + number: 0 skip: True # [py<37] + run_exports: + - {{ pin_subpackage("ppanggolin", max_pin="x") }} requirements: build: - {{ compiler('c') }} + host: - python - pip - - cython + - cython <3 run: - python - tqdm =4 - pytables =3 - - prodigal =2.6 + - pyrodigal =3 - aragorn =1.2 - infernal =1.1 - mmseqs2 - - networkx =2 + - networkx =3 - scipy =1 - - plotly =4 + - plotly =5 - gmpy2 =2 - numpy =1 - - pandas =1 + - pandas =2 - colorlover =0.3 - mafft - - bokeh =2 + - bokeh =3 test: commands: @@ -48,6 +51,7 @@ test: about: license: CeCiLL 2.1 home: https://github.com/labgem/PPanGGOLiN + doc_url: https://ppanggolin.readthedocs.io summary: "PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph" extra: From 3cb6819ca914fb77e10430e9088c905c37d02ff1 Mon Sep 17 00:00:00 2001 From: Justin Sing <32938975+singjc@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:48:07 -0500 Subject: [PATCH 1586/2173] Add recipe for massdash (#45189) * [ADD] recipe for massdash * [FIX] description * [FIX] run_exports, dependency version spacing and matplotlib-base * [FIX] dependency version spacing * [ADD] dev requirements * [ADD] dev requirements * [MOVE] dev requirements to host * [FIX] license --- recipes/massdash/meta.yaml | 56 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 recipes/massdash/meta.yaml diff --git a/recipes/massdash/meta.yaml b/recipes/massdash/meta.yaml new file mode 100644 index 0000000000000..ea81e6b4d1607 --- /dev/null +++ b/recipes/massdash/meta.yaml @@ -0,0 +1,56 @@ +{% set name = "massdash" %} +{% set version = "0.0.5" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: f5258b934d09df5e6d9f22e3dc82bb806aeb28a987b6d90bba49fd7b6fe9f8be + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('massdash', max_pin='x.x') }} + +requirements: + host: + - pip + - python + - flake8 + - flit + - flit-core + - pylint + - snapshottest + run: + - bokeh ==2.4.3 + - click + - joblib + - matplotlib-base + - matplotlib-venn + - upsetplot + - numpy >=1.9.0 + - pandas >=0.17 + - plotly + - psutil + - pyopenms + - scipy + - streamlit + - tqdm + +test: + imports: + - massdash + +about: + home: https://github.com/Roestlab/massdash + license: BSD + license_family: BSD + summary: MassDash is a streamlined DIA mass spec visualization, analysis, optimization, and rapid prototyping. + +extra: + recipe-maintainers: + - singjc From 2988f7f6719e0c7a0ecaff619561f5c6a8b5f347 Mon Sep 17 00:00:00 2001 From: BenoitMorel Date: Fri, 19 Jan 2024 08:49:13 +0100 Subject: [PATCH 1587/2173] update generax (#45153) * update generax * update generax build number * add run exports * Remove patch * Remove patch * recompile * rerun checks * rerun checks --------- Co-authored-by: BenoitMorel --- recipes/generax/meta.yaml | 12 ++++++------ recipes/generax/patch | 12 ------------ 2 files changed, 6 insertions(+), 18 deletions(-) delete mode 100644 recipes/generax/patch diff --git a/recipes/generax/meta.yaml b/recipes/generax/meta.yaml index 6463eb3db5c99..0c662c20d3c3d 100644 --- a/recipes/generax/meta.yaml +++ b/recipes/generax/meta.yaml @@ -1,6 +1,7 @@ {% set name = "generax" %} -{% set version = "2.0.4" %} - +{% set version = "2.1.3" %} + + package: name: {{ name|lower }} version: {{ version }} @@ -9,12 +10,11 @@ source: git_url: https://github.com/benoitmorel/{{ name|lower }}.git git_rev: {{ version }} sha256: unused - patches: - - patch build: - number: 3 - + number: 0 + run_exports: + - {{ pin_subpackage('generax', max_pin="x") }} requirements: build: - make diff --git a/recipes/generax/patch b/recipes/generax/patch deleted file mode 100644 index 20728f85402ef..0000000000000 --- a/recipes/generax/patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/src/core/IO/Model.hpp b/src/core/IO/Model.hpp -index 0eb6ce1..3a16942 100644 ---- a/src/core/IO/Model.hpp -+++ b/src/core/IO/Model.hpp -@@ -6,6 +6,7 @@ - - #include - #include -+#include - extern "C" { - #include - #include From 35ebca0e18f11032c6017542b2bcc9fa52e63fad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:50:12 -0500 Subject: [PATCH 1588/2173] Update pyfaidx to 0.8.1.1 (#45294) * Update pyfaidx to 0.8.1 * Update pyfaidx to 0.8.1.1 --- recipes/pyfaidx/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pyfaidx/meta.yaml b/recipes/pyfaidx/meta.yaml index 9209e777f8e00..eb721ce14f0d7 100644 --- a/recipes/pyfaidx/meta.yaml +++ b/recipes/pyfaidx/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.8.0" %} +{% set version = "0.8.1.1" %} package: name: pyfaidx version: {{ version }} source: - url: https://files.pythonhosted.org/packages/ef/95/aa7e6d1c1b68e64234d5ed985a761edbbce124baea17c2056935626958d2/pyfaidx-0.8.0.tar.gz - sha256: 1eed70f4eafb4ba9c4cf7022cd748947b8ebe0f4c86cb56f42f587ab7f2da027 + url: https://files.pythonhosted.org/packages/0e/32/a89e956d4f27bd8ab4d92f6b27e46386975add4ad13e54504012afa3d025/pyfaidx-0.8.1.1.tar.gz + sha256: 6f0482352619f2cc56003ca22321bdb0d0764b656795bc1e4062b1fa9b08686b build: number: 0 From 16abdd19cafdd730489f03908155e70601f3e514 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:50:42 -0500 Subject: [PATCH 1589/2173] Update protmapper to 0.0.29 (#45301) --- recipes/protmapper/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/protmapper/meta.yaml b/recipes/protmapper/meta.yaml index a7fa1af749531..fe4ac6f625278 100644 --- a/recipes/protmapper/meta.yaml +++ b/recipes/protmapper/meta.yaml @@ -1,6 +1,6 @@ {% set name = "protmapper" %} -{% set version = "0.0.28" %} -{% set sha256 = "0cd18592dc6ae67e2ec723395c6adfe5221f8ce73e7185c3ac85348639c29a1e" %} +{% set version = "0.0.29" %} +{% set sha256 = "d0d10198fb000401d03ba6c271869970caf8e1c8b46db686d2eed153fa8c2257" %} package: name: {{ name|lower }} From 7d494743fccc328443122323c38322702c314496 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:51:08 -0500 Subject: [PATCH 1590/2173] Update pango-designation to 1.24 (#45300) --- recipes/pango-designation/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pango-designation/meta.yaml b/recipes/pango-designation/meta.yaml index 869455a8746fb..3c559b4e5981f 100644 --- a/recipes/pango-designation/meta.yaml +++ b/recipes/pango-designation/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.23" %} +{% set version = "1.24" %} package: name: pango-designation @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pango-designation/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5692d92d4b7ff902464552e81d71fc25dcafd0ada175af3b143246c14fc6d9c1 + sha256: 9b84365c503a71ac5aadf47b977aa022450457492b24955149f26469f733f898 build: number: 0 From c1b1a81e5c4e8142a37f4f2f7c23302bc223d3b8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:51:35 -0500 Subject: [PATCH 1591/2173] Update vg to 1.54.0 (#45289) --- recipes/vg/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml index 8549c995de117..c67d295ba6970 100644 --- a/recipes/vg/meta.yaml +++ b/recipes/vg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vg" %} -{% set version = "1.53.0" %} +{% set version = "1.54.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg - sha256: a86dfc47c143af9f9a89c5e4595ed32b493384aac2b067f97d0684ec2d9a413b + sha256: 84bee2444b3714b5b8672ea4a4e28063c0eb41a22b8b7359641c10467fe8b247 build: number: 0 From 3b7283b4f122b16bb7ae349cba07cd19a1113123 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 02:52:07 -0500 Subject: [PATCH 1592/2173] Update metdatamodel to 0.6.0 (#45276) Co-authored-by: Helge Hecht --- recipes/metdatamodel/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metdatamodel/meta.yaml b/recipes/metdatamodel/meta.yaml index e83742363e601..a36b4b670c13c 100644 --- a/recipes/metdatamodel/meta.yaml +++ b/recipes/metdatamodel/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metdatamodel" %} -{% set version = "0.5.5" %} +{% set version = "0.6.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metDataModel-{{ version }}.tar.gz - sha256: 8ed0c978ffe4e1a75d169ae58687cb86f15c991d05529748791c554c9f1103a9 + sha256: 58bdbf5099c059d6e481921b017bc667e73623c1a1ba840d8b3f42d79e15b2cc build: noarch: python From cbe3607b7c14ad909b72b57b44458cabc565e7a2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 19 Jan 2024 10:38:35 -0500 Subject: [PATCH 1593/2173] Update vsearch to 2.27.0 (#45305) --- recipes/vsearch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index fdfb483ba13ff..d453c4b0d1b98 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.26.1" %} -{% set sha256 = "dc8513376405fc01ca3742624177113752870b05bb682fe1bf62d190d0a696bd" %} +{% set version = "2.27.0" %} +{% set sha256 = "18d6fc919adce684c01fe57797e2adbf5b4d4f6cf5ef169378ad473797be38ae" %} package: name: vsearch From 8a73d4f86b2db9bfc782b57d9f33ce00abe803fc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:38:02 -0500 Subject: [PATCH 1594/2173] Update pyrodigal to 3.2.2 (#45327) --- recipes/pyrodigal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyrodigal/meta.yaml b/recipes/pyrodigal/meta.yaml index 79aae4b1a1021..94764527e29ad 100644 --- a/recipes/pyrodigal/meta.yaml +++ b/recipes/pyrodigal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrodigal" %} -{% set version = "3.2.1" %} +{% set version = "3.2.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7c0bb83eafa888bdc5d931fb3a1f6abc35247f96abc3f9e557a0109e85cbdd35 + sha256: 0e02b2089df29c3c0f1379364664f4a83da12373233bb74d7a95d24a346b02ec build: number: 0 From 9aa5f519ed3f4ad26d0b764354c50b8295d07825 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:38:36 -0500 Subject: [PATCH 1595/2173] Update pyopal to 0.5.1 (#45324) * Update pyopal to 0.5.0 * Update pyopal to 0.5.1 --- recipes/pyopal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyopal/meta.yaml b/recipes/pyopal/meta.yaml index 300e327a6f612..fe7ef5a8f3e0e 100644 --- a/recipes/pyopal/meta.yaml +++ b/recipes/pyopal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyopal" %} -{% set version = "0.4.1" %} +{% set version = "0.5.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: abfc3cb741eaaaf0185af6efb44b56f458f54fe7b1d4d5b9c54bf60da73e245a + sha256: debc526d00f605f1a9f75ece2bb124b6b370f8649857bc33ec7bdc264e8cc6cb build: number: 0 From 0b84e9e84c7730b23c8f21674ba5dfc99b53e000 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:38:48 -0500 Subject: [PATCH 1596/2173] Update pymochi to 1.0 (#45323) --- recipes/pymochi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pymochi/meta.yaml b/recipes/pymochi/meta.yaml index 6d20abd0c7781..7ce09a732e24f 100644 --- a/recipes/pymochi/meta.yaml +++ b/recipes/pymochi/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.9" %} +{% set version = "1.0" %} {% set github = "https://github.com/lehner-lab/MoCHI" %} package: @@ -7,7 +7,7 @@ package: source: url: {{ github }}/archive/v{{ version }}.tar.gz - sha256: cec741cc8cda6affc9f4c2fd470afd28ee7c5ec9282bd59a4d4102a6e3afe005 + sha256: 93bd3c32b5a686d5bacecf3d48678497eeed3bf799198ab453e21accefecbae7 build: noarch: python From 383596c372bf9d46a03796695263567848bb679b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:39:24 -0500 Subject: [PATCH 1597/2173] Update itolapi to 4.1.4 (#45322) --- recipes/itolapi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/itolapi/meta.yaml b/recipes/itolapi/meta.yaml index 14938580238b2..0e664d28481a5 100644 --- a/recipes/itolapi/meta.yaml +++ b/recipes/itolapi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "itolapi" %} -{% set version = "4.1.3" %} +{% set version = "4.1.4" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b4f683630e4c816529b79a326de515809ad6174e473b6a25bc3954aaadd16778 + sha256: 68e87ba51d209da556b0e373b3b0456b644a1a732c193fedbd7785ff37b6a2cb build: noarch: python From 00200e61110cb6eb18763bc102a1a6b2d1149f1e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:39:54 -0500 Subject: [PATCH 1598/2173] Update assemblycomparator2 to 2.5.16 (#45310) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index f0d50c8973c9b..b5640b7519dd6 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.15" %} +{% set version = "2.5.16" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9605f4021710e975365090fba1c13c2005c46978cec48c6cabe678167c86d33e + sha256: 197d157e67a04df4f63b88191106dce7219eab8ee4aa146b74d4fb796a505e93 build: From 5b25b798b6ea00539d3a5ecdd447d23f6a8a631b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:40:53 -0500 Subject: [PATCH 1599/2173] Update dajin2 to 0.4.0 (#45319) --- recipes/dajin2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index eca8b4b9afad9..9c3310af914d4 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "DAJIN2" %} -{% set version = "0.3.6" %} +{% set version = "0.4.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: cf9e686f78041682589c8e90bcac8eb2ad6473987c96bd574faf36e0b461613c + sha256: 0b0abcc8f40679bec605c85643b069b55914ac1ac9031f6ad73c319899abd002 build: entry_points: From 25c1cba337da76e03472ff6a739f541a8de63b4b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:41:01 -0500 Subject: [PATCH 1600/2173] Update orthoflow to 0.3.1 (#45317) --- recipes/orthoflow/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/orthoflow/meta.yaml b/recipes/orthoflow/meta.yaml index ca8111d636967..e693187f59ef0 100644 --- a/recipes/orthoflow/meta.yaml +++ b/recipes/orthoflow/meta.yaml @@ -1,5 +1,5 @@ {% set name = "orthoflow" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/orthoflow-{{ version }}.tar.gz - sha256: bdfb03dbdccec636adee9be5c8a5a8eec682c82f3435da90ae7c504a2899f9e6 + sha256: fb7b14dcc52d3d4ce3ef39cf50a2bf68a43f5cd2b46898b3b50a054b78fc91c8 build: entry_points: From dfd33c18812649d35ed1bc2388eaa00c9105e10e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 14:41:13 -0500 Subject: [PATCH 1601/2173] Update dupsifter to 1.2.1.20240119 (#45315) --- recipes/dupsifter/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dupsifter/meta.yaml b/recipes/dupsifter/meta.yaml index 7a256ef424987..2d91cf55de8e3 100644 --- a/recipes/dupsifter/meta.yaml +++ b/recipes/dupsifter/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.2.0.20230926' %} +{% set version = '1.2.1.20240119' %} package: name: dupsifter @@ -11,7 +11,7 @@ build: source: url: https://github.com/huishenlab/dupsifter/releases/download/v{{ version }}/release-source.zip - sha256: 7a4dfe194d51ac09b30f85f6c77f9e8c31c62e636f56c09748688b32755d9521 + sha256: ca3db67e36f9a3d054acf9fbaf0dee1037781d468d7f094ea5d3852610448e7a patches: - patch From 73793518e5dec508eb89df6c355d6345a192b8aa Mon Sep 17 00:00:00 2001 From: Joerg Fallmann Date: Sun, 21 Jan 2024 20:47:01 +0100 Subject: [PATCH 1602/2173] snakemake pinning, version 8 major changes that break everything (#45302) --- recipes/monsda/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/monsda/meta.yaml b/recipes/monsda/meta.yaml index d923fef7e8211..68ab0c3b3a547 100644 --- a/recipes/monsda/meta.yaml +++ b/recipes/monsda/meta.yaml @@ -11,7 +11,7 @@ source: sha256: "{{ sha256 }}" build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --use-pep517 --no-deps --ignore-installed -vvv" entry_points: - monsda = MONSDA.RunMONSDA:main @@ -35,7 +35,7 @@ requirements: - pandas >=1.4.1 - perl >=5.32.1 - scipy >=1.7.0 - - snakemake >=7.32.3 + - snakemake >=7.32.3,<8.0.0 - versioneer >=0.20 - yaml >=0.2.5 - black >=21.5b2 From 6cfdcafdde15bf01575b50922ee38bd465b25a08 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 15:28:44 -0500 Subject: [PATCH 1603/2173] Update massdash to 0.0.6 (#45303) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/massdash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/massdash/meta.yaml b/recipes/massdash/meta.yaml index ea81e6b4d1607..b3ae8c95452b5 100644 --- a/recipes/massdash/meta.yaml +++ b/recipes/massdash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "massdash" %} -{% set version = "0.0.5" %} +{% set version = "0.0.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f5258b934d09df5e6d9f22e3dc82bb806aeb28a987b6d90bba49fd7b6fe9f8be + sha256: f2b4160745ddcd96698f92c7d9c86b5a354970ace233924a0e26cba88421a761 build: number: 0 From d7bfc49861143d071bb4b24ff7d6cb849e3af17f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 15:44:41 -0500 Subject: [PATCH 1604/2173] Update cyvcf2 to 0.30.27 (#45308) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cyvcf2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cyvcf2/meta.yaml b/recipes/cyvcf2/meta.yaml index b959105c2467d..26df81e5b90b8 100644 --- a/recipes/cyvcf2/meta.yaml +++ b/recipes/cyvcf2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cyvcf2" %} -{% set version = "0.30.26" %} -{% set sha256 = "e8473957181ef7b037213d110217046d107cd6a0eb4671f13c47a7a24412db05" %} +{% set version = "0.30.27" %} +{% set sha256 = "f1b12c1fb78bd039c5d94b0ff2d838edfa0716c0e4902ad3ecec3d48da3d4ff9" %} package: name: {{ name }} From 2dc2d239043753076666081e0f315a676d3c5567 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 15:51:18 -0500 Subject: [PATCH 1605/2173] Update galah to 0.4.0 (#45285) * Update galah to 0.4.0 * add run_exports --------- Co-authored-by: joshuazhuang7 --- recipes/galah/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/galah/meta.yaml b/recipes/galah/meta.yaml index 362a196815042..3259624da0826 100644 --- a/recipes/galah/meta.yaml +++ b/recipes/galah/meta.yaml @@ -1,14 +1,16 @@ -{% set version = "0.3.1" %} +{% set version = "0.4.0" %} {% set name = "galah" %} -{% set sha256 = "78a278a2a4d2e5f074115e41a38c426fab328d3deaac84cb55cded77e9c97428" %} +{% set sha256 = "9b40cc805df15461e5b07fd3108663cc92d286030c17fefe5a33716b5b8fa10a" %} package: name: {{ name }} version: {{ version }} build: - number: 3 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('galah', max_pin="x.x") }} source: url: https://github.com/wwood/{{ name }}/archive/v{{version}}.tar.gz @@ -29,5 +31,6 @@ test: about: home: https://github.com/wwood/galah license: GPL-3.0-only + license_family: GPL3 license_file: LICENCE.txt summary: Galah aims to be a more scalable metagenome assembled genome (MAG) dereplication method. From ef29f7c4d6fc8efe2b0ca6159a1831798bebc962 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sun, 21 Jan 2024 21:53:31 +0100 Subject: [PATCH 1606/2173] bump ampvis2 and update URL (#45313) * bump ampvis2 and update URL * add run_exports * reset build * fix run_exports copy paste error --- recipes/r-ampvis2/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/r-ampvis2/meta.yaml b/recipes/r-ampvis2/meta.yaml index fc5c07195db77..57c01fefc9001 100644 --- a/recipes/r-ampvis2/meta.yaml +++ b/recipes/r-ampvis2/meta.yaml @@ -1,20 +1,22 @@ {% set name = "r-ampvis2" %} -{% set version = "2.7.32" %} +{% set version = "2.8.6" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/MadsAlbertsen/ampvis2/archive/refs/tags/v{{ version }}.tar.gz - sha256: b75f2e92e3d8999e47b8004824b7d1e0a9bb7b0c5fb116296e11a0d87ec0ac4a + url: https://github.com/KasperSkytte/ampvis2/archive/refs/tags/v{{ version }}.tar.gz + sha256: 98ef7a7f899b5d866552f10ae9a005c1c4bd41667e88cb771006811f8d6f50d7 build: - number: 2 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-ampvis2', max_pin="x.x") }} requirements: host: From b2e3ec908fc409ff0c7c8f7a0757e301cdbae946 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sun, 21 Jan 2024 21:55:06 +0100 Subject: [PATCH 1607/2173] add revoluzer (#45296) * add revoluzer * add reun_exports * try 0.1.1 * fix link and sha * add glpk requirement * cmake trace * fix debug and add CMAKE_INCLUDE_PATH * debug * BUILD_PREFIX? * BUILD_PREFIX?? * CXXFLAGS * add boost * bump and test * cleanup * skip osx for now --- recipes/revoluzer/build.sh | 9 ++++++++ recipes/revoluzer/meta.yaml | 44 +++++++++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 recipes/revoluzer/build.sh create mode 100644 recipes/revoluzer/meta.yaml diff --git a/recipes/revoluzer/build.sh b/recipes/revoluzer/build.sh new file mode 100644 index 0000000000000..175ed562969c8 --- /dev/null +++ b/recipes/revoluzer/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash +CXXFLAGS="-I${BUILD_PREFIX}/include $CXXFLAGS" + + +cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' +cmake --build build +mkdir -p $PREFIX/bin +echo "installing: $(find build/src -type f -executable)" +mv $(find build/src -type f -executable) $PREFIX/bin diff --git a/recipes/revoluzer/meta.yaml b/recipes/revoluzer/meta.yaml new file mode 100644 index 0000000000000..1bb05b1981a8b --- /dev/null +++ b/recipes/revoluzer/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "revoluzer" %} +{% set version = "0.1.2" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: https://gitlab.com/Bernt/{{ name }}/-/archive/{{ version }}/{{ name }}-{{ version }}.tar.gz + sha256: f2957266157797c4fe2338e07ea756ad8fc688efe90b6b48a83744a0b82c986a + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('revoluzer', max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - cmake + - make + - boost-cpp + - glpk + host: + run: + - boost-cpp + - glpk + +test: + commands: + - crex --help + - trex -h + +about: + home: https://gitlab.com/Bernt/revoluzer/ + license: GPL-3.0-or-later + license_file: LICENSE + summary: Genome rearrangement analysis tools + +extra: + recipe-maintainers: + - bernt-matthias From 0146964d5e3b318f13c670410e2fe92f1ab5e267 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 15:58:11 -0500 Subject: [PATCH 1608/2173] Update snakemake to 8.2.3 (#45311) * Update snakemake to 8.2.2 * Update snakemake to 8.2.3 --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 1904589e0671a..e40d63fbdb441 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.2.1" %} +{% set version = "8.2.3" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: f177ada98188a10602aa2ed758fc9b7ff13e7107c5e582463ae681c525c28f0c + sha256: d31b7e5ceaa255038475287154b641a973cba9ff7cca6880f109f18ab703351a build: number: 0 From 801dd01e56cb57a562878c9b6283a06976619966 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 16:04:48 -0500 Subject: [PATCH 1609/2173] Update pegasusio to 0.9.0 (#45093) * Update pegasusio to 0.8.2 * add pegasusio * Update pegasusio to 0.9.0 --------- Co-authored-by: joshuazhuang7 --- recipes/pegasusio/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/pegasusio/meta.yaml b/recipes/pegasusio/meta.yaml index 046eedbbb6559..c217cf33b836f 100644 --- a/recipes/pegasusio/meta.yaml +++ b/recipes/pegasusio/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pegasusio" %} -{% set version = "0.8.1" %} +{% set version = "0.9.0" %} package: name: {{ name|lower }} @@ -7,14 +7,16 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "ea18b963315726a18819740b91df316f43c50b87f248092be601756b30f49d44" + sha256: "fc7d1b33d46418a216de50426e29af101268e510ea171b36458498293b5dfdcc" build: number: 0 - skip: True # [py<37] + skip: True # [py < 37] entry_points: - pegasusio = pegasusio.__main__:main - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('pegasusio', max_pin="x.x") }} requirements: build: @@ -56,6 +58,7 @@ about: home: https://github.com/lilab-bcb/pegasusio doc_url: https://pegasusio.readthedocs.io license: BSD-3-Clause + license_family: BSD license_file: LICENSE summary: "PegasusIO is the IO package for Pegasus." From b470d48e7f13d613124d2b5de6eef4de7a69eb50 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 16:06:37 -0500 Subject: [PATCH 1610/2173] Update parsnp to 2.0.2 (#45085) * Update parsnp to 2.0.0 * Update meta.yaml * add tqdm * Update parsnp to 2.0.1 * Update parsnp to 2.0.2 * Update meta.yaml * Update meta.yaml * hack partition into directory (need to change to proper python build) * Update run_test.sh --------- Co-authored-by: Bryce Kille Co-authored-by: joshuazhuang7 --- recipes/parsnp/build.sh | 1 + recipes/parsnp/meta.yaml | 30 +++++++++++++++--------------- recipes/parsnp/run_test.sh | 1 + 3 files changed, 17 insertions(+), 15 deletions(-) diff --git a/recipes/parsnp/build.sh b/recipes/parsnp/build.sh index f8fa0b7b71356..8c6ca7f6a253e 100644 --- a/recipes/parsnp/build.sh +++ b/recipes/parsnp/build.sh @@ -34,6 +34,7 @@ rm -R muscle/m4 cp parsnp $PREFIX/bin cp extend.py $PREFIX/bin cp logger.py $PREFIX/bin +cp partition.py $PREFIX/bin cp src/parsnp_core $PREFIX/bin/bin cp template.ini $PREFIX/bin cp -R bin $PREFIX/bin diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml index acc3bfddfea80..5591dab327142 100644 --- a/recipes/parsnp/meta.yaml +++ b/recipes/parsnp/meta.yaml @@ -1,16 +1,18 @@ -{% set version = "1.7.4" %} +{% set version = "2.0.2" %} package: name: parsnp version: '{{version}}' source: - url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz" - sha256: c24a1b395b1ddb6ab2a1f1c41e7e575b45da2ffed99581225be05fdad761684f + url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz" + sha256: 1d9a4c6e5b414511ebc0052e3c9e6e32984b545ef8816086ed1d74af69c27c8f build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('parsnp', max_pin="x") }} requirements: build: @@ -19,31 +21,29 @@ requirements: - autoconf - libtool - make - - llvm-openmp # [osx] - - openmp # [linux] host: - zlib - llvm-openmp # [osx] - - openmp # [linux] + - openmp # [linux] run: - python >=3.7 - llvm-openmp # [osx] - - openmp # [linux] - - harvesttools - - fasttree - - phipack + - openmp # [linux] - biopython - - numpy + - numpy - zlib - phipack - raxml - fasttree - - fastani # [linux] - - mash + - fastani # [linux] + - mash - harvesttools - - mafft + - pyspoa + - tqdm about: home: https://github.com/marbl/parsnp license: "custom; see https://raw.githubusercontent.com/marbl/parsnp/master/LICENSE" summary: Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. + doc_url: "https://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html" + dev_url: https://github.com/marbl/parsnp diff --git a/recipes/parsnp/run_test.sh b/recipes/parsnp/run_test.sh index d8e2ab432847e..73e2775eda56a 100644 --- a/recipes/parsnp/run_test.sh +++ b/recipes/parsnp/run_test.sh @@ -9,3 +9,4 @@ parsnp -r ! -d mers_virus/genomes/*.fna -o test2 --verbose parsnp -g mers_virus/ref/England1.gbk -d mers_virus/genomes/*.fna -p 2 -C 1000 -c -o test --verbose --use-fasttree parsnp -r ! -d mers_virus/genomes/*.fna -o test2 --verbose -p 2 parsnp -r ! -d mers_virus/genomes/*.fna -o test3 --verbose -p 2 --extend-lcbs +parsnp -r ! -d mers_virus/genomes/*.fna -o test4 --verbose -p 2 --partition --partition-size 10 From 12fdab0cb885600241b3d3a769f148d56545f077 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 16:33:12 -0500 Subject: [PATCH 1611/2173] Update r-pathfindr to 2.3.1 (#45316) --- recipes/r-pathfindr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-pathfindr/meta.yaml b/recipes/r-pathfindr/meta.yaml index 7b75c815daaee..4a76e0d8a98db 100644 --- a/recipes/r-pathfindr/meta.yaml +++ b/recipes/r-pathfindr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '2.3.0' %} +{% set version = '2.3.1' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -11,7 +11,7 @@ source: url: - {{ cran_mirror }}/src/contrib/pathfindR_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/pathfindR/pathfindR_{{ version }}.tar.gz - sha256: e7fc4f10859890af5ab17cc7870efac64614f234059f5734ddd7af705f67281b + sha256: 03b766e4799dbf2083717cd9a8a302beaaa58eaec9499b3b9b9e5e55e50c5694 build: merge_build_host: True # [win] From dfddc22e8177d8082262ea040e0154580fe5fa4c Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sun, 21 Jan 2024 16:50:32 -0600 Subject: [PATCH 1612/2173] Update MOODS to 1.9.4.2 (#45330) --- recipes/moods/build.sh | 24 ++++++++++++------------ recipes/moods/meta.yaml | 28 +++++++++++++++------------- 2 files changed, 27 insertions(+), 25 deletions(-) diff --git a/recipes/moods/build.sh b/recipes/moods/build.sh index 9fd7ba71a6699..689926c02722e 100644 --- a/recipes/moods/build.sh +++ b/recipes/moods/build.sh @@ -1,17 +1,17 @@ #!/bin/bash -cat >setup_compile.patch << EOF ---- setup.py 2018-07-18 09:44:45.000000000 -0700 -+++ new_setup.py 2018-07-18 09:46:32.000000000 -0700 -@@ -7,7 +7,7 @@ - from distutils.core import setup, Extension - +cat > setup.py.patch << EOF +--- a/setup.py ++++ b/setup.py +@@ -4,7 +4,7 @@ from setuptools import setup, Extension + from os import path + common_includes = ["core/"] --common_compile_args = ['-march=native', '-O3', '-fPIC', '--std=c++11'] +-common_compile_args = ['-O3', '-fPIC', '--std=c++11'] +common_compile_args = ['-mtune=generic', '-O3', '-fPIC', '--std=c++11'] - - + tools_mod = Extension('MOODS._tools', + sources=['core/tools_wrap.cxx', EOF -patch setup.py setup_compile.patch -rm setup_compile.patch -$PYTHON setup.py install --record=record.txt +patch setup.py setup.py.patch +rm setup.py.patch +${PYTHON} -m pip install . -vvv --no-deps --no-build-isolation diff --git a/recipes/moods/meta.yaml b/recipes/moods/meta.yaml index d516f94e805d6..01727f6f25eda 100644 --- a/recipes/moods/meta.yaml +++ b/recipes/moods/meta.yaml @@ -1,38 +1,40 @@ -{% set version = "1.9.4.1" %} +{% set name = "moods" %} +{% set version = "1.9.4.2" %} package: - name: moods + name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/jhkorhonen/MOODS/releases/download/v{{ version }}/MOODS-python-{{ version }}.tar.gz - sha256: 7fd4d634bc2258421859d720afb9e38b4015b92d1ffc7aaeeb5422ce8b26d65e + url: https://pypi.io/packages/source/{{ name[0] }}/mira-moods/mira-moods-{{ version }}.tar.gz + sha256: e694e37c7487286801bffcda3e0576157960007919dd5ceb8b5a1626dc2968e1 build: - number: 4 + number: 0 + skip: True # [py < 36] + run_exports: + - {{ pin_subpackage('moods', max_pin="x") }} requirements: build: - - {{ compiler('c') }} - {{ compiler('cxx') }} host: - python - - swig # [py3k] - + - pip run: - python - - swig # [py3k] test: imports: - MOODS.scan about: - home: https://github.com/jhkorhonen/MOODS - license: GPLv3 - license_family: GPL + home: https://www.cs.helsinki.fi/group/pssmfind/ + summary: 'MOODS: Motif Occurrence Detection Suite' + license: GPL-3.0-or-later + license_family: GPL3 license_file: COPYING.GPLv3 - summary: MOODS, Motif Occurrence Detection Suite + dev_url: https://github.com/jhkorhonen/MOODS extra: identifiers: From c8ee098ccfc97d62045cf4b9975312d0cc9dab65 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino <62253982+AndreaGuarracino@users.noreply.github.com> Date: Sun, 21 Jan 2024 18:42:16 -0600 Subject: [PATCH 1613/2173] Update irissv to 1.0.5 (#45329) * update version, sha256 and build number * add `run_exports` * update url --- recipes/irissv/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/irissv/meta.yaml b/recipes/irissv/meta.yaml index 88b85d9548522..842485ab0d1d9 100644 --- a/recipes/irissv/meta.yaml +++ b/recipes/irissv/meta.yaml @@ -1,16 +1,19 @@ -{% set version = "1.0.4" %} +{% set name = "irissv" %} +{% set version = "1.0.5" %} package: - name: irissv + name: "{{ name }}" version: {{ version }} source: - url: https://github.com/mkirsche/Iris/archive/{{ version }}.tar.gz - sha256: 1a7b609fa582abf901ef7392dd84fbcdabdca930be28cb0decb9fd7389aff6a2 + url: https://github.com/mkirsche/Iris/archive/refs/tags/v{{ version }}.tar.gz + sha256: a71718d418fb8b1afacbe2b3a6b91fd50cadc9e12c0b532739b955e455913b0b build: noarch: generic - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: run: From a3ed9d43ff6a4a30f62e7dbe4a4e2ac620cef0fe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 21 Jan 2024 19:58:42 -0500 Subject: [PATCH 1614/2173] Update kingfisher to 0.4.1 (#45281) --- recipes/kingfisher/meta.yaml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/recipes/kingfisher/meta.yaml b/recipes/kingfisher/meta.yaml index 855fa0bd6e4fb..82a4ed31a27c7 100644 --- a/recipes/kingfisher/meta.yaml +++ b/recipes/kingfisher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "kingfisher" %} -{% set version = "0.3.1" %} +{% set version = "0.4.1" %} package: name: {{ name }} @@ -7,12 +7,12 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/kingfisher-{{ version }}.tar.gz - sha256: 2d2dae22f7345a5ad7ba8d64e310a9033667ca09aabdf3bea4ace05a629c388f + sha256: b74510c997db71432b4feb03398b8432b883d873d0d05eb2f0e5a1dafbce42f6 build: noarch: python number: 0 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps -vvv run_exports: - {{ pin_subpackage('kingfisher', max_pin="x") }} @@ -39,15 +39,13 @@ test: imports: - kingfisher commands: - - pip check - kingfisher --version | grep {{ version }} - requires: - - pip about: home: https://github.com/wwood/kingfisher-download summary: Download/extract biological FASTA/Q read data and metadata license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENCE.txt extra: From b1067c5f53e9e94ec44ff5f683bb22adbe61df91 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 00:07:07 -0500 Subject: [PATCH 1615/2173] Update phables to 1.3.0 (#45333) --- recipes/phables/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phables/meta.yaml b/recipes/phables/meta.yaml index a021fa80dec1f..c2f2754b2359c 100644 --- a/recipes/phables/meta.yaml +++ b/recipes/phables/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phables" %} -{% set version = "1.2.2" %} +{% set version = "1.3.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/Vini2/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 316b6f3c9c2a0267745b0ebbaf2f8e82084f3863695274a4c0c6c58d248b4842 + sha256: bded81ddbfdce0b5143da3ebf51e56b1fe61f3b23c282433940c0e357014e642 build: number: 0 From b8e36a2eb3c107ee8270859bd0293d36aad9c7e1 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Mon, 22 Jan 2024 13:15:04 +0100 Subject: [PATCH 1616/2173] new recipe svync (#45338) --- recipes/svync/build.sh | 4 ++++ recipes/svync/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 recipes/svync/build.sh create mode 100644 recipes/svync/meta.yaml diff --git a/recipes/svync/build.sh b/recipes/svync/build.sh new file mode 100644 index 0000000000000..888542f1bb2ed --- /dev/null +++ b/recipes/svync/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +chmod a+x svync* +mkdir -p $PREFIX/bin +cp svync* $PREFIX/bin/svync \ No newline at end of file diff --git a/recipes/svync/meta.yaml b/recipes/svync/meta.yaml new file mode 100644 index 0000000000000..a19463ec08781 --- /dev/null +++ b/recipes/svync/meta.yaml @@ -0,0 +1,36 @@ +{% set version = '0.1.0' %} +{% set name = 'svync' %} + +package: + name: {{ name }} + version: {{ version }} + +source: + - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-darwin-amd64.tar.gz # [osx-amd64] + md5: 62bc02c3f3dc52fd02b998f6f0223216 # [osx] + - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-linux-amd64.tar.gz # [linux] + md5: dbc6b403d5ce1bcef9ba07ad7e1a5dc9 # [linux] + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} + +requirements: + run: + - tabix + +test: + commands: + - "{{ name }} --help" + - bgzip -h + +extra: + skip-lints: + - should_be_noarch_generic # uses per platform binaries + - should_not_be_noarch_source # uses binaries + +about: + home: https://github.com/nvnieuwk/svync + license: MIT + summary: A tool to standardize VCF files from structural variant callers From e98e003636d21df618282b168806e5d55ed21e05 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 07:16:18 -0500 Subject: [PATCH 1617/2173] Update varlociraptor to 8.4.3 (#45337) --- recipes/varlociraptor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varlociraptor/meta.yaml b/recipes/varlociraptor/meta.yaml index 8fb5cf321e92c..a499dd821034d 100644 --- a/recipes/varlociraptor/meta.yaml +++ b/recipes/varlociraptor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.2" %} +{% set version = "8.4.3" %} package: name: varlociraptor @@ -11,7 +11,7 @@ build: source: url: https://github.com/varlociraptor/varlociraptor/archive/v{{ version }}.tar.gz - sha256: 41dd246d34e0e0d277681e9114bbc5bdfa95d0ef01b884be975a8f00bc3b492a + sha256: bbb192ea88f22a85a95273ef425425f2d60686d58ae104c2d182effbd3d61ae9 requirements: build: From ede2bb219e77a9808c128a0147e598ccc2d454cc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 07:27:58 -0500 Subject: [PATCH 1618/2173] Update treetime to 0.11.2 (#45335) --- recipes/treetime/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/treetime/meta.yaml b/recipes/treetime/meta.yaml index 804bad35fbd08..06d0ced896a94 100644 --- a/recipes/treetime/meta.yaml +++ b/recipes/treetime/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.11.1" %} -{% set sha256 = "294cf2f72e145f0642784befa8f31766469d20aeb4b798b78fed211a586577a1" %} +{% set version = "0.11.2" %} +{% set sha256 = "c6fe577580a1ed83dcfc7530f85b678bd9d890366ba83d50444cd8e7371a71af" %} package: name: treetime From e5db34f7fb7c81f3dcb4d1f670cba1e2938b50f5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 09:07:30 -0500 Subject: [PATCH 1619/2173] Update nanometa-live to 0.4.3 (#45342) --- recipes/nanometa-live/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanometa-live/meta.yaml b/recipes/nanometa-live/meta.yaml index 8c98e0ee36a38..4ccbcf3cfba8b 100644 --- a/recipes/nanometa-live/meta.yaml +++ b/recipes/nanometa-live/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanometa-live" %} -{% set version = "0.4.2" %} +{% set version = "0.4.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/FOI-Bioinformatics/nanometa_live/archive/{{ version }}.tar.gz - sha256: 82bbb858a17468c481837bd17a32ec7b9e09789ce32a0dd9ec01dcc4e7dbdbe5 + sha256: 9c8e0cb9eddaf8cfde3a752424717447319afd2af357a815e0ba4d4112e58e5c build: number: 0 From f688814c1d445bf5835915ab37e9a6d476a5214f Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Mon, 22 Jan 2024 16:11:29 +0100 Subject: [PATCH 1620/2173] toil update for 6.0.0 (#45343) - add semantic version run exports - and patch to remove need for ruamel.yaml.string dependency (which is not yet packaged for conda) --- .../drop_ruamel_yaml_string_dependency.patch | 52 +++++++++++++++++++ recipes/toil/meta.yaml | 49 +++++++++-------- 2 files changed, 78 insertions(+), 23 deletions(-) create mode 100644 recipes/toil/drop_ruamel_yaml_string_dependency.patch diff --git a/recipes/toil/drop_ruamel_yaml_string_dependency.patch b/recipes/toil/drop_ruamel_yaml_string_dependency.patch new file mode 100644 index 0000000000000..e2121b54bca4b --- /dev/null +++ b/recipes/toil/drop_ruamel_yaml_string_dependency.patch @@ -0,0 +1,52 @@ +commit 893aa9b3295400829a86054cab028635e9bd2dd2 +Author: Michael R. Crusoe +Date: Mon Jan 22 14:58:45 2024 +0100 + + remove ruamel.yaml.string dependency for a simpler solution + +diff --git a/requirements.txt b/requirements.txt +index c34aceb56..b0e85191d 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -11,6 +11,5 @@ pytz>=2012 + enlighten>=1.5.2, <2 + configargparse>=1.7,<2 + ruamel.yaml>=0.15 +-ruamel.yaml.string>=0.1.1 + pyyaml>=6,<7 + typing-extensions>=4.6.2, <5 +diff --git a/src/toil/common.py b/src/toil/common.py +index d2531d3aa..c8852c8ce 100644 +--- a/src/toil/common.py ++++ b/src/toil/common.py +@@ -23,6 +23,7 @@ import tempfile + import time + import uuid + import warnings ++from io import StringIO + + from ruamel.yaml import YAML + from ruamel.yaml.comments import CommentedMap +@@ -580,15 +581,16 @@ def generate_config(filepath: str) -> None: + with AtomicFileCreate(filepath) as temp_path: + with open(temp_path, "w") as f: + f.write("config_version: 1.0\n") +- yaml = YAML(typ=['rt', 'string']) ++ yaml = YAML(typ='rt') + for data in all_data: + if "config_version" in data: + del data["config_version"] +- for line in yaml.dump_to_string(data).split("\n"): # type: ignore[attr-defined] +- if line: +- f.write("#") +- f.write(line) +- f.write("\n") ++ with StringIO() as data_string: ++ yaml.dump(data, data_string) ++ for line in data_string.readline(): ++ if line: ++ f.write("#") ++ f.write(f"{line}\n") + + + def parser_with_common_options( diff --git a/recipes/toil/meta.yaml b/recipes/toil/meta.yaml index 6baaf6c98595c..0f3965135414e 100644 --- a/recipes/toil/meta.yaml +++ b/recipes/toil/meta.yaml @@ -1,6 +1,6 @@ {% set name = "toil" %} -{% set version = "5.12.0" %} -{% set sha256 = "fb21c85b8654b0e628087ebd403fa5f53644d86a33a4c1e039ba5769dcaf6654" %} +{% set version = "6.0.0" %} +{% set sha256 = "6cf772b744b886a53eaaf700e51ea2fd03bac15d384c34ee9e53455cbe00b33b" %} package: name: {{ name|lower }} @@ -9,39 +9,43 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz sha256: {{ sha256 }} + patches: + - drop_ruamel_yaml_string_dependency.patch # https://github.com/DataBiosphere/toil/pull/4760 build: number: 0 noarch: python script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vvv + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} entry_points: - toil = toil.utils.toilMain:main - _toil_worker = toil.worker:main - toil-cwl-runner = toil.cwl.cwltoil:main [cwl] - toil-wdl-runner = toil.wdl.wdltoil:main [wdl] - - toil-wdl-runner-old = toil.wdl.toilwdl:main [wdl] - toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main [server] - _toil_mesos_executor = toil.batchSystems.mesos.executor:main [mesos] - _toil_contained_executor = toil.batchSystems.contained_executor:executor requirements: host: - - python >=3.7 + - python >=3.8 - pip run: - - python >=3.7 - - dill >=0.3.2 - - requests >=2 - - docker-py >=3.7.2,<6 - - urllib3 >=1.26.0 + - python >=3.8 + - dill >=0.3.2,<0.4 + - requests >=2,<3 + - docker-py >=3.7.2,<8 + - urllib3 >=1.26.0,<3 - python-dateutil - - psutil >=3.0.1 - # - py-tes >=0.4.2,<1 - - pypubsub >=4.0.3 - - addict >=2.2.1 + - psutil >=3.0.1,<6 + - pypubsub >=4.0.3,<5 + - addict >=2.2.1,<2.5 - pytz >=2012 - - enlighten >=1.5.2 - - typing-extensions + - enlighten >=1.5.2,<2 + - configargparse >=1.7,<2 + - typing-extensions >=4.6.2,<5 + - pyyaml >=6,<7 #mesos pymesos isn't available #server reqs # - wes-service is missing @@ -49,8 +53,8 @@ requirements: # - connexion >=2.10.0, <3 # - flask >=2.0,<3 # - werkzeug >=2.0,<3 - # - flask-cors ==3.0.10 - # - gunicorn ==20.1.0 + # - flask-cors ==4.0.0 + # - gunicorn ==21.2.0 # - celery >=5.1.0, <6 #aws reqs # mypy-boto3-{iam,sdb} are not yet in Conda @@ -66,20 +70,19 @@ requirements: - apache-libcloud >=2.2.1 - google-cloud-storage >=2,<=2.8.0 #cwl reqs - - cwltool ==3.1.20230601100705 + - cwltool ==3.1.20240112164112 - schema-salad >=8.4.20230128170514 - - galaxy-tool-util - - ruamel.yaml >=0.15,<=0.17.21 + - galaxy-tool-util <23 + - ruamel.yaml >=0.15,<=0.18.3 - ruamel.yaml.clib >=0.2.6 - - networkx >=2,<2.8.9 + - networkx <4 #htcondor reqs - python-htcondor >=10.2.0.post1 #kubernetes reqs - python-kubernetes >=12.0.1,<22 - idna >=2 #wdl reqs - # - wdlparse ==0.1.0 # not yet packaged for Conda - - mock >=4.0.3 + - miniwdl ==1.11.1 test: imports: From 9691d843fff82623afb3a2f67ec51f8bd5f7260e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 10:12:06 -0500 Subject: [PATCH 1621/2173] Update dimet to 0.2.0 (#45344) --- recipes/dimet/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dimet/meta.yaml b/recipes/dimet/meta.yaml index fcc2e26a6ff37..fd7147d1ce9d8 100644 --- a/recipes/dimet/meta.yaml +++ b/recipes/dimet/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dimet" %} -{% set version = "0.1.4" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dimet-{{ version }}.tar.gz - sha256: 372537f9c9aef2035868357df2c04e5f94bf3f6bef39f69988e25d114a8009ab + sha256: 40d5dee29232deb5722392c745a70f757c78128829b372ce0093fe2fbaf9411e build: noarch: python From b3ab47c70daab9fa5fbc8325097d0f1f5a831349 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 14:40:33 -0500 Subject: [PATCH 1622/2173] Update htslib to 1.19.1 (#45340) --- recipes/htslib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml index de1440505082b..de0c0dc0023c1 100644 --- a/recipes/htslib/meta.yaml +++ b/recipes/htslib/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.19" %} +{% set version = "1.19.1" %} package: name: htslib @@ -11,7 +11,7 @@ build: source: url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2 - sha256: 8751c40c4fa7d1f23a6864c5b20a73744f8be68239535ae7729c5f7d394d0736 + sha256: 222d74d3574fb67b158c6988c980eeaaba8a0656f5e4ffb76b5fa57f035933ec requirements: build: From b428550ee36b1aa63ad776f12efa2bf18028d0ad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 15:47:57 -0500 Subject: [PATCH 1623/2173] Update samtools to 1.19.1 (#45353) --- recipes/samtools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index b17cf299e837e..3d45b94379193 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.19" %} +{% set version = "1.19.1" %} package: name: samtools @@ -11,7 +11,7 @@ build: source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - sha256: fa6b3b18e20851b6f3cb55afaf3205d02fcb79dae3b849fcf52e8fc10ff08b83 + sha256: 1f94915cc32dcb6095049ed57560d99b409ba9297f4316bab551d05bb57ff355 requirements: build: From 46f3966a65c9758a37d6b3b2397e7ebe22ac2c51 Mon Sep 17 00:00:00 2001 From: Bede Constantinides Date: Mon, 22 Jan 2024 22:10:01 +0000 Subject: [PATCH 1624/2173] Update hostile to 1.0.0, add new dep, update DOI (#45352) --- recipes/hostile/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/hostile/meta.yaml b/recipes/hostile/meta.yaml index 4f8c76370bf62..88d7df7ebd535 100644 --- a/recipes/hostile/meta.yaml +++ b/recipes/hostile/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.0" %} +{% set version = "1.0.0" %} package: name: hostile @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/h/hostile/hostile-{{ version }}.tar.gz - sha256: dd003b09a7f17a8fc126bc81c2b402d1ab5946916f1f55dbcffa4c9c3014a56a + sha256: abe985acf384703ff482d5712cc4b3367e7f777818a66cbd389e7bfc6c6ac76a build: noarch: python @@ -25,6 +25,7 @@ requirements: run: - bowtie2 ==2.4.5 - defopt >=6.4.0 + - dnaio >=1.2.0 - gawk >=5.1.0 - httpx >=0.24.1 - minimap2 >=2.26 @@ -50,4 +51,4 @@ about: extra: identifiers: - - doi:10.1101/2023.07.04.547735 + - doi:10.1093/bioinformatics/btad728 From 60b160c7fd04a28a3510f7ecd1d3305bf395fcdd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 20:52:07 -0500 Subject: [PATCH 1625/2173] Update deeplc to 2.2.27 (#45346) --- recipes/deeplc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/deeplc/meta.yaml b/recipes/deeplc/meta.yaml index 51849c0d6507f..053b4fee421bc 100644 --- a/recipes/deeplc/meta.yaml +++ b/recipes/deeplc/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DeepLC" %} -{% set version = "2.2.26" %} -{% set sha256 = "b4cbb3612a89fe82ddac6149a261f7440c721f4b87235ce534c4cbd95d424e1b" %} +{% set version = "2.2.27" %} +{% set sha256 = "611cd06f1a12a543289c4fa0bbb5364bc3dbeeca905464c7c2668f45fa2fa781" %} package: name: {{ name|lower }} From 7726086bf83bb665838d85b4f23b07dda0f5a5a6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 20:52:24 -0500 Subject: [PATCH 1626/2173] Update pangolin-data to 1.24 (#45347) --- recipes/pangolin-data/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangolin-data/meta.yaml b/recipes/pangolin-data/meta.yaml index 99468f431af4a..d8b1f3721fb4d 100644 --- a/recipes/pangolin-data/meta.yaml +++ b/recipes/pangolin-data/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.23.1" %} +{% set version = "1.24" %} package: name: pangolin-data @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pangolin-data/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3a845838cf31131d8bc7e0c19cb3e78e2c99a5894ac44452bfa5f86a91dca056 + sha256: 63e3eb2598b90d0b0c3ab6b9be34cd520c7b060751f5511e653616146407f839 build: number: 0 From 803a6438a4acf9e5930faf40126d8017ee715b04 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 22 Jan 2024 20:53:22 -0500 Subject: [PATCH 1627/2173] Update tides-ml to 1.1.3 (#45354) --- recipes/tides-ml/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tides-ml/meta.yaml b/recipes/tides-ml/meta.yaml index c3a3d4bc436e8..8700a6649354a 100644 --- a/recipes/tides-ml/meta.yaml +++ b/recipes/tides-ml/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tides-ml" %} -{% set version = "1.1.2" %} +{% set version = "1.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/TIdeS-ML-{{ version }}.tar.gz - sha256: 17ad86b841d5e8fca4dbad58d114aa919d332a22190c7d002472ec6c1541609a + sha256: a2a872ac26c24705a6f538823b53081ae456a313fa587520997418fbda8e612e build: entry_points: From aaa38efca76e6960ee89273e69656fe9875f82a3 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Mon, 22 Jan 2024 17:56:06 -0800 Subject: [PATCH 1628/2173] Update augur to 24.0.0 (#45357) Includes dependency changes. --- recipes/augur/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index 21d5c1cf2ebbe..c890f6e104b18 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "23.1.1" %} +{% set version = "24.0.0" %} package: name: augur @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: 1b6f8fb1f20c147d24806764761f8e977c8e100a58e04e06d3110bb72268518f + sha256: 6766330e7db7d6ceab8256b1f815882fdf3a9dccdeb224f316266d7983f2a407 build: - number: 1 + number: 0 noarch: python entry_points: - augur = augur.__main__:main @@ -24,7 +24,7 @@ requirements: run: - python >=3.8 - bcbio-gff >=0.7.0,<0.8 - - biopython >=1.73,!=1.77,!=1.78 + - biopython >=1.73,!=1.77,!=1.78,<1.82 - cvxopt >=1.1.9,<2 - importlib_resources >=5.3.0 # [py<311] - isodate >=0.6.0,<0.7 @@ -35,7 +35,7 @@ requirements: - pandas >=1.0.0,<2 - pyfastx >=1.0.0,<3 - scipy >=1.0.0,<2 - - treetime >=0.10.0,<0.12 + - treetime >=0.11.2,<0.12 - xopen[zstd] >=1.7.0,<2 - fasttree From eb0e85b0caaa301485dc420503a01d2c074aec85 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 03:12:00 -0500 Subject: [PATCH 1629/2173] Update koverage to 0.1.8 (#45360) --- recipes/koverage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/koverage/meta.yaml b/recipes/koverage/meta.yaml index 385acafa06329..e9a66d5265d47 100644 --- a/recipes/koverage/meta.yaml +++ b/recipes/koverage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "koverage" %} -{% set version = "0.1.7" %} +{% set version = "0.1.8" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 75561037d21f1577200b659d097ef72ccb305f2cf5323eabda5d86cee15916ff + sha256: 0680e72916022fbedbf14c9dc5daa0e159e41196f81da15b5e9367d93af0832a build: noarch: python From 5803cf48b487ba90e21a692d5c1c7cc15cebd064 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Tue, 23 Jan 2024 11:15:33 +0100 Subject: [PATCH 1630/2173] Bump svync to v0.1.1 (#45365) --- recipes/svync/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/svync/meta.yaml b/recipes/svync/meta.yaml index a19463ec08781..57d179ecbcf9d 100644 --- a/recipes/svync/meta.yaml +++ b/recipes/svync/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.1.0' %} +{% set version = '0.1.1' %} {% set name = 'svync' %} package: @@ -7,9 +7,9 @@ package: source: - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-darwin-amd64.tar.gz # [osx-amd64] - md5: 62bc02c3f3dc52fd02b998f6f0223216 # [osx] + md5: 2fb00fc49591526cc61e445cc75526d5 # [osx] - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-linux-amd64.tar.gz # [linux] - md5: dbc6b403d5ce1bcef9ba07ad7e1a5dc9 # [linux] + md5: c119b00f23e0e4310e7971fbb6aef9a9 # [linux] build: number: 0 From 403c4b7df97ff2fd5fc5a93c821a34a7ddac84d2 Mon Sep 17 00:00:00 2001 From: aguus8 <139561482+aguus8@users.noreply.github.com> Date: Tue, 23 Jan 2024 14:20:31 +0100 Subject: [PATCH 1631/2173] [biobb_pdb_tools] update 4.1.1 (#45348) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [v4.1.0] update 2023.4 * [v4.1.0] update 2023.4 * [biobb_pdb_tools] update 4.1.1 * [biobb_pdb_tools] update 4.1.1 --------- Co-authored-by: Agustín García Doñate Co-authored-by: Agustin Garcia Doñate Co-authored-by: Genís Bayarri --- recipes/biobb_pdb_tools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biobb_pdb_tools/meta.yaml b/recipes/biobb_pdb_tools/meta.yaml index 2de77d46048e3..44c5d7c9dec38 100644 --- a/recipes/biobb_pdb_tools/meta.yaml +++ b/recipes/biobb_pdb_tools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_pdb_tools" %} -{% set version = "4.1.0" %} +{% set version = "4.1.1" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: a956ceb461219df25154a59c8b319c79802f0f7975095837aef40d6b057c0744 + sha256: 7510052e89c534f935f1b70b575943fe391dc0bc837c4c0982c7cb3d944adb29 build: number: 0 From 12db1c1ed28fc15008511703609916ee0e32566a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 08:22:06 -0500 Subject: [PATCH 1632/2173] Update gget to 0.28.3 (#45355) --- recipes/gget/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gget/meta.yaml b/recipes/gget/meta.yaml index 0c155d5a9aec3..fa18fdcf7a298 100644 --- a/recipes/gget/meta.yaml +++ b/recipes/gget/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gget" %} -{% set version = "0.28.2" %} -{% set sha256 = "2bc24c484e26fdd25646f66089e08edf101c344e9ddb9aaeb1484fac3e1d2a99" %} +{% set version = "0.28.3" %} +{% set sha256 = "4f9e2f3e445b7e898e1a12fa7460604330e73d917c8e357a91a09c0c005b64b9" %} package: name: "{{ name|lower }}" From cf9188ed66f55b4d06491df52cb6bbd6e3e66ec8 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Tue, 23 Jan 2024 16:17:02 +0100 Subject: [PATCH 1633/2173] Bump svync to v0.1.2 (#45371) --- recipes/svync/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/svync/meta.yaml b/recipes/svync/meta.yaml index 57d179ecbcf9d..9430c018d9b6c 100644 --- a/recipes/svync/meta.yaml +++ b/recipes/svync/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.1.1' %} +{% set version = '0.1.2' %} {% set name = 'svync' %} package: @@ -7,9 +7,9 @@ package: source: - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-darwin-amd64.tar.gz # [osx-amd64] - md5: 2fb00fc49591526cc61e445cc75526d5 # [osx] + md5: 2f64a4d9b81124917766bd8a754ea470 # [osx] - url: https://github.com/nvnieuwk/svync/releases/download/{{ version }}/svync-{{ version }}-linux-amd64.tar.gz # [linux] - md5: c119b00f23e0e4310e7971fbb6aef9a9 # [linux] + md5: 298f930c1f30918bd41d07db5bbfd348 # [linux] build: number: 0 From 50d489b7ef5bcbfe367bb7c84473a49dbe8f6b8e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 11:11:53 -0500 Subject: [PATCH 1634/2173] Update sevenbridges-python to 2.10.1 (#45369) --- recipes/sevenbridges-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index 7c534eeee72b4..7bdcd4c93f64a 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.10.0" %} -{% set sha256 = "6e370de45b5af6574a2937e8a8aba76108f779f55982b360eb796a113e9399e6" %} +{% set version = "2.10.1" %} +{% set sha256 = "5db46a3fce7b0235be9273ec070092775be43e4bb1b2787c349f3598eaa3fd07" %} package: name: sevenbridges-python From 041e258e2a5e645a6d79d49f09a50c96ba985dae Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 11:13:31 -0500 Subject: [PATCH 1635/2173] Update assemblycomparator2 to 2.5.17 (#45368) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index b5640b7519dd6..6c929a7075290 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.16" %} +{% set version = "2.5.17" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 197d157e67a04df4f63b88191106dce7219eab8ee4aa146b74d4fb796a505e93 + sha256: 5c15c4882529d33d56678eb3b710e243e3f5adc49b7d0ad1871f26ecab69d97e build: From b2f8c9db39bea461de7026a8f8941627a86c19f6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 11:13:55 -0500 Subject: [PATCH 1636/2173] Update snakemake-interface-common to 1.15.2 (#45367) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index c5e119044e696..4cfc57b3f3c14 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.15.1" %} +{% set version = "1.15.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 5a779c7a0f27412bce26e1dfe4ccc712d04e0c0b9ceaa1640335a35d02509732 + sha256: f2a4908a5ec5d6e657723f90221da3c136e70a1c5897b4e1d65a703bc08e8d7a build: noarch: python From 633beaa108c206dbd3b0e04ca8f1a8d8c29e0f58 Mon Sep 17 00:00:00 2001 From: Samuel Aroney <41124903+AroneyS@users.noreply.github.com> Date: Wed, 24 Jan 2024 06:31:23 +1000 Subject: [PATCH 1637/2173] Update CoverM to v0.7.0 (#45332) * bump CoverM to v0.7.0 * fix name * update sha256 * add cmake to build * add make to build --- recipes/coverm/meta.yaml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/recipes/coverm/meta.yaml b/recipes/coverm/meta.yaml index 7e12b62eb8ef2..90634a04ae368 100644 --- a/recipes/coverm/meta.yaml +++ b/recipes/coverm/meta.yaml @@ -1,14 +1,16 @@ -{% set version = "0.6.1" %} +{% set version = "0.7.0" %} {% set name = "coverm" %} -{% set sha256 = "b6211e6f89ef986691b910d7d7b4c6d1e9eb9beb64e4f71902178ed60d27f4e6" %} +{% set sha256 = "539142529d2590166e98ed399db36913fbf8b256d8c74a1966acae849c18a828" %} package: name: {{ name }} version: {{ version }} build: - number: 6 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage('coverm', max_pin="x.x") }} source: url: https://github.com/wwood/{{ name }}/archive/v{{ version }}.tar.gz @@ -21,6 +23,8 @@ requirements: - {{ compiler('cxx') }} - clangdev # one of the rust submodules explicitly requires clang. As it's statically compiled that will hopefully work - pkg-config + - make + - cmake host: - zlib - gsl @@ -43,4 +47,5 @@ test: about: home: https://github.com/wwood/CoverM license: GPL3 + license_family: GPL3 summary: CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications From 967deffcbe5942490aa42f763313c7675b0eb210 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 19:47:49 -0500 Subject: [PATCH 1638/2173] Update pybiolib to 1.1.1691 (#45383) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index b4b1f16fe1b7d..bbcec685a8ceb 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1689" %} +{% set version = "1.1.1691" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: f33b444bdbde72a8b93f236777544de8d2a5fc0633f7cdb4c1e73f392eae0040 + sha256: 5f25f9028e05b606a32a452fb065288915d94a010481db935ddc2379812abec6 build: noarch: python From c2daddc4b7c9d28d43792a8eea8a620c41bef23f Mon Sep 17 00:00:00 2001 From: "Le (Lena) Huang" Date: Tue, 23 Jan 2024 20:38:36 -0500 Subject: [PATCH 1639/2173] update dbcan to 4.1.4 (#45374) --- recipes/dbcan/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/dbcan/meta.yaml b/recipes/dbcan/meta.yaml index 34d2f399cac8b..4c247128ceb5f 100644 --- a/recipes/dbcan/meta.yaml +++ b/recipes/dbcan/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dbcan" %} -{% set version = "4.1.3" %} +{% set version = "4.1.4" %} package: name: "{{ name|lower }}" @@ -9,7 +9,8 @@ source: # the sha256 sum is generated by doing # wget -0- [URL] | shasum -a 256 url: https://github.com/linnabrown/run_dbcan/releases/download/{{ version }}/dbcan-{{ version }}.tar.gz - sha256: 6346e0b6b2c810e2f808bc0bc901643c16f3eda2652d50b8f8470eb722fb419b + sha256: 12dc906b56c3b1bfea667aa617d46d3f292857fc360730e4fe1d35f5b5557215 + build: number: 0 From 41fe79438923dbb864d41bf679f51d57c448d9cb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 20:40:42 -0500 Subject: [PATCH 1640/2173] Update earlgrey to 4.0.5 (#45361) * Update earlgrey to 4.0.4 * Update earlgrey to 4.0.5 --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index caa4eddb4e6a7..268616558bed9 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.3" %} -{% set sha256 = "5715301151d7d6609aa703c9c174f00e1bde61c6d2f0493f5c01831d95152fb0" %} +{% set version = "4.0.5" %} +{% set sha256 = "5fe1341dad3da2bf322415cb048a846173e386b1998be188828f3c905349daa8" %} package: name: {{ name|lower }} From 96ee4c0cc15ac19dd533358f8f3eacda6ba0fdbd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 20:41:35 -0500 Subject: [PATCH 1641/2173] Update bakta to 1.9.2 (#45373) Co-authored-by: Oliver Schwengers --- recipes/bakta/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml index 98a9068bd9875..f33a11054a52e 100644 --- a/recipes/bakta/meta.yaml +++ b/recipes/bakta/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.9.1" %} +{% set version = "1.9.2" %} package: name: bakta @@ -6,7 +6,7 @@ package: source: url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz - sha256: 'd8eb7ea1321ad6884002cfac670c33031b8dfa219a62b90c556f7cf402a64fe4' + sha256: '145b0209fe6a0c67a1a1a6e5c108e99bad0a86e3b1db0a9d24261744725fe257' build: noarch: python From 16f7d49d3d9bba2523956c57fec6e564239ca444 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 20:43:49 -0500 Subject: [PATCH 1642/2173] Update igv-reports to 1.11.0 (#45378) --- recipes/igv-reports/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/igv-reports/meta.yaml b/recipes/igv-reports/meta.yaml index 6335f9d235f6d..8b464c54de237 100644 --- a/recipes/igv-reports/meta.yaml +++ b/recipes/igv-reports/meta.yaml @@ -1,5 +1,5 @@ {% set name = "igv-reports" %} -{% set version = "1.10.0" %} +{% set version = "1.11.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8cbe26d120ca4d599c7ffb8077dc4501a5ef29cf76a69f187ce1cd948ef0f451 + sha256: 8a524c53f4bbcf93d58a2b2246d8473b22bea1955a492f81365c4c27164efe86 build: noarch: python From 7de974ce291b45f965fa2b0b35058e6554d5fe31 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 20:44:04 -0500 Subject: [PATCH 1643/2173] Update taxmyphage to 0.2.7 (#45379) --- recipes/taxmyphage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxmyphage/meta.yaml b/recipes/taxmyphage/meta.yaml index 0d0b81c087803..379c12a36a2bd 100644 --- a/recipes/taxmyphage/meta.yaml +++ b/recipes/taxmyphage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "taxmyphage" %} -{% set version = "0.2.6" %} +{% set version = "0.2.7" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxmyphage-{{ version }}.tar.gz - sha256: 1058adb02296ec0493b21dedd899447a144804230a4e13f4c98f94dcc0548076 + sha256: 8208758ca9814435a72ffd11ba76538a829c355c73b276f567962c2334b149ec build: entry_points: From 03454712f0e03f9a54113b28ef375ad671367ff0 Mon Sep 17 00:00:00 2001 From: Arafat Rahman Date: Tue, 23 Jan 2024 17:47:06 -0800 Subject: [PATCH 1644/2173] 1.1.0 release update (#45385) --- recipes/beav/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/beav/meta.yaml b/recipes/beav/meta.yaml index 51c26396cf4a7..61b78a68727b4 100644 --- a/recipes/beav/meta.yaml +++ b/recipes/beav/meta.yaml @@ -1,6 +1,6 @@ {% set name = "beav" %} -{% set version = "1.0.0" %} -{% set sha256 = "b0e65b26c2e5760bfa31587d153d3df902ee34606bc0f4059622dbcb8269ffc4" %} +{% set version = "1.1.0" %} +{% set sha256 = "f9a65ac152b33c8649b51e152cc7137036140f5e2d7460f162ebd180aac3f868" %} {% set dbscan_git = "condabeav0.5" %} {% set dbscan_sha256 = "2fe08873026fe63a9992bfb997e59fecce7facb903778983dc6917c962573463" %} {% set gapmind_git = "Beav0.5.1conda" %} From 05de4f0d5f8aee7a399691eada6b2831e07b59da Mon Sep 17 00:00:00 2001 From: Kristy Horan Date: Wed, 24 Jan 2024 13:01:07 +1100 Subject: [PATCH 1645/2173] Add missing deps tbtamr (#45359) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * added in tbtamr * added in tbtamr * added in tbtamr * added in tbtamr * added in tbtamr * added in tbtamr * Update recipes/tbtamr/meta.yaml Co-authored-by: Björn Grüning * addressed issues with licence * adding licence file * added max_pin x.x * adding in missing dependencies tqdm, xlsxwriter, requests * bump build --------- Co-authored-by: Björn Grüning --- recipes/tbtamr/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/tbtamr/meta.yaml b/recipes/tbtamr/meta.yaml index 435271ec684fd..459fa16a643f1 100644 --- a/recipes/tbtamr/meta.yaml +++ b/recipes/tbtamr/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: python - number: 0 + number: 1 entry_points: - tbtamr=tbtamr.tbtamr:main run_exports: @@ -36,6 +36,10 @@ requirements: - bcftools - bedtools - delly + - xlsxwriter + - requests + - tqdm + test: imports: From 000d71e7f2cad288520a48467d0f20089f4f9566 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 21:25:01 -0500 Subject: [PATCH 1646/2173] Update trackplot to 0.3.7 (#45362) * Update trackplot to 0.3.7 * pin python to <3.12 --------- Co-authored-by: mencian --- recipes/trackplot/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/trackplot/meta.yaml b/recipes/trackplot/meta.yaml index 0c723aed874f0..f0d3984428fb9 100644 --- a/recipes/trackplot/meta.yaml +++ b/recipes/trackplot/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trackplot" %} -{% set version = "0.3.6" %} +{% set version = "0.3.7" %} package: name: trackplot @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f1f8706c954abd0f8c426f1c3ed51b458d69940c8a275aa61544864788a93956 + sha256: 5e650448e71d81eaae61fbbdcf88e8130b79f008278128ee1311c2b16a24b803 build: noarch: python @@ -20,11 +20,11 @@ build: requirements: host: - - python >=3.8 + - python >=3.8,<3.12 - pip - poetry-core run: - - python >=3.8 + - python >=3.8,<3.12 - adjusttext >=0.7.3 - cairocffi >=1.4.0 - click From 6b46a407adb4db6fee665fd49d7bc7ba2fd41cf0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 21:49:19 -0500 Subject: [PATCH 1647/2173] Update varfish-cli to 0.6.2 (#45363) --- recipes/varfish-cli/meta.yaml | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/recipes/varfish-cli/meta.yaml b/recipes/varfish-cli/meta.yaml index cc5fa0f456492..30c63c249cf4e 100644 --- a/recipes/varfish-cli/meta.yaml +++ b/recipes/varfish-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.5.3" %} -{% set sha256 = "ae8ee0314f0ebcfacf44518d7dcca4d9aba74d3fa50159fd0adbc04017671677" %} +{% set version = "0.6.2" %} +{% set sha256 = "62633a89b55e8fa0d93acd91deb5d231ac567ecdc76b530ae0e4b000a7c5dea7" %} package: name: varfish-cli @@ -10,9 +10,13 @@ source: sha256: '{{sha256}}' build: - script: python -m pip install --no-deps --ignore-installed . - noarch: python + noarch: python number: 0 + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + entry_points: + - varfish-cli = varfish_cli.__main__:main + run_exports: + - {{ pin_subpackage('varfish-cli', max_pin="x.x") }} requirements: host: @@ -29,9 +33,11 @@ requirements: - tqdm - tabulate - polyleven + - pydantic - python-dateutil - simplejson - typeguard + - typer test: imports: From b871e2bf592177a0e7ae046fc8920c531a6b3153 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 21:50:29 -0500 Subject: [PATCH 1648/2173] Update r-conos to 1.5.1 (#45364) * Update r-conos to 1.5.1 * add run_exports --------- Co-authored-by: mencian --- recipes/r-conos/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/r-conos/meta.yaml b/recipes/r-conos/meta.yaml index 78c4f6043b388..d7c122620cdaf 100644 --- a/recipes/r-conos/meta.yaml +++ b/recipes/r-conos/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.5.0' %} +{% set version = '1.5.1' %} package: name: r-conos @@ -8,13 +8,15 @@ source: url: - {{ cran_mirror }}/src/contrib/conos_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/conos/conos_{{ version }}.tar.gz - sha256: dcf4afbbf3c744e8e4f1bd4472bb4c8f18a1d18d9f2bf854372d12d8e558b0f1 + sha256: bb479d63a2836bfa163b6abc9f8f2bac9e081cdcc5b781f1bee201e7b99da205 build: - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-conos', max_pin="x") }} requirements: build: From 5edfb3a9c742c6355c59ee63fddd5d81ba973b73 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 21:50:45 -0500 Subject: [PATCH 1649/2173] Update r-tinyarray to 2.3.2 (#45336) * Update r-tinyarray to 2.3.2 * add run_exports --------- Co-authored-by: mencian --- recipes/r-tinyarray/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/r-tinyarray/meta.yaml b/recipes/r-tinyarray/meta.yaml index 1a61d8ba0282c..2284c61513a42 100644 --- a/recipes/r-tinyarray/meta.yaml +++ b/recipes/r-tinyarray/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '2.3.1' %} +{% set version = '2.3.2' %} package: name: r-tinyarray @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/tinyarray_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/tinyarray/tinyarray_{{ version }}.tar.gz - sha256: 68ea15eb8d726368919faa54c89e2d18806b94e73e21fdee365c350b7ee79eb3 + sha256: 32d74c2e64b88fb973a2ade4162f4a2c3ec9127d41966768301b518cdcac5654 build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-tinyarray', max_pin="x") }} requirements: host: From 7f69606c4b43e8f0131326a00f553c5bc6616194 Mon Sep 17 00:00:00 2001 From: Guy Assa <78320514+theAguy@users.noreply.github.com> Date: Wed, 24 Jan 2024 04:56:34 +0200 Subject: [PATCH 1650/2173] better translocation detection (#45345) * better translocation detection * better translocation detection take 2 * better translocation detection take 3 * better translocation detection take 4 --- recipes/crispector/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/crispector/meta.yaml b/recipes/crispector/meta.yaml index eead4a143981d..0032615c4b7e3 100644 --- a/recipes/crispector/meta.yaml +++ b/recipes/crispector/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.4" %} +{% set version = "1.0.7" %} package: name: crispector @@ -10,10 +10,12 @@ build: - crispector = crispector.cli:main noarch: python script: python -m pip install . --no-deps -vv + run_exports: + - {{ pin_subpackage('crispector', max_pin="x") }} source: - url: https://github.com/YakhiniGroup/crispector/archive/v{{ version }}.tar.gz - sha256: 66b4ecc6f73958221eed868200c00d3c39718e9a146c389da9fcbd16440f6f1f + url: https://github.com/YakhiniGroup/crispector/archive/refs/tags/V{{ version }}.tar.gz + sha256: f88a8807e9793c7fb9db341f5ba9f130e59f557ecac55b625eb0dcd61ad38b9c requirements: host: @@ -35,6 +37,7 @@ requirements: - pandas >=0.24.2 - statsmodels - jinja2 + - mpmath >=1.3.0 test: commands: From 78d2b88126b8d1ec30943bcdd5a294d76ab911af Mon Sep 17 00:00:00 2001 From: Travis Wrightsman Date: Tue, 23 Jan 2024 21:59:20 -0500 Subject: [PATCH 1651/2173] Build shared library for quicktree (#45326) * Build shared library for quicktree * Make BSD mkdir happy --- recipes/quicktree/build.sh | 9 +++- recipes/quicktree/meta.yaml | 11 +++-- ...001-Add-rule-to-build-shared-library.patch | 43 +++++++++++++++++++ 3 files changed, 59 insertions(+), 4 deletions(-) create mode 100644 recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch diff --git a/recipes/quicktree/build.sh b/recipes/quicktree/build.sh index 6796b7efd05b6..7d776e66d9e68 100644 --- a/recipes/quicktree/build.sh +++ b/recipes/quicktree/build.sh @@ -1,5 +1,12 @@ #!/bin/bash -mkdir -p $PREFIX/bin +set -eux + +mkdir -p "$PREFIX"/{bin,lib,include/quicktree} + make CC=$CC + cp quicktree $PREFIX/bin +cp libquicktree.so "${PREFIX}/lib/" +# some header files are named generic enough to warrant namespacing +cp include/*.h "${PREFIX}/include/quicktree/" diff --git a/recipes/quicktree/meta.yaml b/recipes/quicktree/meta.yaml index b663ce6822c58..5c6cb7814f9f8 100644 --- a/recipes/quicktree/meta.yaml +++ b/recipes/quicktree/meta.yaml @@ -1,21 +1,26 @@ +{% set name = "quicktree" %} {% set version = "2.5" %} package: - name: quicktree + name: {{ name }} version: {{ version }} source: url: https://github.com/khowe/quicktree/archive/v{{ version }}.tar.gz sha256: 731aa845ce3f1f0645bd0df2b54df75f78fce065d6a3ddc47fedf4bdcb11c248 + patches: + - patches/0001-Add-rule-to-build-shared-library.patch build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + requirements: build: - make - {{ compiler('c') }} - run: test: commands: diff --git a/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch b/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch new file mode 100644 index 0000000000000..509748c0811eb --- /dev/null +++ b/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch @@ -0,0 +1,43 @@ +From 390c2db84a0fd0ff3a05d77407d18da3b9c26d63 Mon Sep 17 00:00:00 2001 +From: Travis Wrightsman +Date: Sat, 20 Jan 2024 17:46:20 -0500 +Subject: [PATCH] Add rule to build shared library + +--- + Makefile | 9 ++++++--- + 1 file changed, 6 insertions(+), 3 deletions(-) + +diff --git a/Makefile b/Makefile +index 14e42a4..7fe8385 100644 +--- a/Makefile ++++ b/Makefile +@@ -15,15 +15,18 @@ QUICKTREEOBJ = $(COMMON) $(OBJ)/quicktree.o $(OBJ)/buildtree.o $(OBJ)/tree.o + + + CC = gcc +-CFLAGS = -c -I$(INC) -O2 -Wunused-result ++CFLAGS = -c -I$(INC) -O2 -Wunused-result -fPIC + + LFLAGS = -g + +-all: quicktree ++all: quicktree libquicktree.so + + quicktree : $(QUICKTREEOBJ) + $(CC) $(LFLAGS) -o $@ $(QUICKTREEOBJ) -lm + ++libquicktree.so: $(QUICKTREEOBJ) ++ $(CC) -shared $(LFLAGS) -o $@ $(QUICKTREEOBJ) -lm ++ + $(OBJ)/quicktree.o : $(SRC)/quicktree.c $(INC)/version.h + $(CC) $(CFLAGS) -o $(OBJ)/quicktree.o $(SRC)/quicktree.c + +@@ -52,4 +55,4 @@ $(OBJ)/options.o : $(SRC)/options.c $(INC)/options.h + $(CC) $(CFLAGS) -o $(OBJ)/options.o $(SRC)/options.c + + clean: +- rm $(OBJ)/*.o quicktree ++ rm $(OBJ)/*.o quicktree libquicktree.so +-- +2.39.2 + From 901ab33636ee844b15e55293dc1a39d477d324bc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 23 Jan 2024 23:29:07 -0500 Subject: [PATCH 1652/2173] Update presto to 0.7.2 (#45381) * Update presto to 0.7.2 * add run_exports * add name variable * add packaging --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/presto/build.sh | 9 --------- recipes/presto/meta.yaml | 27 ++++++++++++++++++++------- 2 files changed, 20 insertions(+), 16 deletions(-) delete mode 100755 recipes/presto/build.sh diff --git a/recipes/presto/build.sh b/recipes/presto/build.sh deleted file mode 100755 index 4899c226c8dd0..0000000000000 --- a/recipes/presto/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/presto/meta.yaml b/recipes/presto/meta.yaml index 8db5c41676eea..e3fdd0365f366 100644 --- a/recipes/presto/meta.yaml +++ b/recipes/presto/meta.yaml @@ -1,19 +1,26 @@ +{% set name = "presto" %} +{% set version = "0.7.2" %} +{% set sha256 = "b4f4b34413af4207eb2052316d31d7bc2067b864286498476d89013ad5423dd9" %} + package: - name: presto - version: "0.7.1" + name: {{ name }} + version: {{ version }} source: - url: https://files.pythonhosted.org/packages/ca/12/09123b431758827082924054e03277207067853c6af19803f67d1ad1dea9/presto-0.7.1.tar.gz - sha256: 8b5787b3a3206fda5e5cd0fd1804a6c0ecb8821f9de2b78d9a5e5a5a31ba43e9 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/presto-{{ version }}.tar.gz + sha256: {{ sha256 }} build: number: 0 noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('presto', max_pin="x.x") }} requirements: host: - python >=3 - - setuptools + - pip run: - python >=3 - numpy >=1.8 @@ -23,6 +30,7 @@ requirements: - blast >=2.5 - muscle >=3.8 - vsearch >=2.3.2 + - packaging test: commands: @@ -41,7 +49,12 @@ test: - SplitSeq.py --version about: - home: https://presto.readthedocs.io - license: AGPL-3.0 + home: https://bitbucket.org/kleinstein/presto + license: AGPL-3.0-or-later summary: 'A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.' license_family: AGPL + doc_url: https://presto.readthedocs.io + +extra: + identifier: + - doi:10.1093/bioinformatics/btu138 From fdbbb385540bbdf1160292c94468ff77030a69fa Mon Sep 17 00:00:00 2001 From: Jim Shaw Date: Tue, 23 Jan 2024 23:30:05 -0500 Subject: [PATCH 1653/2173] Add floria recipe. (#45334) * add floria * removed extra file --- recipes/floria/build.sh | 8 ++++++++ recipes/floria/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 recipes/floria/build.sh create mode 100644 recipes/floria/meta.yaml diff --git a/recipes/floria/build.sh b/recipes/floria/build.sh new file mode 100644 index 0000000000000..3662f6efb60db --- /dev/null +++ b/recipes/floria/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --verbose --path . --root $PREFIX diff --git a/recipes/floria/meta.yaml b/recipes/floria/meta.yaml new file mode 100644 index 0000000000000..ff7c268607c96 --- /dev/null +++ b/recipes/floria/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "0.0.1" %} + +package: + name: floria + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('floria', max_pin="x") }} + +source: + url: https://github.com/bluenote-1577/floria/archive/v{{ version }}.tar.gz + sha256: 48430783e411225a90282f65afb05a1e7e3d1d2bfb78fa838e359802530f4be1 + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.62 + - make + - cmake >=3.12 + +test: + commands: + - floria --help + +about: + home: https://github.com/bluenote-1577/floria + license: MIT + summary: Floria is method for recovering strain-level haplotypes and clusters of reads from metagenomic short or long read sequencing data by haplotype phasing. + + +extra: + recipe-maintainers: + - bluenote-1577 + From 1cbbf31b02efee83caf54a85152a7b76c52e0b85 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 00:54:05 -0500 Subject: [PATCH 1654/2173] Update dnaapler to 0.5.2 (#45386) --- recipes/dnaapler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnaapler/meta.yaml b/recipes/dnaapler/meta.yaml index 5737d45fcec6a..699f0fa47dae3 100644 --- a/recipes/dnaapler/meta.yaml +++ b/recipes/dnaapler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dnaapler" %} -{% set version = "0.5.1" %} +{% set version = "0.5.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 9bc6289ebefaa2e9725709cae2dbfa2723ad0d4e7f073f781a23e9b799bac8a8 + sha256: 3e0a03afdf00c20943892184062d9b778d3d8b2b549605a69c883a8f5e68e946 build: number: 0 From e0cd29e585de372d4bd7513340e89e4245ec7466 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 08:36:13 -0500 Subject: [PATCH 1655/2173] Update varfish-cli to 0.6.3 (#45391) --- recipes/varfish-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varfish-cli/meta.yaml b/recipes/varfish-cli/meta.yaml index 30c63c249cf4e..f65d88b9dd723 100644 --- a/recipes/varfish-cli/meta.yaml +++ b/recipes/varfish-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6.2" %} -{% set sha256 = "62633a89b55e8fa0d93acd91deb5d231ac567ecdc76b530ae0e4b000a7c5dea7" %} +{% set version = "0.6.3" %} +{% set sha256 = "7a7344b3d88b8ac303f0a54f7709fa528fe1555dd6e935c45e6ec452d955871d" %} package: name: varfish-cli From d559313cdb417f8650ca4500910c8b7e5555a218 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 10:51:30 -0500 Subject: [PATCH 1656/2173] Update vcf2variants to 1.3 (#45402) --- recipes/vcf2variants/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vcf2variants/meta.yaml b/recipes/vcf2variants/meta.yaml index ce21048d701da..1e86cba1234ab 100644 --- a/recipes/vcf2variants/meta.yaml +++ b/recipes/vcf2variants/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcf2variants" %} -{% set version = "1.2" %} +{% set version = "1.3" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 7830202ec67de08e7b223649365eed4a4a66d1339c985123d21c65cca7283728 + sha256: 152f8e97ae8d23613672e93b33713e4fb620a92bbae72bd052e75e2fc409db12 build: number: 0 From ed9d31bb8134593f670c28b657be5e1f20a6119b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 10:52:40 -0500 Subject: [PATCH 1657/2173] Update scirpy to 0.15.0 (#45395) * Update scirpy to 0.15.0 * Update meta.yaml --------- Co-authored-by: Gregor Sturm --- recipes/scirpy/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/scirpy/meta.yaml b/recipes/scirpy/meta.yaml index 1d42f7a62616a..91d97a5982193 100644 --- a/recipes/scirpy/meta.yaml +++ b/recipes/scirpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "scirpy" %} -{% set version = "0.14.0" %} +{% set version = "0.15.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 26a5a5374503925c1db16595ef67b1814a6389a4932edc2aa48607a47a00bf43 + sha256: 4b0e5ce9fa8a874f0dd502a9493d9201dd6afc673512ab0287644a98c77b3744 folder: "{{ name }}-{{ version }}" build: @@ -45,6 +45,7 @@ requirements: - numba >=0.41.0 - pooch >=1.7.0 - pycairo >=1.20 # [win] + - joblib >=1.3.1 test: imports: From ef91dce8e442b3f3d3306e257d5321ddb7bed14e Mon Sep 17 00:00:00 2001 From: tlacroix Date: Wed, 24 Jan 2024 16:55:07 +0100 Subject: [PATCH 1658/2173] Update icescreen v1.3.1 (#45377) * Update icescreen v1.3.1 * added run_exports section * try rerun tests because of weird CircleCI Pipeline No configuration error --- recipes/icescreen/meta.yaml | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/recipes/icescreen/meta.yaml b/recipes/icescreen/meta.yaml index aac6a83ed3f11..a1d4fdde1d551 100644 --- a/recipes/icescreen/meta.yaml +++ b/recipes/icescreen/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ICEscreen" %} -{% set version = "1.2.0" %} +{% set version = "1.3.1" %} package: name: "{{ name|lower }}" @@ -7,11 +7,13 @@ package: source: url: https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/archive/v{{ version }}/icescreen-v{{ version }}.tar.gz - sha256: 21b163a5dc0f6a745d97aa6185aa94ccc4ecfe14553cc75ed71429ee1da9c122 + sha256: 283fb2bf95eb9066a535a25f7df94f6ec9d4b78083d62bd5237f801e94ac02d5 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('icescreen', max_pin="x") }} requirements: host: @@ -20,10 +22,10 @@ requirements: - hmmer =3.3.2 run: - python - - pandas >=2.0.0 - - snakemake-minimal >=7.25.0 - - biopython >=1.81 - - bcbio-gff >=0.7.0 + - pandas >=2.1.0 + - snakemake-minimal >=7.32 + - biopython =1.81 + - bcbio-gff =0.7.0 - blast =2.12 - hmmer =3.3.2 @@ -35,9 +37,10 @@ about: home: https://forgemia.inra.fr/ices_imes_analysis/icescreen license: AGPL-3.0-or-later license_family: AGPL - summary: "ICEscreen detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes." + summary: "ICEscreen detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes." doc_url: icescreen.migale.inrae.fr extra: recipe-maintainers: - thomas-lacroix + From 1fb02fc8aef42063089a15d220a4a9d5fa561511 Mon Sep 17 00:00:00 2001 From: "Moritz E. Beber" Date: Wed, 24 Jan 2024 16:56:27 +0100 Subject: [PATCH 1659/2173] Add memote (#43071) * feat: add first version of memote recipe * fix: pip install click-configfile * chore: ignore dependencies * fix: add run_exports section * fix: use name directly * fix: pin depinfo * fix: add missing dependencies * fix: use updated version with new dependencies * fix: change how the Python version is pinned * Apparently, <3.11 is not honored. * Statistics is only available for Python <3. This makes use of goodtables impossible for which we currently don't have a replacement. * fix: update dependencies --- recipes/memote/meta.yaml | 77 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 recipes/memote/meta.yaml diff --git a/recipes/memote/meta.yaml b/recipes/memote/meta.yaml new file mode 100644 index 0000000000000..ee4d6467bc3cd --- /dev/null +++ b/recipes/memote/meta.yaml @@ -0,0 +1,77 @@ +{% set name = "memote" %} +{% set version = "0.17.0" %} +{% set sha256 = "b61b222c6fe7719f0f916f01a5c68679567bad8884ed36eb634311ddbc565f19" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + entry_points: + - memote = memote.suite.cli.runner:cli + script: + - {{ PYTHON }} -m pip install --no-deps -vv . + noarch: python + number: 0 + run_exports: + - {{ pin_subpackage("memote", max_pin="x") }} + +requirements: + host: + - python >=3.9,<=3.11 + - setuptools >=40.6.0 + - versioneer-518 + - wheel + - versioneer + - pip + run: + - click + - click-configfile + - click-log + - cobra >=0.28 + - cookiecutter + - depinfo >=2.2 + - future + - git + - gitpython + - importlib_resources + - jinja2 + - jsonschema + - numpy + - numpydoc + - optlang >=1.8 + - pandas + - pandera + - pygithub <2 + - pylru + - pytest + - python >=3.9,<=3.11 + - requests + - ruamel.yaml + - six + - sqlalchemy + - sympy + +test: + imports: + - memote + commands: + - memote --help + - pip check + requires: + - pip + +about: + home: https://memote.readthedocs.io/ + summary: the genome-scale metabolic model test suite + license: Apache-2.0 + license_file: LICENSE + + +extra: + recipe-maintainers: + - Midnighter From e0ef7b2500b12049b317df483354a1ed8849afc3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 10:57:14 -0500 Subject: [PATCH 1660/2173] Update wfmash to 0.12.5 (#45404) --- recipes/wfmash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wfmash/meta.yaml b/recipes/wfmash/meta.yaml index 6aa9d544dff40..8ba197d1380e3 100644 --- a/recipes/wfmash/meta.yaml +++ b/recipes/wfmash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "wfmash" %} -{% set version = "0.10.5" %} +{% set version = "0.12.5" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/waveygang/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 04c779f3e378c64543deefaa14ede67f16d1207d15e21128c9714012a0b55bcb + sha256: 797e2f968c85c631f60835ec63268fed2aba39858e7e3b30f29613b8defc40c1 build: skip: True # [osx] From aa7f4953079a7f5e4b6cf9d27af925e2586d11f3 Mon Sep 17 00:00:00 2001 From: Andrea Telatin <15690844+telatin@users.noreply.github.com> Date: Wed, 24 Jan 2024 16:46:32 +0000 Subject: [PATCH 1661/2173] add rtk2 (#45390) * add rtk2 * run_exports max_pin * Update meta.yaml * Create build.sh * Update build.sh --- recipes/rtk2/build.sh | 15 +++++++++++++++ recipes/rtk2/meta.yaml | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 recipes/rtk2/build.sh create mode 100644 recipes/rtk2/meta.yaml diff --git a/recipes/rtk2/build.sh b/recipes/rtk2/build.sh new file mode 100644 index 0000000000000..7961fbb423e85 --- /dev/null +++ b/recipes/rtk2/build.sh @@ -0,0 +1,15 @@ +#!/bin/sh + +set -euxo pipefail +mkdir -p "$PREFIX"/bin + +echo " Setting environment variables" +# Fix zlib +export CFLAGS="$CFLAGS -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" +export CPATH=${PREFIX}/include + +echo "RUN MAKE" +make test + +mv rtk2 "$PREFIX"/bin/ diff --git a/recipes/rtk2/meta.yaml b/recipes/rtk2/meta.yaml new file mode 100644 index 0000000000000..0aebea2760f7b --- /dev/null +++ b/recipes/rtk2/meta.yaml @@ -0,0 +1,34 @@ +{% set version="2.10" %} +{% set name="rtk2" %} +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/hildebra/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 310cd4bd124f6d976c1f11fdc6a38da2d362942e3ea82a560c0e64cf3f1a9679 + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + - zlib + run: + - zlib + +test: + commands: + - {{ name }} -h + - {{ name }} --version | grep -w {{ version }} + +about: + home: https://github.com/hildebra/rtk2/ + license: 'GPLv2' + license_file: LICENSE + summary: 'rtk2 - a CLI rarefaction toolkit for OTU tables' From fb0a69e0ce6c3af9abfbd3488ca9564a9e68f839 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 12:09:09 -0500 Subject: [PATCH 1662/2173] Update thapbi-pict to 1.0.6 (#45400) * Update thapbi-pict to 1.0.6 * Dependency updates --------- Co-authored-by: Peter Cock --- recipes/thapbi-pict/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index d1eca3abad919..319e783d8d6b0 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.5" %} +{% set version = "1.0.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: c7e42668397ac37b869b2c5774e721635e892ebb99eefc014d634b090d9f7c08 + sha256: a80cc24cce224195e5f613353cfe63020daca949defea4511cef392b7a6f30ed build: noarch: python @@ -21,18 +21,18 @@ build: requirements: host: - pip - - python >=3.7 + - python >=3.8 run: # Python - biom-format >=2.1.14 - - biopython >=1.73 + - biopython >=1.82 - cutadapt >=4.0 - matplotlib-base >=3.7 - networkx >=2.4,!=2.8.3,!=2.8.4 - pydot - - python >=3.7 + - python >=3.8 - rapidfuzz >=2.4.0 - - sqlalchemy + - sqlalchemy >=2.0 - xlsxwriter # Command line - blast From ceb63b031ba77e5c1af382bcfdeb7aafe10152e4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 12:50:18 -0500 Subject: [PATCH 1663/2173] Update fibertools-rs to 0.3.8 (#45407) --- recipes/fibertools-rs/build.sh | 2 ++ recipes/fibertools-rs/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/fibertools-rs/build.sh b/recipes/fibertools-rs/build.sh index 6a4023caabe45..e5418801f8fdf 100644 --- a/recipes/fibertools-rs/build.sh +++ b/recipes/fibertools-rs/build.sh @@ -16,6 +16,8 @@ export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${LIBTORCH}/lib # # download pytorch libraries # +# unfortunetally newish size limits on bioconda packages prevent me from including this. +# keeping this code block here in case the size limits change, or bioconda/conda-forge allow the pytorch channel to be accessed. if [[ "x" == "y" ]]; then export TORCH_VERSION="2.0.1" diff --git a/recipes/fibertools-rs/meta.yaml b/recipes/fibertools-rs/meta.yaml index 078fd91c3b47d..112fffa6d7bc4 100644 --- a/recipes/fibertools-rs/meta.yaml +++ b/recipes/fibertools-rs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.7" %} +{% set version = "0.3.8" %} {% set name = "fibertools-rs" %} {% set build_number = "0" %} @@ -9,7 +9,7 @@ package: source: url: https://github.com/fiberseq/fibertools-rs/archive/v{{ version }}.tar.gz - sha256: 395615d051a322fa08b1d1453691c7d8ece8ca7cc77b91e5c78d3274e1d15498 + sha256: 7e244ceafa5371d21de45a9e6ea5dd66e4922283142bc9a332c1114d5118fa02 build: From 7e63cd2fd8c0fa29b65aaf38aabc508724bf11be Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 13:03:01 -0500 Subject: [PATCH 1664/2173] Update mitos to 2.1.7 (#45406) --- recipes/mitos/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mitos/meta.yaml b/recipes/mitos/meta.yaml index 7523ada0fc540..65d99c42a65c6 100644 --- a/recipes/mitos/meta.yaml +++ b/recipes/mitos/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "2.1.6" %} +{% set version = "2.1.7" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 66d6ca1138bdda459d4ed6271a946ff86ea6298dcf7e3bb6f63c283213f77284 + sha256: b6c6e5173f37a6ff9e5c2b7ac3f45645f0db3093371a7804e3e336e203c5abe4 build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " noarch: python run_exports: From 331d657e4cb63fb13daa73a9d2c884531ea8e68b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 13:38:02 -0500 Subject: [PATCH 1665/2173] Update samtools to 1.19.2 (#45393) --- recipes/samtools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index 3d45b94379193..cd24c1020f76f 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.19.1" %} +{% set version = "1.19.2" %} package: name: samtools @@ -11,7 +11,7 @@ build: source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 - sha256: 1f94915cc32dcb6095049ed57560d99b409ba9297f4316bab551d05bb57ff355 + sha256: 71f60499668e4c08e7d745fbff24c15cc8a0977abab1acd5d2bb419bdb065e96 requirements: build: From 6e3fa672bb5bfa2864836966f55290fea3e38134 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 13:48:08 -0500 Subject: [PATCH 1666/2173] Update varvamp to 1.1 (#45403) --- recipes/varvamp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varvamp/meta.yaml b/recipes/varvamp/meta.yaml index efbed07b77dd9..3c6d6d606e4a2 100644 --- a/recipes/varvamp/meta.yaml +++ b/recipes/varvamp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varvamp" %} -{% set version = "1.0.1" %} +{% set version = "1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/varvamp-{{ version }}.tar.gz - sha256: 422a4a9dc8d5377242731e3027bba4510939e0dc91555d57636d7b45961261ab + sha256: 186b5fd4ca9670c05f977440976348587a5c79d4b79bc4370390fdabb6715d84 build: entry_points: From 31b0722c784e8e5f2d2dd957257cd3b3dd544f54 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 14:02:27 -0500 Subject: [PATCH 1667/2173] Update dnoise to 1.4.1 (#45388) --- recipes/dnoise/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnoise/meta.yaml b/recipes/dnoise/meta.yaml index b706edda05cf0..e8aa73687be78 100644 --- a/recipes/dnoise/meta.yaml +++ b/recipes/dnoise/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DnoisE" %} -{% set version = "1.4.0" %} -{% set sha256 = "bee24dbe42fb884810788bb4ac874d6b664e24a3820e6706406fd8a90b6ac328" %} +{% set version = "1.4.1" %} +{% set sha256 = "39c728faea03732df906cb90bf541efdb8d7ebf4858c9bf2717fa8a75e9157b1" %} package: name: {{ name|lower }} From a6465b6d4c24614b342572d9dcb7711d95ec8ae6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 14:48:28 -0500 Subject: [PATCH 1668/2173] Update virusrecom to 1.1.3.1 (#45398) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/virusrecom/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/virusrecom/meta.yaml b/recipes/virusrecom/meta.yaml index bafd8ea722121..6e9352ffa5415 100644 --- a/recipes/virusrecom/meta.yaml +++ b/recipes/virusrecom/meta.yaml @@ -1,5 +1,5 @@ {% set name = "virusrecom" %} -{% set version = "1.1.3" %} +{% set version = "1.1.3.1" %} package: name: "{{ name }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1950537ea6f2cf83dcfc44dd31b5c524a8e5b6988ca284c1ed291a2234d692c7 + sha256: 3fda39fc84b7a0ffccdfcdb309c2f8bb5e617d7dfc0c5b0cb0fc4a3d245c43b4 build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage('virusrecom', max_pin="x") }} From ced36765922094fca9b17fd3fbab5b06ab325610 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 14:48:52 -0500 Subject: [PATCH 1669/2173] Update last to 1526 (#45394) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 673ba234ef336..c8a7c15ea12ff 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1522" %} +{% set version = "1526" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: 0cc27dce53693c4d97864c012f9b9b34e4c02ebd0c38db23c5c5d978dbfd4d4e + sha256: e1db7307005218cbed0c924d583e4bb7bdee96044cb94867cf73d18249058463 build: number: 0 From a5bd053b68d93bad7dd65f65450230166a387689 Mon Sep 17 00:00:00 2001 From: Bob <55469084+yhhan19@users.noreply.github.com> Date: Wed, 24 Jan 2024 12:28:37 -0800 Subject: [PATCH 1670/2173] Add TREE-QMC package (#43224) * tqmc * build.sh fixed * "folder_and_package_name_must_match" fixed * missing_run_exports fixed * g++ not found fix * build error fixed * build error fix * build.sh fix * osx compilation fix * made the name and version number consistent * minor --- recipes/tree-qmc/build.sh | 9 +++++++ recipes/tree-qmc/conda_build_config.yaml | 5 ++++ recipes/tree-qmc/meta.yaml | 31 ++++++++++++++++++++++++ recipes/treeqmc/build.sh | 9 +++++++ recipes/treeqmc/conda_build_config.yaml | 5 ++++ recipes/treeqmc/meta.yaml | 31 ++++++++++++++++++++++++ 6 files changed, 90 insertions(+) create mode 100644 recipes/tree-qmc/build.sh create mode 100644 recipes/tree-qmc/conda_build_config.yaml create mode 100644 recipes/tree-qmc/meta.yaml create mode 100644 recipes/treeqmc/build.sh create mode 100644 recipes/treeqmc/conda_build_config.yaml create mode 100644 recipes/treeqmc/meta.yaml diff --git a/recipes/tree-qmc/build.sh b/recipes/tree-qmc/build.sh new file mode 100644 index 0000000000000..afeec38073355 --- /dev/null +++ b/recipes/tree-qmc/build.sh @@ -0,0 +1,9 @@ +cd MQLib +make \ + GXX="${CXX}" \ + AR="${AR}" +cd .. +$CXX -std=c++11 -O2 -I MQLib/include -o TREE-QMC src/*.cpp MQLib/bin/MQLib.a +mkdir -p $PREFIX/bin +cp TREE-QMC $PREFIX/bin/ +chmod a+x $PREFIX/bin/TREE-QMC diff --git a/recipes/tree-qmc/conda_build_config.yaml b/recipes/tree-qmc/conda_build_config.yaml new file mode 100644 index 0000000000000..7fe2892e9edfa --- /dev/null +++ b/recipes/tree-qmc/conda_build_config.yaml @@ -0,0 +1,5 @@ +c_compiler_version: # [unix] + - 9.3.0 # [linux] + +cxx_compiler_version: + - 9.3.0 # [linux] diff --git a/recipes/tree-qmc/meta.yaml b/recipes/tree-qmc/meta.yaml new file mode 100644 index 0000000000000..66298530a9cb3 --- /dev/null +++ b/recipes/tree-qmc/meta.yaml @@ -0,0 +1,31 @@ +{% set name = "TREE-QMC" %} +{% set version = "2.0.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/molloy-lab/{{ name|upper }}/releases/download/{{ version }}/{{ name|upper }}-{{ version }}.zip + sha256: f8530dd6d106c63ffde0d728eeef835b8bded16e69620e78bd45f562129f86a9 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('tree-qmc', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + run: + +test: + commands: + - TREE-QMC -h + +about: + home: https://github.com/molloy-lab/TREE-QMC + license: MIT + summary: TREE-QMC is a quartet-based method for estimating species trees from gene trees. diff --git a/recipes/treeqmc/build.sh b/recipes/treeqmc/build.sh new file mode 100644 index 0000000000000..afeec38073355 --- /dev/null +++ b/recipes/treeqmc/build.sh @@ -0,0 +1,9 @@ +cd MQLib +make \ + GXX="${CXX}" \ + AR="${AR}" +cd .. +$CXX -std=c++11 -O2 -I MQLib/include -o TREE-QMC src/*.cpp MQLib/bin/MQLib.a +mkdir -p $PREFIX/bin +cp TREE-QMC $PREFIX/bin/ +chmod a+x $PREFIX/bin/TREE-QMC diff --git a/recipes/treeqmc/conda_build_config.yaml b/recipes/treeqmc/conda_build_config.yaml new file mode 100644 index 0000000000000..7fe2892e9edfa --- /dev/null +++ b/recipes/treeqmc/conda_build_config.yaml @@ -0,0 +1,5 @@ +c_compiler_version: # [unix] + - 9.3.0 # [linux] + +cxx_compiler_version: + - 9.3.0 # [linux] diff --git a/recipes/treeqmc/meta.yaml b/recipes/treeqmc/meta.yaml new file mode 100644 index 0000000000000..2af0d99783ba1 --- /dev/null +++ b/recipes/treeqmc/meta.yaml @@ -0,0 +1,31 @@ +{% set name = "TREEQMC" %} +{% set version = "2.0.0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/molloy-lab/TREE-QMC/releases/download/2.0.0/TREE-QMC-2.0.0.zip + sha256: f8530dd6d106c63ffde0d728eeef835b8bded16e69620e78bd45f562129f86a9 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('treeqmc', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + run: + +test: + commands: + - TREE-QMC -h + +about: + home: https://github.com/molloy-lab/TREE-QMC + license: MIT + summary: TREE-QMC is a quartet-based method for estimating species trees from gene trees. From 9539040c2ff88488082a1abd987705af914386d6 Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Wed, 24 Jan 2024 15:36:37 -0500 Subject: [PATCH 1671/2173] Update gsearch v0.1.8 (#45413) * Update gsearch v0.1.8 * Update BinDash v2.1 --------- Co-authored-by: Jianshu Zhao --- recipes/bindash/meta.yaml | 4 ++-- recipes/gsearch/meta.yaml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/bindash/meta.yaml b/recipes/bindash/meta.yaml index a7667087921b2..47ba2fb182600 100644 --- a/recipes/bindash/meta.yaml +++ b/recipes/bindash/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0" %} +{% set version = "2.1" %} package: name: bindash @@ -6,7 +6,7 @@ package: source: url: https://github.com/jianshu93/bindash/archive/v{{ version }}.tar.gz - sha256: 300fd4709df1d000470feb5af1a7d1ecd95c15f9c35f7535ae9c40dce4a540a8 + sha256: 185903149a2a14a4506f0a60d0f9fc0c03bace6705fb5eca8df4048d1b03592b build: skip: True # [osx] diff --git a/recipes/gsearch/meta.yaml b/recipes/gsearch/meta.yaml index 8e51a1a1372fd..b378ec2e3aee7 100644 --- a/recipes/gsearch/meta.yaml +++ b/recipes/gsearch/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.7" %} +{% set version = "0.1.8" %} package: name: gsearch @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/gsearch/archive/v{{ version }}.tar.gz - sha256: ceec9638cbb2bb8f588375a3c3283ca717ba436e9d550624a1039c9d00a76e8a + sha256: bdb954e52c61baf94f7de574b4a578df19f12508af89996d461aeebb43a39a8f requirements: build: From ca455a133a15a60af976f9d85414f318e8c1422a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 16:04:03 -0500 Subject: [PATCH 1672/2173] Update pyrodigal to 3.3.0 (#45416) --- recipes/pyrodigal/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyrodigal/meta.yaml b/recipes/pyrodigal/meta.yaml index 94764527e29ad..944dd7eb5dd58 100644 --- a/recipes/pyrodigal/meta.yaml +++ b/recipes/pyrodigal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyrodigal" %} -{% set version = "3.2.2" %} +{% set version = "3.3.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 0e02b2089df29c3c0f1379364664f4a83da12373233bb74d7a95d24a346b02ec + sha256: 68f92cd83f9cd2883b99433847a827dd84ccb27edc51cb3f415664f0f08b0325 build: number: 0 From f340648b36f249ea3f6d61bf83330a299470033f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 16:12:44 -0500 Subject: [PATCH 1673/2173] Update genmod to 3.8.2 (#44620) * Update genmod to 3.8.2 * Update meta.yaml * edit python version pinning * lock pypandoc <1.8 --------- Co-authored-by: Thanh Lee <247862+thanhleviet@users.noreply.github.com> Co-authored-by: joshuazhuang7 Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> --- recipes/genmod/meta.yaml | 24 +++++++++--------------- 1 file changed, 9 insertions(+), 15 deletions(-) diff --git a/recipes/genmod/meta.yaml b/recipes/genmod/meta.yaml index 1cd3b5465f5b2..4b226e225aa97 100644 --- a/recipes/genmod/meta.yaml +++ b/recipes/genmod/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genmod" %} -{% set version = "3.8.1" %} +{% set version = "3.8.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d21f072f6c4a34479bc0f1633bd7a15b04a04c87f63f28457dce58615a0a7f14 + sha256: 72921cce29fd8d6b99eea76921a0a71d3846abcb92bcb02dafd24886ab9264a3 build: number: 0 @@ -16,22 +16,15 @@ build: - {{ pin_subpackage('genmod', max_pin="x") }} entry_points: - genmod = genmod.commands.base:cli - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" requirements: host: - - click <7 - - configobj - - extract_vcf >=0.4.2 - - interval_tree >=0.3.2 - - intervaltree - - ped_parser >=1.6.2 - pip - - pytabix - - pytest - - python + - python 3.8.* + - pypandoc <1.8 run: - - click <7 + - click >=8.1.3 - configobj - extract_vcf >=0.4.2 - interval_tree >=0.3.2 @@ -39,7 +32,8 @@ requirements: - ped_parser >=1.6.2 - pytabix - pytest - - python + - python 3.8.* + - vcftoolbox >=1.5.1 test: imports: @@ -61,7 +55,7 @@ about: home: "http://github.com/moonso/genmod" license: MIT license_family: MIT - license_file: + license_file: LICENSE.txt summary: "Annotate genetic inheritance models in variant files" extra: From 9a9c632c9c3f5ccbda9e00eaa43a9a8d6001f0a1 Mon Sep 17 00:00:00 2001 From: Mikko Rautiainen Date: Wed, 24 Jan 2024 23:16:26 +0200 Subject: [PATCH 1674/2173] Update GraphAligner to version 1.0.19 (#45387) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/graphaligner/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/graphaligner/meta.yaml b/recipes/graphaligner/meta.yaml index ff837db9ff3f9..38b34e29495ea 100644 --- a/recipes/graphaligner/meta.yaml +++ b/recipes/graphaligner/meta.yaml @@ -1,13 +1,13 @@ {% set name = "GraphAligner" %} -{% set version = "1.0.18" %} +{% set version = "1.0.19" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/maickrau/{{ name }}/files/13412859/{{ name }}.tar.gz - sha256: 69d248332c1df732b74571f9910d3390bfeb48165fb9d99a892ec0a71ab1291f + url: https://github.com/maickrau/{{ name }}/files/14037134/{{ name }}.tar.gz + sha256: b65d26d415c3fd459bf2fc884b3d48dc0c55f7e9135e700c5c38d62be8ee39fc patches: - version.patch - linux_link.patch # [linux] From a40c9572939617e2a124ae3f463e9a5f916abe4c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 16:21:11 -0500 Subject: [PATCH 1675/2173] Update cazy_webscraper to 2.3.0.2 (#45389) * Update cazy_webscraper to 2.3.0.2 * add run_exports --------- Co-authored-by: mencian --- recipes/cazy_webscraper/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/cazy_webscraper/meta.yaml b/recipes/cazy_webscraper/meta.yaml index f5c23370c9ad7..4e856fcf1d133 100644 --- a/recipes/cazy_webscraper/meta.yaml +++ b/recipes/cazy_webscraper/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cazy_webscraper" %} -{% set version = "2.3.0" %} -{% set sha256 = "08a12134f124622069d4259c55d0bafc618e4f1d4872992529cd495d782fd21e" %} +{% set version = "2.3.0.2" %} +{% set sha256 = "4edd7f8f121bcab1c85af649c40c497490e8b5d5769e748536ce4c965daf5297" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ source: build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - cazy_webscraper = cazy_webscraper.cazy_scraper:main - cw_get_genbank_seqs = cazy_webscraper.expand.genbank.sequences.get_genbank_sequences:main @@ -25,6 +25,8 @@ build: - cw_get_pdb_structures = cazy_webscraper.expand.pdb.get_pdb_structures:main - cw_query_database = cazy_webscraper.api.cw_query_database:main - cw_get_db_schema = cazy_webscraper.sql.get_schema:main + run_exports: + - {{ pin_subpackage('cazy_webscraper', max_pin="x") }} requirements: host: @@ -57,6 +59,7 @@ about: dev_url: "https://github.com/HobnobMancer/cazy_webscraper" summary: "A tool to automate retrieving data from CAZy, build a local CAZyme SQL database, and throughly interrogating the data. Also, automate retrieving protein data, sequences, EC numbers and structure files for specific datasets in the CAZyme database from UniProt, GenBank and PDB." license: MIT + license_family: MIT license_file: LICENSE extra: From 049710f029a75c09d2c94842ac5c878ea5390e6b Mon Sep 17 00:00:00 2001 From: llegregam <75795040+llegregam@users.noreply.github.com> Date: Wed, 24 Jan 2024 22:32:11 +0100 Subject: [PATCH 1676/2173] Added recipe for skyline2isocor v0.1.0 (#45408) * Added recipe for skyline2isocor v0.1.0 * add run_exports --------- Co-authored-by: mencian --- recipes/skyline2isocor/meta.yaml | 45 ++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 recipes/skyline2isocor/meta.yaml diff --git a/recipes/skyline2isocor/meta.yaml b/recipes/skyline2isocor/meta.yaml new file mode 100644 index 0000000000000..3abfb9f8be2a4 --- /dev/null +++ b/recipes/skyline2isocor/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "skyline2isocor" %} +{% set version = "0.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/skyline2isocor-{{ version }}.tar.gz + sha256: 9bf2b6a8c381ced3a5a24838d944bfff016a12c7da6f3627ff31467918e609bc + +build: + entry_points: + - skyline2isocor = skyline2isocor.cli:start_cli + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('skyline2isocor', max_pin="x.x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - pandas >=2.1.4,<3.0.0 + +test: + imports: + - skyline2isocor + commands: + - skyline2isocor --help + +about: + home: https://pypi.org/project/skyline2isocor/ + summary: Convert skyline output to IsoCor input format + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + +extra: + recipe-maintainers: + - llegregam From defdde47b4d35794b6b09fbfc135de69ceeaba54 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 24 Jan 2024 23:07:08 +0100 Subject: [PATCH 1677/2173] Update sativa (#44990) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Updated sativa build, incl. test case * Update meta.yaml with new Sativa release * Linting * Update keggcharter to 1.0.2 (#44992) * Update keggcharter to 1.0.2 * Update meta.yaml Now put all TXTs and TSVs from "resources" folder into "share" folder. --------- Co-authored-by: João Sequeira * Update hictk to v0.0.5 (#44988) * Update conanfile.txt.patch * Bump version * Update perl-minion to 10.28 (#44495) * bugfix: strand deprecated and removed in BioPython 1.82 (#44987) - see: https://github.com/chapmanb/bcbb/issues/138 * bugfix: breaking API change between ruamel.yaml 0.17.x and 0.18 (#44989) * Update tsebra to 1.1.2.2 (#45000) * Update sylph to 0.5.1 (#45001) * add r-misha 3.7.0 (history version) (#44981) * add misha version 3.7.0 (history version) * fix hash * fix compiler settings * use template variable to specify name * add run_export to lock version * add r-misha 3.7.1 (history version) (#44984) * add r-misha 3.7.1 (history version) * fix: incorrect commit and hash * Update viguno to 0.2.0 (#44996) * Update viguno to 0.2.0 * run_exports --------- Co-authored-by: Thanh Lee * Update annonars to 0.32.0 (#45013) * Fix recognizer (#45012) * Update recognizer to 1.10.0 * Update meta.yaml No more build.sh file * Update meta.yaml Forgot about the other TSV files * Removed build.sh --------- Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> * Update last to 1522 (#45011) * Update pcaone to 0.4.1 (#45009) * genoflu version 1.02 (#44995) * genoflu version 1.02 * Update meta.yaml * Update meta.yaml * https://spdx.org/licenses/GPL-3.0-or-later.html --------- Co-authored-by: Thanh Lee * Update chromhmm to 1.25 (#45016) * Update chromhmm to 1.25 * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer * Update ColabFold to 1.5.5 (#45008) * Update ColabFold to 1.5.4 * Use 1.5.5 instead, 1.5.4 had a bug * OpenMM 8.1 causes issues * Update expam to 1.2.2.4 (#45007) * Update expam to 1.2.2.4 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update upimapi to 1.13.1 (#45019) Co-authored-by: João Sequeira * Update raptor (#44952) multiple binaries and a wrapper scripts depending on available instruction sets. * add AnnoSINE2 recipes (#44980) * add strainscan recipes * add annosine2 recipes * Delete recipes/strainscan/meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Bulk (#45014) * a round of fixes and build-skips * add some build failures * correct version for bioconductor-data-packages * add build failure for STdeconvolve * [ci run] trigger bulk run * run_exports on bioconductor-data-packages * [ci run] trigger bulk run * build failure for omnipathr * [ci run] trigger bulk run * Build important packages first * [ci run] trigger bulk run * revert to full build * [ci run] trigger bulk run * build failure files * skip iclusterplus * skip bioconductor-lpsymphony * bump bioconda-repodata-patches build number * [ci run] * build failures * next round of high priority packages * [ci run] trigger bulk run * [ci run] add dependency * [ci run] finish priority packages * re-enable full bulk * [ci run] trigger bulk run * build failures * [ci run] trigger bulk run * next round of high priority packages * [ci run] trigger bulk run * build more high priority packages * [ci run] test local channel fix * [ci run] increase workers * Try building bioconductor-geoquery (#44726) * Delete recipes/bioconductor-geoquery/build_failure.linux-64.yaml * Update meta.yaml * try fixing parsing error * [ci run] try rebuilding bioconductor-coregx (#44727) * try rebuilding bioconductor-coregx * Update meta.yaml * add opencl loading libraries - will this work * [ci run] remove a few build failure files * [ci run] Bioconductor graph (#44733) * remove build failure file * trigger build * Update meta.yaml * add patch back [ci run] * build failures * [ci run] high priority packages * bulk wiki page * [ci run] add missing packges * build failure for bioconductor-sictools * [ci run] missed one * [ci run] full run * Update build.sh * [ci run] fix dexseq * [ci run] next round of high priority packages * [ci run] missing packages * [ci run] high priority package * [ci run] build all bioconductor-bsgenome * [ci run] remove failures associated with bioconductor-bsgenome dependency * full build * use bioconda-common version * build failures: test dev version of utils * escape characters correctly * build failure for bioconductor-pics * use branch * build failure for bioconductor-inspect * try to fix build failure git range * build failure for bioconductor-distinct * use head branch * trigger build failure wf * [ci run] trigger bulk run * build failures fetch depth * build failure for biconductor-benchdamic * build failures * build failures with log * don't run build failures if last commit has ci skip * [ci skip] test build failure wiki * test build failure wiki job * [ci run] reenable record-build-failures * re-add token for build failure updates * build failures add category column * trigger wiki update * fix libsbml version for bioconductor-rsbml * build failure updates * fix bioconductor-glad * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-wppi * [ci skip] add build failure record for recipe recipes/bioconductor-gars * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-metascope * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-msbackendrawfilereader * [ci skip] add build failure record for recipe recipes/bioconductor-omicsviewer * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-micsqtl * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-psygenet2r * [ci skip] add build failure record for recipe recipes/bioconductor-gesper * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-seqcna * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-inpas * [ci skip] add build failure record for recipe recipes/bioconductor-factr * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-doubletrouble * [ci skip] add build failure record for recipe recipes/bioconductor-phyloprofile * [ci skip] add build failure record for recipe recipes/bioconductor-extrachips * [ci skip] add build failure record for recipe recipes/bioconductor-rmassbank * [ci skip] add build failure record for recipe recipes/bioconductor-ularcirc * [ci skip] add build failure record for recipe recipes/bioconductor-umi4cats * [ci skip] add build failure record for recipe recipes/bioconductor-chipqc * [ci skip] add build failure record for recipe recipes/bioconductor-outsplice * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-circseqaligntk * [ci skip] add build failure record for recipe recipes/bioconductor-ritan * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-vulcan * [ci skip] add build failure record for recipe recipes/bioconductor-singlecelltk * [ci skip] add build failure record for recipe recipes/bioconductor-scfeatures * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-deconvr * [ci skip] add build failure record for recipe recipes/bioconductor-ideal * [ci skip] add build failure record for recipe recipes/bioconductor-esatac * [ci skip] add build failure record for recipe recipes/bioconductor-profileplyr * [ci skip] add build failure record for recipe recipes/bioconductor-inetgrate * [ci skip] add build failure record for recipe recipes/bioconductor-ataccogaps * [ci skip] add build failure record for recipe recipes/bioconductor-lemur * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-regionreport * [ci skip] add build failure record for recipe recipes/bioconductor-motifbreakr * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-cageminer * [ci skip] add build failure record for recipe recipes/bioconductor-multicrispr * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-scpipe * Rbowtie2 (#44856) [ci run] fix rbowtie2 builds * [ci run] remove build file * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-biggr * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] remove build failure record for recipe recipes/bioconductor-affycoretools * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * failure for bioconda-multirnaflow * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-proloc * [ci skip] add build failure record for recipe recipes/bioconductor-rcas * [ci skip] add build failure record for recipe recipes/bioconductor-guideseq * [ci skip] add build failure record for recipe recipes/bioconductor-crisprdesign * [ci skip] add build failure record for recipe recipes/bioconductor-fraser * bioconductor-lpsymphony fix from master * remove build failures for finished dependencies * restore skip osx-64 * fix bioconductor-rawrr * high priority packages * [ci run] trigger bulk run * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] remove build failure record for recipe recipes/bioconductor-proloc * fix bioconductor-chemmineob * [ci run] remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * remove easy build failures * [ci run] next round of dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-pigengene * [ci skip] add build failure record for recipe recipes/bioconductor-repitools * [ci skip] add build failure record for recipe recipes/bioconductor-xde * [ci skip] add build failure record for recipe recipes/bioconductor-sctensor * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * build failure updates * [ci run] next batch of fixes * [ci skip] add build failure record for recipe recipes/bioconductor-mitoclone2 * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci run] full build * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci run]remove failures for built dependencies * [ci skip] add build failure record for recipe recipes/bioconductor-ihw * [ci skip] add build failure record for recipe recipes/bioconductor-lpsymphony * [ci skip] add build failure record for recipe recipes/bioconductor-rlseq * [ci skip] add build failure record for recipe recipes/bioconductor-gatom * [ci run] set failures to skip * [ci run] reduce resources that are wasted * [ci skip] add build failure record for recipe recipes/bioconductor-pd.barley1 * fix accidental reverts * add GSL to bioconductor-pics * add back fix from master for omnipathr * remove build failure * [ci run] skip root nodes to spread out builds * [ci run] include more root nodes in blacklist * update build failures * [ci run] add more blacklist items and do osx build * [ci skip] add build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-ping * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * [ci skip] add build failure record for recipe recipes/bioconductor-mumosa * [ci skip] add build failure record for recipe recipes/bioconductor-chromscape * [ci skip] add build failure record for recipe recipes/bioconductor-scmerge * [ci skip] add build failure record for recipe recipes/bioconductor-tadcompare * fix build errors * [ci run] more skipped builds * [ci skip] add build failure record for recipe recipes/bioconductor-cghmcr * [ci skip] add build failure record for recipe recipes/bioconductor-ihwpaper * [ci skip] add build failure record for recipe recipes/bioconductor-ccpromise * [ci skip] remove build failure record for recipe recipes/bioconductor-snapcgh * [ci skip] add build failure record for recipe recipes/bioconductor-interactivedisplay * [ci run] reduce workers * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-tbsignatureprofiler * [ci run] manually distribute packages * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-condiments * [ci skip] add build failure record for recipe recipes/bioconductor-scclassify * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-gcapc * [ci skip] add build failure record for recipe recipes/bioconductor-cepo * [ci skip] add build failure record for recipe recipes/bioconductor-traviz * remove build failures * remove colon that breaks yaml parsing * remove temporary bioconductor bulk skips * [ci run] remaining packages * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci skip] add build failure record for recipe recipes/bioconductor-enrichtf * [ci skip] add build failure record for recipe recipes/bioconductor-promise * [ci skip] add build failure record for recipe recipes/bioconductor-otubase * [ci skip] add build failure record for recipe recipes/bioconductor-cocoa * [ci skip] add build failure record for recipe recipes/bioconductor-rjmcmcnucleosomes * retry http error * [ci run] full bulk build * [ci skip] add build failure record for recipe recipes/bioconductor-deepbluer * [ci skip] remove build failure record for recipe recipes/bioconductor-meb * [ci skip] add build failure record for recipe recipes/bioconductor-distinct * [ci run] categorize failures * add bioconductor-cdi * remove old failure files * update bioconductor-reusedata to 3.18 * remove failures for dependencies that have been built * [ci run] build certain packages * bulk: update bioconductor-ccfindr and bioconductor-rjmcmcnucleosomes with gsl (#44986) * update bioconductor-ccfindr with gsl * update bioconductor-rjmcmcnucleosomes with gsl * [ci run] build updated recipes * [ci skip] add build failure record for recipe recipes/bioconductor-ccfindr * [ci skip] add build failure record for recipe recipes/bioconductor-reusedata * remove temporary changes from workflows * build got bumped in merge * remove temp files --------- Co-authored-by: Ryan Dale Co-authored-by: Björn Grüning Co-authored-by: Bjoern Gruening Co-authored-by: BiocondaBot * Update deeplc to 2.2.26 (#44238) * Update deeplc to 2.2.23 * Update deeplc to 2.2.24 * add pyopenms * Update deeplc to 2.2.25 * Update deeplc to 2.2.26 * try extended base * revert extended base --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Add recipe for CellBender v0.3.0 (#45024) * Add recipe for CellBender v0.3.0 * add run_exports * Fix nrpys to build on python 3.8+ (#45025) * Update oakvar to 2.9.83 (#45026) * Update foldcomp to 0.0.6 (#45018) * Update foldcomp to 0.0.6 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update antismash-lite to 7.1.0 (#45027) * Update jcvi to 1.3.9 (#45029) * Update jcvi to 1.3.9 * Update meta.yaml --------- Co-authored-by: Christian Brueffer * Update recognizer to 1.10.1 (#45031) Co-authored-by: João Sequeira * Update midsv to 0.11.0 (#45028) * Update midsv to 0.11.0 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer * Update meta.yaml (#45041) Snakemake refactored in newer version. * Rebuild unitig caller for new bifrost version (#45035) * Rebuild unitig caller for new bifrost version * Add run_exports * Fix string interpolation in pinning * Update annosine2 build (#45033) * Update meta.yaml * Update meta.yaml * Update rasusa to 0.8.0 (#45042) * Update rasusa to 0.8.0 * add run_export * bump msrv --------- Co-authored-by: Michael Hall * Update annonars to 0.33.0 (#45043) * patch viroconstrictor snakemake requirements to not use version 8.x (#45036) * Add Deepmei version 1.0.0 recipes (#45005) * Update keggcharter to 1.1.0 (#45046) * Update mosca to 2.2.0 (#45054) * Update mosca to 2.2.0 * Update meta.yaml Added run_exports Added pandas as dependency Fixed python version to <3.12 Fixed snakemake version to <8 --------- Co-authored-by: João Sequeira * Update fgbio to 2.2.1 (#45050) * Update fgbio-minimal to 2.2.1 (#45051) * Update viralmsa to 1.1.41 (#45047) * Update ndex2 to 3.7.0 (#45049) * Update expam to 1.2.2.5 (#45053) * Update bustools to 0.43.2 (#45055) * Update kb-python to 0.28.1 (#45056) * Update xengsort to 2.0.5 (#44888) * Update xengsort to 2.0.4 * pin python to 3.11 * Update xengsort to 2.0.5 --------- Co-authored-by: joshuazhuang7 * Update ena-webin-cli to 6.8.0 (#45059) * Update zol to 1.3.17 (#45067) * Update pybiolib to 1.1.1673 (#45057) * Update pybiolib to 1.1.1682 (#45072) * Update adam to 1.0.1 (#45069) * Update adam to 1.0.1 * add pin_subpackage * Update cannoli to 1.0.1 (#45070) * Update cannoli to 1.0.1. * add pin_subpackage * Update keggcharter to 1.1.1 (#45079) * Update galaxy-objectstore to 23.1.4 (#45061) * Update galaxy-files to 23.1.4 (#45062) * Update mashmap to 3.1.3 (#45064) * Update rosella to 0.5.3 (#45075) * Update snakemake-executor-plugin-googlebatch to 0.2.0 (#45039) * Update snakemake-executor-plugin-googlebatch to 0.2.0 * add summary --------- Co-authored-by: mencian * Update hifihla to 0.2.3 (#45066) * Update micom to 0.33.1 (#45071) * Update flight-genome to 1.6.3 (#45073) * Update bioframe to 0.6.0 (#45076) * Update metdatamodel to 0.5.5 (#45082) * Update odgi to 0.8.4 (#45077) * Update odgi to 0.8.4 * run_exports --------- Co-authored-by: Thanh Lee * Update nanovar to 1.5.1 (#45084) * Update r-ldweaver to 1.4 (#45058) * Update r-ldweaver to 1.4 * drop genbankr dependency * it seems genbankr is still needed --------- Co-authored-by: mencian * Update ncbi-datasets-pylib to 16.1.1 (#45090) * Update dbcan to 4.1.0 (#45088) * Update dbcan to 4.1.0 * fix bug * add hatchling and other fixes * edit sha256 --------- Co-authored-by: mencian * Update perl-math-bigint to 2.003002 (#45096) * Update nf-test to 0.8.3 (#45098) * Update foldcomp to 0.0.7 (#45097) * Update meta.yaml (#45086) * Update ltr_retriever to 2.9.8 (#45006) * Update ltr_retriever to 2.9.8 * add run_exports * revert channel specifications * remove channels section --------- Co-authored-by: joshuazhuang7 * prodigal: include upstream patches fixing critical bugs (#45091) * prodigal: freshen up * prodigal: include patches for critical bugs fixed upstream but unreleased The developer has accepted these changes, but no new release has been made in over a year. * Add vcfphasesets (#45092) * Add vcfphasesets. * Change meta.yaml for run exports. * Complexcgr (#45089) * Add complexcgr v0.8.0 * Add complexcgr v0.8.0 * Add complexcgr v0.8.0 * Update ribowaltz to 2.0 (#45065) * Update ribowaltz to 2.0 * add run_exports --------- Co-authored-by: joshuazhuang7 Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update vcf2variants (#45083) * Update to version 1.0. * Add run_exports. * Extra dependency. * Bump version. * Bump version and test import. * Fix import test. * Add additional requirement. --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update snapatac2 to 2.5.2 (#45078) * Update snapatac2 to 2.5.2 * add typing_extensions to run section --------- Co-authored-by: joshuazhuang7 * Update breseq to 0.38.2 (#45103) * Update breseq to 0.38.2 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update mitos to 2.1.6 (#45104) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update harmony-pytorch to 0.1.8 (#45106) * Update harmony-pytorch to 0.1.8 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update snakemake to 8.1.0 (#45108) * Update ltr_retriever to 2.9.9 (#45107) * Update tn93 to 1.0.13 (#45109) * Update hyphy to 2.5.59 (#45111) * Update pyfaidx to 0.8.0 (#45113) * Depend on gcc; new sha256 * Finally a sativa recipe that puts sativa.py in PATH * Update mitgard to 1.1 (#45101) * Update mitgard to 1.1 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update bioframe to 0.6.1 (#45120) * Add virusrecom (#45099) * add virusrecom recipes * add virusrecom recipes xx * Update meta.yaml * add python to run section and use SPDX identifier --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * bump mitos1 (#45112) * bump mitos1 * repin blast-legacy .. add tests first * Update pybiolib to 1.1.1685 (#45119) * Update ncbi-datasets-pylib to 16.1.2 (#45124) * Update das_tool to 1.1.7 (#45123) * Update das_tool to 1.1.7 * add run_exports --------- Co-authored-by: joshuazhuang7 * Update virusrecom to 1.1.3 (#45122) * Update severus to 0.1.2 (#45135) * Update virusrecom (#45130) * add virusrecom recipes * Update meta.yaml * edit recipe-maintainer --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> * Update hybracter to 0.5.0 (#45128) * Update dnaapler to 0.5.1 (#45129) * Update recentrifuge to 1.13.1 (#45132) * Update tissuumaps to 3.2.0.3 (#45137) * mitos: add tests for R packages (#44971) * mitos: add tests for R packages In test with the container I got: Exception: b"Warning message:\npackage \xe2\x80\x98ggplot2\xe2\x80\x99 was built under R version 3.6.3 \nError: package or namespace load failed for \xe2\x80\x98reshape2\xe2\x80\x99 in dyn.load(file, DLLpath = DLLpath, ...):\n unable to load shared object '/usr/local/lib/R/library/stringi/libs/stringi.so':\n libicui18n.so.64: cannot open shared object file: No such file or directory\nIn addition: Warning message:\npackage \xe2\x80\x98reshape2\xe2\x80\x99 was built under R version 3.6.3 \nExecution halted\n" * try to use R directly in tests * try R > 3 * bump and unpin vienna * retry R>3 * another try * try to pin r-stringi * bump * cnt * unpin some more requirements * remove stringi * repin infernal * repin hmmer * repin blast * Revert "repin blast" This reverts commit 6a5717a86f8231c1ced5ca58e21f97f01c264e2f. * Update kb-python to 0.28.2 (#45138) * Update ena-webin-cli to 6.9.0 (#45139) * Update r-seqmagick to 0.1.7 (#45131) * Update r-seqmagick to 0.1.7 * Update meta.yaml --------- Co-authored-by: Christian Brueffer * Update snakefmt to 0.9.0 (#45134) * remove static compilation (#45141) * Update dajin2 to 0.3.6 (#45143) * Update jbrowse2 to 2.10.1 (#45145) * Update ncbi-datasets-pylib to 16.2.0 (#45144) * Add ACI (#45121) * adding aci recipe * fixed entry point typo * fix typo * matplotlib-base * url * revert url * underscore * version --------- Co-authored-by: Thanh Lee * Update ngs-chew to 0.9.0 (#45140) * Update vcfpy to 0.13.7 (#45150) * Avoid building on OS X --------- Co-authored-by: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Co-authored-by: João Sequeira Co-authored-by: Roberto Rossini <71787608+robomics@users.noreply.github.com> Co-authored-by: DrYak Co-authored-by: TPOB <19909103+TTTPOB@users.noreply.github.com> Co-authored-by: Thanh Lee Co-authored-by: stuber Co-authored-by: Christian Brueffer Co-authored-by: Milot Mirdita Co-authored-by: joshuazhuang7 Co-authored-by: Enrico Seiler Co-authored-by: Ray <851836818@qq.com> Co-authored-by: Alicia A. Evans <108547992+aliciaaevans@users.noreply.github.com> Co-authored-by: Ryan Dale Co-authored-by: Björn Grüning Co-authored-by: Bjoern Gruening Co-authored-by: BiocondaBot Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Carl Mathias Kobel Co-authored-by: John Lees Co-authored-by: Michael Hall Co-authored-by: Florian Zwagemaker <49153065+florianzwagemaker@users.noreply.github.com> Co-authored-by: Kanglu123 <64641114+Kanglu123@users.noreply.github.com> Co-authored-by: Michael L Heuer Co-authored-by: Le (Lena) Huang Co-authored-by: Jens Luebeck Co-authored-by: Afif Elghraoui Co-authored-by: Mark Santcroos Co-authored-by: Koke <49822617+jorgeavilacartes@users.noreply.github.com> Co-authored-by: Zhou ZJ <43747306+ZhijianZhou01@users.noreply.github.com> Co-authored-by: M Bernt Co-authored-by: boukn Co-authored-by: Young Co-authored-by: Alexander Peltzer --- recipes/sativa/build.sh | 31 +- recipes/sativa/gpl_license | 674 ++++++++++++++++++++++++++++++++ recipes/sativa/meta.yaml | 18 +- recipes/sativa/sequences.alnfna | 230 +++++++++++ recipes/sativa/taxonomy.tsv | 5 + 5 files changed, 925 insertions(+), 33 deletions(-) create mode 100644 recipes/sativa/gpl_license create mode 100644 recipes/sativa/sequences.alnfna create mode 100644 recipes/sativa/taxonomy.tsv diff --git a/recipes/sativa/build.sh b/recipes/sativa/build.sh index 4c880d868a6ea..9f821444e5974 100644 --- a/recipes/sativa/build.sh +++ b/recipes/sativa/build.sh @@ -3,30 +3,9 @@ export USE_AVX=yes export USE_AVX2=yes -case `uname` in -Darwin) export DARWIN=1;; -Linux) export DARWIN=0;; -*) echo "Unknown architecture"; exit 1;; -esac - -make -C ./raxml CC="$CC" - -install -d ${PREFIX}/tmp -install -d ${PREFIX}/bin - -if [ $DARWIN -eq 1 ]; then - install sativa.cfg *.py ${PREFIX} -else - install -t ${PREFIX} *.py sativa.cfg -fi - -# Place a symlink to sativa.py in bin/ -( cd ${PREFIX}/bin; ln -s ../sativa.py . ) - -mkdir ${PREFIX}/raxml -cp ./raxml/raxmlHPC8* ./raxml/*.sh ${PREFIX}/raxml - -cp -r ./epac ${PREFIX} -cp -r ./tests ${PREFIX} -cp -r ./example ${PREFIX} +make -C raxml +cp -r raxml ${PREFIX}/bin +cp -r epac ${PREFIX}/bin +cp *.py ${PREFIX}/bin +cp sativa.cfg ${PREFIX}/bin diff --git a/recipes/sativa/gpl_license b/recipes/sativa/gpl_license new file mode 100644 index 0000000000000..818433ecc0e09 --- /dev/null +++ b/recipes/sativa/gpl_license @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/sativa/meta.yaml b/recipes/sativa/meta.yaml index 600f238ce24c5..7fa6e1aee16b4 100644 --- a/recipes/sativa/meta.yaml +++ b/recipes/sativa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sativa" %} -{% set version = "0.9.1" %} +{% set version = "0.9.3" %} package: name: {{ name|lower }} @@ -7,10 +7,13 @@ package: source: url: https://github.com/amkozlov/sativa/archive/refs/tags/v{{ version }}.zip - sha256: 14b772c7e1bc242655e1876e7492fd8d50d363058236bdf513aa5afca7d94841 + sha256: 0d0ae82f0f9608f51301ecadc367f85653fe9954855d9ebbbef8f889eef586b8 build: - number: 1 + number: 0 + skip: true # [osx] + run_exports: + - {{ pin_subpackage('sativa', max_pin="x.x") }} requirements: build: @@ -23,16 +26,17 @@ requirements: - python >=3.0.0 test: - imports: - - unittest + files: + - sequences.alnfna + - taxonomy.tsv commands: -# - python sativa.py -h - - python -m unittest discover -v + - sativa.py -s sequences.alnfna -t taxonomy.tsv -x bac -debug about: home: https://github.com/amkozlov/sativa license: GPL-3 license_family: GPL + license_file: gpl_license summary: "SATIVA Semi-Automatic Taxonomy Improvement and Validation Algorithm" extra: diff --git a/recipes/sativa/sequences.alnfna b/recipes/sativa/sequences.alnfna new file mode 100644 index 0000000000000..7e0aa83c9190c --- /dev/null +++ b/recipes/sativa/sequences.alnfna @@ -0,0 +1,230 @@ +>RS_GCF_000019605.1~NC_010482.1 +---GGTTGATCCTGCCGGAGGGAAC-----CCCTATCGGGCTCGCACTAAGCCATGCGAG +TCTGCTGGGGG------------------------------------------------- +------------------------------------CCCCTGCCCCTGGCGGCGCACGGC +TCCGTAATACACGGTCAACCTGTCCTGGGGACCGGGATAA-------------------- +CCTCGGGAAACTGAGGTTAAT---ACCGGATAGGGGTGGATTCCTGGAATGGGTCCACCC +CTAAAGTAGGCGGGGGGACG-GCC-----CCGCTGAGGCCCCAGGGTGGGACCGTGGCCT +AT-CAGG----TAGTAGGTGGGGTA---------ACGGCCCACCTAGCCTAAGACGGGTA +CGGG------CTCTGAGAG-GAGG-AGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGC +C-CTACGGGGCGCAGCAG--------GCGGGAAACTTCCCCAATG-----CGCGCAAGCG +TGAGGGAGTGAGCCCGAGTGCCGCCCGCTGAGGG------CGGCTGTTCCCCTGTGTAA- +--------A-AAG-------CAGGGGGTAGGAAG-GGGAG-------GGTAAGGCTGGTG +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------CCAGCCGCCGCGGTAAAACCAGC---------TCC-CCGA-- +-GGG--GTTCCCACGCATACTGGGCCTAAAGCGTCCGTAGCCGGCCCCGTAAGTCCTCGG +TT---AAATCCGC--CTGAAGACAGG--CGGACCGCCGAGGAT------A--CTGCGGGG +C-TAGGGAGC--GGGAGGGGCCGAGGGTATTCCGGGGGGAGCGGTAAAATGCGT------ +------------------------------------------AGATCCCCGGAGGACC-- +-ACCAGTGGCGAAGGCGCTCGGCTGGAACGCGTCCGACGGTGAGGG--------ACGAAA +GCTGGG-GGAG------------------CAAACCGGATTAGATACCCGGGTAGTCCCAG +CCGTAAACGATGCCGG---CTAGGTGCCG---GCTGAGG---------TTTCGGCCTCAG +CCGGTGTCGA---------------------AGCGAAGGCATTAAGCCGGCCGC-CTGAG +GAGTACAGCCGCAAGGCCGAAA----------CTTAAAGGAATTG-ACGGGGGGGC---- +------------------------------------------------------------ +--------------------------ACCACAAGGGGTGAATGCCTGCGGCTCAATTGGA +CTCAACGCCGGGAATC-TTACCGGGGGCGACAGCAGGATGAAGGTCAGG----------- +------------------------------------------------------------ +--------------------------------------CTG-------AA---------- +-------GACCTTACCTGAC----GCGCTGAG--GG-GTGGTGCATGGC---------CG +TCGCCAGCTCGTGCCGTGAGGTGT--CCTGTTAAGTCAGGC-------AACGAGCGAGAC +-CCCCGCCCTC-AGTTGCCAGCGGGGCCTT-ACGGCTGG-C-CG-GGCAAACTGGGGGGA +CTGCCGGCGAAGA---GCCGGAGGAAGGAGGGGGCTACGGCAGGTCAGTATGCCCCTAAT +C---CCCCGGGCCGCACGCGGGCTGCAATGGGCGGGACA---GCGG---------G-ATG +CGAC-CCCGAGAGGGGGAGCAAATCCCTGAAACCCGCCCGT-G--GTTGGGATCGAGGGT +TGCAACTCGCCCTCGTGA-ACCCGGAATCCCTAGTAACCGCGGTTCTCC-ATAC------ +----------------------------CGCGGTGAATACGTCCCTGCCCCTTGTACACA +CCGCCCGTCAACCCACCCGAGTGGACTTGGGGCGAGGCCCAGCTCAA------------- +-------------------TGGCTGGGTCGAGCTTTGGGTCCGCGAGGGGGGGTAAGTCG +TAACAAGGTAGCCGTAG---GGGAACCTGCGGCTGGATCACCTCCC-------------- +------------------------------------------------------------ +------------------- +>RS_GCF_000092465.1~NC_014205.1 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------AGGTGATCCA----GCCGCAGGTTCCCCTACGGCTACC +TTGTTACGACTTCTCCCCCCTTGGGAGGGGGGAGTTCGACCTGGCCCCC----CGGGTTT +CCCCGGGAGACCAGGCCTCAC---TCCCCCCTCCCTCGGGTGGAGCGACGGGCGGTGTGT +GCAAGGAGCAGGGA--CG---TATTC--ACCGC-GCGATGATGACGCGCGGTTACTAGGG +ATTCCACGTTCACGAGGG-CGAGTT------------------GCAGCCCTCGATCCCAA +CTGCGGCGGGGTTTGAGGGATTGCCTCCCCCTTAC-GGGGTCGGATCCCGCTGTCCCCGC +CATTGTAGCCC---------------GCGTGTAGCCCGGGGGATT-----CGGGGCATGC +TGAC-------------------------------------------------------- +---------------------------------------------CTGCCGTGGCCCCCT +CCTTCCTCCGCCTTATACGGCGGCAGTCCCCCTAGTGTG-CCCC-GG--AGCCGGAGCTC +CGGGTAGCAACTAGGGGCGGGGGT-CTCGCTCGTTGC------------CGGACTTAACC +GGACACCTCACGG----CACGAGCTGGCGACGGCCATGCACCTCCTCTCAGCGCG----- +-TCGGGCAA--------------------------------------------------- +------------------------------------------------------------ +---------------------------GGCCGTTAGCCTGGCCGTCATC-CTGCTG---- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------TCGCCCCCGGTGAGG------------TTCCCGG +CGTTGACTCCAATTAAACCG--CAGGCTCCACC---CCTTGTGGTGCTCCCCCGC----- +-------------------CAATTCCTTTAAGTTTCAGCCTTGCGGCCGTACTCCCCAG- +-GCGGCGGGCTTAACGGCTTCCCTGCGGCACTGGGCGGGCTCT-AA-G-CCCGCCCAACA +CCTAGCCCGCATCGT---------------TTACAGCCGGGACTACCCGGGTATCTAATC +CGGTTCGCTCCCCC------------------GGCTTTCGCCCCTCACCGTCG------- +----------------GGCGCGTTCCAGCCGAGCGCCTTCGCCACTGGTGGTCCTCCCGG +GATTATAGGATTTCGCCCCTAC-----------C------------------CCGGGAGT +ACCCTCGGCCTCTCCCGCCCCCTAGCCTGGCAGTTTCCCCTCCAGTC-C-CCGGGTTGAG +CCCGGGGATTTAGGAGGGGACTTG-CCAGGCCGGCTACGG------GCGCTTTAGGCCCA +ATAATCGTCCCGA----CCACTCGCGGGGCTGGTATTACCGCGGCGGCTGACACCAGTCT +TGCCCCCCGCTTATTCCCCC---------------------------------------- +------------------------------------------------------------ +-----GCCTTCTTACAGCGG-GGAAAAGCCCC------CT-AATTAGGGGGCACTCGGGG +TGACCCCGTCACGGTTGCCCGCAT--TGCGGAGGTTTCGCGCCTGGTGCACCCCGTAGGG +CCTGGGCCCTTGTCT--CAGTGCCCATCTG----GGGGC-----TCCCGCTCTCA-CGGC +CCCTACCCGTTATCGGCTTGGCGGGCCGTTACCCCGCCAACTACCTG-ATGGGCCGCAGC +CCCATCCTCGGGCTGCGCGGCGGCGATAACCCCCGCCGCA--CCC--TTTCGGGGAGGAA +CCCTTCCAGGCGTCCT---CCCCTATGG-GGGATTAGCACC-A--GTTTCCC---GG-TG +TTATCCCCCTCCCGAGGGTAGGTTAGCCACGTGTTACTCAGCCGTCCGCCACGCTCCGCA +GCGG----------CGGAGCGTACGACTCCCATGGCTTAGCCCCACCCCGATAGCGGTCG +GGTCCGGCAGGATCAACCGGAGTT------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------- +>RS_GCF_000970205.1~NZ_CP009512.1-#2 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------GAGGTGATCCA----GCCGCAGATTCCCCTACGGCTACC +TTGTTACGACTTAACCCCCCTTGCAAAGCACAGGTTCGAACACGGCAC-G---------- +----A-AGTCCGTGCCCTCAC---CCATACCTCACTCGGGTGGTTTGACGGGCGGTGTGT +GCAAGGAGCAGGGA--CG---TATTC--ACCGC-GCTATATTGAAACGCGATTACTACGG +ATTCCAGCTTCACGA-GGGCGAGTT------------------ACAGCCCTCGATCCGAA +CTACGAATGGGTTTGTGAGATTAC-CAGCCCTTTTCAGGGGAGGGACCCATTGTCCCATC +CATTGTAGCCC---------------GCGTGTAGCCCGGGAGATT-----CGGGGCATAC +TGAC-------------------------------------------------------- +---------------------------------------------CTACCGTGGCCCGCA +CCTTCCTCCGATTTAACATCGGCGGTCCCCACAGAGTACCCATCGTCCC----GGAGGAC +ATGCTGGTAACAGTGGGCACGGGT-CTCGCTCGTTGC------------CTGACTTAACA +GGATGCTTCACAG----TACGAACTGGCGACGGCCATGCACCTCCTCTCAGCGAT----- +-TCAGGCAA--------------------------------------------------- +------------------------------------------------------------ +---------------------------AGTCTTCAGCTTGGCCTACATA-TTGCTG---- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------TCGCCCCCGGTGAGT------------TGTCCGG +CGTTGAGTCCAATTAAACCG--CAGGCTCCACC---CGTTGTTGTGCTCCCCCGC----- +-------------------CAATTCCTTTAAGTTTCAGCCTTGCGGCCGTACTTCCCAG- +-GTGGCTCGCTTCACGGCTTCCCTGCGGCACCAGACACGGTCG-CG-C-CATGCCTGACA +CCTAGCGAGCATCGT---------------TTACGGCTGGGACTACCCGGGTATCTAATC +CGGTTCGTGCCCCC------------------AGCTTTCGTCCCTCACCGTCG------- +----------------AACCCGTTCTGGTAAGACGCCTTCGCCACAGGTGGTCCCACAGG +GATTACAAGATTTCACTCCTAC-----------C------------------CCTGTAGT +ACCTCTTACCTCTCCCGGTTCCAAGTCTGGCAGTATCCCCCGAAAGCCT-AATAGTTGAG +CTATCAGATTTCCCGGAGGACTGA-CCAAACCGGCTACGG------ACCCTTTAGACCCA +ATAATCACGATCA----CCACTCGGGCCGCCGGTGTTACCGCGGCGGCTGGCACCGGTCT +TGCCCGGCCCTTGCTAACGG---------------------------------------- +------------------------------------------------------------ +-----ATGTATTTTACACATCCGGACAGCCA------GCATATGATGCTGGCACTCGGTG +TCCCCTTATCACGGTTTCCCGCAT--TGTAAAGTTTTCGCGCCTGCTGCGCCCCGTAGGG +CCTGGATTCATGTCT--CAGAATCCATCTC----CGGGC-----TCTTGCTCTCA-CAAC +CCGTACCCGTCGCTGGCTAGTAGGTACATTACACCCACTACTAC-CTGATAGGCCGCAGA +CCCATCCTTGGGCAGACGAATCCTT-------------------T--T--GACGCATAAA +GCATTCCAGCAAATAT---GCGTTATCC-GGAATTATCCCC-A--GTTTCCC---GG-GG +TTATGCCGGTCCCAAGGGCAGGTTATCCACGTGTTACTGAGCAGTACGCCATGTATT--- +---------------GCTACATATGACTCGCATGGCTTAGGCGAACACCGATAGCAGTAA +CCTCTGGCAGGATCAACCAGAATT------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------- +>RS_GCF_000302455.1~NZ_AMPO01000020.1 +-CCGTTTGATCCTGGCGGAGGCCAC-----TGCTATTGGGTTTCGATTAAGCCATGCAAG +TCGTACGATCCT------------------------------------------------ +-----------------------------------TTC----GGGGTCGTGGCATACGGC +TCAGTAACACGTGGATAACCTACCCTTAGGACTGGGATAA-------------------- +CCCCGGGAAACTGGGGACAAT---ACCGGATATGTAGAGTTGCCTGGAATTGGTACTCTA +TTGAAA-------------------T-GTATTCGTGCGCCTAAGGATGGATCTGCGGCAG +AT-TAGG----TAGTTGGCGGGGTA---------AATGCCCACCAAGCCAGTAATCTGTA +CGGG------TTGTGAGAG-CAAG-AGCCCGGAGATGGAACCTGAGACAAGGTTCCAGGC +C-CTACGGGGCGCAGCAG--------GCGCGAAACCTCCGCAATG-----CACGAAAGTG +CGACGGGGGAAACCCAAGTGCCACTCTTAACG--GG----GTGGCTTTTCTTAAGTGTA- +--------AAAAG-------CTTTTGGAATAAGA-GCTGG-------GC-AAGACCGGTG +C----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------CAGCCGCCGCGGTAACACCGGC---------AGC-TCAA-- +-GTG--GTGGCCATTTTTATTGGGCCTAAAGCGTTCGTAGCCGGTTTGATAAGTCTCTGG +TG---AAATCTCA--CGGCTTAACCGTGAGAATTGCTGGAGAT------A--CTATTAGG +C-TTGAGGCC--GGGAGAGGTTAGCGGTACTCCCAGGGTAGGGGTGAAATCCTA------ +------------------------------------------TAATCCTGGGAGGACC-- +-ACCTGTGGCGAAGGCGGCTAACTGGAACGGACCTGACGGTGAGTA--------ACGAAA +GCCAGG-GGCG------------------CGAACCGGATTAGATACCCGGGTAGTCCTGG +CCGTAAACGATGTGGA---CTTGGTGTTG---GGATGGC--------------------- +------------------------------------------------------------ +---------------------------------TCCGAGCTGCCC-CAGTGCCGAAGGGA +AGCTGTTAAGTCCACC-------GCCTGGGAAGTACG-GTCGCAAGACTGAAACTTAAAG +G------AATTGGCGGGGGAG----CACCACAACGCGTGGAGCCT-GCGGTTTAATTGGA +TTCAACGCCGGACATC-TCACCAGGGGCGACAGCAGAATGATAGCCAGG----------- +------------------------------------------------------------ +--------------------------------------TTG-------AT---------- +-------GACCTTGCTTGAC----AAGCTGAG--AG-GAGGTGCATGGC---------CG +CCGTCAGCTCGTACCGTGAGGCGT--CCTGTTAAGTCAGGC-------AACGAGCGAGAC +-CCACGCCCTT-AGTTACCAGCGGATCCTT-T--GGGAT-G-CCGGGCACACTAAGGGGA +CCGCCAGTGATAA---ACTGGAGGAAGGAGTGGACGACGGTAGGTCCGTATGCCCCGAAT +C---CCCTGGGCTACACGCGGGCTACAATGGCTAGGACA---ATGG---------G-TTC +CGACACTGAA-AAGTGAAGGTAATCTCCTAAACCTAGCCTT-A--GTTCGGATTGAGGGC +TGTAACTCGCCCTCATGA-AGCTGGAATGCGTAGTAATCGCGTGTCATA-ACCG------ +----------------------------CGCGGTGAATACGTCCCTGCTCCTTGCACACA +CCGCCCGTCACGCCACCCAAAAAGGGTTTGGATGAGGCCATAGTCTTT------------ +--G--------------TTGGTTATGGTCGAATCTGGGTTCTTTGAGGAGGGCGAAGTCG +TAACAAGGTAGCCGTAG---GGGAACCTGCGGCTGGATCACCTCCTT------------- +------------------------------------------------------------ +------------------- +>RS_GCF_000993805.1~NZ_CP009961.1 +TCCGGTTGATCCTGCCGGACCCGAC-----TGCTATCAGGGTGGGGCTAACCCATGGAAG +TCTAGGAGCCGGG----------------------------------------------- +---------------------------------GC--TACGGCCGGCTCCGGCGGACGGC +TCAGTAGCACGTGGCTAACCTACCCTCGGGAGGGGGATAA-------------------- +CCCCGGGAAACTGGGGCTAAT---CCCCCATAGGCGCAGACTCCTGGAATGGGTCCGCGC +CGAAAAGGCTGCAACGCCAT-GCCCG---TTGCAGCCGCCCGAGGATGGGGCTGCGCCCC +AT-CAGG----TAGTTGGCGGGGTA---------ACGGCCCGCCAAGCCGATAACGGGTG +GGGG------CCGTGAGAG-CGGG-AGCCCCGAGATGGGCACTGAGACAAGGGCCCAGGC +C-CTACGGGGCGCACCAG--------GGGCGAAACTTCCGCAATG-----CGGGAAACCG +TGACGGAGCCACCCTGAGTGCCACCCGATGAGGG------TGGCTTTTGCCCGGTCTAA- +--------A-AAG-------CCGGGCGAATAAGC-GGGG--------GGCAAGCCTGGTG +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------TCAGCCGCCGCGGTAATACCAGC---------CCC-GCGA-- +-GTG--GTCGGGACGATTATTGGGCCTAAAGCGTCCGTAGCCGGCCCGGCAAGTCCCCCT +TT---AAAGCCCA--CGGCTCAACCG--TGGGAGCGGGGGGAT------A--CTGTCGGG +C-TAGGGGGC--GGGAGAGGCCGGGGGTACTCCTGGGGTAGGGGCGAAATCCTA------ +------------------------------------------TAATCCCAGGAGGACC-- +-ACCAGTGGCGAAGGCGCCCGGCTGGAACGCGCCCGACGGTGAGGG--------ACGAAA +GCTGGG-GGAG------------------CAAAGGGGATTAGATACCCCCGTAGTCCCAG +CTGTAAACGATGCGGG---CTAGGTGTTG---GGTGGG----------CCTCGAGCCCGC +CCAGTGTCGT---------------------AGGGAAGCCGTTAAGCCCGCCGC-CTGGG +GAGTACGGCCGCAAGGCTGAAA----------CTTAAAGGAATTG-GCGGGGGAGC---- +------------------------------------------------------------ +--------------------------ACCACAAGGGGTGAAGCTT-GCGGTTTAATTGGA +GTCAACGCCGGAAACC-TCACCGGGGGCGACAGCAGGATGAAGGCCAGG----------- +------------------------------------------------------------ +--------------------------------------CTA-------AC---------- +-------GACCTTGCCAGAC----GAGCTGAG--AG-GAGGTGCATGGC---------CG +TCGCCGGCTCGTGCCGTGAGGTGT--CCTGTTAAGTCAGGG-------AACGAGCGAGAC +-CCCCGCCCCT-AGTTGCAACCCAGCCTTT-CGGGGCTG-G-GG--CACTCTAGGGGGAC +TGCCGGCGA-TAA---GCCGGAGGAAGGTGGGGGCTACGGCAGGTCAGTATGCCCCGAAA +C---CCCCGGGCTACACGCGAGCTGCAATGGCGGGGACA---GCGG---------G-CTC +CG-ACCCCGAAAGGGGAAGGAAATCCCGTAAACCCCGCCTC-A--GTAGGAATCGAGGGC +TGCAACTCGCCCTCGTGA-ACGTGGAATCCCTAGTAACCGCGTGTCACC-AACG------ +----------------------------CGCGGTGAATACGTCCCTGCTCCTTGCACACA +CCGCCCGTCGCTCCACCCGAGGGAGGCCCAGGTGAGGCCTCTCGCCGAAAG--------- +-------------------GTGGGAGGTCGAATCTGGGCCTCCCAAGGGGGGAGAAGTCG +TAACAAGGTGGCCGTAG---GGGAACCTGCGGCCGGATCACCTCCTT------------- +------------------------------------------------------------ +------------------- diff --git a/recipes/sativa/taxonomy.tsv b/recipes/sativa/taxonomy.tsv new file mode 100644 index 0000000000000..349a7c83c9d8d --- /dev/null +++ b/recipes/sativa/taxonomy.tsv @@ -0,0 +1,5 @@ +RS_GCF_000019605.1~NC_010482.1 d__Archaea;p__Crenarchaeota;c__Korarchaeia;o__Korarchaeales;f__Korarchaeaceae;g__Korarchaeum;s__Korarchaeum +RS_GCF_000092465.1~NC_014205.1 d__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Desulfurococcales;f__Desulfurococcaceae;g__Staphylothermus;s__Staphylothermus +RS_GCF_000970205.1~NZ_CP009512.1-#2 d__Archaea;p__Halobacterota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina;s__Methanosarcina +RS_GCF_000302455.1~NZ_AMPO01000020.1 d__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium;s__Methanobacterium +RS_GCF_000993805.1~NZ_CP009961.1 d__Archaea;p__Crenarchaeota;c__Thermoprotei;o__Thermofilales;f__Thermofilaceae;g__Thermofilum_A;s__Thermofilum_A From 5bcda20c5275995789ca3a211359429d0b7b5769 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 17:28:10 -0500 Subject: [PATCH 1678/2173] Update yacht to 1.2.1 (#45410) * Update yacht to 1.2.1 * add pandas to host * add scipy to host * add tqdm to host * add biom-format and pytaxonkit to host --------- Co-authored-by: mencian --- recipes/yacht/meta.yaml | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/recipes/yacht/meta.yaml b/recipes/yacht/meta.yaml index c7f12473b7254..c8f57cc59af75 100644 --- a/recipes/yacht/meta.yaml +++ b/recipes/yacht/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.0" %} +{% set version = "1.2.1" %} package: name: yacht @@ -6,13 +6,13 @@ package: source: url: https://github.com/KoslickiLab/YACHT/releases/download/v{{ version }}/yacht-{{ version }}.tar.gz - sha256: 0655301d2ecb949fe75799b8ee67b4032e8a778a03f2edc3572b48066d0e4007 + sha256: 248c85c52e88c576d7afd9842b06fec2a6f89fbb9b1150885486e6adf72ac3ca build: number: 0 noarch: python skip: True # [win or osx] - script: "{{ PYTHON }} -m pip install . --ignore-installed --no-cache-dir -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('yacht', max_pin="x") }} @@ -20,7 +20,14 @@ requirements: host: - python >3.6 - pip - - setuptools + - pandas + - pytaxonkit + - scipy + - sourmash + - loguru + - tqdm + - biom-format + - numpy run: - python >3.6 - sourmash >=4.8.3,<5 @@ -46,6 +53,8 @@ about: home: https://github.com/KoslickiLab/YACHT summary: 'YACHT is a mathematically rigorous hypothesis test for the presence or absence of organisms in a metagenomic sample, based on average nucleotide identity (ANI).' license: MIT + license_family: MIT + license_file: LICENSE.txt dev_url: https://github.com/KoslickiLab/YACHT doc_url: https://github.com/KoslickiLab/YACHT/wiki From 40bf344303eaa2b6f267f4d1c172c01b1b5c659b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 18:57:07 -0500 Subject: [PATCH 1679/2173] Update intarna to 3.4.0 (#45399) * Update intarna to 3.4.0 * run_exports added * disable test build on osx to avoid timeout in package build --------- Co-authored-by: Martin Raden --- recipes/intarna/build.sh | 4 +++- recipes/intarna/meta.yaml | 8 +++++--- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/intarna/build.sh b/recipes/intarna/build.sh index fd174c6efa2cd..5e5ab3a2b0308 100644 --- a/recipes/intarna/build.sh +++ b/recipes/intarna/build.sh @@ -34,5 +34,7 @@ export LDFLAGS=${LDFLAGS} make -j ${CPU_COUNT} -make tests -j ${CPU_COUNT} +if [ `uname` != Darwin ] ; then # skip tests for osx to avoid timeout + make tests -j ${CPU_COUNT} +fi make install diff --git a/recipes/intarna/meta.yaml b/recipes/intarna/meta.yaml index 26009b219a7b8..8177abc6959ae 100644 --- a/recipes/intarna/meta.yaml +++ b/recipes/intarna/meta.yaml @@ -1,5 +1,5 @@ -{% set INTARNA_VERSION = "3.3.2" %} -{% set INTARNA_SHA256 = "57d273fa5bb6b62636e316465240b95089273e7e9e34224ea48c9cd747e88ed1" %} +{% set INTARNA_VERSION = "3.4.0" %} +{% set INTARNA_SHA256 = "4b0c53472dad49f3fbe6f0d3b1613d22d7b438bf650936da6a351a25fa9d535c" %} {% set VRNA_VERSION = "2.4.14" %} package: @@ -12,7 +12,9 @@ about: summary: Efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites build: - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('intarna', max_pin="x.x") }} source: url: "https://github.com/BackofenLab/IntaRNA/releases/download/v{{INTARNA_VERSION}}/intaRNA-{{INTARNA_VERSION}}.tar.gz" From 08e7826f3c17e073e90e3376113f29e9f573d911 Mon Sep 17 00:00:00 2001 From: Andrea Telatin <15690844+telatin@users.noreply.github.com> Date: Thu, 25 Jan 2024 02:28:15 +0000 Subject: [PATCH 1680/2173] [seqfu] Re-add macOS support (#45401) * Test OSX * Update build.sh * Update meta.yaml * skip patch on osx --- recipes/seqfu/build.sh | 20 ++++++++++++-------- recipes/seqfu/meta.yaml | 1 - 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/recipes/seqfu/build.sh b/recipes/seqfu/build.sh index 41e15120f4793..3857c7e750166 100644 --- a/recipes/seqfu/build.sh +++ b/recipes/seqfu/build.sh @@ -14,19 +14,23 @@ export CFLAGS="$CFLAGS -I$PREFIX/include" export LDFLAGS="$LDFLAGS -L$PREFIX/lib" export CPATH=${PREFIX}/include -echo "GXX: $GXX" -echo "GCC: $GCC" +echo "GXX: ${GXX:-'not set'}" +echo "GCC: ${GCC:-'not set'}" echo "----------" -echo "Patching makefile" -# Trying to fix build when gcc or g++ are required -sed -i 's/gcc/$(GCC)/g' Makefile -sed -i 's/g++/$(GXX)/g' Makefile -sed -i '1iGCC ?= gcc' Makefile -sed -i '1iGXX ?= g++' Makefile + + if [[ $OSTYPE == "darwin"* ]]; then + echo "OSX" export HOME="/Users/distiller" export HOME=`pwd` +else + # Trying to fix build when gcc or g++ are required + echo "LINUX: Patching makefile" + sed -i 's/gcc/$(GCC)/g' Makefile + sed -i 's/g++/$(GXX)/g' Makefile + sed -i '1iGCC ?= gcc' Makefile + sed -i '1iGXX ?= g++' Makefile fi mkdir -p "$PREFIX"/bin diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml index b8c6278466772..9d494a364ba0b 100644 --- a/recipes/seqfu/meta.yaml +++ b/recipes/seqfu/meta.yaml @@ -12,7 +12,6 @@ source: build: number: 0 - skip: True # Let's skip MacOS until we find out more run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} From 4584f23a61800b1498e8db32f0c57ec14f62618d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 24 Jan 2024 22:44:29 -0500 Subject: [PATCH 1681/2173] Update aster to 1.16 (#45412) * Update aster to 1.16 * add run_exports * updating the names of the binaries for ASTER since authors changed them --------- Co-authored-by: mencian Co-authored-by: worku005 --- recipes/aster/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/aster/meta.yaml b/recipes/aster/meta.yaml index 74e9391b7ffa2..30d17f22be13c 100644 --- a/recipes/aster/meta.yaml +++ b/recipes/aster/meta.yaml @@ -1,13 +1,15 @@ -{% set version = "1.15" %} +{% set version = "1.16" %} {% set name = "ASTER" %} -{% set sha256 = "71618824a0f39135977709f21f3b6374815407411fb44474442a1a9c88a6c919" %} +{% set sha256 = "c6e80de483a0a59fc0d3a74465b1f793e773b9d79cbd20756c6766136ffbb1a7" %} package: name: "{{ name|lower }}" version: "{{ version }}" build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('aster', max_pin="x") }} source: url: "https://github.com/chaoszhang/ASTER/archive/refs/tags/v{{ version }}.tar.gz" @@ -20,15 +22,17 @@ requirements: test: commands: - - master-site -h &> /dev/null # [linux] - - master-pair -h &> /dev/null # [linux] + - caster-site -h &> /dev/null # [linux] + - caster-pair -h &> /dev/null # [linux] + - waster-site -h &> /dev/null # [linux] - astral -h &> /dev/null - astral-pro -h &> /dev/null - astral-hybrid -h &> /dev/null about: home: https://github.com/chaoszhang/ASTER - license: AGPL-3.0 + license: AGPL-3.0-or-later + license_family: AGPL license_file: LICENSE summary: | Accurate Species Tree EstimatoR series; a family of optimation algorithms From 35d992f6bb29e9d0856b5550cb0ed26f17728868 Mon Sep 17 00:00:00 2001 From: John Lees Date: Thu, 25 Jan 2024 11:21:42 +0000 Subject: [PATCH 1682/2173] Add recipe for cgt (#45372) * Add recipe for cgt * Fix license file name * Change executable name --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/cgt/meta.yaml | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 recipes/cgt/meta.yaml diff --git a/recipes/cgt/meta.yaml b/recipes/cgt/meta.yaml new file mode 100644 index 0000000000000..9afec628b546a --- /dev/null +++ b/recipes/cgt/meta.yaml @@ -0,0 +1,31 @@ +{% set name = "cgt" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower}} + version: {{ version }} + +source: + url: https://github.com/bacpop/{{ name }}/archive/v{{ version }}.tar.gz + sha256: d79750878e45853e46a3e991e8f7274a2de248bca58476b2be7e527caac3ab2b + +build: + number: 0 + script: "cargo install --no-track --locked --verbose --root \"${PREFIX}\" --path ." + run_exports: + - {{ pin_subpackage("cgt", max_pin="x") }} + +requirements: + build: + - {{ compiler('rust') }} + +test: + commands: + - cgt_bacpop -V + +about: + home: https://github.com/bacpop/cgt + license: Apache-2.0 + license_family: APACHE + license_file: LICENSE.txt + summary: Calculate a core genome threshold (cgt) from metagenome data From 6859495b36bce89062686d83792fc10c4a786885 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 Jan 2024 13:44:29 +0100 Subject: [PATCH 1683/2173] add orthanq 1.1.0 (#44940) * [ci skip] add orthanq draft recipe * fix * fix * add checksum * Update meta.yaml * Update meta.yaml * fixes --- recipes/orthanq/build.sh | 8 ++++++ recipes/orthanq/meta.yaml | 58 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 recipes/orthanq/build.sh create mode 100644 recipes/orthanq/meta.yaml diff --git a/recipes/orthanq/build.sh b/recipes/orthanq/build.sh new file mode 100644 index 0000000000000..9dca7213beca0 --- /dev/null +++ b/recipes/orthanq/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -eu + +# Make sure bindgen passes on our compiler flags. +export BINDGEN_EXTRA_CLANG_ARGS="${CPPFLAGS} ${CFLAGS} ${LDFLAGS}" +export HDF5_DIR=${PREFIX} +export RUSTFLAGS="-C link-args=-Wl,-rpath,$HDF5_DIR/lib" + +cargo install --no-track --locked --verbose --root "${PREFIX}" --path . diff --git a/recipes/orthanq/meta.yaml b/recipes/orthanq/meta.yaml new file mode 100644 index 0000000000000..946b26b7f0fd4 --- /dev/null +++ b/recipes/orthanq/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.1.0" %} + +package: + name: orthanq + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("orthanq", max_pin="x") }} + +source: + url: https://github.com/orthanq/orthanq/archive/v{{ version }}.tar.gz + sha256: 5ce1d2826404c04f1de8e5c543c0e23cc23b693f5d190c2602e654d510375bbd + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{ compiler('rust') }} + - rust >=1.54 + - pkg-config + - make + - cmake + - perl-findbin + host: + - gsl + - libcblas + - openssl + - zlib + - bzip2 + - xz + - clangdev + - coincbc + - hdf5 =1.10.5 + - fontconfig + run: + - gsl + - libcblas + - openssl + - zlib + - bzip2 + - xz + - clangdev + - coincbc + - hdf5 =1.10.5 + - fontconfig + +test: + commands: + - orthanq -h + +about: + home: https://github.com/orthanq/orthanq + license: MIT + license_family: MIT + license_file: LICENSE + summary: Uncertainty aware HLA typing and general haplotype quantification From 57577c98f659be6ed8bdd0ab36372594ac82ef4f Mon Sep 17 00:00:00 2001 From: M Bernt Date: Thu, 25 Jan 2024 13:49:07 +0100 Subject: [PATCH 1684/2173] bump mitos1 (#45421) --- recipes/mitos/mitos1/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mitos/mitos1/meta.yaml b/recipes/mitos/mitos1/meta.yaml index c1a015275ecc6..0e010a1780797 100644 --- a/recipes/mitos/mitos1/meta.yaml +++ b/recipes/mitos/mitos1/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mitos" %} -{% set version = "1.1.4" %} +{% set version = "1.1.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4f541044977dd3b33628ff780f6435094f1d633a031a88b5bda80342efa05bae + sha256: 1727e5037c679648b4633b4bd811d9f818a2b41d2c8d322bd51ec5b6a94faa02 build: number: 0 From 5b3ea17c324c85e48d7bd0bcd5194b35468cc573 Mon Sep 17 00:00:00 2001 From: Charlie Date: Thu, 25 Jan 2024 07:51:09 -0500 Subject: [PATCH 1685/2173] Add pycov3 recipe (#45409) --- recipes/pycov3/meta.yaml | 45 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 recipes/pycov3/meta.yaml diff --git a/recipes/pycov3/meta.yaml b/recipes/pycov3/meta.yaml new file mode 100644 index 0000000000000..e9435f67e8e41 --- /dev/null +++ b/recipes/pycov3/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "pycov3" %} +{% set version = "2.0.4b0" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 22a3b35bd589e967bf3041356436c652913a64c601efb2af2149375fb095a8e4 + +build: + number: 0 + noarch: python + entry_points: + - pycov3 = pycov3.cli:main + script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage('pycov3', max_pin="x") }} + +requirements: + host: + - pip + - python + run: + - python + +test: + imports: + - pycov3 + commands: + - pycov3 --help + +about: + home: https://github.com/Ulthran/pycov3 + license: MIT + license_family: MIT + license_file: + summary: "Generate cov3 files used in DEMIC" + doc_url: + dev_url: https://github.com/Ulthran/pycov3 + +extra: + recipe-maintainers: + - Ulthran From 8132498cb48ec246b16b36fe04e1d319052c7f29 Mon Sep 17 00:00:00 2001 From: Eric Kutschera Date: Thu, 25 Jan 2024 08:03:21 -0500 Subject: [PATCH 1686/2173] Update ucsc-twobitinfo to 455 (#45418) --- recipes/ucsc-twobitinfo/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ucsc-twobitinfo/meta.yaml b/recipes/ucsc-twobitinfo/meta.yaml index f3fcd9757c185..782f34538d8c9 100644 --- a/recipes/ucsc-twobitinfo/meta.yaml +++ b/recipes/ucsc-twobitinfo/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-twobitinfo" %} {% set program = "twoBitInfo" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -19,6 +19,8 @@ build: ignore_run_exports: - libpng - libuuid + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: From cd164fbc6329141791f8a6dc98542a6cb3bc6eb5 Mon Sep 17 00:00:00 2001 From: Eric Kutschera Date: Thu, 25 Jan 2024 08:04:16 -0500 Subject: [PATCH 1687/2173] Update ucsc-bedgraphtobigwig to 455 (#45419) --- recipes/ucsc-bedgraphtobigwig/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ucsc-bedgraphtobigwig/meta.yaml b/recipes/ucsc-bedgraphtobigwig/meta.yaml index 96ba38c44d3e8..14a8480f5135d 100644 --- a/recipes/ucsc-bedgraphtobigwig/meta.yaml +++ b/recipes/ucsc-bedgraphtobigwig/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedgraphtobigwig" %} {% set program = "bedGraphToBigWig" %} -{% set version = "445" %} -{% set sha256 = "c7abb5db6a5e16a79aefcee849d2b59dbc71ee112ca1e41fea0afb25229cf56c" %} +{% set version = "455" %} +{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} package: name: "{{ package }}" @@ -15,6 +15,8 @@ source: build: number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: From 8ef8c98ee8f04cc01f12cdb075b9d2811de7fc12 Mon Sep 17 00:00:00 2001 From: Jeremy Volkening Date: Thu, 25 Jan 2024 07:21:30 -0600 Subject: [PATCH 1688/2173] add run_exports to perl-biox-seq (#45115) --- recipes/perl-biox-seq/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/perl-biox-seq/meta.yaml b/recipes/perl-biox-seq/meta.yaml index 8abda5e2b51b4..3f0b26b9a0481 100644 --- a/recipes/perl-biox-seq/meta.yaml +++ b/recipes/perl-biox-seq/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-biox-seq" %} -{% set version = "0.008008" %} -{% set sha256 = "a301c51f5d58c02ed4d7b1d5e2914666ebb00cc669073242f8d123a8a771a44a" %} +{% set version = "0.008009" %} +{% set sha256 = "93d45421823619317aed195f7f19c486358248d8fe79d3dea7bd91b1fc49e8f5" %} package: name: {{ name }} @@ -13,6 +13,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: From 68e5dd08822d217a95577ed511093aa598c9f472 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Jan 2024 09:52:09 -0500 Subject: [PATCH 1689/2173] Update snakemake to 8.3.2 (#45366) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake to 8.2.4 * Update snakemake to 8.3.1 * Update meta.yaml * Update snakemake to 8.3.2 --------- Co-authored-by: Johannes Köster Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snakemake/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index e40d63fbdb441..5f0761641c24b 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.2.3" %} +{% set version = "8.3.2" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: d31b7e5ceaa255038475287154b641a973cba9ff7cca6880f109f18ab703351a + sha256: 2959b72891d0c842faa019aba35726090db97f3513b6d78bd668fdbe92056628 build: number: 0 @@ -110,6 +110,7 @@ outputs: - toposort >=1.10 - yte >=1.5.1,<2.0 - wrapt + - dpath >=2.1.6,<3.0.0 test: imports: From 666c8df93e7c706407f7180da8043eee5928a53d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Jan 2024 10:17:50 -0500 Subject: [PATCH 1690/2173] Update oakvar to 2.9.85 (#45063) * Update oakvar to 2.9.84 * Update oakvar to 2.9.85 --------- Co-authored-by: Brandon Seah --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 3980d2f261a57..15f40af72b4d6 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.83" %} -{% set sha256 = "b7157f768ee6b631a202ac50a05a6b69c233320c036437f484ebeb2660422f77" %} +{% set version = "2.9.85" %} +{% set sha256 = "ff8f8f8a6ab8cd9c9307edf2cb710a9ccdb9649f3c46ff656f336678419e514b" %} package: name: {{ name|lower }} From a035983320b7c2b8cf04f3c417fdd4fbdc4763a8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Jan 2024 10:18:11 -0500 Subject: [PATCH 1691/2173] Update mkdesigner to 0.3.4 (#45423) * Update mkdesigner to 0.3.2 * Update mkdesigner to 0.3.3 * Update mkdesigner to 0.3.4 --- recipes/mkdesigner/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mkdesigner/meta.yaml b/recipes/mkdesigner/meta.yaml index 45a3fb5756df4..3585d115b792d 100644 --- a/recipes/mkdesigner/meta.yaml +++ b/recipes/mkdesigner/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mkdesigner" %} -{% set version = "0.3.1" %} +{% set version = "0.3.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mkdesigner-{{ version }}.tar.gz - sha256: db3adaf00bbf6cb906c56ecee29ee233445255c7c7759ae42bd1f0e8262bd7f8 + sha256: 832372167e966e12cc0551cad936ed8049555da474fa3a4ef71574215001bf3a build: entry_points: From 0f96e182131cc02ebec50bd1dadaf9c21171d0f7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 25 Jan 2024 17:42:10 -0500 Subject: [PATCH 1692/2173] Update hiphase to 1.2.0 (#45428) --- recipes/hiphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index e6d8bad778424..89033d92be5b2 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "1.1.0" %} -{% set hiphase_sha256 = "b5034e3adc53c0314ac9b8b5b205553830e43c65f77169e91635f18559c5be3b" %} +{% set version = "1.2.0" %} +{% set hiphase_sha256 = "e57455275a42a5679895a95f997c132064164343c0ef949946b28cac356c9a3a" %} package: name: {{ name }} From 33c29829a92a5cd11f33a8447123cbb430bfa7ab Mon Sep 17 00:00:00 2001 From: Alex Petty Date: Fri, 26 Jan 2024 02:21:36 -0600 Subject: [PATCH 1693/2173] Add recipe r-deconcell (#45426) --- recipes/r-deconcell/build.sh | 4 +++ recipes/r-deconcell/meta.yaml | 53 +++++++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 recipes/r-deconcell/build.sh create mode 100644 recipes/r-deconcell/meta.yaml diff --git a/recipes/r-deconcell/build.sh b/recipes/r-deconcell/build.sh new file mode 100644 index 0000000000000..6d23e7f876394 --- /dev/null +++ b/recipes/r-deconcell/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +pushd Decon2/DeconCell +$R CMD INSTALL --build . diff --git a/recipes/r-deconcell/meta.yaml b/recipes/r-deconcell/meta.yaml new file mode 100644 index 0000000000000..211669e1ffeda --- /dev/null +++ b/recipes/r-deconcell/meta.yaml @@ -0,0 +1,53 @@ +{% set name = "r-deconcell" %} +{% set version = "0.1.0" %} +{% set vcommit = "335bf320df9c7dd15f636cff2c089d89ba6b786e" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/molgenis/systemsgenetics/archive/{{ vcommit }}.tar.gz + sha256: 9dadbe65cdbe72ca6f7bb6869770f40dc4fcea45945fbfb76ace61e41feb5b14 + + +build: + number: 0 + noarch: generic + rpaths: + - lib/R/lib/ + - lib/ + run_exports: + - {{ pin_subpackage('r-deconcell', max_pin="x") }} + +requirements: + host: + - bioconductor-deconrnaseq + - bioconductor-edger + - r-base + - r-data.table + - r-devtools + - r-glmnet + run: + - bioconductor-deconrnaseq + - bioconductor-edger + - r-base + - r-data.table + - r-glmnet + +test: + commands: + - $R -e "library(\"DeconCell\")" + +about: + home: https://github.com/molgenis/systemsgenetics/tree/master/Decon2/DeconCell + license: GPL-3.0-or-later + license_family: GPL3 + summary: DeconCell is an statitsical framework for generating cell proportions predictive models using bulk expresion data. It currently has pre-calculated models + description: | + DeconCell is an statitsical framework for generating cell proportions predictive models using bulk expresion data. It currently has pre-calculated models + dev_url: https://github.com/molgenis/systemsgenetics/tree/master/Decon2/DeconCell + +extra: + recipe-maintainers: + - pettyalex From 749ba06fdded478714c333429f8dd6dc42e38efa Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Fri, 26 Jan 2024 14:22:14 +0100 Subject: [PATCH 1694/2173] Update seqan3 (#45405) --- recipes/seqan3/fix_glibcxx_debug.patch | 25 +++++++++++++++++++++++++ recipes/seqan3/meta.yaml | 4 +++- 2 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 recipes/seqan3/fix_glibcxx_debug.patch diff --git a/recipes/seqan3/fix_glibcxx_debug.patch b/recipes/seqan3/fix_glibcxx_debug.patch new file mode 100644 index 0000000000000..529cc94d0f3f9 --- /dev/null +++ b/recipes/seqan3/fix_glibcxx_debug.patch @@ -0,0 +1,25 @@ +From 47b77ef92911ff1667f4487edb3961f0c28f407b Mon Sep 17 00:00:00 2001 +From: Simon Gene Gottlieb +Date: Wed, 17 Jan 2024 12:09:11 +0100 +Subject: [PATCH] [FIX] Do not use constexpr vector with _GLIBCXX_DEBUG + +--- + include/seqan3/core/platform.hpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/seqan3/core/platform.hpp b/include/seqan3/core/platform.hpp +index 1fd92faa7..e0c7687fe 100644 +--- a/include/seqan3/core/platform.hpp ++++ b/include/seqan3/core/platform.hpp +@@ -252,7 +252,7 @@ static_assert(sdsl::sdsl_version_major == 3, "Only version 3 of the SDSL is supp + #endif + + //!\brief Our char literals returning std::vector should be constexpr if constexpr std::vector is supported. +-#if defined(__cpp_lib_constexpr_vector) && __cpp_lib_constexpr_vector >= 201907L ++#if __cpp_lib_constexpr_vector >= 201907L && !defined(_GLIBCXX_DEBUG) + # define SEQAN3_WORKAROUND_LITERAL constexpr + #else + # define SEQAN3_WORKAROUND_LITERAL inline +-- +2.43.0 + diff --git a/recipes/seqan3/meta.yaml b/recipes/seqan3/meta.yaml index c5f14a78f7ae3..abb3a201426e9 100644 --- a/recipes/seqan3/meta.yaml +++ b/recipes/seqan3/meta.yaml @@ -8,10 +8,12 @@ package: source: url: https://github.com/seqan/{{ name|lower }}/releases/download/{{ version }}/seqan3-{{ version }}-Source.tar.xz sha256: da2fb621268ebc52b9cc26087e96f4a94109db1f4f28d363d19c7c9cdbd788b1 + patches: + - fix_glibcxx_debug.patch # Fix will be included in 3.4.0 build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('seqan3', max_pin="x") }} From 0b4ce3ef92deee10a183db2aab377e018ecb28ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Jan 2024 10:19:21 -0500 Subject: [PATCH 1695/2173] Update varvamp to 1.1.1 (#45435) --- recipes/varvamp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varvamp/meta.yaml b/recipes/varvamp/meta.yaml index 3c6d6d606e4a2..98241a40fce99 100644 --- a/recipes/varvamp/meta.yaml +++ b/recipes/varvamp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varvamp" %} -{% set version = "1.1" %} +{% set version = "1.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/varvamp-{{ version }}.tar.gz - sha256: 186b5fd4ca9670c05f977440976348587a5c79d4b79bc4370390fdabb6715d84 + sha256: 3036bb0b0f9f1453e2978b95c75a5adf3c9f08cec9f3a4a2f38affa28b1fd04b build: entry_points: From e9173f70db0adc629a2d812fe319808c4e0e4662 Mon Sep 17 00:00:00 2001 From: Yiming Yang Date: Fri, 26 Jan 2024 07:31:46 -0800 Subject: [PATCH 1696/2173] Update Pegasuspy to 1.9.0 (#45321) * upgrade Pegasuspy to 1.9.0 * resolve issue * Remove unnecessary dependency * try removing git status * remove duplicated 'run_exports' key * simplify --- recipes/pegasuspy/meta.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/recipes/pegasuspy/meta.yaml b/recipes/pegasuspy/meta.yaml index 9b3e42df1b209..f0485e29a84ec 100644 --- a/recipes/pegasuspy/meta.yaml +++ b/recipes/pegasuspy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pegasuspy" %} -{% set version = "1.8.1" %} +{% set version = "1.9.0" %} package: name: {{ name|lower }} @@ -7,17 +7,17 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3897e1048d6ce3547028c0e4220fea7145573e6f62805918c7f7002f683f4105 + sha256: ace00d403d43c91094706a8de85c6c7806e5dce8049c902f6262c808e0089c9f build: number: 0 - skip: True # [py<37] + skip: True # [py<38] entry_points: - pegasus = pegasus.__main__:main - run_exports: - - {{ pin_subpackage(name, max_pin='x') }} script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: @@ -35,8 +35,7 @@ requirements: - loompy >=3 - docopt - scipy >=1.7 - - importlib_metadata >=0.7 - - pegasusio >=0.5.1 + - pegasusio >=0.9.0 - psutil - threadpoolctl - adjusttext @@ -54,12 +53,13 @@ requirements: - python-igraph >=0.8.0 - scikit-learn >=0.23.2 - scikit-misc - - seaborn + - seaborn >=0.13.0 - statsmodels - pyfit-sne >=1.1.1 - umap-learn >=0.5.2 - xlsxwriter - wordcloud + - forceatlas2-python # brought in by numba, trying to ensure it comes from conda-forge rather than defaults - tbb From e20a67d4925b0ae2ac97ba39aeb7ed2995483ca4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Jan 2024 10:37:35 -0500 Subject: [PATCH 1697/2173] Update biocode to 0.11.0 (#44304) * Update biocode to 0.11.0 * run_export * Remove outdated patch --------- Co-authored-by: Thanh Lee Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: Brandon Seah Co-authored-by: Brandon Seah --- recipes/biocode/biocode.patch | 23 ----------------------- recipes/biocode/meta.yaml | 8 ++++---- 2 files changed, 4 insertions(+), 27 deletions(-) delete mode 100644 recipes/biocode/biocode.patch diff --git a/recipes/biocode/biocode.patch b/recipes/biocode/biocode.patch deleted file mode 100644 index 2b3d9f2ded9f8..0000000000000 --- a/recipes/biocode/biocode.patch +++ /dev/null @@ -1,23 +0,0 @@ -From 028ea8130db125bcb546bbc90dbdf44c5b5b0d5b Mon Sep 17 00:00:00 2001 -From: Gerry Tonkin-Hill -Date: Mon, 15 Aug 2022 12:26:17 +0100 -Subject: [PATCH] remove old script - ---- - setup.py | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/setup.py b/setup.py -index 5a96f71..ec9f63d 100644 ---- a/setup.py -+++ b/setup.py -@@ -22,7 +22,7 @@ setup(name='biocode', - license='MIT', - long_description=read('README.rst'), - packages=['biocode'], -- scripts=['bin/append_to_column_9_value.py', 'bin/prepend_to_fasta_header.py', 'bin/download_assemblies_from_genbank.py', 'bin/convert_augustus_to_gff3.py', 'bin/convert_gff3_to_ncbi_tbl.py', 'bin/mark_partial_genes.py', 'bin/filter_fasta_by_abundance.py', 'bin/validate_feature_boundaries_on_molecules.py', 'bin/add_polypeptide_to_gff3_gene_models.py', 'bin/select_training_and_evaluation_transcripts.py', 'bin/filter_fasta_by_type.py', 'bin/filter_uniref_by_taxonomy.py', 'bin/remove_orphaned_features.py', 'bin/convert_blast_btab_to_bed.py', 'bin/replace_gff_type_column_value.py', 'bin/convert_blast_btab_to_gff3.py', 'bin/interleave_fastq.py', 'bin/split_isoforms_into_individual_genes.py', 'bin/make_cufflinks_ids_unique.py', 'bin/convert_gff3_to_gbk.py', 'bin/make_go_slim_index.py', 'bin/eggnog_to_sqlite3.py', 'bin/convert_metagenemark_gff_to_gff3.py', 'bin/append_to_fasta_header.py', 'bin/merge_bam_files.py', 'bin/remove_masked_gene_models.py', 'bin/filter_fastq_by_N_content.py', 'bin/uniref_to_sqlite3.py', 'bin/uniprot_sprot_to_sqlite3.py', 'bin/reverse_misordered_cds_coords.py', 'bin/update_selected_column9_values.py', 'bin/convert_gff3_to_gene_association_format.py', 'bin/interleave_fasta.py', 'bin/make_go_slim.py', 'bin/join_columnar_files.py', 'bin/split_interleaved_sequence_file.py', 'bin/merge_masked_fasta_files.py', 'bin/hmmlib_to_sqlite3.py', 'bin/fasta_size_distribution_plot.py', 'bin/report_gff3_statistics.py', 'bin/reformat_fasta_residue_lengths.py', 'bin/convert_cufflinks_gtf_to_gff3.py', 'bin/list_biocode.py', 'bin/fasta_simple_stats.py', 'bin/fastq_simple_stats.py', 'bin/convert_prodigal_to_gff3.py', 'bin/convert_scipio_gff_to_gff3.py', 'bin/filter_gff3_by_id_list.py', 'bin/reorient_sequences_by_id.py', 'bin/convert_fastq_to_fasta.py', 'bin/create_rsem_html_table.py', 'bin/convert_glimmerHMM_gff_to_gff3.py', 'bin/convert_genbank_to_gff3.py', 'bin/replace_homopolymeric_repeats_with_Ns.py', 'bin/split_fasta_into_even_files.py', 'bin/get_mpilup_from_id_list.py', 'bin/convert_gff_to_ncbi_gff3.py', 'bin/create_taxonomic_profile_from_blast.py', 'bin/convert_fasta_contigs_to_gff3.py', 'bin/merge_fasta_files_and_uniquify_ids.py', 'bin/merge_predicted_gff3.py', 'bin/filter_fasta_by_header_regex.py', 'bin/convert_pasa_gff_to_models.py', 'bin/extract_fasta_regions.py', 'bin/set_source_column.py', 'bin/tigrfam_info_to_sqlite3.py', 'bin/add_gff3_locus_tags.py', 'bin/fasta_base_content.py', 'bin/subsample_fasta.py', 'bin/convert_gff3_to_bed.py', 'bin/compare_gene_structures.py', 'bin/validate_fasta.py', 'bin/randomly_subsample_fastq.py', 'bin/append_to_fastq_read_header.py', 'bin/convert_aat_btab_to_gff3.py', 'bin/check_for_embedded_fasta_headers.py', 'bin/convert_htab_to_bed.py', 'bin/correct_gff3_CDS_phase_column.py', 'bin/report_coverage_gaps.py', 'bin/detect_inverted_repeats.py', 'bin/convert_cegma_gff_to_gff3.py', 'bin/remove_duplicate_features.py', 'bin/remove_duplicate_sequences.py', 'bin/create_taxonomy_db.py', 'bin/calculate_query_coverage_by_blast.py', 'bin/report_or_replace_nonstandard_residues.py', 'bin/write_fasta_from_gff.py', 'bin/filter_uniref_by_repid.py', 'bin/check_gff_for_internal_stops.py', 'bin/report_basic_gff_model_agreement.py', 'bin/calculate_gene_coverage_from_assembly.py', 'bin/report_gff_intron_and_intergenic_stats.py', 'bin/extend_genes_to_stops.py', 'bin/report_go_slim_counts.py', 'bin/make_go_index.py', 'bin/split_molecules_on_gaps.py'], -+ scripts=['bin/append_to_column_9_value.py', 'bin/prepend_to_fasta_header.py', 'bin/download_assemblies_from_genbank.py', 'bin/convert_augustus_to_gff3.py', 'bin/convert_gff3_to_ncbi_tbl.py', 'bin/mark_partial_genes.py', 'bin/filter_fasta_by_abundance.py', 'bin/validate_feature_boundaries_on_molecules.py', 'bin/add_polypeptide_to_gff3_gene_models.py', 'bin/select_training_and_evaluation_transcripts.py', 'bin/filter_fasta_by_type.py', 'bin/filter_uniref_by_taxonomy.py', 'bin/remove_orphaned_features.py', 'bin/convert_blast_btab_to_bed.py', 'bin/replace_gff_type_column_value.py', 'bin/convert_blast_btab_to_gff3.py', 'bin/interleave_fastq.py', 'bin/split_isoforms_into_individual_genes.py', 'bin/make_cufflinks_ids_unique.py', 'bin/convert_gff3_to_gbk.py', 'bin/make_go_slim_index.py', 'bin/eggnog_to_sqlite3.py', 'bin/convert_metagenemark_gff_to_gff3.py', 'bin/append_to_fasta_header.py', 'bin/merge_bam_files.py', 'bin/remove_masked_gene_models.py', 'bin/filter_fastq_by_N_content.py', 'bin/uniref_to_sqlite3.py', 'bin/uniprot_sprot_to_sqlite3.py', 'bin/reverse_misordered_cds_coords.py', 'bin/update_selected_column9_values.py', 'bin/convert_gff3_to_gene_association_format.py', 'bin/make_go_slim.py', 'bin/join_columnar_files.py', 'bin/split_interleaved_sequence_file.py', 'bin/merge_masked_fasta_files.py', 'bin/hmmlib_to_sqlite3.py', 'bin/fasta_size_distribution_plot.py', 'bin/report_gff3_statistics.py', 'bin/reformat_fasta_residue_lengths.py', 'bin/convert_cufflinks_gtf_to_gff3.py', 'bin/list_biocode.py', 'bin/fasta_simple_stats.py', 'bin/fastq_simple_stats.py', 'bin/convert_prodigal_to_gff3.py', 'bin/convert_scipio_gff_to_gff3.py', 'bin/filter_gff3_by_id_list.py', 'bin/reorient_sequences_by_id.py', 'bin/convert_fastq_to_fasta.py', 'bin/create_rsem_html_table.py', 'bin/convert_glimmerHMM_gff_to_gff3.py', 'bin/convert_genbank_to_gff3.py', 'bin/replace_homopolymeric_repeats_with_Ns.py', 'bin/split_fasta_into_even_files.py', 'bin/get_mpilup_from_id_list.py', 'bin/convert_gff_to_ncbi_gff3.py', 'bin/create_taxonomic_profile_from_blast.py', 'bin/convert_fasta_contigs_to_gff3.py', 'bin/merge_fasta_files_and_uniquify_ids.py', 'bin/merge_predicted_gff3.py', 'bin/filter_fasta_by_header_regex.py', 'bin/convert_pasa_gff_to_models.py', 'bin/extract_fasta_regions.py', 'bin/set_source_column.py', 'bin/tigrfam_info_to_sqlite3.py', 'bin/add_gff3_locus_tags.py', 'bin/fasta_base_content.py', 'bin/subsample_fasta.py', 'bin/convert_gff3_to_bed.py', 'bin/compare_gene_structures.py', 'bin/validate_fasta.py', 'bin/randomly_subsample_fastq.py', 'bin/append_to_fastq_read_header.py', 'bin/convert_aat_btab_to_gff3.py', 'bin/check_for_embedded_fasta_headers.py', 'bin/convert_htab_to_bed.py', 'bin/correct_gff3_CDS_phase_column.py', 'bin/report_coverage_gaps.py', 'bin/detect_inverted_repeats.py', 'bin/convert_cegma_gff_to_gff3.py', 'bin/remove_duplicate_features.py', 'bin/remove_duplicate_sequences.py', 'bin/create_taxonomy_db.py', 'bin/calculate_query_coverage_by_blast.py', 'bin/report_or_replace_nonstandard_residues.py', 'bin/write_fasta_from_gff.py', 'bin/filter_uniref_by_repid.py', 'bin/check_gff_for_internal_stops.py', 'bin/report_basic_gff_model_agreement.py', 'bin/calculate_gene_coverage_from_assembly.py', 'bin/report_gff_intron_and_intergenic_stats.py', 'bin/extend_genes_to_stops.py', 'bin/report_go_slim_counts.py', 'bin/make_go_index.py', 'bin/split_molecules_on_gaps.py'], - url='http://github.com/jorvis/biocode', - version='0.10.0', - zip_safe=False) --- diff --git a/recipes/biocode/meta.yaml b/recipes/biocode/meta.yaml index 2d3c8dc8fe5d8..42ff93ce5a92a 100644 --- a/recipes/biocode/meta.yaml +++ b/recipes/biocode/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biocode" %} -{% set version = "0.10.0" %} +{% set version = "0.11.0" %} package: name: "{{ name|lower }}" @@ -7,14 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: ab48e0ea92f52c7fe48c6c947d4d5aa43437f16cd42a804546c71ef0e5ba2265 - patches: biocode.patch + sha256: 5c0df506d07e6b073b56da360bba4dad8e0b90e4ceb6f62009ae51c56a83b162 build: noarch: python number: 0 script: "{{ PYTHON }} -m pip install . --no-deps -vv" - + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: - pip From 902a417f5b0a40cd1efff64051468f9c4356d967 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Jan 2024 11:09:17 -0500 Subject: [PATCH 1698/2173] Update whatshap to 2.2 (#45436) --- recipes/whatshap/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/whatshap/meta.yaml b/recipes/whatshap/meta.yaml index 7c3aeef9ad35c..f8554c9bb5021 100644 --- a/recipes/whatshap/meta.yaml +++ b/recipes/whatshap/meta.yaml @@ -1,10 +1,10 @@ package: name: whatshap - version: "2.1" + version: "2.2" source: - url: https://files.pythonhosted.org/packages/35/1a/d6fedb787eac8d616ec598f6a42cf2289bcc11dbbfdeae65afdf1dcb7bfc/whatshap-2.1.tar.gz - sha256: 9b61812eda1dd5251ba8d02db16d7ddda152ccc813cb3db6a1ec796f1865fe8d + url: https://files.pythonhosted.org/packages/00/f3/2e2c850755629a151c2027b636f253745bbbfeee052870f03e99f94a4996/whatshap-2.2.tar.gz + sha256: 4cd34e9b82930c4f42e9e6b7dce2e321e4c81f934fdb980b6093ad91a06ae30a build: number: 0 From 9cf088755387c095e0368e5655d0987a6a9f5e7d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Jan 2024 14:51:07 -0500 Subject: [PATCH 1699/2173] Update hiphase to 1.2.1 (#45443) --- recipes/hiphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index 89033d92be5b2..5f949dfe8a40b 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "1.2.0" %} -{% set hiphase_sha256 = "e57455275a42a5679895a95f997c132064164343c0ef949946b28cac356c9a3a" %} +{% set version = "1.2.1" %} +{% set hiphase_sha256 = "a5bd4926bb57f934fae5d72859d530991ce804ca7127fc134ca7e4c8245fe9f0" %} package: name: {{ name }} From 8c2fd6a0acdc6de21419aeb8b2400e3410d7b75c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 26 Jan 2024 15:50:54 -0500 Subject: [PATCH 1700/2173] Update viralmsa to 1.1.42 (#45422) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index 78d60f0913045..51aad2edd4c70 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.41" %} +{% set version = "1.1.42" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: 1475eb3497823fd85febd5bb983c919b830b1e367aa7cf21af19fb33d437404b + sha256: dd4ba1779681479f86c3fa38c486ee36ee8f2ca5d66301e583125dc9767d1171 requirements: run: From 59c100637b996733b411c533a7e40b63cb032b43 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 05:56:18 -0500 Subject: [PATCH 1701/2173] Update ncbi-datasets-pylib to 16.4.3 (#45424) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 150d6075f3184..cc7f56893916a 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.3.0" %} -{% set sha256 = "9dafbff2b355d0b28f3621cdab580e5cadc8299d2ceeb845bb474d8413d14b85" %} +{% set version = "16.4.3" %} +{% set sha256 = "3155f0ebc388c30208315f253e0e36ea3df1bf83c89c97ea9765386fd3829d5d" %} package: name: {{ name|lower }} From 736d52b0b4763b99cd8f6f8b3258d01fd27bb806 Mon Sep 17 00:00:00 2001 From: Bryce Kille Date: Sat, 27 Jan 2024 12:45:57 -0600 Subject: [PATCH 1702/2173] Enable macos build for parsnp (#45444) * Enable macos build * update build number * Add patch for osx cpu count --- recipes/parsnp/cpu_count.patch | 52 ++++++++++++++++++++++++++++++++++ recipes/parsnp/meta.yaml | 7 +++-- 2 files changed, 56 insertions(+), 3 deletions(-) create mode 100644 recipes/parsnp/cpu_count.patch diff --git a/recipes/parsnp/cpu_count.patch b/recipes/parsnp/cpu_count.patch new file mode 100644 index 0000000000000..eac0bdea42d0f --- /dev/null +++ b/recipes/parsnp/cpu_count.patch @@ -0,0 +1,52 @@ +diff --git a/parsnp b/parsnp +index 85fd9c9..9501ab8 100755 +--- a/parsnp ++++ b/parsnp +@@ -8,6 +8,7 @@ + import os, sys, string, random, subprocess, time, operator, math, datetime, numpy #pysam + from collections import defaultdict + import shutil ++import multiprocessing + import shlex + from tempfile import TemporaryDirectory + import re +@@ -1210,8 +1211,13 @@ SETTINGS: + (len(outputDir)+17)*"*")) + + # If we requested more threads than available, give a warning. +- if len(os.sched_getaffinity(0)) < threads: +- logger.warning("You have asked to use more threads than you have available on your machine. This may lead to serious performance degredation with RAxML.") ++ try: ++ if len(os.sched_getaffinity(0)) < threads: ++ logger.warning("You have asked to use more threads than you have available on your machine. This may lead to serious performance degredation with RAxML.") ++ except AttributeError: ++ if multiprocessing.cpu_count() < threads: ++ logger.warning("You have asked to use more threads than you have available on your machine. This may lead to serious performance degredation with RAxML.") ++ + logger.info("<>") + + #1)read fasta files (contigs/scaffolds/finished/DBs/dirs) +@@ -1614,19 +1620,16 @@ SETTINGS: + else: + import partition + +- full_query_list_path = f"{outputDir}/config/input-list.txt" +- with open(full_query_list_path, 'w') as input_list_handle: +- random_seeded.shuffle(finalfiles) +- for qf in finalfiles: +- input_list_handle.write(qf + "\n") +- + if len(finalfiles) % args.partition_size == 1: + logger.warning("Incrementing partition size by 1 to avoid having a remainder partition of size 1") + args.partition_size += 1 + partition_output_dir = f"{outputDir}/partition" + partition_list_dir = f"{partition_output_dir}/input-lists" + os.makedirs(partition_list_dir, exist_ok=True) +- run_command(f"split -l {args.partition_size} -a 5 --additional-suffix '.txt' {full_query_list_path} {partition_list_dir}/{partition.CHUNK_PREFIX}-") ++ for partition_idx in range(math.ceil(len(finalfiles) / args.partition_size)): ++ with open(f"{partition_list_dir}/{partition.CHUNK_PREFIX}-{partition_idx:010}.txt", 'w') as part_out: ++ for qf in finalfiles[partition_idx*args.partition_size : (partition_idx+1)*args.partition_size]: ++ part_out.write(f"{qf}\n") + + chunk_label_parser = re.compile(f'{partition.CHUNK_PREFIX}-(.*).txt') + chunk_labels = [] diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml index 5591dab327142..4d0c7af0086ec 100644 --- a/recipes/parsnp/meta.yaml +++ b/recipes/parsnp/meta.yaml @@ -7,10 +7,11 @@ package: source: url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz" sha256: 1d9a4c6e5b414511ebc0052e3c9e6e32984b545ef8816086ed1d74af69c27c8f + patches: + - cpu_count.patch build: - skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('parsnp', max_pin="x") }} @@ -35,7 +36,7 @@ requirements: - phipack - raxml - fasttree - - fastani # [linux] + - fastani - mash - harvesttools - pyspoa From ec7bcfaa2212f81649e59b7d0d8b9d5f3443d501 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:08:12 -0500 Subject: [PATCH 1703/2173] Update dimet to 0.2.1 (#45442) --- recipes/dimet/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dimet/meta.yaml b/recipes/dimet/meta.yaml index fd7147d1ce9d8..8a230316e2d32 100644 --- a/recipes/dimet/meta.yaml +++ b/recipes/dimet/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dimet" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dimet-{{ version }}.tar.gz - sha256: 40d5dee29232deb5722392c745a70f757c78128829b372ce0093fe2fbaf9411e + sha256: e5ad617a5f45072bfd4257cc09b965cf27341a252de979864462c3a8e0ba94dc build: noarch: python From 0fb475eca0e7d39c35189811e4db36c5e059a2e7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:08:29 -0500 Subject: [PATCH 1704/2173] Update annembed to 0.1.3 (#45441) --- recipes/annembed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml index 5a2b606fcd0b3..44ad55f01bd75 100644 --- a/recipes/annembed/meta.yaml +++ b/recipes/annembed/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: annembed @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/annembed/archive/v{{ version }}.tar.gz - sha256: 68d08b42f06d873a3b301cb609530cb1072cd97cd8ccefa8d0331d857f692352 + sha256: 9a9175f728bb46ada240989060d7687e551c387288151186ae327b51965e4945 requirements: build: From 18fce7ad9232bcbab353f3d9c3aac15be1959c32 Mon Sep 17 00:00:00 2001 From: stuber Date: Sat, 27 Jan 2024 13:09:56 -0700 Subject: [PATCH 1705/2173] vsnp3 version 3.19 (#45440) --- recipes/vsnp3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsnp3/meta.yaml b/recipes/vsnp3/meta.yaml index 9fe286418fdbe..7daba8dea3820 100644 --- a/recipes/vsnp3/meta.yaml +++ b/recipes/vsnp3/meta.yaml @@ -1,7 +1,7 @@ {% set user = "USDA-VS" %} {% set name = "vsnp3" %} -{% set version = "3.18" %} -{% set sha256 = "46c6d760d4e7ad6e437bbd1096cd9ae681a33c90c1be7c410439b0a1a0ba7769" %} +{% set version = "3.19" %} +{% set sha256 = "cc1c282094fc4cfcf8fdf865a954807eabe5f45a9cd1218041bd03ce2e13648d" %} package: name: {{ name|lower }} From 6f6a83170dee87c4e8129489ea4d7e0a6650eb12 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:11:58 -0500 Subject: [PATCH 1706/2173] Update sirius-csifingerid to 5.8.6 (#45451) --- recipes/sirius-csifingerid/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sirius-csifingerid/meta.yaml b/recipes/sirius-csifingerid/meta.yaml index ef47cac572991..818c2dd93a169 100644 --- a/recipes/sirius-csifingerid/meta.yaml +++ b/recipes/sirius-csifingerid/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "5.8.5" %} +{% set version = "5.8.6" %} {% set siriusDistDir = "sirius_gui_dist" %} package: @@ -15,7 +15,7 @@ build: source: - url: https://github.com/boecker-lab/sirius/archive/refs/tags/v{{ version }}.zip - sha256: 72bf7762f143740c6f2be06a268149e85787c97064586791348b8a27f9e9f5c8 + sha256: f769a474140d6e28168d6d1526afc9e923e66eaeb0ace400e6c2ae77aa7f9202 requirements: build: From 4e42da9acb0c055ac08b8ce5b2b02034fe7a6809 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:13:08 -0500 Subject: [PATCH 1707/2173] Update comebin to 1.0.4 (#45439) --- recipes/comebin/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/comebin/meta.yaml b/recipes/comebin/meta.yaml index 655515c4b5f9f..3b95de96aefd5 100644 --- a/recipes/comebin/meta.yaml +++ b/recipes/comebin/meta.yaml @@ -1,10 +1,10 @@ package: name: comebin - version: "1.0.3" + version: "1.0.4" source: - url: https://github.com/ziyewang/COMEBin/archive/refs/tags/1.0.3.tar.gz - sha256: 27001cff1029ddf492da18ba8f4db18c055f48e062237bb9e17ad65ed7602930 + url: https://github.com/ziyewang/COMEBin/archive/refs/tags/1.0.4.tar.gz + sha256: 63726b4ae450c0ca366845d46f2065326a83454b2c7f87cec5b53adc9527be22 build: number: 0 From d97fa28517a9cbfb01ee0f14a9f86ebe3299215b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:13:29 -0500 Subject: [PATCH 1708/2173] Update zdb to 1.2.3 (#45434) --- recipes/zdb/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/zdb/meta.yaml b/recipes/zdb/meta.yaml index d410159bdd9f4..508c74054ba0c 100644 --- a/recipes/zdb/meta.yaml +++ b/recipes/zdb/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.1" %} +{% set version = "1.2.3" %} package: name: zdb @@ -6,13 +6,13 @@ package: build: noarch: generic - number: 1 + number: 0 run_exports: - {{ pin_subpackage('zdb', max_pin="x.x") }} source: - url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.2.1.tar.gz - sha256: 621146aa73de7bf04dd05da4e226eb558d07eb1f79e04760456c84e00ae9be0c + url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.2.3.tar.gz + sha256: b73a72cce424c1db28ccb0f1be20cbf61855260bb957e2829a6d9f991a20c029 requirements: run: From 08c4551db89f048cfabeb35f49414c4ff7297a21 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:13:44 -0500 Subject: [PATCH 1709/2173] Update sneep to 0.9 (#45437) --- recipes/sneep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sneep/meta.yaml b/recipes/sneep/meta.yaml index 97578dcf17ba2..6158e18019de4 100644 --- a/recipes/sneep/meta.yaml +++ b/recipes/sneep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SNEEP" %} -{% set version = "0.8" %} +{% set version = "0.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/SchulzLab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 147e10e6f64056f6fde4fec609f7019d0a765a5b4b14ead954e1ef3071d95d49 + sha256: 3d1f0a20f4d54ae91dd555d0fb8f9d25e980be9399bf6cbec5a5ddeedf47961d build: skip: True # [py2k] From e2f1b989e2f2affed5ba31be979702d725cffe53 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 27 Jan 2024 15:14:34 -0500 Subject: [PATCH 1710/2173] Update tides-ml to 1.1.4 (#45427) Co-authored-by: Brandon Seah --- recipes/tides-ml/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tides-ml/meta.yaml b/recipes/tides-ml/meta.yaml index 8700a6649354a..ff653618f6ed2 100644 --- a/recipes/tides-ml/meta.yaml +++ b/recipes/tides-ml/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tides-ml" %} -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/TIdeS-ML-{{ version }}.tar.gz - sha256: a2a872ac26c24705a6f538823b53081ae456a313fa587520997418fbda8e612e + sha256: 393f24ce18a58f40b2387e2a2fc2d45eb0088c8231c3d533f647deaf4b38c6ee build: entry_points: From 60412141fe8c0e666044abff7df2c40491df352b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Jan 2024 12:02:21 -0500 Subject: [PATCH 1711/2173] Update r-oncopharmadb to 1.5.1 (#45452) * Update r-oncopharmadb to 1.5.1 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-oncopharmadb/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/r-oncopharmadb/meta.yaml b/recipes/r-oncopharmadb/meta.yaml index 58e8fc471ae38..bbfbdc7933bbf 100644 --- a/recipes/r-oncopharmadb/meta.yaml +++ b/recipes/r-oncopharmadb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "r-oncopharmadb" %} -{% set version = "1.4.6" %} +{% set version = "1.5.1" %} {% set github = "https://github.com/sigven/oncoPharmaDB" %} package: @@ -8,7 +8,7 @@ package: source: url: https://github.com/sigven/pharmOncoX/archive/refs/tags/{{ version }}.tar.gz - sha256: 5c0c708828cc91f032018e5ff2c42a391a9f98bb411038b1fa431ef6992d3095 + sha256: 7765b9122063aeacd96db0c536141ab2e23a116a84e313b7264d707a09c92316 build: number: 0 @@ -24,6 +24,7 @@ requirements: - r-stringr - r-lgr - r-tidyr + - r-ggplot2 - r-googledrive - r-rlang - r-assertthat @@ -35,6 +36,7 @@ requirements: - r-stringr - r-lgr - r-tidyr + - r-ggplot2 - r-googledrive - r-rlang - r-assertthat From c4f8dbf6ca9d69e692f70c5164531f2080f3797d Mon Sep 17 00:00:00 2001 From: Mingfu Shao Date: Sun, 28 Jan 2024 15:48:36 -0500 Subject: [PATCH 1712/2173] aletsch 1.1.0 (#45454) * init for coral * update meta * Update meta.yaml * add recipes for aletsch * Update meta.yaml * update meta.yaml --------- Co-authored-by: Devon Ryan --- recipes/aletsch/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/aletsch/meta.yaml b/recipes/aletsch/meta.yaml index d456e3db645dd..f97373d1f61d4 100644 --- a/recipes/aletsch/meta.yaml +++ b/recipes/aletsch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "aletsch" %} -{% set version = "1.0.3" %} +{% set version = "1.1.0" %} package: name: "{{ name }}" @@ -7,10 +7,12 @@ package: source: url: "https://github.com/Shao-Group/aletsch/releases/download/v{{ version }}/aletsch-{{ version }}.tar.gz" - sha256: "1eae28ae32f40097320ef14c8dd65e30319cae5f1cb11533905b4330b5b76478" + sha256: "075e514da0b8e264fb7822d065061f406d5f73bea95c60ab31f08d2c498010a2" build: - number: 6 + number: 0 + run_exports: + - {{ pin_subpackage('aletsch', max_pin="x") }} requirements: build: @@ -32,7 +34,7 @@ about: home: "https://github.com/Shao-Group/aletsch" license: BSD-3-Clause license_file: LICENSE - summary: "Aletsch is a scalable, accurate, and versatile assembler for multiple RNA-seq samples." + summary: "Aletsch is an accurate, versatile assembler for multiple RNA-seq samples." extra: recipe-maintainers: From 3e249e65bf514bd7935e523cbb0a813c1786ee15 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 28 Jan 2024 15:59:37 -0500 Subject: [PATCH 1713/2173] Update cpat to 3.0.5 (#45425) * Update cpat to 3.0.5 * Add run_exports; use SPDX abbrev for license * Link executables to old names with .py suffix --------- Co-authored-by: Brandon Seah Co-authored-by: Brandon Seah --- recipes/cpat/build.sh | 9 +++++++++ recipes/cpat/meta.yaml | 11 ++++++----- 2 files changed, 15 insertions(+), 5 deletions(-) create mode 100644 recipes/cpat/build.sh diff --git a/recipes/cpat/build.sh b/recipes/cpat/build.sh new file mode 100644 index 0000000000000..ea41484c36517 --- /dev/null +++ b/recipes/cpat/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +${PYTHON} -m pip install . --no-deps --ignore-installed -vv + +# Prefix '.py' has been removed from v3.0.5 +# symlinking for reverse compatibility, as suggested in release notes +ln -s ${PREFIX}/bin/cpat ${PREFIX}/bin/cpat.py +ln -s ${PREFIX}/bin/make_hexamer_tab ${PREFIX}/bin/make_hexamer_tab.py +ln -s ${PREFIX}/bin/make_logitModel ${PREFIX}/bin/make_logitModel.py diff --git a/recipes/cpat/meta.yaml b/recipes/cpat/meta.yaml index 7303729af7f68..749a4451c6ab6 100644 --- a/recipes/cpat/meta.yaml +++ b/recipes/cpat/meta.yaml @@ -1,18 +1,19 @@ {% set name = "CPAT" %} -{% set version = "3.0.4" %} +{% set version = "3.0.5" %} package: name: "{{ name|lower }}" version: "{{ version }}" build: - number: 2 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " + number: 0 skip: True # [py2k or py > 39] + run_exports: + - {{ pin_subpackage('cpat', max_pin="x") }} source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 6d832f20729f8fc814384a27a4fcebcf81b11c0e6d80a404b4c4860d17e7d935 + sha256: ea7c9216208221f68055f962073622939ff90bbe52ebe36c305ead9f91ed24bc requirements: build: @@ -40,6 +41,6 @@ test: about: home: https://cpat.readthedocs.io/en/latest/ - license: GNU General Public v2 or later (GPLv2+) + license: GPL-2.0-or-later license_file: LICENSE.txt summary: Coding Potential Assessment Tool From 94ace5d6987e83efca0e0fe057a9ec6294d54969 Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Mon, 29 Jan 2024 09:12:41 +1000 Subject: [PATCH 1714/2173] Update syri (#45284) * add mummer to run dependencies * add run_exports * try different install method * Update meta.yaml * add patch for missing sys * try old install method * adjust pinnings to match upstream * remove test skip * attempt custon config * try pinning numpy * shot in the dark * pin cython based on open PR * remove custom config, make note on cython * trigger CI, mac test was stuck --------- Co-authored-by: Robert A. Petit III --- recipes/syri/import-sys.patch | 12 ++++++++++++ recipes/syri/meta.yaml | 30 ++++++++++++++++++------------ 2 files changed, 30 insertions(+), 12 deletions(-) create mode 100644 recipes/syri/import-sys.patch diff --git a/recipes/syri/import-sys.patch b/recipes/syri/import-sys.patch new file mode 100644 index 0000000000000..001ae2d87f0e3 --- /dev/null +++ b/recipes/syri/import-sys.patch @@ -0,0 +1,12 @@ +diff --git a/syri/pyxFiles/findshv.pyx b/syri/pyxFiles/findshv.pyx +index b23bd33..4bc3372 100644 +--- a/syri/pyxFiles/findshv.pyx ++++ b/syri/pyxFiles/findshv.pyx +@@ -9,6 +9,7 @@ from collections import defaultdict + import pandas as pd + from functools import partial + import os ++import sys + import logging + from re import findall + \ No newline at end of file diff --git a/recipes/syri/meta.yaml b/recipes/syri/meta.yaml index 583b8c738ccee..3ab1f4198571e 100755 --- a/recipes/syri/meta.yaml +++ b/recipes/syri/meta.yaml @@ -8,31 +8,37 @@ package: source: url: https://github.com/schneebergerlab/syri/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} + patches: + - import-sys.patch build: - number: 1 - skip: True # [py < 38 or py > 39] + number: 2 script: "{{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt" + run_exports: + - {{ pin_subpackage('syri', max_pin="x") }} requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} host: - - python + - python 3.8 - setuptools - - numpy >=1.20 - - cython + - numpy >=1.21.2 + # Please review cython pinning on future releases + # see: https://github.com/schneebergerlab/syri/pull/217 + - cython <=0.29.36 run: - - python - - numpy >=1.20 - - pandas - - scipy - - psutil - - python-igraph - - pysam + - python 3.8 + - numpy >=1.21.2 + - pandas >=1.2.4 + - scipy >=1.6.2 + - psutil >=5.8 + - python-igraph >=0.9.1 + - pysam >=0.16.0.1 - longestrunsubsequence - pulp + - mummer4 test: commands: From 234e5cb64fd32245b349393a5dfb24febf26fb80 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 03:22:13 -0500 Subject: [PATCH 1715/2173] Update annembed to 0.1.4 (#45459) --- recipes/annembed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml index 44ad55f01bd75..5b9b7bcc27166 100644 --- a/recipes/annembed/meta.yaml +++ b/recipes/annembed/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: annembed @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/annembed/archive/v{{ version }}.tar.gz - sha256: 9a9175f728bb46ada240989060d7687e551c387288151186ae327b51965e4945 + sha256: 0f923798db3843aac0352eba5d2b169673ee087fce2cc37981bd19a1ecb878d0 requirements: build: From abcefe22bbcd6221f9cd53c50fd48faeefbc92e0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 03:22:36 -0500 Subject: [PATCH 1716/2173] Update pycov3 to 2.1.0 (#45456) --- recipes/pycov3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pycov3/meta.yaml b/recipes/pycov3/meta.yaml index e9435f67e8e41..f5ac7f49a1a19 100644 --- a/recipes/pycov3/meta.yaml +++ b/recipes/pycov3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pycov3" %} -{% set version = "2.0.4b0" %} +{% set version = "2.1.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 22a3b35bd589e967bf3041356436c652913a64c601efb2af2149375fb095a8e4 + sha256: 7fcd34f840fb93b0e951eca51f23b4df7548412577d9bc4a6e1fbf855b97329a build: number: 0 From a12a831054d9ea233615a3b4a9467463a11fa187 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 05:27:51 -0500 Subject: [PATCH 1717/2173] Update ppanggolin to 2.0.2 (#45460) --- recipes/ppanggolin/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ppanggolin/meta.yaml b/recipes/ppanggolin/meta.yaml index fe77191e7d636..16e09e9ca169c 100644 --- a/recipes/ppanggolin/meta.yaml +++ b/recipes/ppanggolin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: ppanggolin @@ -6,7 +6,7 @@ package: source: url: https://github.com/labgem/PPanGGOLiN/archive/{{ version }}.tar.gz - sha256: 0e13410a03f825894ceccb7c7a85f8acee060cd98c720486fbb90df71cbd5275 + sha256: a655b378b05da41c5d2b7e8e8269af722681854c5d6c7c9589d01bea636035a1 build: number: 0 From 543c057fc0bbee877fd4a375494e4a3b3176ca41 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 07:00:11 -0500 Subject: [PATCH 1718/2173] Update snakemake to 8.4.0 (#45461) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 5f0761641c24b..2bd9541d59cd1 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.3.2" %} +{% set version = "8.4.0" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 2959b72891d0c842faa019aba35726090db97f3513b6d78bd668fdbe92056628 + sha256: c875e88c561370c5b545622fe7397cc0d7d2399c285044c83d1309816d0d224f build: number: 0 From bf858dca2feabc229f19a52709b607bd74a38589 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 09:49:32 -0500 Subject: [PATCH 1719/2173] Update bcbio-gff to 0.7.1 (#45464) --- recipes/bcbio-gff/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bcbio-gff/meta.yaml b/recipes/bcbio-gff/meta.yaml index ff55d1753cf3b..173e1c0c2cda6 100644 --- a/recipes/bcbio-gff/meta.yaml +++ b/recipes/bcbio-gff/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bcbio-gff" %} -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/b/{{ name|lower }}/{{ name }}-{{ version }}.tar.gz - sha256: f7b3922ee274106f8716703f41f05a1795aa9d73e903f4e481995ed8f5f65d2d + sha256: d1dc3294147b95baced6033f6386a0fed45c43767ef02d1223df5ef497e9cca6 build: - number: 1 + number: 0 noarch: python run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} From 432ff92a397dbf117ffaca924fa710f823c6591c Mon Sep 17 00:00:00 2001 From: Jose Figueroa Date: Mon, 29 Jan 2024 11:18:52 -0500 Subject: [PATCH 1720/2173] Update metacerberus (#45448) * Update metacerberus * Update metacerberus * Update metacerberus --- recipes/metacerberus/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/metacerberus/meta.yaml b/recipes/metacerberus/meta.yaml index 5983b3673b124..79300581b533d 100644 --- a/recipes/metacerberus/meta.yaml +++ b/recipes/metacerberus/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MetaCerberus" %} -{% set version = "1.1" %} +{% set version = "1.2" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 65610ac32ca00ad7917cb5fa49fc2282db66590fc5310115c32e0090600eff90 + sha256: 6103002803d448df349f770a38e0da9a261a688993b5d33afbf1a9024ecbba07 build: - number: 1 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_compatible('MetaCerberus', max_pin="x") }} requirements: host: @@ -54,7 +56,7 @@ about: home: "https://github.com/raw-lab/metacerberus" license: BSD-3-Clause license_family: BSD - license_file: + license_file: LICENSE.txt summary: "Versatile Functional Ontology Assignments for Metagenomes via Hidden Markov Model (HMM) searching with environmental focus of shotgun meta'omics data" doc_url: dev_url: From dc7470493d0887713e525ea6ea3fed64e329d104 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 11:43:05 -0500 Subject: [PATCH 1721/2173] Update thapbi-pict to 1.0.7 (#45467) --- recipes/thapbi-pict/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 319e783d8d6b0..176bda0e09969 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.6" %} +{% set version = "1.0.7" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: a80cc24cce224195e5f613353cfe63020daca949defea4511cef392b7a6f30ed + sha256: 30381e97d0af98fd4d0924130f4efaa722e8e5a3cc7a4719c7bc597d87d9e5fa build: noarch: python From 4cb6313d16e4073ed99e7db7500ec27cfe3457a5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 14:16:53 -0500 Subject: [PATCH 1722/2173] Update simpleaf to 0.16.0 (#45471) * Update simpleaf to 0.16.0 * Update meta.yaml requires piscem unless we're on osx-arm64 --------- Co-authored-by: Rob Patro --- recipes/simpleaf/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index 689fa08030ddc..fa26b7bab51b4 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.15.1" %} +{% set version = "0.16.0" %} package: name: simpleaf @@ -12,7 +12,7 @@ build: source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: 888ebb199a27ef4f009fa890fce221da3ed8b08420269faee3169e48d754932a + sha256: 1939d27ca19e7e01b951b619aa16d564935227e6f1ea14c8b730dee1faafe26b requirements: build: @@ -25,6 +25,7 @@ requirements: run: - alevin-fry >=0.8.1 - salmon >=1.10.1 + - piscem >=0.7.0 # [not osx-arm64] test: commands: From df0e13c5384ee22e3ae473544958e7207ed037c0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 14:17:08 -0500 Subject: [PATCH 1723/2173] Update parsnp to 2.0.3 (#45466) * Update parsnp to 2.0.3 * Remove osx patch --------- Co-authored-by: Bryce Kille --- recipes/parsnp/meta.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml index 4d0c7af0086ec..80b3d3aff5598 100644 --- a/recipes/parsnp/meta.yaml +++ b/recipes/parsnp/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.2" %} +{% set version = "2.0.3" %} package: name: parsnp @@ -6,12 +6,10 @@ package: source: url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz" - sha256: 1d9a4c6e5b414511ebc0052e3c9e6e32984b545ef8816086ed1d74af69c27c8f - patches: - - cpu_count.patch + sha256: 8e0c71662f69fc77eeb10a8c4687ff75dfb9d37daf7fca1a4ca410b1c1b1f7cb build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('parsnp', max_pin="x") }} From e527e3c1490b09a49c3e4a1ea3071fb0525b3647 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 14:37:43 -0500 Subject: [PATCH 1724/2173] Update star to 2.7.11b (#45429) * Update star to 2.7.11b * Include gzip * Include zlib * Include zlib --------- Co-authored-by: Michael Steinbaugh --- recipes/star/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/star/meta.yaml b/recipes/star/meta.yaml index 08e21507fba8d..fd2d21ffee404 100644 --- a/recipes/star/meta.yaml +++ b/recipes/star/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.7.11a" %} -{% set sha256 = "542457b1a4fee73f27a581b1776e9f73ad2b4d7e790388b6dc71147bd039f99a" %} +{% set version = "2.7.11b" %} +{% set sha256 = "3f65305e4112bd154c7e22b333dcdaafc681f4a895048fa30fa7ae56cac408e7" %} package: name: star @@ -27,8 +27,10 @@ requirements: - vim host: - htslib + - zlib run: - htslib + - zlib test: commands: @@ -46,3 +48,5 @@ extra: - biotools:star - usegalaxy-eu:rna_starsolo - usegalaxy-eu:rna_star + recipe-maintainers: + - mjsteinbaugh From cb9e0d6b223fd5ee3adf68873696052e26369b47 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 15:05:06 -0500 Subject: [PATCH 1725/2173] Update last to 1540 (#45462) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index c8a7c15ea12ff..0bb421e9f8b58 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1526" %} +{% set version = "1540" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: e1db7307005218cbed0c924d583e4bb7bdee96044cb94867cf73d18249058463 + sha256: 047d5ec2f3745f14e29de72c606fa9e74393723ebac9286584435650201de0cf build: number: 0 From 20484339686bb2cd589bdd08805d1036cba4412f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 15:05:15 -0500 Subject: [PATCH 1726/2173] Update pyfamsa to 0.3.2 (#45450) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/pyfamsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyfamsa/meta.yaml b/recipes/pyfamsa/meta.yaml index 14d799d24909a..587c9a9ee11d7 100644 --- a/recipes/pyfamsa/meta.yaml +++ b/recipes/pyfamsa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyfamsa" %} -{% set version = "0.3.1" %} +{% set version = "0.3.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 1122a8b06bbbe1045a185d7671e87be0030e3db8e2dd0cb885ff21744c9d24a6 + sha256: c926d6fe00029d712dd277a1544e632c2b20546da322e13bd92780ea3f756dae build: number: 0 From 84ad871ef1638eda56697b187b8f41f773c67c52 Mon Sep 17 00:00:00 2001 From: Jean Mainguy Date: Mon, 29 Jan 2024 22:41:13 +0100 Subject: [PATCH 1727/2173] Update Binette to v0.1.7 (#45469) * update binette recipe to v0.1.7 * add run_exports * update sha256 --- recipes/binette/meta.yaml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/recipes/binette/meta.yaml b/recipes/binette/meta.yaml index dbeca042db483..ff3604957f999 100644 --- a/recipes/binette/meta.yaml +++ b/recipes/binette/meta.yaml @@ -1,16 +1,20 @@ {% set name = "Binette" %} -{% set version = "0.1.6" %} +{% set version = "0.1.7" %} package: name: {{ name|lower }} version: {{ version }} source: url: https://github.com/genotoul-bioinfo/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 97f2bb4f9d8e0c06fadb4b1bc4097cc3bfeb80fe84d3c63424ae080b8ac4086d + sha256: a3ede9f274e8eec53401ee92727922ff08a8d89116bed411391b5671616e1d1e + build: noarch: python number: 0 script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv . + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + requirements: host: @@ -23,14 +27,13 @@ requirements: - numpy =1.19.2 - diamond =2.0.4 - pandas =1.4.0 - - prodigal =2.6.3 - checkm2 - requests - packaging - tqdm - - networkx + - networkx >=3 - pyfastx - - pyrodigal + - pyrodigal >=2 test: imports: @@ -40,7 +43,8 @@ test: about: home: https://github.com/genotoul-bioinfo/{{ name|lower }} + doc_url: https://binette.readthedocs.io license: MIT license_family: MIT license_file: LICENSE - summary: A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. + summary: "A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools." From a9dc305c86741a5125a5cee20412c47ff00aa276 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 17:21:05 -0500 Subject: [PATCH 1728/2173] Update nf-core to 2.12 (#45465) * Update nf-core to 2.12 * add trogon depends * add pillow depend --------- Co-authored-by: Robert A. Petit III --- recipes/nf-core/meta.yaml | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml index df210d833f8d2..c5f20958f1b84 100644 --- a/recipes/nf-core/meta.yaml +++ b/recipes/nf-core/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nf-core" %} -{% set version = "2.11.1" %} -{% set sha256 = "f81e411a66a417b9355657eec4337e8d004b166d8690e39f337994763b0ecc63" %} +{% set version = "2.12" %} +{% set sha256 = "a1af4ad7407cc7b65097b066e2593bdfc302b4c61301dd7476c2203924e92e46" %} package: name: {{ name|lower }} @@ -27,26 +27,28 @@ requirements: run: - python >=3.8 - click + - filetype + - galaxy-tool-util - git - - pyyaml - - requests - - requests-cache - - tabulate - gitpython - - markdown >=3.3 - - jsonschema >=3.0 - jinja2 - - rich >=13.3.1 - - rich-click >=1.6.1 + - jsonschema >=3.0 + - markdown >=3.3 + - packaging + - pillow - pre-commit - prompt_toolkit >=3.0.3 - pytest >=7.0.0 - pytest-workflow >=1.6.0 + - pyyaml - questionary >=1.8.0 - - packaging - - galaxy-tool-util - refgenie - - filetype + - requests + - requests-cache + - rich >=13.3.1 + - rich-click >=1.6.1 + - tabulate + - trogon test: commands: From bfb4341f583eb1f998bb69710f196fc2d2c33941 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 17:49:49 -0500 Subject: [PATCH 1729/2173] Update tksm to 0.5.0 (#44839) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update tksm to 0.4.0 * add run_exports * add make * add lld to build reqs * Update tksm to 0.5.0 * remove python pinning * Update TKSM to v0.5 (#45473) Fix python build + add more tests --------- Co-authored-by: joshuazhuang7 Co-authored-by: Fatih Karaoglanoglu Co-authored-by: Baraa Orabi /baraːʔ ʕraːbi/ --- recipes/tksm/meta.yaml | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/recipes/tksm/meta.yaml b/recipes/tksm/meta.yaml index 1d3bc532de1b6..df1add61a6a93 100644 --- a/recipes/tksm/meta.yaml +++ b/recipes/tksm/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.2" %} -{% set sha256 = "e965a8e932698570b6bc7c2ea15ebecaf7e0a50985c26cf87ece7869eaf44c83" %} +{% set version = "0.5.0" %} +{% set sha256 = "d2e0abc0ca378945fc2165d489dbe189c71fe0fc7d50bf8fb3be1bd9ce1e7bf3" %} package: name: tksm @@ -11,23 +11,24 @@ source: build: number: 0 - skip: True # [py<3.8 or osx] + skip: True # [py < 3.8 or osx] + run_exports: + - {{ pin_subpackage('tksm', max_pin="x.x") }} requirements: build: + - python - {{ compiler('cxx') }} - - python {{ python }} - - zlib - make - vim - lld host: - - python {{ python }} + - python - zlib - cxxopts >=3.1.0 - fmt >=9.1.0 run: - - python {{ python }} + - python - zlib - python-edlib - numpy @@ -37,11 +38,14 @@ requirements: test: commands: + - tksm list - tksm sequence --help - + - tksm abundance --help + - tksm model-truncation --help about: home: https://github.com/vpc-ccg/tksm license: MIT + license_family: MIT license_file: LICENSE summary: Very modular, very cool long-read transcriptomic simulator From 622fb04f1236d585379b796215829267057da8ef Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 17:58:19 -0500 Subject: [PATCH 1730/2173] Update koverage to 0.1.9 (#45475) --- recipes/koverage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/koverage/meta.yaml b/recipes/koverage/meta.yaml index e9a66d5265d47..a05f96e6afbb5 100644 --- a/recipes/koverage/meta.yaml +++ b/recipes/koverage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "koverage" %} -{% set version = "0.1.8" %} +{% set version = "0.1.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 0680e72916022fbedbf14c9dc5daa0e159e41196f81da15b5e9367d93af0832a + sha256: 45e3e3ae21669f0c7a45f023ee130d4494ebc2637c0aa4529e95a3867c4b488a build: noarch: python From 3f3fae394b71d047ae89940991e09303821d3cee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 17:58:39 -0500 Subject: [PATCH 1731/2173] Update ena-webin-cli to 6.10.0 (#45468) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index 98bc27a785056..aa7f4b8f4abec 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.9.0" %} -{% set sha256 = "13218491e3d0dce8b28360606e23ffd54bd491452449c996e7f05944bf352217" %} +{% set version = "6.10.0" %} +{% set sha256 = "3fd887d5fc5a1fbb28060f55e3903051aa9b15cc85cafd5bedb6e2c2645df1c4" %} package: name: ena-webin-cli From 4471192f0caf4ede0740d77b79ee75d24db7dd38 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 17:59:44 -0500 Subject: [PATCH 1732/2173] Update protgraph to 0.3.10 (#45457) * Update protgraph to 0.3.10 * Add run_exports statement --------- Co-authored-by: Brandon Seah --- recipes/protgraph/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/protgraph/meta.yaml b/recipes/protgraph/meta.yaml index 1837064bfc1d0..49cc0bb70b774 100644 --- a/recipes/protgraph/meta.yaml +++ b/recipes/protgraph/meta.yaml @@ -1,5 +1,5 @@ {% set name = "protgraph" %} -{% set version = "0.3.9" %} +{% set version = "0.3.10" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a1e69aed7dc57c8dcde2a70605a7ed0b39e36bcb03800f0dfecad476cbce143d + sha256: 52d0449eea53c8f113d1287fd5f40e837bf3bd6ed13193974fbd0c3bd358f800 build: number: 0 @@ -15,6 +15,8 @@ build: script: {{ PYTHON }} -m pip install . -vv entry_points: - protgraph=protgraph.protgraph:main + run_exports: + - {{ pin_subpackage('protgraph', max_pin="x.x") }} requirements: host: From c5003a903595021b13a55972b3d1fe4d5b57aff0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 29 Jan 2024 18:01:00 -0500 Subject: [PATCH 1733/2173] Update nextstrain-cli to 8.0.1 (#45472) --- recipes/nextstrain-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml index ea7189f07bb13..e0bbbca25862b 100644 --- a/recipes/nextstrain-cli/meta.yaml +++ b/recipes/nextstrain-cli/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.0.0" %} +{% set version = "8.0.1" %} package: name: nextstrain-cli @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain-cli-{{ version }}.tar.gz - sha256: 515fb4be3c013a9a30ef8cc28d8e7430d20e2edd840a9a3aa3419764b57e8268 + sha256: b552463d4c4195c9b2e57cf20bfc72e9e6927231715d88ebaec13481328fb080 build: number: 0 From cbe4c62b59e50aa4631b834e10736b1729891df5 Mon Sep 17 00:00:00 2001 From: Zak <52193148+zclaas@users.noreply.github.com> Date: Tue, 30 Jan 2024 01:01:28 +0200 Subject: [PATCH 1734/2173] Update bbmap to 39.06 (#45449) * Update bbmap to 39.06 * Copy resources to path without version number for consistency * Added run_exports --- recipes/bbmap/build.sh | 4 ++++ recipes/bbmap/meta.yaml | 12 +++++++----- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/recipes/bbmap/build.sh b/recipes/bbmap/build.sh index e1f2e8a16fe49..3cad42d6b4a27 100755 --- a/recipes/bbmap/build.sh +++ b/recipes/bbmap/build.sh @@ -4,12 +4,16 @@ set -x -e -o pipefail BINARY_HOME=$PREFIX/bin BBMAP_HOME=$PREFIX/opt/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +DATA_HOME=$PREFIX/share/$PKG_NAME mkdir -p $BINARY_HOME mkdir -p $BBMAP_HOME +mkdir -p $DATA_HOME chmod a+x *.sh cp -R * $BBMAP_HOME/ find *.sh -type f -exec ln -s $BBMAP_HOME/{} $BINARY_HOME/{} \; + +cp -R $BBMAP_HOME/resources $DATA_HOME diff --git a/recipes/bbmap/meta.yaml b/recipes/bbmap/meta.yaml index 68499749c3bf0..0ddc96a75784f 100644 --- a/recipes/bbmap/meta.yaml +++ b/recipes/bbmap/meta.yaml @@ -1,9 +1,6 @@ {% set name = "BBMap" %} -{% set version = "39.01" %} -{% set sha256 = "98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6" %} - -build: - number: 1 +{% set version = "39.06" %} +{% set sha256 = "61d45bd59a543b90a143c5c7dbfec0ff6163dce54194b8c4b648fb6aac67d42e" %} package: name: {{ name|lower }} @@ -13,6 +10,11 @@ source: url: http://downloads.sourceforge.net/project/{{ name|lower }}/{{ name }}_{{ version }}.tar.gz sha256: {{ sha256 }} +build: + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + requirements: build: - {{ compiler('c') }} From 540635bf9fe186717be25c33fd847722574b3006 Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Tue, 30 Jan 2024 00:04:11 +0100 Subject: [PATCH 1735/2173] Update nextclade to 3.0.1 (#45474) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index 1a01d3d0d15c5..2bf851ea44aee 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "3.0.0" %} +{% set version = "3.0.1" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: b5f40f1ef809ad17bdb1fe31661b965c861115325ea2d73beadc86550ffccf16 # [linux64] + sha256: 181d0ff48fe09e67f3a1e186ec0f89b15aa08eba779089f7837fc15c7b6501b1 # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: a5763a28d4b1da627aac358156923650b3ea21dae1b1c3bbfb5f5e617c2ed3a4 # [osx and x86_64] + sha256: bd21bfb9ae40be1e4a839519718b7127f146b2f8bc831771359844e27ae649f0 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: ce156efb5f5a9ead01ac140d6f701f4b780b224cc64c27cb15a4dcfd13dbdc7a # [arm64] + sha256: 20cebf5b8494645f915dddb24b87540634df31bf321c20ff97a091f85c06932d # [arm64] build: number: 0 From ede007aeac0abea10e16bf25a933b7fe985190ce Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Mon, 29 Jan 2024 18:07:41 -0500 Subject: [PATCH 1736/2173] Update annembed v0.1.4 (#45458) --- recipes/annembed/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml index 5b9b7bcc27166..8b87e6aa37968 100644 --- a/recipes/annembed/meta.yaml +++ b/recipes/annembed/meta.yaml @@ -26,7 +26,7 @@ test: - annembed -h about: - home: https://github.com/jean-pierreBoth/gsearch + home: https://github.com/jianshu93/annembed license: MIT summary: annembed is an ultra-fast and scalable non-linear dimension reduction algorithm (similar to UMAP or t-SNE) for large-scale biological data From c510aa19850e1ea6e24aae0e868da2987af10868 Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Tue, 30 Jan 2024 00:12:09 +0100 Subject: [PATCH 1737/2173] Update hictk to v0.0.7 (#45433) * Bump hictk to v0.0.7 * Try to reduce the level of parallelism during build * Update URL * Update checksum * Update patch * Bugfix * Bugfix --- recipes/hictk/build.sh | 2 +- recipes/hictk/conanfile.txt.patch | 14 ++++++++------ recipes/hictk/meta.yaml | 12 +++++++++--- recipes/hictk/run_test.sh | 12 ++++-------- 4 files changed, 22 insertions(+), 18 deletions(-) diff --git a/recipes/hictk/build.sh b/recipes/hictk/build.sh index 81e494d834d06..237a19ba2e1ad 100755 --- a/recipes/hictk/build.sh +++ b/recipes/hictk/build.sh @@ -2,7 +2,7 @@ export CONAN_NON_INTERACTIVE=1 -export CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT} +export CMAKE_BUILD_PARALLEL_LEVEL=1 # ${CPU_COUNT} export CTEST_PARALLEL_LEVEL=${CPU_COUNT} if [[ ${DEBUG_C} == yes ]]; then diff --git a/recipes/hictk/conanfile.txt.patch b/recipes/hictk/conanfile.txt.patch index 05ea419f8ae85..7925b911e0e70 100644 --- a/recipes/hictk/conanfile.txt.patch +++ b/recipes/hictk/conanfile.txt.patch @@ -1,29 +1,31 @@ diff --git a/conanfile.txt b/conanfile.txt -index 0ea6184..eb94f2c 100644 +index c3cfb89..163ff31 100644 --- a/conanfile.txt +++ b/conanfile.txt -@@ -3,72 +3,11 @@ +@@ -3,74 +3,11 @@ # SPDX-License-Identifier: MIT [requires] --boost/1.83.0#7825569cd0622461dec7bc87dfdf47ae +-boost/1.83.0#39551a6ba03b4fe2c7a86b9a6d80cd67 bshoshany-thread-pool/3.5.0#5aaea7ccf37107d3c1ba9ca9ab246e42 +-catch2/3.5.2#9554dc3c4ffcab50daf8f2cac4b79308 -cli11/2.3.2#1424b9b1d9e3682a7122f415b078b4d7 + concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502 -eigen/3.4.0#2e192482a8acff96fe34766adca2b24c -fast_float/6.0.0#6c8a953c57879453982a6ce69c0ba87c --fmt/10.1.1#cd63809a79574a2f9eb73ca35f16a243 +-fmt/10.2.1#9199a7a0611866dea5c8849a77467b25 -hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1 -highfive/2.8.0#b1de99f678ff5699cce6fb5fcac44d2d -libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602 parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7 readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83 span-lite/0.10.3#1967d71abb32b314387c2ab9c558dd22 --spdlog/1.12.0#0e390a2f5c3e96671d0857bc734e4731 +-spdlog/1.13.0#2775cc949e26b339029a852785b6b276 -zstd/1.5.5#b87dc3b185caa4b122979ac4ae8ef7e8 [generators] CMakeDeps - +- -[options] -boost*:system_no_deprecated=True -boost*:asio_no_deprecated=True diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index aaa53c1d48491..2efb3189fdfa5 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.6" %} -{% set sha256 = "5913792f858304ff82996c9e9720442736b443d56c53aa8eb2a1ac2ae8ccc88f" %} +{% set version = "0.0.7" %} +{% set sha256 = "f3aaa80a399074f29747d99f5779d5a8221947044ef6946de3d7b9425d29d415" %} package: name: {{ name|lower }} @@ -22,6 +22,7 @@ requirements: - cmake >=3.25 - conan >=2 - make + - catch2 >=3.5 - cli11 >=2.3 - eigen >=3.4 - fast_float >=5 @@ -53,11 +54,13 @@ test: requires: - curl - cooler>=0.9.3 - - openjdk>=11 - perl-digest-sha1 - xz source_files: - cmake/FetchTestDataset.cmake + - test/scripts/check_test_files_exist.sh + - test/scripts/compare_matrix_files.sh + - test/scripts/compare_plain_files.sh - test/scripts/hictk_balance.sh - test/scripts/hictk_convert_hic2cool.sh - test/scripts/hictk_convert_cool2hic.sh @@ -78,6 +81,9 @@ test: - test/scripts/hictk_rename_chromosomes.sh - test/scripts/hictk_validate.sh - test/scripts/hictk_zoomify.sh + - test/scripts/nproc.sh + - test/scripts/readlink.sh + - test/scripts/shuffle.sh commands: - hictk --help - hictk --version diff --git a/recipes/hictk/run_test.sh b/recipes/hictk/run_test.sh index 045b9c4db17c7..9d039acef9489 100755 --- a/recipes/hictk/run_test.sh +++ b/recipes/hictk/run_test.sh @@ -16,16 +16,12 @@ shasum -c checksum.sha256 tar -xf hictk_test_dataset.tar.xz -# Download hictools -hictools_url='https://github.com/aidenlab/HiCTools/releases/download/v3.30.00/hic_tools.3.30.00.jar' -hictools_sha256='2b09b0642a826ca5730fde74e022461a708caf62ed292bc5baaa841946721867' -curl -L "$hictools_url" -o hic_tools.jar -echo "$hictools_sha256 hic_tools.jar" | tee checksum.sha256 -shasum -c checksum.sha256 - hictk="$(which hictk)" # Run integration tests + +test/scripts/hictk_balance.sh "$hictk" + test/scripts/hictk_dump_chroms.sh "$hictk" test/scripts/hictk_dump_bins.sh "$hictk" test/scripts/hictk_dump_gw.sh "$hictk" @@ -34,7 +30,7 @@ test/scripts/hictk_dump_trans.sh "$hictk" test/scripts/hictk_dump_balanced.sh "$hictk" test/scripts/hictk_convert_hic2cool.sh "$hictk" -test/scripts/hictk_convert_cool2hic.sh "$hictk" hic_tools.jar +test/scripts/hictk_convert_cool2hic.sh "$hictk" test/scripts/hictk_load_coo.sh "$hictk" sorted test/scripts/hictk_load_coo.sh "$hictk" unsorted From 7f88484e7b9e8959b5e436a07d3d8c5f67682e6d Mon Sep 17 00:00:00 2001 From: Jody Phelan Date: Tue, 30 Jan 2024 02:31:50 +0000 Subject: [PATCH 1738/2173] add itol-config (#45476) --- recipes/itol-config/meta.yaml | 46 +++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/itol-config/meta.yaml diff --git a/recipes/itol-config/meta.yaml b/recipes/itol-config/meta.yaml new file mode 100644 index 0000000000000..069a6ee5a623a --- /dev/null +++ b/recipes/itol-config/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "itol-config" %} +{% set version = "0.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/jodyphelan/itol-config/archive/v{{ version }}.tar.gz + sha256: e4fb28eb6c434a7a2c823f0d34b86a483c67a7f139e2c18832d564b9b4555bb6 + +build: + number: 0 + noarch: python + entry_points: + - itol-config = itol_config.cli:cli + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('itol-config', max_pin="x.x") }} + +requirements: + host: + - python >=3.8 + - flit-core >=3.2,<4 + - pip + run: + - python >=3.8 + - tomli + +test: + imports: + - itol_config + commands: + - itol-config --help + +about: + home: https://github.com/jodyphelan/itol-config + license: MIT + license_family: MIT + license_file: LICENSE + doc_url: https://jodyphelan.github.io/itol-config/ + summary: Package to create iTOL config files + +extra: + recipe-maintainers: + - jodyphelan From d7f4c2bed9c25c09fb6c47e3e586aedebc1402d7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 03:36:35 -0500 Subject: [PATCH 1739/2173] Update simpleaf to 0.16.1 (#45478) --- recipes/simpleaf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index fa26b7bab51b4..2a135224532ca 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.16.0" %} +{% set version = "0.16.1" %} package: name: simpleaf @@ -12,7 +12,7 @@ build: source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: 1939d27ca19e7e01b951b619aa16d564935227e6f1ea14c8b730dee1faafe26b + sha256: f6204577500063f89c55de9d496c6aeb58ef9048fb5ef8904efaa4f2850b31cc requirements: build: From 725560dbd497e800ebf124c4dfcfd040db0f29d7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 06:02:32 -0500 Subject: [PATCH 1740/2173] Update snakemake to 8.4.1 (#45483) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 2bd9541d59cd1..5a553102e641a 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.0" %} +{% set version = "8.4.1" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: c875e88c561370c5b545622fe7397cc0d7d2399c285044c83d1309816d0d224f + sha256: 476f1f979b98dc2cd10d774e7e5319262dc2559a4f36013459e94d03e076ab4a build: number: 0 From 602ed4b089cf02af7198bbac9ce04ab757b05c5c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 07:15:19 -0500 Subject: [PATCH 1741/2173] Update varlociraptor to 8.4.4 (#45486) --- recipes/varlociraptor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varlociraptor/meta.yaml b/recipes/varlociraptor/meta.yaml index a499dd821034d..98b3bb7d447fc 100644 --- a/recipes/varlociraptor/meta.yaml +++ b/recipes/varlociraptor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.3" %} +{% set version = "8.4.4" %} package: name: varlociraptor @@ -11,7 +11,7 @@ build: source: url: https://github.com/varlociraptor/varlociraptor/archive/v{{ version }}.tar.gz - sha256: bbb192ea88f22a85a95273ef425425f2d60686d58ae104c2d182effbd3d61ae9 + sha256: e95294fb7dcefc1f61e26fac3fceedb8355138ff386e5ffd76236f3aea083cb3 requirements: build: From fcda95f9091dbaf6628baca856dcfcee738eec04 Mon Sep 17 00:00:00 2001 From: Martin Raden Date: Tue, 30 Jan 2024 13:50:18 +0100 Subject: [PATCH 1742/2173] rebuild locarna 2.0 (#45432) using recent viennarna package --- recipes/locarna/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/locarna/meta.yaml b/recipes/locarna/meta.yaml index 6575d3c121e45..8b20692981d04 100644 --- a/recipes/locarna/meta.yaml +++ b/recipes/locarna/meta.yaml @@ -13,7 +13,9 @@ about: summary: Multiple alignment of RNAs build: - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage('locarna', max_pin="x.x") }} source: url: "https://github.com/s-will/LocARNA/releases/download/v{{ version }}/locarna-{{ version }}.tar.gz" @@ -27,9 +29,9 @@ requirements: - make - {{ compiler('cxx') }} host: - - viennarna =={{ vrnaversion }} + - viennarna >={{ vrnaversion }},<3 run: - - viennarna =={{ vrnaversion }} + - viennarna >={{ vrnaversion }},<3 - perl test: From 27c852fc01ef7d227a21be2a7f275be94eb96685 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 09:11:16 -0500 Subject: [PATCH 1743/2173] Update ccsmeth to 0.5.0 (#45490) * Update ccsmeth to 0.5.0 * Update meta.yaml * add run_exports --------- Co-authored-by: Peng Ni <543943952@qq.com> --- recipes/ccsmeth/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/ccsmeth/meta.yaml b/recipes/ccsmeth/meta.yaml index 2d8d97c2f3349..b31d55381a2a0 100644 --- a/recipes/ccsmeth/meta.yaml +++ b/recipes/ccsmeth/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ccsmeth" %} -{% set version = "0.4.1" %} -{% set hash = "783382fc3f3a108d7b1f4de8f60c06a45c049d8de797251d14cadb1ae69b6aa7" %} +{% set version = "0.5.0" %} +{% set hash = "9f6bd61ebf1e7e7a4b6d0690658ccf0a70936faf3229db7998ef3ad6ef3e3a54" %} package: name: "{{ name|lower }}" @@ -16,6 +16,8 @@ build: entry_points: - ccsmeth=ccsmeth.ccsmeth:main script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage("ccsmeth", max_pin="x.x") }} requirements: host: @@ -28,7 +30,7 @@ requirements: - numpy >=1.20.0 - scikit-learn >=1.0.2 - statsmodels >=0.13.2 - - pytorch >=1.2.0,<=1.12.1 + - pytorch >=1.2.0,<=2.1.0 - pysam >=0.19.0 - tqdm >=4.64.0 - bedtools =2.30.0 From 1d13a1583252aa120ad395aaec808d34dcb59e8d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 11:48:31 -0500 Subject: [PATCH 1744/2173] Update nf-test to 0.8.4 (#45494) --- recipes/nf-test/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-test/meta.yaml b/recipes/nf-test/meta.yaml index 21bcaf9fe3c08..280a8e4979ddd 100644 --- a/recipes/nf-test/meta.yaml +++ b/recipes/nf-test/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.3" %} +{% set version = "0.8.4" %} package: @@ -13,7 +13,7 @@ build: source: url: https://github.com/askimed/nf-test/releases/download/v{{version}}/nf-test-{{version}}.tar.gz - sha256: af48883e8d0cd2d65b0846b3f60a476a5ec28a3799ba9374e0cb307a2a2d634d + sha256: 8023bbe6e354294fba514493f423f80e75869e5daf7e51f4cb808877fdc84381 requirements: host: From 9081ec45161207f80fe489dc553a5f900466b87b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 11:52:37 -0500 Subject: [PATCH 1745/2173] Update hictk to 0.0.8 (#45479) --- recipes/hictk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml index 2efb3189fdfa5..8045e185b4dd9 100644 --- a/recipes/hictk/meta.yaml +++ b/recipes/hictk/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hictk" %} -{% set version = "0.0.7" %} -{% set sha256 = "f3aaa80a399074f29747d99f5779d5a8221947044ef6946de3d7b9425d29d415" %} +{% set version = "0.0.8" %} +{% set sha256 = "4bdadf49cb053731ea31f50312c9e4fcbcdcbaf94c39715f7b325641629bed4b" %} package: name: {{ name|lower }} From f0c9fc08fbe3ea688645f6a07d5d56872ce74915 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=A3o=20Sequeira?= Date: Tue, 30 Jan 2024 20:20:29 +0000 Subject: [PATCH 1746/2173] Update mosca (#45485) * Update mosca to 2.3.0 * Add txt files from resources * build.sh removed * Update meta.yaml Updated license name --------- Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> --- recipes/mosca/build.sh | 5 ----- recipes/mosca/meta.yaml | 11 ++++++++--- 2 files changed, 8 insertions(+), 8 deletions(-) delete mode 100644 recipes/mosca/build.sh diff --git a/recipes/mosca/build.sh b/recipes/mosca/build.sh deleted file mode 100644 index 4582f8c0c8704..0000000000000 --- a/recipes/mosca/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -echo "Storing MOSCA's files in the Conda environment at: ${PREFIX}" -mkdir -p "${PREFIX}/share/MOSCA" "${PREFIX}/bin" -cp -r workflow/* resources/*.json "${PREFIX}/share/MOSCA" -chmod +x "${PREFIX}/share/MOSCA/mosca.py" -ln -s "${PREFIX}/share/MOSCA/mosca.py" "${PREFIX}/bin/mosca" diff --git a/recipes/mosca/meta.yaml b/recipes/mosca/meta.yaml index d4ec74195aabd..d5f6fa74f4ac4 100644 --- a/recipes/mosca/meta.yaml +++ b/recipes/mosca/meta.yaml @@ -1,6 +1,6 @@ {% set name = "mosca" %} -{% set version = "2.2.1" %} -{% set sha256 = "c2b66c9cb0d55edf1c452fd23e31965ce9fb45793007521b372a1229ab5ed254" %} +{% set version = "2.3.0" %} +{% set sha256 = "1eba9c082273dd46badd2d5ff8df56aabdc496214e337331d000f54399893a94" %} package: name: {{ name|lower }} @@ -15,6 +15,11 @@ build: number: 0 run_exports: - {{ pin_subpackage("mosca", max_pin="x.x") }} + script: > + mkdir -p $PREFIX/share/MOSCA $PREFIX/bin && + cp -r workflow/* resources/*.json resources/*.txt $PREFIX/share/MOSCA && + chmod +x $PREFIX/share/MOSCA/mosca.py && + ln -s $PREFIX/share/MOSCA/mosca.py $PREFIX/bin/mosca requirements: run: @@ -28,7 +33,7 @@ test: about: home: https://github.com/iquasere/MOSCA - license: GNU General Public License v3 (GPL-3.0) + license: GPL-3.0-or-later license_family: GPL license_file: LICENSE summary: 'MOSCA - Meta-Omics Software for Community Analysis' From 920a17f6d16507f3712568999252358cb402d049 Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Tue, 30 Jan 2024 16:25:08 -0500 Subject: [PATCH 1747/2173] Update meta.yaml (#45500) Bump piscem to 0.7.1 --- recipes/piscem/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/piscem/meta.yaml b/recipes/piscem/meta.yaml index c8a3c44e6338e..d1158ff26aa29 100644 --- a/recipes/piscem/meta.yaml +++ b/recipes/piscem/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.0" %} -{% set git_commit = "c2b7489018f5b146d7206b3f080ca949cc6427fc" %} +{% set version = "0.7.1" %} +{% set git_commit = "db091893716b1709d97cdf4a8659607e99f5b534" %} {% set sha256 = "a72af2ab728e95aa6766a3bb4520af6273a9ea3be44a6a8dc260cd97615877df" %} package: From 143a8b1bc26e82456b26a2287d28914c6d8b110a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 16:25:28 -0500 Subject: [PATCH 1748/2173] Update cyvcf2 to 0.30.28 (#45499) --- recipes/cyvcf2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cyvcf2/meta.yaml b/recipes/cyvcf2/meta.yaml index 26df81e5b90b8..2ebb65713d6f9 100644 --- a/recipes/cyvcf2/meta.yaml +++ b/recipes/cyvcf2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "cyvcf2" %} -{% set version = "0.30.27" %} -{% set sha256 = "f1b12c1fb78bd039c5d94b0ff2d838edfa0716c0e4902ad3ecec3d48da3d4ff9" %} +{% set version = "0.30.28" %} +{% set sha256 = "dde7771570e210df9ca6d21c171a8aa376f191966826241fdcdf960befb9cc0f" %} package: name: {{ name }} From 95fc11f93f0f97e69debf3caffa65a71aa19c849 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 16:25:49 -0500 Subject: [PATCH 1749/2173] Update snakemake to 8.4.2 (#45497) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 5a553102e641a..614c8729ad5bc 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.1" %} +{% set version = "8.4.2" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 476f1f979b98dc2cd10d774e7e5319262dc2559a4f36013459e94d03e076ab4a + sha256: ea9273d7a27706b635fafae87bb21100dad02275570e138fdcff125cb3cba4f4 build: number: 0 From 73823b6b0816be91d1ff1b6de407c309eac57172 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 16:26:13 -0500 Subject: [PATCH 1750/2173] Update gubbins to 3.3.3 (#45495) --- recipes/gubbins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml index 8305801f9caa9..34c62e3484b4a 100644 --- a/recipes/gubbins/meta.yaml +++ b/recipes/gubbins/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gubbins" %} -{% set version = "3.3.1" %} -{% set sha256 = "1794ba37780f1444131f84fa34fb144e709ec1af239c46f7f18636d8b1b73edf" %} +{% set version = "3.3.3" %} +{% set sha256 = "b1d878130a6f07ff133efa55f0d6ed2ec3bcfa64029352ce5050c6a162b9a0b2" %} package: name: {{ name|lower }} From 3f52153a10cfbcfc5788c05b536b5975536cbcc1 Mon Sep 17 00:00:00 2001 From: Jean Mainguy Date: Tue, 30 Jan 2024 23:32:57 +0100 Subject: [PATCH 1751/2173] update binette to v1.0.0 (#45482) --- recipes/binette/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/binette/meta.yaml b/recipes/binette/meta.yaml index ff3604957f999..f666ea8f6e0f9 100644 --- a/recipes/binette/meta.yaml +++ b/recipes/binette/meta.yaml @@ -1,12 +1,12 @@ {% set name = "Binette" %} -{% set version = "0.1.7" %} +{% set version = "1.0.0" %} package: name: {{ name|lower }} version: {{ version }} source: url: https://github.com/genotoul-bioinfo/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: a3ede9f274e8eec53401ee92727922ff08a8d89116bed411391b5671616e1d1e + sha256: 121cff275fac2bbec2062863fa074c7f4f2a16eb52cada89bc46c87b7429d63d build: noarch: python From 03faab73a38ebabaffd01db1a36f664cc024f4db Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 17:38:20 -0500 Subject: [PATCH 1752/2173] Update ncbi-datasets-pylib to 16.4.4 (#45503) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index cc7f56893916a..ed48d3f17a024 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.3" %} -{% set sha256 = "3155f0ebc388c30208315f253e0e36ea3df1bf83c89c97ea9765386fd3829d5d" %} +{% set version = "16.4.4" %} +{% set sha256 = "34db22fd526188b0c819c1b9487a183c98c33f65ca940876b52e1debb8a8e450" %} package: name: {{ name|lower }} From 28f0a2e8e45acc97fb117c0613032f82e59a58ea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 30 Jan 2024 18:22:35 -0500 Subject: [PATCH 1753/2173] Update augur to 24.1.0 (#45502) * Update augur to 24.1.0 * Bump minimum bcbio-gff to 0.7.1, biopython 1.80 --------- Co-authored-by: Cornelius Roemer --- recipes/augur/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index c890f6e104b18..9d585bfd5ce39 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "24.0.0" %} +{% set version = "24.1.0" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: 6766330e7db7d6ceab8256b1f815882fdf3a9dccdeb224f316266d7983f2a407 + sha256: 22d349581fbbdfdcca0df02ce5d093965c9963931ef42c946a63b87d79a7ab08 build: number: 0 @@ -23,13 +23,13 @@ requirements: - pip run: - python >=3.8 - - bcbio-gff >=0.7.0,<0.8 - - biopython >=1.73,!=1.77,!=1.78,<1.82 + - bcbio-gff >=0.7.1,<0.8 + - biopython >=1.80,<2 - cvxopt >=1.1.9,<2 - importlib_resources >=5.3.0 # [py<311] - isodate >=0.6.0,<0.7 - jsonschema >=3.0.0,<4 - - networkx >=2.5, <3 + - networkx >=2.5,<3 - numpy >=1.0.0,<2 - packaging >=19.2 - pandas >=1.0.0,<2 From c54e8843fd2a3cc89d9306fed719cca59787217c Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 31 Jan 2024 09:23:01 +0100 Subject: [PATCH 1754/2173] adjust GitHub org for annonars (#45504) --- recipes/annonars/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 61ae02aad9578..a7e856b889433 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -5,13 +5,13 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("annonars", max_pin="x.x") }} source: - url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz sha256: 8b0725fc8d7e861bc08c96882f6e9e489b5079c10eb723295b26d2100e6e86f9 requirements: @@ -37,7 +37,7 @@ test: - annonars --help about: - home: https://github.com/bihealth/annonars + home: https://github.com/varfish-org/annonars license: Apache-2.0 license_file: LICENSE.txt summary: 'Genome annotation based on Rust and RocksDB.' From 8a0e8ea807ec07d40df5b3e07b126b5bcd8e0a09 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 31 Jan 2024 09:23:30 +0100 Subject: [PATCH 1755/2173] move viguno to other org (#45505) --- recipes/viguno/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/viguno/meta.yaml b/recipes/viguno/meta.yaml index aee151869b737..44a32ed9707e4 100644 --- a/recipes/viguno/meta.yaml +++ b/recipes/viguno/meta.yaml @@ -7,12 +7,12 @@ package: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage("viguno", max_pin="x.x") }} source: - url: https://github.com/bihealth/viguno/archive/v{{ version }}.tar.gz + url: https://github.com/varfish-org/viguno/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: @@ -38,6 +38,6 @@ test: - viguno -h about: - home: https://github.com/bihealth/viguno + home: https://github.com/bihealth/varfish-org license: MIT summary: Lookup OMIM genes and HPO terms and compute similarities From d70cccb6c9a32b52e9c6ec154341b70bcf196b76 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 31 Jan 2024 09:23:54 +0100 Subject: [PATCH 1756/2173] adjust GitHub org (#45506) --- recipes/mehari/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index c36b6f1c6475a..a9745e92008b9 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -7,12 +7,12 @@ package: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage("mehari", max_pin="x.x") }} source: - url: https://github.com/bihealth/mehari/archive/v{{ version }}.tar.gz + url: https://github.com/varfish-org/mehari/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: @@ -38,6 +38,6 @@ test: - mehari -h about: - home: https://github.com/bihealth/mehari + home: https://github.com/bihealth/varfish-org license: MIT summary: VEP-like tool for sequence ontology and HGVS annotation of VCF files written in Rust. From 05d3c955b86d110902d8d9376d526d2c111c8540 Mon Sep 17 00:00:00 2001 From: Felix Becker Date: Wed, 31 Jan 2024 11:59:22 +0100 Subject: [PATCH 1757/2173] Update learnMSA to version 1.3.4 (#45493) * added run_exports * changed package name to lower case --- recipes/learnmsa/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/learnmsa/meta.yaml b/recipes/learnmsa/meta.yaml index dacfbf73ca0a2..2ddcc263cfca5 100644 --- a/recipes/learnmsa/meta.yaml +++ b/recipes/learnmsa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "learnMSA" %} -{% set version = "1.3.2" %} +{% set version = "1.3.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: da7ec9b5f89685098cbeb272918e9c89f2e67bd6698dbbc7bfa49a036d06d73c + sha256: b942cc9f2c6835f8a067ad647e542fe1f2b12517a4b1b81ac70e120b0385637d build: number: 0 @@ -15,6 +15,8 @@ build: - learnMSA = learnMSA.run:run_main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv" noarch: python + run_exports: + - {{ pin_subpackage('learnmsa', max_pin="x") }} requirements: host: From e97713676f983166c2335a2e8c34e5bfbb6eaeb0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 07:13:48 -0500 Subject: [PATCH 1758/2173] Update cellqc to 0.0.7 (#45501) --- recipes/cellqc/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/cellqc/meta.yaml b/recipes/cellqc/meta.yaml index 898e630900d0c..0582defd01a18 100644 --- a/recipes/cellqc/meta.yaml +++ b/recipes/cellqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cellqc" %} -{% set version = "0.0.6" %} +{% set version = "0.0.7" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3da8ed9e2c275626ab2eb2c779cdb8eacf1429fce212357c0dd29c9753e08764 + sha256: d637e51cf5bbe5dae7b3fd8dc85f32af1e8b9c379882351878673bdd3ff6bf6d build: - number: 1 + number: 0 entry_points: - cellqc=cellqc.cellqc:main run_exports: From ba7737f350b0dcf51aca1a0074c380a3c39b644c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 07:14:18 -0500 Subject: [PATCH 1759/2173] Update massdash to 0.0.8 (#45509) --- recipes/massdash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/massdash/meta.yaml b/recipes/massdash/meta.yaml index b3ae8c95452b5..dcbbef4ea0961 100644 --- a/recipes/massdash/meta.yaml +++ b/recipes/massdash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "massdash" %} -{% set version = "0.0.6" %} +{% set version = "0.0.8" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: f2b4160745ddcd96698f92c7d9c86b5a354970ace233924a0e26cba88421a761 + sha256: 9e03e23c7f2f9c84c30ba7aef936d2f26b0284b4fa0dd330618e6fd6fb40cbef build: number: 0 From 39ce391c399b6365a1fff0e188c83487a6318541 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 07:14:48 -0500 Subject: [PATCH 1760/2173] Update skyline2isocor to 0.1.1 (#45516) --- recipes/skyline2isocor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skyline2isocor/meta.yaml b/recipes/skyline2isocor/meta.yaml index 3abfb9f8be2a4..cd67bddec37b2 100644 --- a/recipes/skyline2isocor/meta.yaml +++ b/recipes/skyline2isocor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skyline2isocor" %} -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/skyline2isocor-{{ version }}.tar.gz - sha256: 9bf2b6a8c381ced3a5a24838d944bfff016a12c7da6f3627ff31467918e609bc + sha256: 276d9ced9a3f69c9692a7803ec3cd84f16466aac1bbab9ec4c827ea599db7f8e build: entry_points: From 66a18ed4c1e007cf90d4b8a420a163c5f6e5d48c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 07:16:16 -0500 Subject: [PATCH 1761/2173] Update earlgrey to 4.0.6 (#45515) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index 268616558bed9..19c3246edd5ab 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.5" %} -{% set sha256 = "5fe1341dad3da2bf322415cb048a846173e386b1998be188828f3c905349daa8" %} +{% set version = "4.0.6" %} +{% set sha256 = "bc4ba13a2f7cf10ef6eedec17529bf8e191ecdd81d85d9db8a788467e282d655" %} package: name: {{ name|lower }} From 3f075b402b677ad7e859f396c1a4ce3ae60f9ada Mon Sep 17 00:00:00 2001 From: Jesus Garcia Garcia <44952878+garci1294@users.noreply.github.com> Date: Wed, 31 Jan 2024 06:19:32 -0600 Subject: [PATCH 1762/2173] Update bioconductor-infercnv (#45481) * Update meta.yaml `htmltools >=0.5.7' package is required by infercnv. * increased build no --------- Co-authored-by: Thanh Lee --- recipes/bioconductor-infercnv/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bioconductor-infercnv/meta.yaml b/recipes/bioconductor-infercnv/meta.yaml index 846a226731767..cca8ee52d9314 100644 --- a/recipes/bioconductor-infercnv/meta.yaml +++ b/recipes/bioconductor-infercnv/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d5bce5518c27e86b3fb26b6fedad5d7b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -27,6 +27,7 @@ requirements: - 'bioconductor-edger >=4.0.0,<4.1.0' - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'r-htmltools >=0.5.7' - r-ape - r-argparse - r-base @@ -61,6 +62,7 @@ requirements: - 'bioconductor-edger >=4.0.0,<4.1.0' - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - 'r-htmltools >=0.5.7' - r-ape - r-argparse - r-base From 6ff11650016c021322beb14282df5ea1201ed987 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 12:15:19 -0500 Subject: [PATCH 1763/2173] Update zol to 1.3.18 (#45519) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index ce26b14a3821b..b2c6b239d2e12 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.17" %} +{% set version = "1.3.18" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 71205d5144d4489d863d63dd0e4eb5b4341e66b71bf4bc7fc186e9bed98fa17b + sha256: 7c5a9693a0ca4225581b8f31da73b154d415067c5619a882a7b1d6b99efdc6f7 build: number: 0 From 1083a2b5f2a825c300065a93ac808588b124289e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 16:48:45 -0500 Subject: [PATCH 1764/2173] Update gw to 0.9.3 (#45525) --- recipes/gw/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gw/meta.yaml b/recipes/gw/meta.yaml index 7bf6ab483b790..b76079b337bc9 100644 --- a/recipes/gw/meta.yaml +++ b/recipes/gw/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.9.1" %} -{% set sha256 = "10a65107717811179a124e8bac5b2f202bdbde6679a9e6eb67ef97c990b7cf9d" %} +{% set version = "0.9.3" %} +{% set sha256 = "43445ef6d96bd8a09a9a45cd18e21481d7fefe7e9ab26aec4abd8d1f4bff3fcd" %} package: name: gw From 24bdc9ee04962958bc44d21b3cbd69ad105f9eb4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 16:52:12 -0500 Subject: [PATCH 1765/2173] Update skyline2isocor to 0.1.2 (#45520) --- recipes/skyline2isocor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skyline2isocor/meta.yaml b/recipes/skyline2isocor/meta.yaml index cd67bddec37b2..a888d3d122ba4 100644 --- a/recipes/skyline2isocor/meta.yaml +++ b/recipes/skyline2isocor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skyline2isocor" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/skyline2isocor-{{ version }}.tar.gz - sha256: 276d9ced9a3f69c9692a7803ec3cd84f16466aac1bbab9ec4c827ea599db7f8e + sha256: de1516845912f31ecb84ddd19c28f3ff6f6db2dd11ca834a42424276d795ec74 build: entry_points: From a32307bd70575691441302054881432fd904cfa9 Mon Sep 17 00:00:00 2001 From: Mingfu Shao Date: Wed, 31 Jan 2024 16:57:17 -0500 Subject: [PATCH 1766/2173] terrace (#45526) * init for coral * update meta * Update meta.yaml * add recipes for aletsch * Update meta.yaml * update meta.yaml * Create build.sh for TERRACE * Create meta.yaml --------- Co-authored-by: Devon Ryan --- recipes/terrace/build.sh | 5 +++++ recipes/terrace/meta.yaml | 41 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 recipes/terrace/build.sh create mode 100644 recipes/terrace/meta.yaml diff --git a/recipes/terrace/build.sh b/recipes/terrace/build.sh new file mode 100644 index 0000000000000..7a0d70011ef7a --- /dev/null +++ b/recipes/terrace/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +./configure --prefix=$PREFIX +make LIBS+=-lhts +make install diff --git a/recipes/terrace/meta.yaml b/recipes/terrace/meta.yaml new file mode 100644 index 0000000000000..136afdf510081 --- /dev/null +++ b/recipes/terrace/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "terrace" %} +{% set version = "1.1.1" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: "https://github.com/Shao-Group/TERRACE/releases/download/v{{ version }}/terrace-{{ version }}.tar.gz" + sha256: "2014bce67e6d05cf7c71ba16033f044c7043dc60217ca390741cff8818538664" + +build: + number: 0 + run_exports: + - {{ pin_subpackage('terrace', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - htslib + - boost-cpp + run: + - htslib + - boost-cpp + +test: + commands: + - terrace --help + +about: + home: "https://github.com/Shao-Group/TERRACE" + license: BSD-3-Clause + license_file: LICENSE + summary: "TERRACE is an assembler for circular RNAs." + +extra: + recipe-maintainers: + - shaomingfu From 00d1a9fbbf7c8ff04f615e3130d6bc194fc60431 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 17:15:58 -0500 Subject: [PATCH 1767/2173] Update varcode to 1.2.0 (#45498) * Update varcode to 1.2.0 * add run_exports --------- Co-authored-by: mencian --- recipes/varcode/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/varcode/meta.yaml b/recipes/varcode/meta.yaml index 01e085d867ed8..061bbf466712d 100644 --- a/recipes/varcode/meta.yaml +++ b/recipes/varcode/meta.yaml @@ -1,5 +1,5 @@ {% set name = "varcode" %} -{% set version = "1.1.0" %} +{% set version = "1.2.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: ed2c81a322e13f4b9fcfc15fc1dba87dbeef8ab4cd808f22188ec67db9159512 + sha256: e3ae050bf772fca49417044f7dfc5f68c373b11ace7afea106d4f35b4721091f build: number: 0 @@ -15,7 +15,9 @@ build: entry_points: - varcode-genes = varcode.cli.genes_script:main - varcode = varcode.cli.effects_script:main - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('varcode', max_pin="x") }} requirements: host: @@ -44,8 +46,9 @@ test: about: home: "https://github.com/openvax/varcode" - license: Apache Software + license: Apache-2.0 license_family: APACHE + license_file: LICENSE summary: "Variant annotation in Python" extra: From 4693f89724b6c07c7d374f8a81e0f2fcdba33d2e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 17:26:02 -0500 Subject: [PATCH 1768/2173] Update diamond to 2.1.9 (#45518) * Update diamond to 2.1.9 * add run_exports --------- Co-authored-by: mencian --- recipes/diamond/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/diamond/meta.yaml b/recipes/diamond/meta.yaml index 0fe8f5553d59f..d35213fa65257 100644 --- a/recipes/diamond/meta.yaml +++ b/recipes/diamond/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.1.8" %} -{% set sha256 = "b6088259f2bc92d1f9dc4add44590cff68321bcbf91eefbc295a3525118b9415" %} +{% set version = "2.1.9" %} +{% set sha256 = "4cde9df78c63e8aef9df1e3265cd06a93ce1b047d6dba513a1437719b70e9d88" %} package: name: diamond @@ -11,6 +11,8 @@ source: build: number: 0 + run_exports: + - {{ pin_subpackage('diamond', max_pin="x") }} requirements: build: @@ -32,10 +34,11 @@ test: about: home: https://github.com/bbuchfink/diamond - license: GPL-3.0 - license_family: GPL + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: Accelerated BLAST compatible local sequence aligner + doc_url: https://github.com/bbuchfink/diamond/wiki extra: identifiers: From 817c68cd56448299a4c2bd5f093d8b5a8b6ca2b8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 19:32:07 -0500 Subject: [PATCH 1769/2173] Update ephemeris to 0.10.9 (#45523) * Update ephemeris to 0.10.9 * add run_exports * edit tests --------- Co-authored-by: mencian --- recipes/ephemeris/meta.yaml | 51 ++++++++++++++++++++++++------------- 1 file changed, 33 insertions(+), 18 deletions(-) diff --git a/recipes/ephemeris/meta.yaml b/recipes/ephemeris/meta.yaml index 23825c1b8f8f3..7afc256a6fbd3 100644 --- a/recipes/ephemeris/meta.yaml +++ b/recipes/ephemeris/meta.yaml @@ -1,42 +1,53 @@ +{% set name = "ephemeris" %} +{% set version = "0.10.9" %} + package: - name: ephemeris - version: "0.10.8" + name: {{ name }} + version: {{ version }} source: - url: https://files.pythonhosted.org/packages/92/56/0544ef43ecb994e543a81f68bbe65dd0ccaf1a21eaa3706a75190f4ba256/ephemeris-0.10.8.tar.gz - sha256: dd19c739ddb83ffbfa7d23b63e979f26602af2282c21a799cc52ea4342d62d37 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ephemeris-{{ version }}.tar.gz + sha256: fdc09b71f902f638fb74bbb1a4b22fcaf76869c4aa3ec6739c4be25c856e45b7 build: number: 0 noarch: python - preserve_egg_dir: True entry_points: - - get-tool-list=ephemeris.get_tool_list_from_galaxy:main - - shed-tools=ephemeris.shed_tools:main - - workflow-install=ephemeris.workflow_install:main - - run-data-managers=ephemeris.run_data_managers:main - - workflow-to-tools=ephemeris.generate_tool_list_from_ga_workflow_files:main - - setup-data-libraries=ephemeris.setup_data_libraries:main - - galaxy-wait=ephemeris.sleep:main - script: python -m pip install --no-deps --ignore-installed . + - get-tool-list = ephemeris.get_tool_list_from_galaxy:main + - shed-tools = ephemeris.shed_tools:main + - workflow-install = ephemeris.workflow_install:main + - run-data-managers = ephemeris.run_data_managers:main + - workflow-to-tools = ephemeris.generate_tool_list_from_ga_workflow_files:main + - setup-data-libraries = ephemeris.setup_data_libraries:main + - galaxy-wait = ephemeris.sleep:main + - install_tool_deps = ephemeris.install_tool_deps:main + - install-tool-deps = ephemeris.install_tool_deps:main + - set-library-permissions = ephemeris.set_library_permissions:main + - _idc-lint = ephemeris._idc_lint:main + - _idc-split-data-manager-genomes = ephemeris._idc_split_data_manager_genomes:main + - _idc-data-managers-to-tools = ephemeris._idc_data_managers_to_tools:main + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv + run_exports: + - {{ pin_subpackage('ephemeris', max_pin="x.x") }} requirements: host: - - python + - python >=3.7 - pip run: - - python + - python >=3.7 - pyyaml - six >=1.9.0 - bioblend >=0.10.0 - jinja2 - - galaxy-tool-util >=20.5.0 - - galaxy-util >=20.5.0 + - galaxy-tool-util >=20.9.1 + - galaxy-util >=20.9.0 + - pysam + - rich test: imports: - ephemeris - commands: - get-tool-list --help - shed-tools --help @@ -45,9 +56,13 @@ test: - workflow-to-tools --help - setup-data-libraries --help - galaxy-wait --help + - install_tool_deps --help + - install-tool-deps --help + - set-library-permissions --help about: home: https://github.com/galaxyproject/ephemeris license: Academic Free License (AFL) summary: 'Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows.' license_family: OTHER + doc_url: https://ephemeris.readthedocs.io/en/latest/ From c02286b651fa62bf2ac4550c452ce301824e062e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 22:00:52 -0500 Subject: [PATCH 1770/2173] Update dnaapler to 0.6.0 (#45533) --- recipes/dnaapler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnaapler/meta.yaml b/recipes/dnaapler/meta.yaml index 699f0fa47dae3..3417697c03deb 100644 --- a/recipes/dnaapler/meta.yaml +++ b/recipes/dnaapler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dnaapler" %} -{% set version = "0.5.2" %} +{% set version = "0.6.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 3e0a03afdf00c20943892184062d9b778d3d8b2b549605a69c883a8f5e68e946 + sha256: b68c138bf11285f5f09add09ae44e5342c8809ce349a1bce6446d8e64f06510d build: number: 0 From 67f2b2816f5ce20c66d5abfcd661c60a7d0bf6d0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 31 Jan 2024 23:20:27 -0500 Subject: [PATCH 1771/2173] Update snakefmt to 0.10.0 (#45529) * Update snakefmt to 0.10.0 * Update black version --------- Co-authored-by: Michael Hall --- recipes/snakefmt/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/snakefmt/meta.yaml b/recipes/snakefmt/meta.yaml index 399a36ceda420..a86a8e347327b 100644 --- a/recipes/snakefmt/meta.yaml +++ b/recipes/snakefmt/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.9.0" %} +{% set version = "0.10.0" %} package: name: snakefmt @@ -6,10 +6,10 @@ package: source: url: https://pypi.io/packages/source/s/snakefmt/snakefmt-{{ version }}.tar.gz - sha256: 54c78050edead20cea5f87a6c9674ee1b5e4e38faac2852b45d0650faf9cb319 + sha256: 53eae69fc81425e2192684eba76171bd648b05dcba93c9d5f45746d3fadb8617 build: - number: 1 + number: 0 noarch: python entry_points: - snakefmt = snakefmt.snakefmt:main @@ -19,14 +19,14 @@ build: requirements: host: - - black >=23.12.1,<24.0 + - black >=24.1,<25.0 - click >=8.0.0,<9.0.0 - pip - python >=3.8 - toml >=0.10.2,<0.11.0 - poetry >=1.3,<2.0 run: - - black >=23.12.1,<24.0 + - black >=24.1,<25.0 - click >=8.0.0,<9.0.0 - python >=3.8 - toml >=0.10.2,<0.11.0 From b92e5b7cb9ca28c99e657b039671cdde5e2b8801 Mon Sep 17 00:00:00 2001 From: Daniel DW Kim <49298377+endixk@users.noreply.github.com> Date: Thu, 1 Feb 2024 14:09:07 +0900 Subject: [PATCH 1772/2173] Update ezaai to 1.2.3 (#45531) * Update ezaai to 1.2.3 * add run_exports * improve exec command * posix sh * heredoc * heredoc style script writer --- recipes/ezaai/build.sh | 10 +++++++--- recipes/ezaai/meta.yaml | 10 ++++++---- 2 files changed, 13 insertions(+), 7 deletions(-) diff --git a/recipes/ezaai/build.sh b/recipes/ezaai/build.sh index 125996f06d360..1c8fd24997d5c 100644 --- a/recipes/ezaai/build.sh +++ b/recipes/ezaai/build.sh @@ -2,7 +2,8 @@ EZ_AAI_JAR_NAME="EzAAI.jar" EZ_AAI_LICENSE="LICENSE.md" -EZ_AAI_BIN="${PREFIX}/bin/EzAAI" +EZ_AAI_BIN="${PREFIX}/bin/ezaai" +EZ_AAI_BIN_ALT="${PREFIX}/bin/EzAAI" # Copy the JAR to the resource directory TARGET="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}" @@ -12,6 +13,9 @@ cp "${EZ_AAI_LICENSE}" "${TARGET}" # Alias the JAR in the bin directory mkdir -p "${PREFIX}/bin" -echo '#!/usr/bin/env bash' > "${EZ_AAI_BIN}" -echo "java -jar ${TARGET}/${EZ_AAI_JAR_NAME} \$@" >> "${EZ_AAI_BIN}" +cat << EOF > "${EZ_AAI_BIN}" +#!/bin/sh +exec java -jar "${TARGET}/${EZ_AAI_JAR_NAME}" "\${@}" +EOF chmod +x "${EZ_AAI_BIN}" +cp "${EZ_AAI_BIN}" "${EZ_AAI_BIN_ALT}" diff --git a/recipes/ezaai/meta.yaml b/recipes/ezaai/meta.yaml index f2ac8a0971924..c3376bf7614bf 100644 --- a/recipes/ezaai/meta.yaml +++ b/recipes/ezaai/meta.yaml @@ -1,16 +1,18 @@ {% set name = "EzAAI" %} -{% set version = "1.2.2" %} -{% set sha256 = "657f2b131e2564f291ef22417cabcd6615cdf88c59f3c553ceccd3ea3b86e564" %} +{% set version = "1.2.3" %} +{% set sha256 = "dbf2433928edb223f5fb6c105e3a32ae7784bac7f2ab506a5d9470d13d240332" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/endixk/ezaai/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/endixk/ezaai/releases/download/v{{ version }}/ezaai-bin.tar.gz sha256: {{ sha256 }} build: + run_exports: + - {{ pin_subpackage('ezaai', max_pin="x") }} noarch: generic number: 0 @@ -24,7 +26,7 @@ requirements: test: commands: - - EzAAI -h + - ezaai -h about: home: http://leb.snu.ac.kr/ezaai From d7f0b9d0e464cb7d2cdd6fe93947c572262deab4 Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Thu, 1 Feb 2024 07:54:50 +0000 Subject: [PATCH 1773/2173] Update SeqKit to v2.7.0 (#45527) --- recipes/seqkit/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/seqkit/meta.yaml b/recipes/seqkit/meta.yaml index 845a461c51f7a..a3be4a4ee909e 100644 --- a/recipes/seqkit/meta.yaml +++ b/recipes/seqkit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.6.1" %} +{% set version = "2.7.0" %} package: name: seqkit @@ -6,10 +6,10 @@ package: source: url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_darwin_amd64.tar.gz # [osx] - md5: c3596d65d5fa973a7c65485a97d735ac # [osx] + md5: 2d0bd16060b100c90abd216eaf6c9947 # [osx] url: https://github.com/shenwei356/seqkit/releases/download/v{{ version }}/seqkit_linux_amd64.tar.gz # [linux] - md5: c48e7806a03cb9e3f2c1a091c9113908 # [linux] + md5: 78311f53ecebbcd4acd5455ae46debbe # [linux] build: number: 0 From 5ba347c694777884990aae9ee14ba3a90c2b431a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 1 Feb 2024 09:06:16 +0100 Subject: [PATCH 1774/2173] update chromograph (#45521) --- recipes/chromograph/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/chromograph/meta.yaml b/recipes/chromograph/meta.yaml index 17ef1fb5263cb..559bb6398e177 100644 --- a/recipes/chromograph/meta.yaml +++ b/recipes/chromograph/meta.yaml @@ -7,8 +7,10 @@ package: build: noarch: python - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + run_exports: + - {{ pin_subpackage('chromograph', max_pin="x.x") }} source: url: https://github.com/Clinical-Genomics/chromograph/archive/refs/tags/v{{version}}.tar.gz @@ -16,11 +18,11 @@ source: requirements: host: - - python >=3.7,<3.10 + - python ==3.9 - pip run: - - python >=3.7,<3.10 - - matplotlib-base + - python ==3.9 + - matplotlib-base ==3.5.3 - numpy >=1.15 - pyaml - pandas From 33c569a7de9f5aa7ec9e6cca11d2d04aca736027 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 03:08:54 -0500 Subject: [PATCH 1775/2173] Update annonars to 0.34.1 (#45539) --- recipes/annonars/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index a7e856b889433..49388dd1ed49a 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,18 +1,18 @@ -{% set version = "0.34.0" %} +{% set version = "0.34.1" %} package: name: annonars version: {{ version }} build: - number: 1 + number: 0 skip: True # [osx] run_exports: - {{ pin_subpackage("annonars", max_pin="x.x") }} source: url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 8b0725fc8d7e861bc08c96882f6e9e489b5079c10eb723295b26d2100e6e86f9 + sha256: 55f4d7fff2f94eaf94e7752a426ee2532f88ffb25a0d2bb0cf0b4127212bf3e1 requirements: build: From 15cc1f41f05b6857a37c825b34fa75ad2032bee3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 03:53:33 -0500 Subject: [PATCH 1776/2173] Update simpleaf to 0.16.2 (#45536) Co-authored-by: Rob Patro --- recipes/simpleaf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index 2a135224532ca..3d1763a882e62 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.16.1" %} +{% set version = "0.16.2" %} package: name: simpleaf @@ -12,7 +12,7 @@ build: source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: f6204577500063f89c55de9d496c6aeb58ef9048fb5ef8904efaa4f2850b31cc + sha256: e35fb2773b3f4f158d23ebc6d0b51aed29ea54206a3c57a56931325e67add720 requirements: build: From 58aef112ece5644032d8c79ed08abc126c537518 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:43:32 -0500 Subject: [PATCH 1777/2173] Update gget to 0.28.4 (#45530) --- recipes/gget/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gget/meta.yaml b/recipes/gget/meta.yaml index fa18fdcf7a298..f47038aae5141 100644 --- a/recipes/gget/meta.yaml +++ b/recipes/gget/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gget" %} -{% set version = "0.28.3" %} -{% set sha256 = "4f9e2f3e445b7e898e1a12fa7460604330e73d917c8e357a91a09c0c005b64b9" %} +{% set version = "0.28.4" %} +{% set sha256 = "bab45530f72b189b233a72be20421176fbc4ca7ed407e36eec758086c2cda7c6" %} package: name: "{{ name|lower }}" From 6401c8f429f1202cb2e0a87a844406a179d19ecd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:44:09 -0500 Subject: [PATCH 1778/2173] Update hecatomb to 1.3.0 (#45537) * Update hecatomb to 1.3.0 * Update meta.yaml lint fix and update run dependencies * Update meta.yaml --------- Co-authored-by: Michael Roach --- recipes/hecatomb/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/hecatomb/meta.yaml b/recipes/hecatomb/meta.yaml index 52fb463a7f9b2..b5783bce3c181 100644 --- a/recipes/hecatomb/meta.yaml +++ b/recipes/hecatomb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "Hecatomb" %} -{% set version = "1.2.0" %} +{% set version = "1.3.0" %} package: name: "{{ name|lower }}" @@ -7,11 +7,13 @@ package: source: url: "https://github.com/shandley/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 20da6871131a01222d4374194188f766bfdd3ab164ab4dbdd4307db0b80341a7 + sha256: ad53c9ab16b9db9a8d6bff2874c96727cffd030d3f5f8d7213496248a8f3659e build: number: 0 noarch: python + run_exports: + - {{ pin_subpackage('hecatomb', max_pin='x.x') }} script: "{{ PYTHON }} -m pip install . -vv " requirements: @@ -19,12 +21,13 @@ requirements: - python - pip run: - - python >=3.8,<3.11 - - snakemake >=7.14.0 + - python >=3.9,<=3.12 + - snakemake >=7.14.0,<8 + - pulp <2.8 - pyyaml >=6.0 - click >=8.1.3 - - jinja2 >=3.0.2 - - mamba >=0.15.3 + - metasnek >=0.0.7 + - snaketool-utils >=0.0.4 test: commands: From 21cb03de0cb4aa1a5243794080fe8668e4eeb34f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:45:16 -0500 Subject: [PATCH 1779/2173] Update mehari to 0.21.2 (#45540) --- recipes/mehari/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index a9745e92008b9..91cc370330ddc 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.21.1" %} -{% set sha256 = "6dcdd453ca44a531e4b4903ebf32921707bebe9d51f389a463dc2df3b3042f12" %} +{% set version = "0.21.2" %} +{% set sha256 = "37fc1ef33d8d7f49886312283ac1e4009fba92db40e254cb03356e0e6f643774" %} package: name: mehari @@ -7,7 +7,7 @@ package: build: skip: True # [osx] - number: 1 + number: 0 run_exports: - {{ pin_subpackage("mehari", max_pin="x.x") }} From a9d925fc33951ce242788e96d6d90bdd8e37776e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:45:29 -0500 Subject: [PATCH 1780/2173] Update viguno to 0.2.1 (#45538) --- recipes/viguno/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/viguno/meta.yaml b/recipes/viguno/meta.yaml index 44a32ed9707e4..cfeec69d90f06 100644 --- a/recipes/viguno/meta.yaml +++ b/recipes/viguno/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.0" %} -{% set sha256 = "a4217f7ba34d55cda76b392e774be8392c18d550e752eb9db81e6cc3afa53010" %} +{% set version = "0.2.1" %} +{% set sha256 = "00da4730a4dd63b05eeb8e7ae0b58ba829e7145cc41f0f9194470376f367b937" %} package: name: viguno @@ -7,7 +7,7 @@ package: build: skip: True # [osx] - number: 1 + number: 0 run_exports: - {{ pin_subpackage("viguno", max_pin="x.x") }} From 92f89a4f47056b10950d525d1d955ff2482e903e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:46:21 -0500 Subject: [PATCH 1781/2173] Update skyline2isocor to 0.2.0 (#45541) --- recipes/skyline2isocor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/skyline2isocor/meta.yaml b/recipes/skyline2isocor/meta.yaml index a888d3d122ba4..ce4c92b00b71e 100644 --- a/recipes/skyline2isocor/meta.yaml +++ b/recipes/skyline2isocor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "skyline2isocor" %} -{% set version = "0.1.2" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/skyline2isocor-{{ version }}.tar.gz - sha256: de1516845912f31ecb84ddd19c28f3ff6f6db2dd11ca834a42424276d795ec74 + sha256: 7f8e122e4ffe2cb66d02fe1d5ee06d97846d120ffb4987ed46075f0267784796 build: entry_points: From 3e23b0d5a0ffd4b63fd7f9fa50c1e974ab479a41 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:46:48 -0500 Subject: [PATCH 1782/2173] Update scirpy to 0.16.0 (#45545) --- recipes/scirpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scirpy/meta.yaml b/recipes/scirpy/meta.yaml index 91d97a5982193..fd3cf450186d3 100644 --- a/recipes/scirpy/meta.yaml +++ b/recipes/scirpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "scirpy" %} -{% set version = "0.15.0" %} +{% set version = "0.16.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 4b0e5ce9fa8a874f0dd502a9493d9201dd6afc673512ab0287644a98c77b3744 + sha256: 169d71fcb26da1adac33be0e30541eb09ed9ae32d484f16a194c2fa07bf9a4fb folder: "{{ name }}-{{ version }}" build: From 5f5c5bc4222723074be1c64a40e395eb6d4382c6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 05:47:34 -0500 Subject: [PATCH 1783/2173] Update sevenbridges-python to 2.10.2 (#45546) --- recipes/sevenbridges-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index 7bdcd4c93f64a..34b191fef1cfc 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.10.1" %} -{% set sha256 = "5db46a3fce7b0235be9273ec070092775be43e4bb1b2787c349f3598eaa3fd07" %} +{% set version = "2.10.2" %} +{% set sha256 = "4402b7b874f97532c5156a68b45ebb9554a774ffd182ef346876cca83db791a9" %} package: name: sevenbridges-python From 069cfc067e4e940da653454d7e29ff1ffec2ad8e Mon Sep 17 00:00:00 2001 From: Kez Cleal <42997789+kcleal@users.noreply.github.com> Date: Thu, 1 Feb 2024 10:48:52 +0000 Subject: [PATCH 1784/2173] GW v0.9.3 (#45524) From fb327c8f689b2bbd85239cfb5a2b2e76829e513e Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Thu, 1 Feb 2024 02:50:16 -0800 Subject: [PATCH 1785/2173] Update ntLink build (#45522) --- recipes/ntlink/meta.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/recipes/ntlink/meta.yaml b/recipes/ntlink/meta.yaml index 609bc60ac8087..f67d1d7829657 100644 --- a/recipes/ntlink/meta.yaml +++ b/recipes/ntlink/meta.yaml @@ -9,20 +9,18 @@ source: sha256: 3a6fe7ca9c7a0226cf51b7e55804e235ac2b959e82a30f9bce55b9caea5bb03b build: - number: 2 - skip: True # [py<38 or py > 39] + number: 3 + noarch: generic run_exports: - {{ pin_subpackage('ntlink', max_pin="x") }} requirements: - build: - - {{ compiler('cxx') }} host: - make - python - pip - zlib - - btllib <=1.4.10 + - btllib run: - python - zlib From edc236506f550eec8d0d68fa40dca50868436776 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 1 Feb 2024 12:36:30 +0100 Subject: [PATCH 1786/2173] Update MALT to 0.62 (#45193) * Update meta.yaml * Update build.sh * Add run_exports * Apply suggestions from code review --- recipes/malt/build.sh | 4 ++-- recipes/malt/meta.yaml | 8 +++++--- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/malt/build.sh b/recipes/malt/build.sh index 49b33d38c0310..61ca8fc5e25e0 100755 --- a/recipes/malt/build.sh +++ b/recipes/malt/build.sh @@ -1,9 +1,9 @@ #!/bin/bash # call installer -chmod u+x MALT_unix_0_6_1.sh +chmod u+x MALT_unix_0_6_2.sh MALT="$PREFIX/opt/$PKG_NAME-$PKG_VERSION" -./MALT_unix_0_6_1.sh -q -dir "$MALT" +./MALT_unix_0_6_2.sh -q -dir "$MALT" ln -s "$MALT"/malt-build "$PREFIX"/bin/malt-build ln -s "$MALT"/malt-run "$PREFIX"/bin/malt-run diff --git a/recipes/malt/meta.yaml b/recipes/malt/meta.yaml index 154885195a594..28c4fe7bffb80 100755 --- a/recipes/malt/meta.yaml +++ b/recipes/malt/meta.yaml @@ -1,12 +1,14 @@ package: name: malt - version: 0.61 # Keep without patch release decimal. Versioning style changed in 0.5 causing latest-version sorting problems when installing from bioconda. + version: 0.62 # Keep without patch release decimal. Versioning style changed in 0.5 causing latest-version sorting problems when installing from bioconda. build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage("malt", max_pin="x.x") }} source: - md5: 41573f8c652fc81f3745729dee2d5e2d - url: https://software-ab.informatik.uni-tuebingen.de/download/malt/MALT_unix_0_6_1.sh + md5: 3e9b7516c722ca959d92722bea209b04 + url: https://maira.cs.uni-tuebingen.de/download/malt/MALT_unix_0_6_2.sh requirements: build: - openjdk From 829c9146fca79be3a2252b6578bc3846d851f513 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 06:47:17 -0500 Subject: [PATCH 1787/2173] Update nf-core to 2.12.1 (#45547) --- recipes/nf-core/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml index c5f20958f1b84..bdfc0e175394a 100644 --- a/recipes/nf-core/meta.yaml +++ b/recipes/nf-core/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nf-core" %} -{% set version = "2.12" %} -{% set sha256 = "a1af4ad7407cc7b65097b066e2593bdfc302b4c61301dd7476c2203924e92e46" %} +{% set version = "2.12.1" %} +{% set sha256 = "29503365111d5f760fe178cb0db317f9196af5340e649e68e345eb06c95be211" %} package: name: {{ name|lower }} From 67479197501b2dae3f09c3563e030f12d64823bb Mon Sep 17 00:00:00 2001 From: Marco Matthies <71844+marcom@users.noreply.github.com> Date: Thu, 1 Feb 2024 13:41:08 +0100 Subject: [PATCH 1788/2173] Update linearfold to 1.0.1.dev20220829 (#45470) * Update linearfold to 1.0.1.dev20220829 This is a release from the last commit on github from 2022-08-29, git-sha1 c3ee9bd80c06c2fc39a7bb7ae5e77b9566227cac. Changes since the last release 1.0 (my summary): - driver script works with python3 - fixes for dangles - SHAPE support - other bugfixes There hasn't yet been an upstream release that doesn't require python2 for the driver script, making it difficult to use the package with other packages depending on python3. Upstream issue: https://github.com/LinearFold/LinearFold/issues/14 * Add missing run_exports line * Try and fix linting issues * Simplify version string to try and fix post-build error --- ...IX-command-broken-with-symbolic-link.patch | 22 +++++-------------- recipes/linearfold/meta.yaml | 13 ++++++----- 2 files changed, 13 insertions(+), 22 deletions(-) diff --git a/recipes/linearfold/0001-FIX-command-broken-with-symbolic-link.patch b/recipes/linearfold/0001-FIX-command-broken-with-symbolic-link.patch index 3709632b08a68..2efbe34655620 100644 --- a/recipes/linearfold/0001-FIX-command-broken-with-symbolic-link.patch +++ b/recipes/linearfold/0001-FIX-command-broken-with-symbolic-link.patch @@ -1,25 +1,13 @@ -From bb95a8f98b874fb9061c5ee1b3178f4d40f96416 Mon Sep 17 00:00:00 2001 -From: Fabien Pertuy -Date: Fri, 21 May 2021 09:23:34 +0000 -Subject: [PATCH] FIX command broken with symbolic link - ---- - linearfold | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - diff --git a/linearfold b/linearfold -index f5541d2..2c86b63 100755 +index fca4a30..7e68544 100755 --- a/linearfold +++ b/linearfold -@@ -28,7 +28,7 @@ def main(): - zuker_subopt = '1' if FLAGS.zuker else '0' - delta = str(FLAGS.delta) +@@ -38,7 +38,7 @@ def main(): + + dangles = str(FLAGS.dangles) - path = os.path.dirname(os.path.abspath(__file__)) + path = os.path.dirname(os.path.realpath(__file__)) - cmd = ["%s/%s" % (path, ('bin/linearfold_v' if use_vienna else 'bin/linearfold_c')), beamsize, is_sharpturn, is_verbose, is_eval, is_constraints, zuker_subopt, delta] + cmd = ["%s/%s" % (path, ('bin/linearfold_v' if use_vienna else 'bin/linearfold_c')), beamsize, is_sharpturn, is_verbose, is_eval, is_constraints, zuker_subopt, delta, shape_file_path, is_fasta, dangles] subprocess.call(cmd, stdin=sys.stdin) --- -2.30.2 - diff --git a/recipes/linearfold/meta.yaml b/recipes/linearfold/meta.yaml index 68bd8d83073a7..62e614174d93e 100644 --- a/recipes/linearfold/meta.yaml +++ b/recipes/linearfold/meta.yaml @@ -1,17 +1,20 @@ {% set name = "LinearFold" %} -{% set version = "1.0" %} -{% set sha256 = "2ae56b5f183472c2de96782e770a91e57f82e0ab511dfc0d9d612aa4e6155f60" %} +{% set git_sha1 = "c3ee9bd80c06c2fc39a7bb7ae5e77b9566227cac" %} +{% set version = "1.0.1.dev20220829" %} +{% set sha256 = "cad8b93ba961820ca3701a1d931944bd307b1d1f92d74e1b02d5bd34d4ffe998" %} package: name: {{ name | lower }} version: {{ version }} build: - number: 3 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage(name | lower, max_pin="x.x.x") }} source: - url: https://github.com/{{ name }}/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/{{ name }}/{{ name }}/archive/{{ git_sha1 }}.tar.gz sha256: {{ sha256 }} patches: - 0001-FIX-command-broken-with-symbolic-link.patch @@ -23,7 +26,7 @@ requirements: run: - python-gflags - - python=2.7 + - python >=3,<4 test: source_files: From 72f32eb76d75b6a0e5171c76fe6e0663c02f7e65 Mon Sep 17 00:00:00 2001 From: Ray <851836818@qq.com> Date: Thu, 1 Feb 2024 21:48:08 +0800 Subject: [PATCH 1789/2173] Update meta.yaml (#45549) * Update meta.yaml * Update meta.yaml --- recipes/strainscan/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/strainscan/meta.yaml b/recipes/strainscan/meta.yaml index e4bb6caf0e437..a16796f4a5b47 100644 --- a/recipes/strainscan/meta.yaml +++ b/recipes/strainscan/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 2d927c5ac4d9b89a166afeca2aabaf4086d49b097e357ed0feb34181295cf243 build: - number: 0 + number: 1 entry_points: - strainscan = StrainScan.StrainScan:main - strainscan_build = StrainScan.StrainScan_build:main @@ -25,7 +25,7 @@ requirements: - python ==3.7.3 run: - python ==3.7.3 - - sibeliaz ==1.2.2 + - sibeliaz ==1.2.3 - r-base ==4.0.2 - numpy ==1.17.3 - pandas ==1.0.1 From 12959549fd3824bd58f75129dd7cf453d53a4ae6 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 1 Feb 2024 14:50:15 +0100 Subject: [PATCH 1790/2173] Update MEGAN to 6.25.9 (#45548) * Update MEGAN to 6.25.9 * Add pin subpackage for linting * Apply suggestions from code review --- recipes/megan/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/megan/meta.yaml b/recipes/megan/meta.yaml index b630ebb5fdfad..d3014d47e4e3c 100644 --- a/recipes/megan/meta.yaml +++ b/recipes/megan/meta.yaml @@ -1,13 +1,13 @@ {% set name = "megan" %} -{% set version = "6.24.20" %} +{% set version = "6.25.9" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://software-ab.cs.uni-tuebingen.de/download/megan6/MEGAN_Community_unix_{{ version|replace(".", "_") }}.sh # [linux] - sha256: 4eaf7797b4a2b9cdc2157b2780810504b9b8b539dd81bb6130f4b69e453f009b # [linux] + url: https://maira.cs.uni-tuebingen.de/download/megan6/MEGAN_Community_unix_{{ version|replace(".", "_") }}.sh # [linux] + sha256: 09975351baff29e620d49f14145bde7840ec5d58828ba9ddf187c9ba54e46b4b # [linux] # url: https://software-ab.informatik.uni-tuebingen.de/download/megan6/MEGAN_Community_macos_{{ version|replace(".", "_") }}.dmg # [osx] # sha256: dd843e823f358f496834a2034e1b638e9602ba83251a5f0542f20b0d22d7dc70 # [osx] @@ -15,6 +15,8 @@ build: # detect_binary_files_with_prefix: true number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage("megan", max_pin="x.x") }} requirements: host: From cdfa7f897f017970fa733e553bd1c731529289d9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 09:21:06 -0500 Subject: [PATCH 1791/2173] Update cmat to 3.1.1 (#45550) --- recipes/cmat/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/cmat/meta.yaml b/recipes/cmat/meta.yaml index 69e11aa455e27..22556a626dd0c 100644 --- a/recipes/cmat/meta.yaml +++ b/recipes/cmat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cmat" %} -{% set version = "3.1.0" %} +{% set version = "3.1.1" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/EBIvariation/CMAT/archive/v{{version}}.tar.gz - sha256: 1e46a83d3d7e46a41f9f62ff4af0c151851fbbebc1c6b129255f987d75b64079 + sha256: 0ff44acd1a9c1df9ed76804faf62d49716edcc1376679a19b1ef1b5003cde535 build: number: 0 @@ -61,4 +61,4 @@ about: extra: recipe-maintainers: - - apriltuesday \ No newline at end of file + - apriltuesday From 13799e6ff47775ddfedffa5d8fa6f603c75cfc30 Mon Sep 17 00:00:00 2001 From: Martin Raden Date: Thu, 1 Feb 2024 16:11:34 +0100 Subject: [PATCH 1792/2173] rebuild pourRNA (#45511) * rebuild pourRNA * name via variable --- recipes/pourrna/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/pourrna/meta.yaml b/recipes/pourrna/meta.yaml index 993b810c88dc6..4313accff6e9c 100644 --- a/recipes/pourrna/meta.yaml +++ b/recipes/pourrna/meta.yaml @@ -11,7 +11,9 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage( name, max_pin="x.x") }} requirements: build: From b5bf6d72dacf9f45cb69defd63509c821b50d80e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 10:23:37 -0500 Subject: [PATCH 1793/2173] Update ephemeris to 0.10.10 (#45552) --- recipes/ephemeris/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ephemeris/meta.yaml b/recipes/ephemeris/meta.yaml index 7afc256a6fbd3..e6929208c86a9 100644 --- a/recipes/ephemeris/meta.yaml +++ b/recipes/ephemeris/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ephemeris" %} -{% set version = "0.10.9" %} +{% set version = "0.10.10" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ephemeris-{{ version }}.tar.gz - sha256: fdc09b71f902f638fb74bbb1a4b22fcaf76869c4aa3ec6739c4be25c856e45b7 + sha256: 397599341949e359c5dc1cb6bf8b4be06b14cc3d2e8fb404a3421f37d17c2b44 build: number: 0 From 1d75c6125643b5d2d22ac731f0f23800b463c9d5 Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Thu, 1 Feb 2024 18:46:47 +0100 Subject: [PATCH 1794/2173] Update nextclade to 3.1.0 (#45560) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index 2bf851ea44aee..fa81294b44098 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "3.0.1" %} +{% set version = "3.1.0" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: 181d0ff48fe09e67f3a1e186ec0f89b15aa08eba779089f7837fc15c7b6501b1 # [linux64] + sha256: 949ec8ea1eb9705529425543292347ce7fbf9c799ec9f82fb3a9dab5f9e39450 # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: bd21bfb9ae40be1e4a839519718b7127f146b2f8bc831771359844e27ae649f0 # [osx and x86_64] + sha256: 878523f7c278c16bb19c47ab6421c63ccb876bbd2820cc997bcda62dcf3eb4d4 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: 20cebf5b8494645f915dddb24b87540634df31bf321c20ff97a091f85c06932d # [arm64] + sha256: 967ed5de693aa162ba010521d397462c7a73ff9430b2d70af42bc05b52782881 # [arm64] build: number: 0 From 9953a3cd48c11cbe4fc8fd4a383a7414d87071fd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 15:33:51 -0500 Subject: [PATCH 1795/2173] Update attotree to 0.1.2 (#45559) --- recipes/attotree/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/attotree/meta.yaml b/recipes/attotree/meta.yaml index 3cd8f4c661f08..577c993650692 100644 --- a/recipes/attotree/meta.yaml +++ b/recipes/attotree/meta.yaml @@ -1,5 +1,5 @@ {% set name = "attotree" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: ada454ac2a9392667476816c466c005935d5ffe73f87b2b7bc7960a0ec0753a4 + sha256: 8ae3799fd513595a0d05625e420b17b7745a0fa067e2e100302a2ddefe438ebf build: number: 0 From 6bf81c3a2387a03a563413f94fd691c4e8e96a32 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 1 Feb 2024 15:18:35 -0600 Subject: [PATCH 1796/2173] Update kma to 1.4.14 (#45566) --- recipes/kma/build.sh | 4 +++- recipes/kma/meta.yaml | 12 ++++++++---- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/recipes/kma/build.sh b/recipes/kma/build.sh index 202febb333a5e..20626f6691fb4 100755 --- a/recipes/kma/build.sh +++ b/recipes/kma/build.sh @@ -1,5 +1,7 @@ +#!/bin/bash + BINARIES="kma kma_index kma_shm kma_update" -make CFLAGS="-w -O3 -I$PREFIX/include -L$PREFIX/lib" +make CFLAGS="${CFLAGS} -w -O3 -I${PREFIX}/include -L${PREFIX}/lib" mkdir -p ${PREFIX}/bin cp $BINARIES $PREFIX/bin diff --git a/recipes/kma/meta.yaml b/recipes/kma/meta.yaml index 8cfa498075d15..9805f97f9b6e5 100644 --- a/recipes/kma/meta.yaml +++ b/recipes/kma/meta.yaml @@ -1,6 +1,6 @@ {% set name = "kma" %} -{% set version = "1.4.9" %} -{% set sha256 = "6434e6fcc23420edc29922baf289e4a6d923f31949c34d8efd2331f3bb5e8e8b" %} +{% set version = "1.4.14" %} +{% set sha256 = "85971fcb2e806d2ee95d3499cd9b358f313b1635d5d71cb189eabc503be4b10f" %} package: name: {{ name|lower }} @@ -11,7 +11,9 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('kma', max_pin="x") }} requirements: build: @@ -21,7 +23,7 @@ requirements: - zlib run: - zlib - + test: commands: - kma -h | grep KMA >/dev/null @@ -33,6 +35,8 @@ about: home: https://bitbucket.org/genomicepidemiology/kma summary: 'KMA is mapping a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.' license: Apache-2.0 + license_family: APACHE + extra: identifiers: - doi:10.1186/s12859-018-2336-6 From 1145bc8784ba4e2af268ecc71433b60131286998 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 17:00:54 -0500 Subject: [PATCH 1797/2173] Update centrifuge-core to 1.0.4.1 (#45557) * Update centrifuge-core to 1.0.4.1 * Apply suggestions from code review * test if custom build config is still needed * skip osx builds --------- Co-authored-by: James A. Fellows Yates Co-authored-by: Robert A. Petit III --- recipes/centrifuge-core/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/centrifuge-core/meta.yaml b/recipes/centrifuge-core/meta.yaml index dfb689b988214..5381ccdd5d741 100644 --- a/recipes/centrifuge-core/meta.yaml +++ b/recipes/centrifuge-core/meta.yaml @@ -1,16 +1,19 @@ {% set name = "centrifuge-core" %} -{% set version = "1.0.4" %} +{% set version = "1.0.4.1" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 2 + number: 0 + skip: true # [osx] + run_exports: + - {{ pin_subpackage("centrifuge-core", max_pin="x.x") }} source: url: https://github.com/DaehwanKimLab/centrifuge/archive/refs/tags/v{{ version }}.tar.gz - sha256: 929daed0f84739f7636cc1ea2757527e83373f107107ffeb5937a403ba5201bc + sha256: 638cc6701688bfdf81173d65fa95332139e11b215b2d25c030f8ae873c34e5cc requirements: build: From 7cc4b8645c1d357cc16cfd61a3bbac70f973b1a2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 18:35:41 -0500 Subject: [PATCH 1798/2173] Update pybiolib to 1.1.1703 (#45563) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index bbcec685a8ceb..9676b29d9dd02 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1691" %} +{% set version = "1.1.1703" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 5f25f9028e05b606a32a452fb065288915d94a010481db935ddc2379812abec6 + sha256: fce4db168dccecd6500d5967d307a3fbd26bd4c4d586668a189f72103b75edbf build: noarch: python From bb6535573220753b9ad7604b23d28f49700333a6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:05:06 -0500 Subject: [PATCH 1799/2173] Update npstructures to 0.2.16 (#45556) --- recipes/npstructures/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/npstructures/meta.yaml b/recipes/npstructures/meta.yaml index aabf2fa368189..41873871a5cd0 100644 --- a/recipes/npstructures/meta.yaml +++ b/recipes/npstructures/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.15" %} +{% set version = "0.2.16" %} {% set name = "npstructures" %} package: name: {{ name }} @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 6266b74fae8f58d1cdc8967e5a85f557610df4956fae28e6b3eb39ddebb46aae + sha256: 0964520dfb11789635ceae36c9ab477e60cd4fbc99f069656fafbdcb3878a0be build: From c987d518bb577e079b8f32ac09ce660066af6032 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:05:26 -0500 Subject: [PATCH 1800/2173] Update htsinfer to 0.10.0 (#45555) --- recipes/htsinfer/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/htsinfer/meta.yaml b/recipes/htsinfer/meta.yaml index a88775a875d23..1a4e250b5331b 100644 --- a/recipes/htsinfer/meta.yaml +++ b/recipes/htsinfer/meta.yaml @@ -1,13 +1,13 @@ {% set name = "HTSinfer" %} -{% set version = "0.9.0" %} +{% set version = "0.10.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/zavolanlab/htsinfer/archive/refs/tags/v0.9.0.tar.gz - sha256: f4708d43e56389240752e45ac3f4cdcb620ab3783b57ff068599eec0adbd91f3 + url: https://github.com/zavolanlab/htsinfer/archive/refs/tags/v0.10.0.tar.gz + sha256: a851d00a47ef5a47e9c2540599ff2c16723dfac95c12ac85f7152b0ad4c295a7 build: number: 0 @@ -54,4 +54,4 @@ about: extra: recipe-maintainers: - - balajtimate \ No newline at end of file + - balajtimate From e5b89cc439af563b1002356b5e37ffea5c59311c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:05:39 -0500 Subject: [PATCH 1801/2173] Update bionumpy to 1.0.2 (#45553) --- recipes/bionumpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index 30519b96389e1..e150ab834eebc 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.1" %} +{% set version = "1.0.2" %} package: name: bionumpy @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9e00254dc1c2ee2669048b7fd0bb6309e6caa218f8a330b00e3929f1dfeee58c + sha256: 0052120fb3c07a83d5064b680246b2b8ddf251dac526ac60d6d1c18f4ee944eb build: noarch: python From 074e7ec5ba0701d59282f1be8e6f1ae8e70b440e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:05:54 -0500 Subject: [PATCH 1802/2173] Update snakemake-executor-plugin-slurm to 0.3.0 (#45554) * Update snakemake-executor-plugin-slurm to 0.2.2 * Update snakemake-executor-plugin-slurm to 0.3.0 --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index a7cdccccdb508..3d08d331ed1ed 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.2.1" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: dd484fcb136612a3f2bdcccf15ca4ebffc2f5fcdfa7f1fcc14416dd272812999 + sha256: 0200006e4860d4966ed092e0b2d335068a2b0aef33f8938bca435890b790e5fa build: noarch: python From ac8f7b47ed18f252e115e40a99373a8faff8b51e Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 1 Feb 2024 18:54:55 -0600 Subject: [PATCH 1803/2173] Add recipe for dropkick v1.2.8 (#45569) * Add recipe for dropkick v1.2.8 * add run_exports * skip OSX --- recipes/dropkick/meta.yaml | 51 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 recipes/dropkick/meta.yaml diff --git a/recipes/dropkick/meta.yaml b/recipes/dropkick/meta.yaml new file mode 100644 index 0000000000000..8454489e5b6ba --- /dev/null +++ b/recipes/dropkick/meta.yaml @@ -0,0 +1,51 @@ +{% set name = "dropkick" %} +{% set version = "1.2.8" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dropkick-{{ version }}.tar.gz + sha256: 4bfbd23984ac11669691818f29e1f0033e32dd7c2236b16d8a2f20fe60c923c6 + +build: + number: 0 + # "Failed to find libgfortran.3.dylib" build error on OSX + skip: True # [py < 36 or osx] + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + entry_points: + - dropkick = dropkick.__main__:main + run_exports: + - {{ pin_subpackage('dropkick', max_pin="x") }} + +requirements: + build: + - {{ compiler('fortran') }} + - {{ compiler('c') }} + host: + - python + - pip + - numpy + run: + - python + - scipy >=0.14.1 + - pandas + - scikit-learn >=0.18.0 + - scikit-image + - matplotlib-base >=3.0.3 + - scanpy + - {{ pin_compatible('numpy') }} + +test: + imports: + - dropkick + commands: + - dropkick --help + +about: + home: https://github.com/KenLauLab/dropkick + summary: Automated scRNA-seq filtering + license: MIT + license_family: MIT + license_file: LICENSE From b30ccf0877357f4160fedf5012ed635b710fdbb3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:55:22 -0500 Subject: [PATCH 1804/2173] Update tides-ml to 1.2.0 (#45561) * Update tides-ml to 1.2.0 * pin python to <3.12 --------- Co-authored-by: mencian --- recipes/tides-ml/meta.yaml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/recipes/tides-ml/meta.yaml b/recipes/tides-ml/meta.yaml index ff653618f6ed2..75f14a4175336 100644 --- a/recipes/tides-ml/meta.yaml +++ b/recipes/tides-ml/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tides-ml" %} -{% set version = "1.1.4" %} +{% set version = "1.2.0" %} package: name: {{ name|lower }} @@ -7,23 +7,23 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/TIdeS-ML-{{ version }}.tar.gz - sha256: 393f24ce18a58f40b2387e2a2fc2d45eb0088c8231c3d533f647deaf4b38c6ee + sha256: 8c31f4429303e5d34c031b243963fae3eec1f0d9c97e856949a7eac17f82452c build: entry_points: - tides = tides.tides:main noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: - - python >=3.8 + - python <3.12 - pip run: - - python >=3.8 + - python <3.12 - biopython >=1.79 - ete3 >=3.1.2 - optuna >=3.0 @@ -33,7 +33,7 @@ requirements: - diamond >=2.1.3 - cd-hit >=4.8.1 - barrnap >=0.9 - - kraken2 >=2.0.0 + - kraken2 >=2.0.0 test: imports: @@ -44,12 +44,12 @@ test: - (barrnap --help 2>&1; true) | grep -q Options - tides --help - kraken2 --version - about: home: https://github.com/xxmalcala/TIdeS summary: Tool for ORF-calling and ORF-classification using ML approaches license: MIT + license_family: MIT license_file: LICENSE extra: From 969f57da0bc859053e0025eede38b2769dde6428 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 19:55:32 -0500 Subject: [PATCH 1805/2173] Update clonalframeml to 1.13 (#45542) * Update clonalframeml to 1.13 * add run_exports --------- Co-authored-by: mencian --- recipes/clonalframeml/meta.yaml | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/recipes/clonalframeml/meta.yaml b/recipes/clonalframeml/meta.yaml index e90bef289093c..eb47de77ebb1c 100644 --- a/recipes/clonalframeml/meta.yaml +++ b/recipes/clonalframeml/meta.yaml @@ -1,13 +1,18 @@ +{% set name = "clonalframeml" %} +{% set version = "1.13" %} + package: - name: clonalframeml - version: "1.12" + name: {{ name }} + version: {{ version }} build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage('clonalframeml', max_pin="x") }} source: - url: https://github.com/xavierdidelot/ClonalFrameML/archive/v1.12.tar.gz - sha256: ef76705c1a0f1343184f956cd0bdc96c2cfdbb998177330b09b6df84c74c2de6 + url: https://github.com/xavierdidelot/ClonalFrameML/archive/refs/tags/v{{ version }}.tar.gz + sha256: 6056109380c695020afa0c26f4ce49dcb9267f1a8f26dfb42629bfa63ac25e6e requirements: build: @@ -20,6 +25,8 @@ test: about: home: https://github.com/xavierdidelot/ClonalFrameML - license: GPLv3 + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE summary: Efficient inferencing of recombination in bacterial genomes - + doc_url: https://github.com/xavierdidelot/clonalframeml/wiki From ef7c2945c9aecd431627c28007814af7e146b574 Mon Sep 17 00:00:00 2001 From: Daniel Standage Date: Thu, 1 Feb 2024 19:56:20 -0500 Subject: [PATCH 1806/2173] lusSTR: pin snakemake =1.0,<2.0 - xlrd >=1.0,<2.0 - openpyxl >=3.0.6 - - snakemake-minimal >=7.22.0 + - snakemake-minimal >=7.22.0,<8.0 - pyyaml >=6.0 - matplotlib-base >=3.5.3 From 40ea994c1cfb6ba182f0da6bbe30583ace5cdc46 Mon Sep 17 00:00:00 2001 From: Manuel Tognon <51021763+ManuelTgn@users.noreply.github.com> Date: Fri, 2 Feb 2024 02:01:43 +0100 Subject: [PATCH 1807/2173] Update CRISPRme to v2.1.2 (#45544) * Update CRISPRme to v2.1.1 * update SHA256 * Update CRISPRme to v2.1.2 * add run_exports to recipe * Update sha256 --- recipes/crisprme/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/crisprme/meta.yaml b/recipes/crisprme/meta.yaml index 42d75db4871bf..8645e64e2d3dd 100644 --- a/recipes/crisprme/meta.yaml +++ b/recipes/crisprme/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.1.1" %} +{% set version = "2.1.2" %} package: name: crisprme @@ -6,9 +6,11 @@ package: source: url: https://github.com/pinellolab/CRISPRme/archive/refs/tags/v{{ version }}.tar.gz - sha256: d59a970c8210cbc5854d77101fe23b5f0ead899b53bcc4c9e6cfb3579c02db26 + sha256: 4f04cc791d2c562dffe6f88345a41795e5a0109490a9f33d91376677e41becc5 build: + run_exports: + - {{ pin_subpackage('crisprme', max_pin="x.x.x") }} number: 0 noarch: generic @@ -48,4 +50,4 @@ about: home: https://github.com/pinellolab/CRISPRme license: AGPL-3.0 license_file: LICENSE - summary: CRISPRme, tool package for CRISPR experiments assessment and analysis. \ No newline at end of file + summary: CRISPRme, tool package for CRISPR experiments assessment and analysis. From 65118c0846e0cdaac534f861da7fc691e78698e4 Mon Sep 17 00:00:00 2001 From: nickjcroucher Date: Fri, 2 Feb 2024 01:38:31 +0000 Subject: [PATCH 1808/2173] Update Gubbins (#45488) * Update version and dependencies * Whitespace versions * Correct URL * Change to codeload URL * Correct version number * Update version number * Update shasum256 * Update shasum256 again * Increment build number * Consistent numpy version --- recipes/gubbins/meta.yaml | 29 ++++++++++++++--------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml index 34c62e3484b4a..41884170f7d23 100644 --- a/recipes/gubbins/meta.yaml +++ b/recipes/gubbins/meta.yaml @@ -7,13 +7,13 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [py < 38] run_exports: - {{ pin_subpackage('gubbins', max_pin="x") }} source: - url: https://github.com/nickjcroucher/{{ name|lower }}/archive/v{{ version }}.tar.gz + url: https://github.com/nickjcroucher/gubbins/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: @@ -28,28 +28,27 @@ requirements: host: - perl - zlib - - python - - scipy >=1.5.3 + - python >=3.8 + - scipy - setuptools - - dendropy >=4.0.2 - - biopython >=1.59 + - dendropy + - biopython - numpy <=1.23.0 - - numba >=0.53 + - numba run: - - python - - scipy >=1.5.3 - - reportlab >=3.0 - - dendropy >=4.0.2 - - biopython >=1.59 - - multiprocess >=0.70 + - python >=3.8 + - scipy + - dendropy + - biopython + - multiprocess - setuptools - raxml =8.2.12 - iqtree >=2.2 - rapidnj - raxml-ng =1.0.1 - fasttree =2.1.10 - - numpy >=1.2 - - numba >=0.56 + - numpy <=1.23.0 + - numba - ska2 >=0.3.0 - r-argparser - r-magrittr From 6e4573dc2dce8568a4c881eab3cf477511ac357e Mon Sep 17 00:00:00 2001 From: Yasuhiro Tanizawa <30499043+nigyta@users.noreply.github.com> Date: Fri, 2 Feb 2024 10:40:16 +0900 Subject: [PATCH 1809/2173] Updated submission-excel2xml recipe (#45528) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: 谷沢靖洋 --- recipes/submission-excel2xml/build.sh | 86 ++++++++++---------------- recipes/submission-excel2xml/meta.yaml | 26 ++++---- recipes/submission-excel2xml/patch | 60 ------------------ 3 files changed, 48 insertions(+), 124 deletions(-) delete mode 100644 recipes/submission-excel2xml/patch diff --git a/recipes/submission-excel2xml/build.sh b/recipes/submission-excel2xml/build.sh index e94caa89de577..a873d246167d1 100644 --- a/recipes/submission-excel2xml/build.sh +++ b/recipes/submission-excel2xml/build.sh @@ -1,58 +1,40 @@ #! /bin/bash -gem install date -v "3.0.0" -gem install open3 -v "0.1.2" -gem install mini_portile2 -v "2.4.0" -gem install nokogiri -v "1.15.3" -gem install rubyzip -v "2.3.2" -gem install roo -v "2.10.0" -gem install builder -v "3.2.4" -gem install rexml -v "3.2.5" +APPROOT=$PREFIX/opt/$PKG_NAME -APPROOT=$PREFIX/opt/submission-excel2xml +mkdir -p $APPROOT +bundle install && \ + bundle exec rake install && \ + bundle exec rake clobber + + +sed -i '1s|^.*$|#! /usr/bin/env ruby|' $PREFIX/share/rubygems/bin/excel2xml_dra +sed -i '1s|^.*$|#! /usr/bin/env ruby|' $PREFIX/share/rubygems/bin/excel2xml_jga +sed -i '1s|^.*$|#! /usr/bin/env ruby|' $PREFIX/share/rubygems/bin/submission-excel2xml +sed -i '1s|^.*$|#! /usr/bin/env ruby|' $PREFIX/share/rubygems/bin/validate_meta_dra +sed -i '1s|^.*$|#! /usr/bin/env ruby|' $PREFIX/share/rubygems/bin/validate_meta_jga + + + +# Downloading xsd files +# Files will be downloaded to $PREFIX/opt/submission-excel2xml/data +# "submission-excel2xml/data" is hard-coded in the source code. +export XDG_DATA_HOME=$PREFIX/opt +submission-excel2xml download_xsd + +# copy sample files +cp -r example/ $APPROOT/ + + +## Set variables on env activation +mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d +cat <> ${PREFIX}/etc/conda/activate.d/${PKG_NAME}.sh +export XDG_DATA_HOME=$PREFIX/opt +EOF + +cat <> ${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}.sh +unset XDG_DATA_HOME +EOF -mkdir -p $APPROOT -# sed -i.bak '1 s|^.*$|#!/usr/bin/env ruby|g' *.rb - -cp excel2xml_dra.rb $APPROOT/ -cp validate_meta_dra.rb $APPROOT/ -cp excel2xml_jga.rb $APPROOT/ -cp validate_meta_jga.rb $APPROOT/ - -chmod a+x $APPROOT/excel2xml_dra.rb -chmod a+x $APPROOT/validate_meta_dra.rb -chmod a+x $APPROOT/excel2xml_jga.rb -chmod a+x $APPROOT/validate_meta_jga.rb - - -mkdir -p $APPROOT/xsd - -cd $APPROOT/xsd - -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.analysis.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.annotation.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.common.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.experiment.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.package.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.run.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.sample.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.study.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/dra/xsd/1-5/SRA.submission.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.analysis.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.common.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.dac.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.data.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.dataset.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.experiment.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.policy.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.sample.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.study.xsd -curl -LO https://raw.githubusercontent.com/ddbj/pub/master/docs/jga/xsd/1-2/JGA.submission.xsd - -cd $PREFIX/bin -ln -s ../opt/submission-excel2xml/excel2xml_dra.rb ./ -ln -s ../opt/submission-excel2xml/validate_meta_dra.rb ./ -ln -s ../opt/submission-excel2xml/excel2xml_jga.rb ./ -ln -s ../opt/submission-excel2xml/validate_meta_jga.rb ./ diff --git a/recipes/submission-excel2xml/meta.yaml b/recipes/submission-excel2xml/meta.yaml index fe1bdec983d3e..aaa47188eaa55 100644 --- a/recipes/submission-excel2xml/meta.yaml +++ b/recipes/submission-excel2xml/meta.yaml @@ -1,6 +1,9 @@ +{% set version = "2.5" %} + package: name: submission-excel2xml - version: "2.0.0" + version: {{ version }} + build: number: 0 noarch: generic @@ -8,26 +11,25 @@ build: - {{ pin_subpackage('submission-excel2xml', max_pin="x") }} source: - url: https://github.com/ddbj/submission-excel2xml/archive/refs/heads/master.zip - md5: 746ef9a1e1bd13f20a0b348fd080eb45 - patches: - - patch + url: https://github.com/ddbj/submission-excel2xml/archive/refs/tags/v{{ version }}.tar.gz + md5: 14369dca823b18bc4c345913d689ae64 requirements: - build: - - make host: - - ruby 3.2.2 + - make + - ruby >=3.0 - compilers - - libxml2 run: - - ruby 3.2.2 - - compilers + - ruby >=3.0 - libxml2 test: commands: - - "excel2xml_jga.rb -h" + # - excel2xml_dra -h + # - excel2xml_jga -h + - excel2xml_dra -a example -i 0001 -p PRJDB7252 ${XDG_DATA_HOME}/submission-excel2xml/example/example-0001_dra_metadata.xlsx && validate_meta_dra -a example -i 0001 + - excel2xml_dra -a example -i 0002 -p PRJDB7252 -c "National Institute of Genetics" ${XDG_DATA_HOME}/submission-excel2xml/example/example-0002_dra_metadata.xlsx && validate_meta_dra -a example -i 0002 + - excel2xml_jga -j JSUB999999 ${XDG_DATA_HOME}/submission-excel2xml/example/JSUB999999_jga_metadata.xlsx && validate_meta_jga -j JSUB999999 about: home: https://github.com/ddbj/submission-excel2xml diff --git a/recipes/submission-excel2xml/patch b/recipes/submission-excel2xml/patch deleted file mode 100644 index 59faa15a8cfa7..0000000000000 --- a/recipes/submission-excel2xml/patch +++ /dev/null @@ -1,60 +0,0 @@ -diff --git a/excel2xml_dra.rb b/excel2xml_dra.rb -index ff30c77..2dbf2ba 100644 ---- a/excel2xml_dra.rb -+++ b/excel2xml_dra.rb -@@ -1,4 +1,4 @@ --#! /usr/bin/ruby -+#! /usr/bin/env ruby - # -*- coding: utf-8 -*- - - require 'rubygems' -diff --git a/excel2xml_jga.rb b/excel2xml_jga.rb -index 8bd6b32..0cdfebe 100644 ---- a/excel2xml_jga.rb -+++ b/excel2xml_jga.rb -@@ -1,4 +1,4 @@ --#! /usr/bin/ruby -+#! /usr/bin/env ruby - # -*- coding: utf-8 -*- - - require 'rubygems' -diff --git a/validate_meta_dra.rb b/validate_meta_dra.rb -index 47d417d..8256cfb 100644 ---- a/validate_meta_dra.rb -+++ b/validate_meta_dra.rb -@@ -1,4 +1,4 @@ --#! /usr/bin/ruby -+#! /usr/bin/env ruby - # -*- coding: utf-8 -*- - - require 'rubygems' -@@ -53,7 +53,7 @@ end - - ## Validate DRA XML against xsd - #xsd_path = "/opt/submission-excel2xml/" --xsd_path = "xsd/" -+xsd_path = __dir__ + "/xsd/" - - puts "\n== XML validation against SRA xsd ==" - if FileTest.exist?("#{submission_id}_dra_Submission.xml") -diff --git a/validate_meta_jga.rb b/validate_meta_jga.rb -index 055bc61..1d3d2f6 100644 ---- a/validate_meta_jga.rb -+++ b/validate_meta_jga.rb -@@ -1,4 +1,4 @@ --#! /usr/bin/ruby -+#! /usr/bin/env ruby - # -*- coding: utf-8 -*- - - require 'rexml/document' -@@ -41,8 +41,8 @@ meta_object = ['Submission', 'Study', 'Sample', 'Experiment', 'Data', 'Analysis' - ## - - ## Validate XMLs against JGA xsd --xsd_path = "/opt/submission-excel2xml/" --#xsd_path = "xsd/" -+#xsd_path = "/opt/submission-excel2xml/" -+xsd_path = __dir__ + "/xsd/" - - xml_a = [] - Dir.glob("#{submission_id}*xml").each{|xml| From 70adb6e0c1b7018b0973e4549552035dd3546a29 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 20:56:11 -0500 Subject: [PATCH 1810/2173] Update plassembler to 1.5.1 (#45572) --- recipes/plassembler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/plassembler/meta.yaml b/recipes/plassembler/meta.yaml index 85b1484bc031b..6eeca0a86bd9e 100644 --- a/recipes/plassembler/meta.yaml +++ b/recipes/plassembler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "plassembler" %} -{% set version = "1.5.0" %} +{% set version = "1.5.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 35496f09241e9c5eb45e66146e0c24b1e77598c84a61db8bc9fbf0d11c3db5d5 + sha256: ab3a4f7b3b0cb391df9e8189bbf5af4ea6fbdd919da65467053f70ad0a7f9c12 build: number: 0 From 22d983c95ac2162ed6b71e3882bbc662b1dae286 Mon Sep 17 00:00:00 2001 From: SantaMcCloud <100047964+SantaMcCloud@users.noreply.github.com> Date: Fri, 2 Feb 2024 02:58:17 +0100 Subject: [PATCH 1811/2173] Update bigscape to 1.1.8 (#45292) * update bigscape to the newest version * Update bigscape to 1.1.8 --- recipes/bigscape/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bigscape/meta.yaml b/recipes/bigscape/meta.yaml index 78c95f18aa48d..7915ed0a1a506 100644 --- a/recipes/bigscape/meta.yaml +++ b/recipes/bigscape/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.6" %} -{% set sha256 = "c38f633d4f1c5b9034c9ee2c96a14b7994884e2fc005fbead219068a618580a4" %} +{% set version = "1.1.8" %} +{% set sha256 = "9a9c256cb0464ca23408fe5a1738db21b8818b487216fb939d7aef037339a598" %} package: name: bigscape From 82cdbf9258cb833c826a334675f1559ba35949cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 21:10:08 -0500 Subject: [PATCH 1812/2173] Update ucsc-cell-browser to 1.2.4 (#45445) * Update ucsc-cell-browser to 1.2.4 * add run_exports * try pinning python to <3.12 --------- Co-authored-by: mencian --- recipes/ucsc-cell-browser/meta.yaml | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/recipes/ucsc-cell-browser/meta.yaml b/recipes/ucsc-cell-browser/meta.yaml index b2e4b40352f61..a86e0702e4f9c 100644 --- a/recipes/ucsc-cell-browser/meta.yaml +++ b/recipes/ucsc-cell-browser/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.2.3' %} +{% set version = '1.2.4' %} {% set name = "cellbrowser" %} package: @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "081d55d1ecc3701c20b1f0275915e9b472b8b71eaa9cb1de7dcba1a0cd0501b1" + sha256: "9c7414dd377ce36c290b1eef0763d0e9d0b8fa9ddc697f6bcfd1e2efa49e67f9" build: number: 0 @@ -25,14 +25,16 @@ build: - cbGenes = cellbrowser.genes:cbGenesCli - cbHub = cellbrowser.hubmaker:cbHubCli noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('ucsc-cell-browser', max_pin="x") }} requirements: host: - - python >=3.6 + - python >=3.6,<3.12 - pip run: - - python >=3.6 + - python >=3.6,<3.12 - numpy - anndata @@ -53,7 +55,14 @@ test: - which cbGenes about: - home: http://cells.ucsc.edu - license: GPL + home: https://cells.ucsc.edu + license: GPL-3.0-or-later + license_family: GPL3 license_file: LICENSE summary: A browser for single-cell data, main site at http://cells.ucsc.edu. UCSC Cellbrowser, an interactive browser for single cell data. Includes importers and basic pipelines for text files, Seurat, Scanpy and Cellranger. All Javascript - does not require a server backend. + doc_url: https://cellbrowser.readthedocs.io/en/master/ + dev_url: https://github.com/maximilianh/cellBrowser + +extra: + identifiers: + - doi:10.1093/bioinformatics/btab503 From 1fa384b366a81dcc0ddd4059228604e56423fbaf Mon Sep 17 00:00:00 2001 From: John Blischak Date: Thu, 1 Feb 2024 21:40:41 -0500 Subject: [PATCH 1813/2173] Package htslib LICENSE and update about section (#45048) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/htslib/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml index de0c0dc0023c1..db620cbb24b61 100644 --- a/recipes/htslib/meta.yaml +++ b/recipes/htslib/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('htslib', max_pin='x.x') }} @@ -40,7 +40,10 @@ test: about: home: https://github.com/samtools/htslib license: MIT + license_family: MIT + license_file: LICENSE summary: C library for high-throughput sequencing data formats. + doc_url: http://www.htslib.org/ extra: identifiers: From 3fc34657a70994e83fc9a0d7079fdb72afed1756 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 1 Feb 2024 21:51:07 -0500 Subject: [PATCH 1814/2173] Update regenie to 3.4.1 (#45564) * Update regenie to 3.4.1 * Update regenie to 3.4.1 * add patch for v3.4.1 --------- Co-authored-by: Joelle Mbatchou Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/regenie/meta.yaml | 7 +- ...013-update-cmakelist-file-for-v3.4.1.patch | 343 ++++++++++++++++++ 2 files changed, 347 insertions(+), 3 deletions(-) create mode 100644 recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch diff --git a/recipes/regenie/meta.yaml b/recipes/regenie/meta.yaml index 3cdfe87d4c7b0..0ee50bfab1262 100644 --- a/recipes/regenie/meta.yaml +++ b/recipes/regenie/meta.yaml @@ -1,6 +1,6 @@ {% set name = "regenie" %} -{% set version = "3.4" %} -{% set sha256 = "c4c87f86ac42dc0ebc57f701e24cc88acd5fbf6cb9e6e3dac8c1b1c9ba4e6922" %} +{% set version = "3.4.1" %} +{% set sha256 = "e2683cd4078015ece44cfbea28957695155dbad3b6a5ef6017654b1d8254f214" %} package: name: {{ name|lower }} @@ -22,7 +22,8 @@ source: # - patches/0009-update-cmake-file-for-conda.patch # - patches/0010-update-cmakelist-file-for-v3.2.7.patch # - patches/0011-update-cmakelist-file-for-v3.2.9.patch - - patches/0012-update-cmakelist-file-for-v3.4.patch + # - patches/0012-update-cmakelist-file-for-v3.4.patch + - patches/0013-update-cmakelist-file-for-v3.4.1.patch build: number: 0 diff --git a/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch b/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch new file mode 100644 index 0000000000000..a3072766dad91 --- /dev/null +++ b/recipes/regenie/patches/0013-update-cmakelist-file-for-v3.4.1.patch @@ -0,0 +1,343 @@ +From 40a095edbac9478fe818b43ae49c0d5e958d632f Mon Sep 17 00:00:00 2001 +From: Joelle Mbatchou +Date: Thu, 1 Feb 2024 17:14:05 -0500 +Subject: [PATCH] update cmakelist file for v3.4.1 + +--- + CMakeLists.txt | 228 +++++++++++++++++++++---------------------------- + 1 file changed, 95 insertions(+), 133 deletions(-) + mode change 100755 => 100644 CMakeLists.txt + +diff --git a/CMakeLists.txt b/CMakeLists.txt +old mode 100755 +new mode 100644 +index 4368ce0..2dc15fd +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -1,11 +1,3 @@ +-# For Intel MKL, set MKLROOT= when running cmake +-# e.g. MKLROOT=/opt/mkl/ cmake -S regenie_dir/ -B regenie_dir/build/ +-# For OpenBLAS, set OPENBLAS_ROOT= when running cmake +-# note: it also requires lapacke library +-# For static compilation on Linux systems, set STATIC=1 when running cmake +-# -> this excludes GLIBC +- +- + cmake_minimum_required(VERSION 3.13) + + # detect OS architecture +@@ -33,57 +25,16 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Ensures -std=c++11 + ###################################### + ######## check input variables + +-# check BGEN_PATH +-if("$ENV{BGEN_PATH}" STREQUAL "") +- message( FATAL_ERROR "Must specify path to BGEN library in 'BGEN_PATH'") +-else() +- set(BGEN_PATH "$ENV{BGEN_PATH}" CACHE INTERNAL "Set BGEN library path") +- if (NOT EXISTS ${BGEN_PATH}) +- message( FATAL_ERROR "Specified BGEN library directory '${BGEN_PATH}' does not exist") +- endif() +-endif() +- + # check for static compilation +-if($ENV{STATIC}) ++if(BUILD_SHARED_LIBS) ++ set(BUILD_STATIC OFF CACHE INTERNAL "Dynamic compilation") ++ set(Boost_USE_STATIC_LIBS OFF) ++else() + set(BUILD_STATIC ON CACHE INTERNAL "Static compilation") ++ set(Boost_USE_STATIC_LIBS ON) + message( STATUS "Static compilation mode") + endif() + +-# check Boost IOStreams +-if($ENV{HAS_BOOST_IOSTREAM}) +- set(HAS_BOOST_IOSTREAM 1 CACHE INTERNAL "Add Boost IO") +- set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") +-else() +- set(HAS_BOOST_IOSTREAM 0 CACHE INTERNAL "Skip Boost IO") +-endif() +- +-# check MKL +-if(NOT "$ENV{MKLROOT}" STREQUAL "") +- set(MKLROOT "$ENV{MKLROOT}" CACHE INTERNAL "Set MKL library path") +- if (NOT EXISTS ${MKLROOT}) +- message( FATAL_ERROR "Specified MKL library directory '${MKLROOT}' does not exist") +- endif() +- message( STATUS "Will compile with Intel MKL library") +-endif() +- +-# check HTSlib +-if(NOT "$ENV{HTSLIB_PATH}" STREQUAL "") +- set(HTSLIB_PATH "$ENV{HTSLIB_PATH}" CACHE INTERNAL "Set HTSlib library path") +- if (NOT EXISTS ${HTSLIB_PATH}) +- message( FATAL_ERROR "Specified HTSlib library directory '${HTSLIB_PATH}' does not exist") +- endif() +- message( STATUS "Will compile with HTSlib") +-endif() +- +-# check OpenBLAS +-if(NOT "$ENV{OPENBLAS_ROOT}" STREQUAL "") +- set(OPENBLAS_ROOT "$ENV{OPENBLAS_ROOT}" CACHE INTERNAL "Set OpenBLAS library path") +- if (NOT EXISTS ${OPENBLAS_ROOT}) +- message( FATAL_ERROR "Specified OpenBLAS library directory '${OPENBLAS_ROOT}' does not exist") +- endif() +- message( STATUS "Will compile with OpenBLAS library") +-endif() +- + ###################################### + ######## set flags and required libraries + +@@ -92,9 +43,10 @@ set(Boost_USE_STATIC_LIBS ${BUILD_STATIC}) + set(Boost_USE_DEBUG_LIBS OFF) + set(Boost_USE_MULTITHREADED ON) + set(Boost_USE_STATIC_RUNTIME OFF) ++set(MKLROOT "${CMAKE_PREFIX_PATH}") + +-# list each file specifically +-add_executable(regenie ++# list each file specifically ++add_executable(regenie + ${CMAKE_SOURCE_DIR}/src/Data.cpp + ${CMAKE_SOURCE_DIR}/src/Files.cpp + ${CMAKE_SOURCE_DIR}/src/Geno.cpp +@@ -112,32 +64,54 @@ add_executable(regenie + ${CMAKE_SOURCE_DIR}/src/MCC.cpp + ${CMAKE_SOURCE_DIR}/src/Ordinal.cpp + ) +-target_include_directories(regenie PRIVATE ${CMAKE_SOURCE_DIR}/src) ++target_include_directories(regenie PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_PREFIX_PATH}/include) + + set(CMAKE_CXX_FLAGS "-O3 -Wall -pedantic -ffast-math -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC") +-add_definitions(-DVERSION_NUMBER="${RG_VERSION}") + ++find_package(OpenMP REQUIRED) ++target_link_libraries(regenie OpenMP::OpenMP_CXX) + if("${UNAME_S}" STREQUAL "Linux") +- find_package(OpenMP REQUIRED) +- target_link_libraries(regenie PRIVATE OpenMP::OpenMP_CXX) + if(${BUILD_STATIC}) +- target_link_options(regenie BEFORE PRIVATE -static-libgcc PRIVATE -static-libstdc++) ++ target_link_options(regenie BEFORE -static-libgcc -static-libstdc++) + endif() + elseif("${UNAME_S}" STREQUAL "Darwin") +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++") + endif() + +-set(EXTERN_LIBS_PATH "${CMAKE_SOURCE_DIR}/external_libs") +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/) ++set(EXTERN_LIBS_PATH "${CMAKE_CURRENT_SOURCE_DIR}/external_libs") ++target_include_directories(regenie PUBLIC ${EXTERN_LIBS_PATH}/) ++ ++# for BGEN (choose static if present first) ++find_library(ZSTD_LIBRARY zstd REQUIRED) ++find_library(DB_LIBRARY ++ NAMES libdb.a db ++ REQUIRED ++ ) ++find_library(SQLITE3_LIBRARY sqlite3 REQUIRED) ++find_package(Boost ++ REQUIRED COMPONENTS system filesystem thread ++ OPTIONAL_COMPONENTS iostreams ++ ) ++find_library(BGEN_LIBRARY ++ NAMES libbgen.a ++ REQUIRED ++ ) ++target_link_libraries(regenie ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARIES}) ++target_include_directories(regenie ++ PUBLIC ++ $ ++ $ ++ $ ++ $ ++ ) ++add_definitions(${Boost_DEFINITIONS}) + +-# BGEN library and its dependencies +-find_library(ZSTD_LIBRARY libzstd.a HINTS "${BGEN_PATH}/build/3rd_party/zstd-1.1.0" REQUIRED) +-find_library(DB_LIBRARY libdb.a HINTS "${BGEN_PATH}/build/db" REQUIRED) +-find_library(SQLITE3_LIBRARY libsqlite3.a HINTS "${BGEN_PATH}/build/3rd_party/sqlite3" REQUIRED) +-find_library(Boost_LIBRARY libboost.a HINTS "${BGEN_PATH}/build/3rd_party/boost_1_55_0" REQUIRED) +-find_library(BGEN_LIBRARY libbgen.a HINTS "${BGEN_PATH}/build" REQUIRED) +-target_link_libraries(regenie PRIVATE ${ZSTD_LIBRARY} ${BGEN_LIBRARY} ${DB_LIBRARY} ${SQLITE3_LIBRARY} ${Boost_LIBRARY}) +-target_include_directories(regenie PRIVATE ${BGEN_PATH} ${BGEN_PATH}/genfile/include/ ${BGEN_PATH}/3rd_party/boost_1_55_0/ ${BGEN_PATH}/3rd_party/zstd-1.1.0/lib ${BGEN_PATH}/db/include/ ${BGEN_PATH}/3rd_party/sqlite3) ++# Boost IO ++if(Boost_iostreams_FOUND) ++ add_definitions(-DHAS_BOOST_IOSTREAM) ++ set(RG_VERSION "${RG_VERSION}.gz" CACHE INTERNAL "Update version") ++ message( STATUS "Will compile with Boost Iostreams library") ++endif() + + # MVTNorm library + set(MVTN_PATH "${EXTERN_LIBS_PATH}/mvtnorm") +@@ -146,7 +120,7 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${MVTN_PATH} + ) +-target_link_libraries(regenie PRIVATE ${MVTN_PATH}/libMvtnorm.a) ++target_link_libraries(regenie ${MVTN_PATH}/libMvtnorm.a) + add_dependencies(regenie libMvtnorm) + + # QF library +@@ -156,7 +130,7 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${QF_PATH} + ) +-target_link_libraries(regenie PRIVATE ${QF_PATH}/qf.a) ++target_link_libraries(regenie ${QF_PATH}/qf.a) + add_dependencies(regenie libqf) + + # Quadpack library +@@ -166,7 +140,7 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${QUAD_PATH} + ) +-target_link_libraries(regenie PRIVATE ${QUAD_PATH}/libquad.a) ++target_link_libraries(regenie ${QUAD_PATH}/libquad.a) + add_dependencies(regenie libquad) + + # PGEN library +@@ -176,12 +150,12 @@ add_custom_target( + COMMAND make + WORKING_DIRECTORY ${PGEN_PATH} + ) +-target_link_libraries(regenie PRIVATE ${PGEN_PATH}/pgenlib.a) +-target_include_directories(regenie PRIVATE ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) ++target_link_libraries(regenie ${PGEN_PATH}/pgenlib.a) ++target_include_directories(regenie PUBLIC ${PGEN_PATH} ${PGEN_PATH}/simde/ ${PGEN_PATH}/include/) + add_dependencies(regenie pgenlib) + + # REMETA library +-if(EXISTS ${HTSLIB_PATH}) ++if(DEFINED HTSLIB_PATH) + set(REMETA_PATH "${EXTERN_LIBS_PATH}/remeta") + add_custom_target( + remeta +@@ -198,78 +172,66 @@ if(EXISTS ${HTSLIB_PATH}) + endif() + + # Intel MKL +-if(EXISTS ${MKLROOT}) ++if(DEFINED MKLROOT) + add_definitions(-DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) +- target_include_directories(regenie PRIVATE ${MKLROOT}/include/) +- if(${BUILD_STATIC}) # specify static libs +- find_library(MKL_LP64_LIB libmkl_intel_lp64.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_THREAD_LIB libmkl_gnu_thread.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_CORE_LIB libmkl_core.a HINTS "${MKLROOT}/lib/intel64" REQUIRED) +- target_link_libraries(regenie PRIVATE "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) ++ target_include_directories(regenie PUBLIC ${MKLROOT}/include/) ++ find_library(MKL_LP64_LIB mkl_intel_lp64 ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ if("${UNAME_S}" STREQUAL "Linux") ++ find_library(MKL_THREAD_LIB mkl_gnu_thread ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ elseif("${UNAME_S}" STREQUAL "Darwin") ++ find_library(MKL_THREAD_LIB mkl_intel_thread ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ endif() ++ find_library(MKL_CORE_LIB mkl_core ++ HINTS "${MKLROOT}/lib/" ++ REQUIRED ++ ) ++ if("${UNAME_S}" STREQUAL "Darwin") ++ target_link_libraries(regenie ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB}) ++ elseif(${BUILD_STATIC}) ++ target_link_libraries(regenie "-Wl,--start-group" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} "-Wl,--end-group" -lgomp) + else() # use dynamic libs +- find_library(MKL_LP64_LIB mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_THREAD_LIB mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" REQUIRED) +- find_library(MKL_CORE_LIB mkl_core PATHS "${MKLROOT}/lib/intel64" REQUIRED) +- target_link_libraries(regenie PRIVATE "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) ++ target_link_libraries(regenie "-Wl,--no-as-needed" ${MKL_LP64_LIB} ${MKL_THREAD_LIB} ${MKL_CORE_LIB} -lgomp) + endif() +-elseif(EXISTS ${OPENBLAS_ROOT}) # OpenBLAS +- add_definitions(-DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE) +- target_include_directories(regenie PRIVATE ${OPENBLAS_ROOT}/include/) +- find_library(LAPACK_LIB lapack REQUIRED) +- find_library(BLAS_LIB openblas HINTS "${OPENBLAS_ROOT}/lib/" REQUIRED) +- target_link_libraries(regenie PRIVATE ${LAPACK_LIB} -llapacke ${BLAS_LIB}) ++ message( STATUS "Will compile with Intel MKL library") + endif() + + # cxxopts (header-only) +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/cxxopts/include/) ++target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/cxxopts/include/) + + # LBFGS (header-only) +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/LBFGSpp/include/) ++target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/LBFGSpp/include/) + + # Eigen (header-only) +-target_include_directories(regenie PRIVATE ${EXTERN_LIBS_PATH}/eigen-3.4.0/) +- +-# Boost IO +-if(${HAS_BOOST_IOSTREAM}) +- if("${UNAME_S}" STREQUAL "Darwin") +- find_library(BOOST_LIB_IO libboost_iostreams libboost_iostreams.a REQUIRED) +- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) +- elseif(${BUILD_STATIC}) +- find_library(BOOST_LIB_IO libboost_iostreams.a REQUIRED) +- target_link_libraries(regenie PRIVATE ${BOOST_LIB_IO}) +- else() +- target_link_libraries(regenie PRIVATE -lboost_iostreams) +- endif() +- add_definitions(-DHAS_BOOST_IOSTREAM) +- message( STATUS "Will compile with Boost Iostreams library") +-endif() ++target_include_directories(regenie PUBLIC ${CMAKE_SOURCE_DIR}/external_libs/eigen-3.4.0/) + + # Other libraries +-find_library(ZLIB_LIBRARY libz.a z REQUIRED) +-find_library(M_LIB m REQUIRED) +-find_library(DL_LIB dl REQUIRED) +-find_library(BZ2_LIB bz2) +-find_library(LZMA_LIB lzma) +-find_library(CURL_LIB curl) +-find_library(CRYPTO_LIB crypto) ++find_library(ZLIB_LIBRARY z REQUIRED) ++find_library(M_LIB m REQUIRED) ++find_library(DL_LIB dl REQUIRED) + if("${UNAME_S}" STREQUAL "Linux") + set(GFORTRAN_LIBRARY "-lgfortran") + elseif("${UNAME_S}" STREQUAL "Darwin") + find_library(GFORTRAN_LIBRARY gfortran REQUIRED) + endif() +-target_link_libraries( +- regenie PRIVATE +- ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} +- ${BZ2_LIB} ${LZMA_LIB} +- ${CURL_LIB} ${CRYPTO_LIB} ${GFORTRAN_LIBRARY} +-) ++target_link_libraries(regenie ${ZLIB_LIBRARY} ${M_LIB} ${DL_LIB} ${PTHREAD_LIB} ${GFORTRAN_LIBRARY}) + +-install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}) ++add_definitions(-DVERSION_NUMBER="${RG_VERSION}") ++install(TARGETS regenie RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} OPTIONAL) + message( STATUS "REGENIE v" ${RG_VERSION}) + +-add_custom_target(full-clean +- COMMAND cd "${MVTN_PATH}" && make clean +- COMMAND cd "${QF_PATH}" && make clean +- COMMAND cd "${QUAD_PATH}" && make clean +- COMMAND cd "${PGEN_PATH}" && make clean +- ) ++write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake COMPATIBILITY SameMajorVersion) ++install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake DESTINATION share/${PROJECT_NAME}) ++ ++set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR}) ++set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR}) ++set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH}) ++include(CPack) +-- +2.34.1 + From 50d60d3fbbecb55d1ed9bf375e8efc4a8f312c1d Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren <78838419+alejandrogzi@users.noreply.github.com> Date: Thu, 1 Feb 2024 22:01:12 -0500 Subject: [PATCH 1815/2173] Add gtfsort recipe (#45535) * new: gtfsort recipe * clean up recipe --------- Co-authored-by: mencian --- recipes/gtfsort/build.sh | 9 +++++++++ recipes/gtfsort/meta.yaml | 39 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 recipes/gtfsort/build.sh create mode 100644 recipes/gtfsort/meta.yaml diff --git a/recipes/gtfsort/build.sh b/recipes/gtfsort/build.sh new file mode 100644 index 0000000000000..8e10cdc3e3237 --- /dev/null +++ b/recipes/gtfsort/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/gtfsort/meta.yaml b/recipes/gtfsort/meta.yaml new file mode 100644 index 0000000000000..33e2dc96045a2 --- /dev/null +++ b/recipes/gtfsort/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "gtfsort" %} +{% set version = "0.2.1" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz + sha256: 0fdaa15e22bd34193e2b16b53697b413af0fcf485401f45d48ac48054f1d70f4 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('gtfsort', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.39 + - pkg-config + +test: + commands: + - gtfsort --help + - gtfsort --version + +about: + home: https://github.com/alejandrogzi/gtfsort + license: MIT + license_family: MIT + license_file: LICENSE + summary: "A chr/pos/feature GTF sorter that uses a lexicographically-based index ordering algorithm." + +extra: + recipe-maintainers: + - alejandrogzi + identifiers: + - doi:10.1101/2023.10.21.563454 From f59886a0bc57f415b8f0d475740c00f7c9f6d1e3 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 1 Feb 2024 23:02:15 -0600 Subject: [PATCH 1816/2173] Add recipe for cgelib v0.7.4 (#45576) --- recipes/cgelib/meta.yaml | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 recipes/cgelib/meta.yaml diff --git a/recipes/cgelib/meta.yaml b/recipes/cgelib/meta.yaml new file mode 100644 index 0000000000000..ddbcd260e9cc1 --- /dev/null +++ b/recipes/cgelib/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "cgelib" %} +{% set version = "0.7.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cgelib-{{ version }}.tar.gz + sha256: 213181bba24856ec367bdfd1e4615eeefff88243f8d29ad9446150927a434aed + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('cgelib', max_pin="x.x") }} + +requirements: + host: + - python >=3.6 + - pip + - wheel + run: + - python >=3.6 + - python-dateutil + - gitpython + +test: + imports: + - cgelib + +about: + home: https://genomicepidemiology.org/ + summary: "This package will in time replace the cgecore package. The package contains classes and functions intended to be utilized across the CGE tools." + license: Apache-2.0 + license_family: APACHE + license_file: LICENSE.txt + dev_url: https://bitbucket.org/genomicepidemiology/cgelib From ea0419040180e4125d517c073c778ab13d66d47a Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 1 Feb 2024 23:02:28 -0600 Subject: [PATCH 1817/2173] Update gmap to 2023.12.01 (#45574) --- recipes/gmap/build.sh | 5 ++--- recipes/gmap/meta.yaml | 9 ++++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/gmap/build.sh b/recipes/gmap/build.sh index ed5ed8319b2d8..f7a0c51aced84 100644 --- a/recipes/gmap/build.sh +++ b/recipes/gmap/build.sh @@ -16,8 +16,7 @@ export LANGUAGE=en_US.UTF-8 export LANG=en_US.UTF-8 export LC_ALL=en_US.UTF-8 -autoconf -autoheader +autoreconf -i ./configure CC="${CC}" CFLAGS="${CFLAGS}" \ CPPFLAGS="${CPPFLAGS}" \ LDFLAGS="${LDFLAGS}" \ @@ -48,5 +47,5 @@ sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/md_coords sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/psl_genes sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/psl_introns sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/psl_splicesites +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/snpindex sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/vcf_iit - diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index 13f1ad8b29cb3..cceb395e938e3 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GMAP" %} -{% set version = "2023.10.10" %} -{% set sha256 = "f76cc3d0024c6c963ea1c13e46236b62a548d965ad8e295a181f138b82aca36e" %} +{% set version = "2023.12.01" %} +{% set sha256 = "878193a4ec16539d4aa2594424e55a9670e2bdae607e63e088962c904ec6ef69" %} package: name: {{ name|lower }} @@ -13,7 +13,8 @@ source: - single_quote_paths.patch build: - number: 1 + number: 0 + skip: True # [osx] run_exports: - {{ pin_subpackage('gmap', max_pin=None) }} @@ -22,6 +23,8 @@ requirements: - make - {{ compiler('c') }} - autoconf + - automake + - libtool - perl host: - zlib From cacfc83d364d6730b8b93a2371990cf2eb8cf3e7 Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren <78838419+alejandrogzi@users.noreply.github.com> Date: Fri, 2 Feb 2024 00:03:52 -0500 Subject: [PATCH 1818/2173] Add bed2gtf recipe (#45573) * new: gtfsort recipe * new: bed2gtf recipe * fix: clean recipe * feat: add build.sh * fix: delete gtfsort --- recipes/bed2gtf/build.sh | 9 +++++++++ recipes/bed2gtf/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 recipes/bed2gtf/build.sh create mode 100644 recipes/bed2gtf/meta.yaml diff --git a/recipes/bed2gtf/build.sh b/recipes/bed2gtf/build.sh new file mode 100644 index 0000000000000..8e10cdc3e3237 --- /dev/null +++ b/recipes/bed2gtf/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/bed2gtf/meta.yaml b/recipes/bed2gtf/meta.yaml new file mode 100644 index 0000000000000..9ce15cb1fe6a5 --- /dev/null +++ b/recipes/bed2gtf/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "bed2gtf" %} +{% set version = "1.9.0" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz + sha256: ae09861fa3474b3298a0469ad6d58bced91667792b5a20fdafe7b0dde6a05351 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('bed2gtf', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.39 + - pkg-config + +test: + commands: + - bed2gtf --help + - bed2gtf --version + +about: + home: https://github.com/alejandrogzi/bed2gtf + license: MIT + license_family: MIT + license_file: LICENSE + summary: "A high-performance BED-to-GTF converter written in Rust" + +extra: + recipe-maintainers: + - alejandrogzi From 3a7549681b3a0f28bce7f5157cde725d886fe880 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=B8ren=20Heidelbach?= <42008781+SorenHeidelbach@users.noreply.github.com> Date: Fri, 2 Feb 2024 06:36:06 +0100 Subject: [PATCH 1819/2173] nanomotif (#45287) * nanomotif * add run_exports * add home URL --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: mencian --- recipes/nanomotif/meta.yaml | 52 +++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/nanomotif/meta.yaml diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml new file mode 100644 index 0000000000000..7e7f621cae175 --- /dev/null +++ b/recipes/nanomotif/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "nanomotif" %} +{% set version = "0.1.7" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz + sha256: 81ebdc88ad0147b48f20385079a10a6ba91f088e9d4325fd7f5206bdde800991 + +build: + entry_points: + - nanomotif = nanomotif.main:main + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('nanomotif', max_pin="x.x") }} + +requirements: + host: + - python + - pip + run: + - python + - wheel + - requests + - numpy ==1.24.4 + - pandas ==2.0.2 + - polars >=0.19 + - seaborn ==0.12.2 + - scipy ==1.10.1 + - networkx ==3.1 + - progressbar2 ==3.53.1 + +test: + imports: + - nanomotif + commands: + - nanomotif --help + +about: + home: https://pypi.org/project/nanomotif/ + summary: Identifying methlyation motifs in nanopore data + license: MIT + license_family: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - SorenHeidelbach From 99151712bbff85d11e544142faa8b011363b8923 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 2 Feb 2024 00:29:27 -0600 Subject: [PATCH 1820/2173] Update resfinder to 4.4.2 (#45579) --- recipes/resfinder/LICENSE-2.0.txt | 202 ------------------ recipes/resfinder/build.sh | 6 +- recipes/resfinder/meta.yaml | 50 +++-- recipes/resfinder/python_path.patch | 6 +- .../resfinder/remove_version_git_tag.patch | 36 ---- 5 files changed, 31 insertions(+), 269 deletions(-) delete mode 100644 recipes/resfinder/LICENSE-2.0.txt delete mode 100644 recipes/resfinder/remove_version_git_tag.patch diff --git a/recipes/resfinder/LICENSE-2.0.txt b/recipes/resfinder/LICENSE-2.0.txt deleted file mode 100644 index d645695673349..0000000000000 --- a/recipes/resfinder/LICENSE-2.0.txt +++ /dev/null @@ -1,202 +0,0 @@ - - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/recipes/resfinder/build.sh b/recipes/resfinder/build.sh index 9cecba2f5985c..3c65803ffd5ac 100644 --- a/recipes/resfinder/build.sh +++ b/recipes/resfinder/build.sh @@ -1,10 +1,6 @@ #!/bin/bash -mkdir -p ${PREFIX}/bin - -cp *.py ${PREFIX}/bin -chmod +x ${PREFIX}/bin/*.py -cp -r cge/ ${PREFIX}/bin/ +${PYTHON} -m pip install . -vvv --no-deps --no-build-isolation # create folder for database download target=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION} diff --git a/recipes/resfinder/meta.yaml b/recipes/resfinder/meta.yaml index a4795a5d6cf2c..53c3e5a68befa 100644 --- a/recipes/resfinder/meta.yaml +++ b/recipes/resfinder/meta.yaml @@ -1,47 +1,51 @@ -{% set name = "ResFinder" %} -{% set version = "4.1.11" %} -{% set sha256 = "e312ff8dc23f329baf8b0a4dc3c41f0006778772e8f736086cf12d03bc76c9c8" %} +{% set name = "resfinder" %} +{% set version = "4.4.2" %} package: - name: '{{ name|lower }}' - version: '{{ version }}' + name: {{ name|lower }} + version: {{ version }} source: - url: https://bitbucket.org/genomicepidemiology/{{ name|lower }}/get/{{ version }}.tar.gz - sha256: '{{ sha256 }}' + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/resfinder-{{ version }}.tar.gz + sha256: 9660e58c3b3f63cf08335c0058f7ef3c56320be852009b714e773c71e8ea2659 patches: - python_path.patch - - remove_version_git_tag.patch build: number: 0 - noarch: generic + noarch: python + run_exports: + - {{ pin_subpackage('resfinder', max_pin="x") }} requirements: host: - - git - - kma + - python >=3.8 + - pip + - pdm-pep517 >=0.12.0 run: - - python >=3 + - python >=3.8 + # Needs cgelib in conda-forge/bioconda + - cgelib >=0.7.3 + - cgecore ==1.5.6 + - tabulate >=0.8.9 + - pandas >=1.4.2 + - biopython >=1.79 + - python-dateutil - kma - - biopython - blast >=2.8.1 - - cgecore 1.5.5 - - tabulate 0.7.7 - - gitpython - - python-dateutil - - git test: - commands: - - run_resfinder.py --help + imports: + - resfinder about: home: https://bitbucket.org/genomicepidemiology/resfinder - license: APACHE-2.0 + summary: "ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria." + license: Apache-2.0 license_family: APACHE - license_file: LICENSE-2.0.txt - summary: ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria. + license_file: LICENSE extra: notes: "ResFinder requires databases that can be downloaded with download-db.sh." + identifiers: + - doi:10.1093/jac/dkaa345 diff --git a/recipes/resfinder/python_path.patch b/recipes/resfinder/python_path.patch index a6b2bea47370b..59543ff0ea533 100644 --- a/recipes/resfinder/python_path.patch +++ b/recipes/resfinder/python_path.patch @@ -1,8 +1,8 @@ ---- run_resfinder.py.old 2022-03-24 02:00:31.990686268 -0500 -+++ run_resfinder.py 2022-03-24 02:01:00.924797159 -0500 +--- a/src/resfinder/run_resfinder.py ++++ b/src/resfinder/run_resfinder.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/opt/anaconda1anaconda2anaconda3/bin/python + import io import sys import os - import re diff --git a/recipes/resfinder/remove_version_git_tag.patch b/recipes/resfinder/remove_version_git_tag.patch deleted file mode 100644 index f1b80390791fe..0000000000000 --- a/recipes/resfinder/remove_version_git_tag.patch +++ /dev/null @@ -1,36 +0,0 @@ ---- run_resfinder.py.old 2022-03-24 02:18:37.191844209 -0500 -+++ run_resfinder.py 2022-03-24 02:19:40.497086660 -0500 -@@ -27,24 +27,6 @@ - # ######### FUNCTIONS ######### # - # ########################################################################### # - --def get_git_tag(): -- git_folders_path = os.path.dirname(os.path.realpath(__file__)) -- try: -- git_tag = str( -- subprocess.check_output( -- ['git', 'describe', '--tags', '--abbrev=0'], -- stderr=subprocess.STDOUT, cwd=git_folders_path, -- )).strip('\'b\\n') -- except subprocess.CalledProcessError as exc_info: -- match = re.search( -- 'fatal: no tag exactly matches \'(?P[a-z0-9]+)\'', str(exc_info.output)) -- if match: -- raise Exception( -- 'Bailing: there is no git tag for the current commit, {commit}'.format( -- commit=match.group('commit'))) -- raise Exception(str(exc_info.output)) -- return git_tag -- - def eprint(*args, **kwargs): - print(*args, file=sys.stderr, **kwargs) - -@@ -178,7 +160,7 @@ - ResFinder will be used.", - type=float, - default=None) --parser.add_argument("-v", "--version", action="version", version=get_git_tag(), -+parser.add_argument("-v", "--version", action="version", version="4.1.11", - help="Show program's version number and exit") - # Temporary option only available temporary - parser.add_argument("--pickle", From 9a9347e1eb984e41fd8a4a4e42cc1bdd77546ba3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 01:54:35 -0500 Subject: [PATCH 1821/2173] Update nanomotif to 0.1.13 (#45580) --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index 7e7f621cae175..a9d41641151cb 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.7" %} +{% set version = "0.1.13" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: 81ebdc88ad0147b48f20385079a10a6ba91f088e9d4325fd7f5206bdde800991 + sha256: 97a236a5f8d56f7150292c043af057e44c8625ab92cef5e1046f3ba40a84b5d7 build: entry_points: From 31447f4087299dce52924e00667b23ab5e4732b0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 04:08:23 -0500 Subject: [PATCH 1822/2173] Update trimnami to 0.1.2 (#45578) * Update trimnami to 0.1.2 * Update meta.yaml update dependencies --------- Co-authored-by: Michael Roach --- recipes/trimnami/meta.yaml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/trimnami/meta.yaml b/recipes/trimnami/meta.yaml index 34ec5afd44ed6..74c441bf5757e 100644 --- a/recipes/trimnami/meta.yaml +++ b/recipes/trimnami/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trimnami" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 594d14c9535ed21270afb3c56f146cad786e9e619c25a89b30556d2284f8f461 + sha256: 5a045d74b3a3e388d32ef2b43429f3742adaa90566d44a52f7cd9bb70d428e69 build: noarch: python @@ -18,12 +18,13 @@ build: requirements: host: - - python >=3.8 + - python >=3.9 - pip run: - - python >=3.8 - - snaketool-utils >=0.0.3 - - snakemake >=7.14.0 + - python >=3.9 + - snaketool-utils >=0.0.4 + - snakemake >=7.14.0,<8 + - pulp <2.8 - pyyaml >=6.0 - Click >=8.1.3 - metasnek >=0.0.8 From f67ad45908a29f4bc10c1ef7f4ad9b169263cd59 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 05:00:38 -0500 Subject: [PATCH 1823/2173] Update pypolca to 0.3.1 (#45581) --- recipes/pypolca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pypolca/meta.yaml b/recipes/pypolca/meta.yaml index 84b6e54e58dca..05b761f65d25c 100644 --- a/recipes/pypolca/meta.yaml +++ b/recipes/pypolca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pypolca" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8f65a6f010a65ced2f0e470d6f1ae9703236fece666674afe76cfb4475bfa440 + sha256: bb48e81a8a3a11979a3edc8091dbfac4b14ec3a57f0952075ae44c8638bac620 build: number: 0 From 781ef4544b4887d12640b9054523672b0a018760 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 2 Feb 2024 11:02:19 +0100 Subject: [PATCH 1824/2173] Update centrifuge to 1.0.4.1 (#45577) * Update centrifuge * Apply suggestions from code review * Correct hash * Update meta.yaml * Update build-fail-blacklist * Sync with centrifuge-core --- build-fail-blacklist | 1 - recipes/centrifuge/meta.yaml | 10 +++++++--- recipes/centrifuge/patch | 13 +++++++++++++ 3 files changed, 20 insertions(+), 4 deletions(-) create mode 100644 recipes/centrifuge/patch diff --git a/build-fail-blacklist b/build-fail-blacklist index 31d92e56cbae9..743eb04f0d076 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -175,7 +175,6 @@ recipes/bwa/0.6.2 # fails compilation in bulk on Linux recipes/paragraph recipes/selectsequencesfrommsa -recipes/centrifuge recipes/nasp recipes/mmvc recipes/gemma diff --git a/recipes/centrifuge/meta.yaml b/recipes/centrifuge/meta.yaml index 2156e793478fb..9aa11c129bd5c 100644 --- a/recipes/centrifuge/meta.yaml +++ b/recipes/centrifuge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "centrifuge" %} -{% set version = "1.0.4" %} +{% set version = "1.0.4.1" %} package: name: {{ name|lower }} @@ -7,10 +7,13 @@ package: build: number: 0 + skip: true # [osx] + run_exports: + - {{ pin_subpackage("centrifuge", max_pin="x.x") }} source: url: https://github.com/DaehwanKimLab/centrifuge/archive/refs/tags/v{{ version }}.tar.gz - sha256: 929daed0f84739f7636cc1ea2757527e83373f107107ffeb5937a403ba5201bc + sha256: 638cc6701688bfdf81173d65fa95332139e11b215b2d25c030f8ae873c34e5cc requirements: build: @@ -23,7 +26,7 @@ requirements: - perl - wget - tar - - python <3 + - python >=3.6 test: commands: @@ -32,6 +35,7 @@ test: about: home: https://github.com/DaehwanKimLab/centrifuge license: GPL3 + license_file: LICENSE summary: 'Classifier for metagenomic sequences.' extra: diff --git a/recipes/centrifuge/patch b/recipes/centrifuge/patch new file mode 100644 index 0000000000000..5a968e69311d7 --- /dev/null +++ b/recipes/centrifuge/patch @@ -0,0 +1,13 @@ +diff --git a/processor_support.h b/processor_support.h +index f68ee65..135a768 100644 +--- a/processor_support.h ++++ b/processor_support.h +@@ -49,7 +49,7 @@ public: + #elif defined(USING_GCC_COMPILER) + __get_cpuid(0x1, ®s.EAX, ®s.EBX, ®s.ECX, ®s.EDX); + #else +- std::cerr << “ERROR: please define __cpuid() for this build.\n”; ++ std::cerr << "ERROR: please define __cpuid() for this build.\n"; + assert(0); + #endif + if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false; \ No newline at end of file From 354218b1237c076f050f2262cef73b9d4ae69352 Mon Sep 17 00:00:00 2001 From: VinzentRisch <100149044+VinzentRisch@users.noreply.github.com> Date: Fri, 2 Feb 2024 16:44:48 +0100 Subject: [PATCH 1825/2173] Add RNAnorm recipe (#45512) * added recipe for rnanorm * Revert "added recipe for rnanorm" This reverts commit 6c3b14b96a68c2be4c92a1928831313d5e272673. * added recipe for rnanorm * added home url and run_exports * removed LICENSE.txt and changed run_export statement --- recipes/rnanorm/meta.yaml | 52 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/rnanorm/meta.yaml diff --git a/recipes/rnanorm/meta.yaml b/recipes/rnanorm/meta.yaml new file mode 100644 index 0000000000000..ee38e16598b55 --- /dev/null +++ b/recipes/rnanorm/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "rnanorm" %} +{% set version = "2.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/rnanorm-{{ version }}.tar.gz + sha256: 651bce77059548b907a4719615646898b6b51fe6915ba713686d2e6aa42d687f + +build: + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + entry_points: + - rnanorm = rnanorm.cli:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + +requirements: + host: + - python >=3.8,<3.13 + - setuptools >=64.0.0 + - setuptools-scm >=6.4.0 + - pip + run: + - python >=3.8,<3.13 + - click + - numpy >=1.0.0 + - pandas >=1.0.0 + - scikit-learn >=1.0.0 + - pandera + +test: + imports: + - rnanorm + commands: + - pip check + - rnanorm --help + requires: + - pip + +about: + summary: Common RNA-seq normalization methods + license: Apache-2.0 + license_file: LICENSE + home: https://github.com/genialis/RNAnorm + +extra: + recipe-maintainers: + - VinzentRisch From 77baeaa796b02823119b3238f5c87de780ce2214 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 10:54:45 -0500 Subject: [PATCH 1826/2173] Update hiphase to 1.3.0 (#45585) --- recipes/hiphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index 5f949dfe8a40b..59ee793e0ae92 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "1.2.1" %} -{% set hiphase_sha256 = "a5bd4926bb57f934fae5d72859d530991ce804ca7127fc134ca7e4c8245fe9f0" %} +{% set version = "1.3.0" %} +{% set hiphase_sha256 = "dd2708f5dd057009be555bf548aecfe30b189c4da086d026bdbb226bd4fb576e" %} package: name: {{ name }} From 44fef08d3ba4a8411515cc600e6333e817773cba Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 15:17:58 -0500 Subject: [PATCH 1827/2173] Update cptac to 1.5.11 (#45589) --- recipes/cptac/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cptac/meta.yaml b/recipes/cptac/meta.yaml index 8a64077d86dde..bab54c17e1958 100644 --- a/recipes/cptac/meta.yaml +++ b/recipes/cptac/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cptac" %} -{% set version = "1.5.10" %} +{% set version = "1.5.11" %} package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 85176554062e73dd0226027baa876357056acd4c81e233082403817252e4fa1e + sha256: f890f69e78193a61f0017f1f2585d1d4bca0a4af5221baeb624b08177f9d0b5b build: number: 0 From facd9b3e97f55dec59826fa628c56338946b4d07 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 15:18:19 -0500 Subject: [PATCH 1828/2173] Update snakemake-interface-common to 1.15.3 (#45587) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 4cfc57b3f3c14..525b28533b34c 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.15.2" %} +{% set version = "1.15.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: f2a4908a5ec5d6e657723f90221da3c136e70a1c5897b4e1d65a703bc08e8d7a + sha256: 7587c5e553c6ddaf0e2542bad1ffda55c3adf5b8ca651f4bc359a17d3f747ceb build: noarch: python From 81c68eedf69aab1ba5ef9b847dcb0263929ecd98 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 15:18:39 -0500 Subject: [PATCH 1829/2173] Update snakemake to 8.4.3 (#45582) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 614c8729ad5bc..d3b7e490033f6 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.2" %} +{% set version = "8.4.3" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: ea9273d7a27706b635fafae87bb21100dad02275570e138fdcff125cb3cba4f4 + sha256: 2c1aad84792beeed8f05933978849b787409d8b96b44890fb96baee737844fbc build: number: 0 From cc8e0f8391d21307f3f2199c76572d8b14fa867a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 2 Feb 2024 15:19:01 -0500 Subject: [PATCH 1830/2173] Update matchms to 0.24.2 (#45584) --- recipes/matchms/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 9cb15af6297b8..051eb033c05c7 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.24.1" %} +{% set version = "0.24.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8cb7098f0e5149c3ab5ad7b39789472b35e12f7668a79c12a3c58e51b50c255c + sha256: 1fe2b241b7d07e066ee92ddf549b22d135c16634b2755aadb774855a46ff55c3 build: number: 0 From 9c6f0adf52ce64c76bedcee5132e4f798c81173f Mon Sep 17 00:00:00 2001 From: Marco Matthies <71844+marcom@users.noreply.github.com> Date: Sat, 3 Feb 2024 10:59:59 +0100 Subject: [PATCH 1831/2173] Update rnastructure to 6.4 (#45594) * Update rnastructure to 6.4 Changelog: https://rna.urmc.rochester.edu/Overview/Updates.html * Add missing jinja template definition --- recipes/rnastructure/meta.yaml | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/recipes/rnastructure/meta.yaml b/recipes/rnastructure/meta.yaml index d994092a66833..10976d6e6a4e0 100644 --- a/recipes/rnastructure/meta.yaml +++ b/recipes/rnastructure/meta.yaml @@ -1,13 +1,19 @@ +{% set name = "RNAstructure" %} +{% set version = "6.4" %} +{% set sha256 = "e2a372a739153293185eeffee3d3265f9f50dc6976053a1d013ccf086b06d975" %} + package: - name: rnastructure - version: '6.3' + name: {{ name | lower }} + version: {{ version }} source: - sha256: e922591ceaa99e0db8ab4572a8716ff625fc0109906650415e92d099d927b310 - url: http://rna.urmc.rochester.edu/Releases/6.3/RNAstructureSource.tgz + sha256: {{ sha256 }} + url: http://rna.urmc.rochester.edu/Releases/{{ version }}/RNAstructureSource.tgz build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage(name | lower, max_pin="x.x") }} requirements: build: From 025ea80d4d2a76b70274bc532561fa247cc6fddd Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Sat, 3 Feb 2024 02:02:15 -0800 Subject: [PATCH 1832/2173] Update unikseq to 1.3.5 (#45591) * Update unikseq to 1.3.5 Needed to add run_exports section * Update summary --- recipes/unikseq/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/unikseq/meta.yaml b/recipes/unikseq/meta.yaml index 7acad68484a8d..6eee8a084f202 100644 --- a/recipes/unikseq/meta.yaml +++ b/recipes/unikseq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.4" %} +{% set version = "1.3.5" %} package: name: unikseq @@ -6,7 +6,7 @@ package: source: url: https://github.com/bcgsc/unikseq/releases/download/v{{ version }}/unikseq-{{ version }}.tar.gz - sha256: e5abe93ccd3bd4b66a67516cde0d877fe82d0ac275833d7d3cc9d95c19f68cf4 + sha256: 9b497384ce023a06fd79353c2488455f1517f10e575c86f1f5df1e21463d09e8 patches: - unikseq-bloom.patch - unikseq-write-bloom.patch @@ -14,6 +14,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('unikseq', max_pin="x") }} requirements: run: @@ -27,7 +29,7 @@ test: - writeBloom.pl |grep "Usage" about: - summary: Unique DNA sequence region identification, using a k-mer approach + summary: Unique DNA sequence region identification using a k-mer approach home: https://github.com/bcgsc/unikseq license: GPL-3.0 license_file: LICENSE From 170412a31697269cea1f518fa6f5cdedabba7d1a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 3 Feb 2024 22:52:38 -0500 Subject: [PATCH 1833/2173] Update koverage to 0.1.10 (#45597) * Update koverage to 0.1.10 * Update meta.yaml update dependencies --------- Co-authored-by: Michael Roach --- recipes/koverage/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/koverage/meta.yaml b/recipes/koverage/meta.yaml index a05f96e6afbb5..d7047f608650d 100644 --- a/recipes/koverage/meta.yaml +++ b/recipes/koverage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "koverage" %} -{% set version = "0.1.9" %} +{% set version = "0.1.10" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 45e3e3ae21669f0c7a45f023ee130d4494ebc2637c0aa4529e95a3867c4b488a + sha256: 46d7d444350932a88f6d0158c946671f2f0a6b4769f3c9c68e4b13fa76ecefc2 build: noarch: python @@ -18,18 +18,18 @@ build: requirements: host: - - python >=3.8 + - python >=3.10 - pip run: - - python >=3.8 + - python >=3.10 - snaketool-utils >=0.0.4 - metasnek >=0.0.8 - - snakemake >=7.14.0 + - snakemake >=7.14.0,<8 + - pulp <2.8 - pyyaml >=6.0 - Click >=8.1.3 - zstandard >=0.21.0 - numpy >=1.24.3 - - py-spy >=0.3.14 - datapane >=0.16.7 - plotly >=5.15.0 From 5ecf67c7d40d51c5e986cad0f92c06c18f769c3a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 12:08:51 -0500 Subject: [PATCH 1834/2173] Update olivar to 1.1.4 (#45604) --- recipes/olivar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/olivar/meta.yaml b/recipes/olivar/meta.yaml index 312f353f707f4..cacb4b80f87e8 100644 --- a/recipes/olivar/meta.yaml +++ b/recipes/olivar/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: olivar @@ -6,7 +6,7 @@ package: source: url: 'https://github.com/treangenlab/Olivar/archive/refs/tags/v{{version}}.tar.gz' - sha256: f7a04661321a33c8c4142fcb65397e13fdbcc3be2e6f429d2a5056e3f16fb567 + sha256: d671e9cc3befd34ccaefc46dbf01d20de7de3bc7a23b66c30c47409509fb18de build: number: 0 From 89d978af24fe4308eb524ab9686a5b72872e8692 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 19:23:02 -0500 Subject: [PATCH 1835/2173] Update breseq to 0.38.3 (#45606) --- recipes/breseq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/breseq/meta.yaml b/recipes/breseq/meta.yaml index 2b9c00862c815..8696fa41b547e 100644 --- a/recipes/breseq/meta.yaml +++ b/recipes/breseq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.38.2" %} +{% set version = "0.38.3" %} package: name: breseq @@ -6,7 +6,7 @@ package: source: url: https://github.com/barricklab/breseq/releases/download/v{{ version }}/breseq-{{ version }}-Source.tar.gz - sha256: "d451670b9e7e3c87b76d3107efe7f1a9a94904011a32e5d407f4cce7ee3b2892" + sha256: "4d0c772fb87947e028094839f090ee130c87d0d5951adf5b845b79ac87449900" build: number: 0 From dd239458c9b46109cff9b0898c450479dda170cc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 19:23:11 -0500 Subject: [PATCH 1836/2173] Update hecatomb to 1.3.1 (#45603) --- recipes/hecatomb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hecatomb/meta.yaml b/recipes/hecatomb/meta.yaml index b5783bce3c181..6793fb605bf02 100644 --- a/recipes/hecatomb/meta.yaml +++ b/recipes/hecatomb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "Hecatomb" %} -{% set version = "1.3.0" %} +{% set version = "1.3.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/shandley/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: ad53c9ab16b9db9a8d6bff2874c96727cffd030d3f5f8d7213496248a8f3659e + sha256: ce078b0d8327e07ba2a814d054b3f7b8c09ec76ad8dd421549676c792ff35ab1 build: number: 0 From eb6681f9a13d47e5bd8f8d103600ea123dd4b05d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 19:23:19 -0500 Subject: [PATCH 1837/2173] Update sage-proteomics to 0.14.6 (#45599) --- recipes/sage-proteomics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sage-proteomics/meta.yaml b/recipes/sage-proteomics/meta.yaml index 75e03453a0b0e..c6e19501ae077 100644 --- a/recipes/sage-proteomics/meta.yaml +++ b/recipes/sage-proteomics/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sage-proteomics" %} -{% set version = "0.14.5" %} -{% set sha256 = "a85b91c6651dfd028d5807163bdb62aa4a8eb222cac03348bd607323af1238c9" %} +{% set version = "0.14.6" %} +{% set sha256 = "5df02517d7c3e4f99785177d595c3106db8df6e443618837bab840c664886f54" %} package: name: {{ name }} From 37a43cca185ebb1a798435b5203db7e5feca95cc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 19:23:30 -0500 Subject: [PATCH 1838/2173] Update pxblat to 1.1.18 (#45595) --- recipes/pxblat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index 2a0c29693aa1f..62cb7b33e4200 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "1.1.10" %} -{% set sha256 = "d20b48ac4c761ad26c680cd1a10e7fb22f581212d5221cbfc2bc7f522a6b81d2" %} +{% set version = "1.1.18" %} +{% set sha256 = "b5d0c4f3ca6e92e01aac24503212760501bd812bff7886b2a28e1219c1511f4d" %} package: name: {{ name|lower }} From 99b513e685140dcac9c248847f963ee3a912f0ae Mon Sep 17 00:00:00 2001 From: Paimon Goulart Date: Sun, 4 Feb 2024 16:44:42 -0800 Subject: [PATCH 1839/2173] Update vcfsim (#45601) * Removed skip true from meta.yaml * Small change * Small change * Small changes * Small changes * Small changes * Small changes * Small changes * Small changes * Small changes * Small changes * Small changes --- recipes/vcfsim/meta.yaml | 45 ++++++++++++++-------------------------- 1 file changed, 15 insertions(+), 30 deletions(-) diff --git a/recipes/vcfsim/meta.yaml b/recipes/vcfsim/meta.yaml index 4123c6047645d..96d58274dcb6d 100644 --- a/recipes/vcfsim/meta.yaml +++ b/recipes/vcfsim/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcfsim" %} -{% set version = "1.0.5.alpha" %} +{% set version = "1.0.8.alpha" %} package: name: {{ name|lower }} @@ -7,62 +7,47 @@ package: source: url: https://github.com/Pie115/VCFSimulator-SamukLab/archive/{{ version }}.tar.gz - sha256: 3930958c2e52f62e5dd9e685307ff03e5387ae80158339806152da7f7aaa57ac + sha256: 67a2be52bb06b44dfb3cb96cff766cae866181b0b1e136d1d8737a229438068c build: + noarch: python entry_points: - vcfsim=vcfsim.__main__:main script: {{ PYTHON }} -m pip install . -vv number: 0 - skip: True run_exports: - {{ pin_subpackage('vcfsim', max_pin="x") }} - -requirements: - build: - - {{ compiler('c') }} - - cross-python_{{ target_platform }} - - python - - pybind11 - - numpy +requirements: host: - - python >=3.8 - - cython + - python >=3.6 - pip - setuptools - numpy - - setuptools_scm - - gsl - + - pandas + - msprime + - ipython # Include this only if IPython features are used outside notebooks + run: - - python >=3.8 - - pandas >=1.5.2 + - python >=3.6 - numpy - - msprime >=1.0.1 - - tskit >=0.4 - - demes >=0.2 - - gsl - - scikit-allel >=1.3.5 - - scikit-learn >=1.2.0 - - scipy >=1.9.3 + - pandas + - msprime + - ipython # Include this only if IPython features are used outside notebooks test: imports: - vcfsim commands: - - pip check - vcfsim --help - requires: - - pip about: home: https://github.com/Pie115/VCFSimulator-SamukLab license: MIT license_file: LICENSE.txt - summary: "Script for generating simulated VCF's" + summary: "Script for generating simulated VCF's leveraging a coalescent simulating backend." description: | - "vcfsim is a new command-line tool for generating simulated VCF's(variant call format files for encoding genetic data). Leveraging a coalescent simulating backend and providing an interface from Msprime coalescent simulating package to pandas. VCF's can now be easily simulated with just a few command line arguments!" + "VCFSim is a new command-line tool for generating simulated VCF's(variant call format files for encoding genetic data). Leveraging a coalescent simulating backend and providing an interface from Msprime coalescent simulating package to pandas. VCF's can now be easily simulated with just a few command line arguments!" extra: recipe-maintainers: From d0468db9408a21e0c204257b2d0e9996ea096185 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 20:21:35 -0500 Subject: [PATCH 1840/2173] Update novoplasty to 4.3.5 (#45605) * Update novoplasty to 4.3.5 * add run_exports --------- Co-authored-by: mencian --- recipes/novoplasty/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/novoplasty/meta.yaml b/recipes/novoplasty/meta.yaml index dac1892e5cb5e..ded9b844226cf 100644 --- a/recipes/novoplasty/meta.yaml +++ b/recipes/novoplasty/meta.yaml @@ -1,5 +1,5 @@ {% set name = "NOVOPlasty" %} -{% set version = "4.3.3" %} +{% set version = "4.3.5" %} package: name: {{ name|lower }} @@ -7,17 +7,18 @@ package: source: url: https://github.com/ndierckx/NOVOPlasty/archive/NOVOPlasty{{ version }}.tar.gz - sha256: 305759167b63d08f8f8191c1f735aa29c90b0a9de9e8c67cdca9ab43c8c13490 + sha256: b2555f2c10548a882d397a3c18d59d41905c0693ecf417d63aee24d5ac738d36 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('novoplasty', max_pin="x") }} requirements: host: - perl - perl-module-build - run: - perl @@ -30,10 +31,11 @@ test: about: home: https://github.com/ndierckx/NOVOPlasty summary: "The organelle assembler and heteroplasmy caller" - license: other + license: Other license_file: LICENSE description: | NOVOPlasty is a de novo assembler for short circular genomes. + extra: identifiers: - doi:10.1093/nar/gkw955 From de1448a3694e24eb464c606123d19a133207b30a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 20:21:51 -0500 Subject: [PATCH 1841/2173] Update somaticseq to 3.7.4 (#45602) * Update somaticseq to 3.7.4 * add run_exports --------- Co-authored-by: mencian --- recipes/somaticseq/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/somaticseq/meta.yaml b/recipes/somaticseq/meta.yaml index 7dd1f0e852f15..cd81c589f93e9 100644 --- a/recipes/somaticseq/meta.yaml +++ b/recipes/somaticseq/meta.yaml @@ -1,6 +1,6 @@ {% set name = "somaticseq" %} -{% set version = "3.7.3" %} -{% set sha256 = "3721c03646496980a17141fe63a90e09ee10328edc1b692aae57bc07c2477e3c" %} +{% set version = "3.7.4" %} +{% set sha256 = "d072300bc403f12265fcadba74c4e6ba82175e749f22f66b46a1e32bf851e24d" %} package: name: {{ name|lower }} @@ -13,7 +13,9 @@ source: build: number: 0 noarch: python - script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv + run_exports: + - {{ pin_subpackage('somaticseq', max_pin="x") }} requirements: host: @@ -25,7 +27,7 @@ requirements: - pysam - scipy - pandas - - xgboost + - xgboost >=1.4 - r-base - r-ada - bedtools @@ -45,7 +47,7 @@ test: - makeSomaticScripts.py --help about: - home: http://bioinform.github.io/somaticseq/ + home: https://bioinform.github.io/somaticseq/ license: BSD-2-Clause license_file: LICENSE.txt license_family: BSD From 8903a66a8f339a85dff89ab2739462630b14f429 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 20:22:17 -0500 Subject: [PATCH 1842/2173] Update ipyrad to 0.9.94 (#45592) * Update ipyrad to 0.9.94 * add run_exports --------- Co-authored-by: mencian --- recipes/ipyrad/meta.yaml | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/recipes/ipyrad/meta.yaml b/recipes/ipyrad/meta.yaml index 4375514b5f3e1..f1cf832e4036c 100644 --- a/recipes/ipyrad/meta.yaml +++ b/recipes/ipyrad/meta.yaml @@ -1,21 +1,23 @@ {% set name = "ipyrad" %} -{% set version = "0.9.93" %} -{% set sha256 = "7f42396c0baa284dde0e9896270006f3c7e2211fa93bb149decccd39b4ab557e" %} +{% set version = "0.9.94" %} +{% set sha256 = "7a9ed2982cdec30afe480d38ae3208458c513f6302ca2a6c947935e5c03736cf" %} package: - name: {{name}} - version: {{version}} + name: {{ name }} + version: {{ version }} source: - url: https://github.com/dereneaton/{{name}}/archive/{{version}}.tar.gz - sha256: {{sha256}} + url: https://github.com/dereneaton/{{ name }}/archive/{{ version }}.tar.gz + sha256: {{ sha256 }} build: number: 0 - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " - noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vv" + noarch: python entry_points: - ipyrad = ipyrad.__main__:main + run_exports: + - {{ pin_subpackage('ipyrad', max_pin="x.x") }} requirements: host: @@ -36,7 +38,7 @@ requirements: - mpi4py >=3.0 # [ py >= 37 ] - notebook - bedtools - - muscle <5 # Pin muscle < v5 see issue #477 + - muscle <5 # Pin muscle < v5 see issue #477 - vsearch >=2.13 - bwa - samtools @@ -52,5 +54,6 @@ test: about: home: http://github.com/dereneaton/ipyrad license: GPL-3.0-only + license_family: GPL3 license_file: LICENSE.txt summary: Interactive assembly and analysis of RAD-seq data sets. From bd961292b4d1c47d6b5e83814b0487981176f5e1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 20:41:23 -0500 Subject: [PATCH 1843/2173] Update cogent3 to 2024.2.5a1 (#45607) --- recipes/cogent3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cogent3/meta.yaml b/recipes/cogent3/meta.yaml index 8b5b4792d7e2f..a113597567360 100644 --- a/recipes/cogent3/meta.yaml +++ b/recipes/cogent3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cogent3" %} -{% set version = "2023.12.15a1" %} +{% set version = "2024.2.5a1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8cccfdb39aff746c9225b1e063a6506502c840276c843bcb93fea10bb2f31bfb + sha256: 4b0d59ba1c31b8257a56258d992fb201b53f265aa6f041da24ed9dc412a7782f build: noarch: python From d714c3a980b73a1d91a0fe21f48c24e3e9b24800 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sun, 4 Feb 2024 20:13:32 -0600 Subject: [PATCH 1844/2173] Add recipe for Monopogen v1.1.0 (#45608) --- recipes/monopogen/LICENSE | 674 ++++++++++++++++++++++++++++++++++++ recipes/monopogen/meta.yaml | 56 +++ 2 files changed, 730 insertions(+) create mode 100644 recipes/monopogen/LICENSE create mode 100644 recipes/monopogen/meta.yaml diff --git a/recipes/monopogen/LICENSE b/recipes/monopogen/LICENSE new file mode 100644 index 0000000000000..f288702d2fa16 --- /dev/null +++ b/recipes/monopogen/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/monopogen/meta.yaml b/recipes/monopogen/meta.yaml new file mode 100644 index 0000000000000..974c5c784f73d --- /dev/null +++ b/recipes/monopogen/meta.yaml @@ -0,0 +1,56 @@ +{% set name = "Monopogen" %} +{% set version = "1.1.0" %} +{% set sha256 = "d6d049792ae277327e2c08ba675af3c9ae2bfccfbee14bed4ab2e20da2be4805" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/KChen-lab/Monopogen/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('monopogen', max_pin="x") }} + +requirements: + host: + - python >=3.6 + - pip + run: + - python >=3.6 + - pandas >=1.2.3 + - pysam >=0.16.0.1 + - numpy >=1.19.5 + - scipy >=1.6.3 + - pillow >=8.2.0 + - openjdk + - samtools + - bcftools + - beagle + - tabix + - r-base + - r-data.table + - r-e1071 + - r-ggplot2 + +test: + imports: + - Monopogen + +about: + home: https://github.com/KChen-lab/Monopogen + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: "Monopogen is an analysis package for SNV calling from single-cell sequencing datasets generated from single cell RNA 10x 5', 10x 3', single ATAC-seq technoloiges, scDNA-seq, etc." + +extra: + recipe-maintainers: + - mencian + identifiers: + - doi:10.1038/s41587-023-01873-x From 5d678a8d8911552425a70774afdacafc6ecee0ab Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 4 Feb 2024 21:33:48 -0500 Subject: [PATCH 1845/2173] Update ashlar to 1.18.0 (#45588) * Update ashlar to 1.18.0 * add run_exports * pin python to <3.12 --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/ashlar/meta.yaml | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/recipes/ashlar/meta.yaml b/recipes/ashlar/meta.yaml index 56f3226e440d9..0f70c9431a7f1 100644 --- a/recipes/ashlar/meta.yaml +++ b/recipes/ashlar/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ashlar" %} -{% set version = "1.17.0" %} +{% set version = "1.18.0" %} package: name: "{{ name|lower }}" @@ -7,31 +7,34 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 3c4fb3a2d1ffee986f86c633d12f753544904ddccbd8499851badbdeec3142be + sha256: 2c0e8997a49daf64fc56b3afabc2e58a0eb2f6f9985d0c3c22be957bf8b03760 build: number: 0 entry_points: - ashlar=ashlar.scripts.ashlar:main - script: "{{ PYTHON }} -m pip install . -vv" + - preview_slide=ashlar.scripts.preview_slide:main + - make_alignment_movie=ashlar.scripts.make_alignment_movie:main + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('ashlar', max_pin="x") }} requirements: host: - pip - - python + - python <3.12 run: - blessed >=1.17 - matplotlib-base >=3.1.2 - networkx >=2.4 - numpy >=1.18.1 - - pip - pyjnius >=1.2.1 - - python + - python <3.12 - scikit-image ==0.19 - scikit-learn >=0.21.1 - scipy >=1.4.1 - - tifffile>=2022.4.8 + - tifffile >=2022.4.8 - zarr test: @@ -44,6 +47,8 @@ test: about: home: "https://github.com/sorgerlab/ashlar" license: MIT + license_family: MIT + license_file: LICENSE summary: "Alignment by Simultaneous Harmonization of Layer/Adjacency Registration" doc_url: https://labsyspharm.github.io/ashlar/ From 1a1f8a5008a9e1b5709944e76b45169e5ffe9d40 Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren <78838419+alejandrogzi@users.noreply.github.com> Date: Sun, 4 Feb 2024 21:40:45 -0500 Subject: [PATCH 1846/2173] Add bed2gff recipe (#45575) * new: gtfsort recipe * new: bed2gtf recipe * new: bed2gff recipe * fix: clean recipe * feat: add build.sh * fix: clean recipe; add build.sh * fix: delete other recipes already in PRs * fix spacing * Update meta.yaml --------- Co-authored-by: mencian --- recipes/bed2gff/build.sh | 9 +++++++++ recipes/bed2gff/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 recipes/bed2gff/build.sh create mode 100644 recipes/bed2gff/meta.yaml diff --git a/recipes/bed2gff/build.sh b/recipes/bed2gff/build.sh new file mode 100644 index 0000000000000..8e10cdc3e3237 --- /dev/null +++ b/recipes/bed2gff/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/bed2gff/meta.yaml b/recipes/bed2gff/meta.yaml new file mode 100644 index 0000000000000..8dd9a3b9338c3 --- /dev/null +++ b/recipes/bed2gff/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "bed2gff" %} +{% set version = "0.1.3" %} + +package: + name: bed2gff + version: {{ version }} + +source: + url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz + sha256: c278185aba8c352ec2b14cc7db6eb08afb5b81e000b0acb9330bfccdad10506c + +build: + number: 0 + run_exports: + - {{ pin_subpackage('bed2gff', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.39 + - pkg-config + +test: + commands: + - bed2gff --help + - bed2gff --version + +about: + home: https://github.com/alejandrogzi/bed2gff + license: MIT + license_family: MIT + license_file: LICENSE + summary: "BED-to-GFF3 converter that runs in parallel" + +extra: + recipe-maintainers: + - alejandrogzi From 6a75d09a104c8ef0d0a2d47c4675011ccf550693 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 5 Feb 2024 11:56:36 +0100 Subject: [PATCH 1847/2173] Restrict version of python in centrifuge due to python 2 evaluation scripts (#45611) --- recipes/centrifuge/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/centrifuge/meta.yaml b/recipes/centrifuge/meta.yaml index 9aa11c129bd5c..e3d21ca909841 100644 --- a/recipes/centrifuge/meta.yaml +++ b/recipes/centrifuge/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage("centrifuge", max_pin="x.x") }} @@ -26,7 +26,7 @@ requirements: - perl - wget - tar - - python >=3.6 + - python <3 test: commands: @@ -36,7 +36,7 @@ about: home: https://github.com/DaehwanKimLab/centrifuge license: GPL3 license_file: LICENSE - summary: 'Classifier for metagenomic sequences.' + summary: 'Classifier for metagenomic sequences. Supports classifier scripts' extra: identifiers: From d8ba2a80dc79e71c764754fe6833fb518533e9ab Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 12:44:23 -0500 Subject: [PATCH 1848/2173] Update r-easydifferentialgenecoexpression to 1.4 (#45613) * Update r-easydifferentialgenecoexpression to 1.4 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-easydifferentialgenecoexpression/meta.yaml | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/recipes/r-easydifferentialgenecoexpression/meta.yaml b/recipes/r-easydifferentialgenecoexpression/meta.yaml index 3ca98180e3570..da710a321155f 100644 --- a/recipes/r-easydifferentialgenecoexpression/meta.yaml +++ b/recipes/r-easydifferentialgenecoexpression/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.0' %} +{% set version = '1.4' %} package: name: r-easydifferentialgenecoexpression @@ -8,41 +8,39 @@ source: url: - {{ cran_mirror }}/src/contrib/easyDifferentialGeneCoexpression_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/easyDifferentialGeneCoexpression/easyDifferentialGeneCoexpression_{{ version }}.tar.gz - sha256: 19156037a2fa498dc28d8db8d53797d74007135c43e53bc5f20d61a66100f5b7 + sha256: d0e1653a311d5e5834ef4b9c333ae3fe5aee8333c1201517ee5f6cb556b054c7 build: - number: 2 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-easydifferentialgenecoexpression', max_pin='x') }} requirements: host: - r-base - bioconductor-biobase - bioconductor-geoquery - - r-r.utils - bioconductor-annotate - bioconductor-diffcoexp - r-geneexpressionfromgeo - r-jetset - bioconductor-limma - r-magrittr - - r-stringi - r-xml2 run: - r-base - bioconductor-biobase - bioconductor-geoquery - - r-r.utils - bioconductor-annotate - bioconductor-diffcoexp - r-geneexpressionfromgeo - r-jetset - bioconductor-limma - r-magrittr - - r-stringi - r-xml2 test: From 9d64299daac4cf409679f36eefd04526daab1de2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 14:22:49 -0500 Subject: [PATCH 1849/2173] Update seq2science to 1.2.2 (#45614) --- recipes/seq2science/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seq2science/meta.yaml b/recipes/seq2science/meta.yaml index dd78a09be0e26..87aeaebd5f332 100644 --- a/recipes/seq2science/meta.yaml +++ b/recipes/seq2science/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} package: name: seq2science @@ -6,7 +6,7 @@ package: source: url: https://github.com/vanheeringen-lab/seq2science/archive/v{{ version }}.tar.gz - sha256: f4543413118f9bdf69e1143f14708f4debf2f1089952569d55a1ca539d676bff + sha256: 5adbaf1689e8f302ec2d5c98f85a206b51f17d0e70e3fc0f16d872ae2099fdc5 build: noarch: python From cc21da441a1de29187f0a99a491e28fc48516ea3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 14:59:45 -0500 Subject: [PATCH 1850/2173] Update dxpy to 0.369.0 (#45625) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 2f93229ada451..5dd102f8d5615 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.368.1" %} +{% set version = "0.369.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: e8fd366edfbe7c9ffd86be14e89d1a0086843442807bea3c404146ca7e96de62 + sha256: dc2f58723d70c6d02155c08d4ac65f41f63aeb05000e4782940d2196b05a962b build: number: 0 From 5b2d1d1ae1bcac05855f14e0a93285cd66a6f27a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 15:00:05 -0500 Subject: [PATCH 1851/2173] Update degenotate to 1.3 (#45624) --- recipes/degenotate/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/degenotate/meta.yaml b/recipes/degenotate/meta.yaml index f66a7025ab294..df8b230b1460e 100644 --- a/recipes/degenotate/meta.yaml +++ b/recipes/degenotate/meta.yaml @@ -1,6 +1,6 @@ {% set name = "degenotate" %} -{% set version = "1.2.4" %} -{% set sha256 = "46359a6d33e660b21c0a0384c641e1aac15f7546f1fbb7463f01d94ad27abf60" %} +{% set version = "1.3" %} +{% set sha256 = "1c12673fd743c24845fec1dd503bf01114faa6b7f4545429e62747e65d323a66" %} package: name: {{ name|lower }} From 46cdc95c07270bc1945beb65cb075ecf4bb8f9cb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 15:00:34 -0500 Subject: [PATCH 1852/2173] Update ncbi-amrfinderplus to 3.12.8 (#45621) --- recipes/ncbi-amrfinderplus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-amrfinderplus/meta.yaml b/recipes/ncbi-amrfinderplus/meta.yaml index a1c878034c0f5..1e8066c9c665a 100644 --- a/recipes/ncbi-amrfinderplus/meta.yaml +++ b/recipes/ncbi-amrfinderplus/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.11.26" %} -{% set sha256 = "49d98d0f66e121d3ed5a3d9a817089ee69399b0bd06af52f79d796bfe8b2d8b2" %} +{% set version = "3.12.8" %} +{% set sha256 = "a199bc332877bad9033a7620bc5e8e849db1f19a9ba8b7357ec5451a6a283aa0" %} package: name: ncbi-amrfinderplus From ebfa13d62c7679f2b05991153e5c09163a42fd17 Mon Sep 17 00:00:00 2001 From: Chenkai Li Date: Mon, 5 Feb 2024 12:04:37 -0800 Subject: [PATCH 1853/2173] Update amplify to 2.0.0 (#45596) * Update amplify to 2.0.0 * Specify package version * Add run_exports * Specify version information for all packages * Add more detailed version information * Change everything back * Add run_exports * Update version * update tensorflow version * change order * try host * change back * try channels * change back * try * change back * try * try * change back * try * change back * try * change back * try * try * try * switch source * try * try * try * try * try * try * try * try * try * try * try * try * update version * remove pip --------- Co-authored-by: mark0428 --- recipes/amplify/build.sh | 4 ++-- recipes/amplify/meta.yaml | 10 +++++++--- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/recipes/amplify/build.sh b/recipes/amplify/build.sh index 94a9322f414cc..3795944d08f32 100644 --- a/recipes/amplify/build.sh +++ b/recipes/amplify/build.sh @@ -4,8 +4,8 @@ mkdir -p ${PREFIX}/bin/ mkdir -p ${PREFIX}/share/amplify/ mkdir -p ${PREFIX}/share/amplify/src/ mkdir -p ${PREFIX}/share/amplify/models/ -cp -r src/. ${PREFIX}/share/amplify/src -cp -r models/. ${PREFIX}/share/amplify/models +cp -r src/. ${PREFIX}/share/amplify/src/ +cp -r models/. ${PREFIX}/share/amplify/models/ echo "#!/bin/bash" > ${PREFIX}/bin/AMPlify echo "${PREFIX}/share/amplify/src/AMPlify.py \$@" >> ${PREFIX}/bin/AMPlify diff --git a/recipes/amplify/meta.yaml b/recipes/amplify/meta.yaml index 28e7d52ba1728..ec02b944b75d4 100644 --- a/recipes/amplify/meta.yaml +++ b/recipes/amplify/meta.yaml @@ -1,5 +1,5 @@ {% set name = "amplify" %} -{% set version = "1.1.0" %} +{% set version = "2.0.0" %} package: name: '{{ name|lower }}' @@ -7,17 +7,21 @@ package: source: url: https://github.com/bcgsc/AMPlify/archive/v{{ version }}.tar.gz - sha256: 8ce9cc10fbb73048b8d8906a387130d9a1ac24928c4762cd190861d44ebb4466 + sha256: 94418a9e2f09b1cfc63eff047fab6d15cce5a7afae5283e50ab809dac2de8752 build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: + host: + - python =3.6 run: - python =3.6 - keras =2.2.4 - - tensorflow =1.12 + - tensorflow >=1.10, <1.13 - numpy <1.17 - biopython - pandas From 9ce540addaa68b6ffc42a39094a87fabafac6da1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 15:06:05 -0500 Subject: [PATCH 1854/2173] Update cadd-scripts to 1.7 (#45615) --- recipes/cadd-scripts/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cadd-scripts/meta.yaml b/recipes/cadd-scripts/meta.yaml index 97cc5f5adcd16..57183b15af886 100644 --- a/recipes/cadd-scripts/meta.yaml +++ b/recipes/cadd-scripts/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.6.post1" %} -{% set sha256 = "0f83361c2e3b0f4bbd096d2e07a8cda4593a0d8b82f68ebff3153b161cad78a4" %} +{% set version = "1.7" %} +{% set sha256 = "46f06c31adc7bdde612c60120f892f2a622494b02812fc047e0d3cee6bd25a0f" %} package: name: cadd-scripts From e7f8e277ffbdb1ebc1d7a846d7006fecd940bc59 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 15:06:51 -0500 Subject: [PATCH 1855/2173] Update pyteomics to 4.7 (#45618) --- recipes/pyteomics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyteomics/meta.yaml b/recipes/pyteomics/meta.yaml index 1f42dfe14a83d..3a7d5dfd42122 100644 --- a/recipes/pyteomics/meta.yaml +++ b/recipes/pyteomics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.6.3" %} +{% set version = "4.7" %} package: name: pyteomics @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/p/pyteomics/pyteomics-{{ version }}.tar.gz - sha256: e3bb11e57da3e52ca768d94fed12c9f66d7300fd58bccbc6736dfc0707fd9546 + sha256: 9f3f83da617c9e7576a927f1dd668f0725789384545e3bc1fd53401d829534c2 build: noarch: python From 6737a8a0111150da9d306b00b87ae2b81bf5e706 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Mon, 5 Feb 2024 15:10:21 -0800 Subject: [PATCH 1856/2173] Update ntjoin (#45626) --- recipes/ntjoin/meta.yaml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/recipes/ntjoin/meta.yaml b/recipes/ntjoin/meta.yaml index 6d7500b02bc9f..d49a1ecaaa371 100644 --- a/recipes/ntjoin/meta.yaml +++ b/recipes/ntjoin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.3" %} +{% set version = "1.1.4" %} package: name: ntjoin @@ -6,16 +6,15 @@ package: source: url: https://github.com/bcgsc/ntJoin/releases/download/v{{ version }}/ntJoin-{{ version }}.tar.gz - sha256: 5c54522841730f454dbdf2ea2ffee01ba647276022d01ecbe74273a1a705265b + sha256: ec24330e11ea63948d1b124273dae79e80088d672f7e536e7d97787f0c2bb644 build: number: 0 - skip: True # [py<38] - run_exports: {{ pin_subpackage("ntjoin", max_pin="x") }} + noarch: generic + run_exports: + - {{ pin_subpackage("ntjoin", max_pin="x") }} requirements: - build: - - {{ compiler('cxx') }} host: - make - python From 05d8d17e1c1835ddf3f7ab4be797a72aa1eb37d7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 18:48:48 -0500 Subject: [PATCH 1857/2173] Update pxblat to 1.1.19 (#45632) --- recipes/pxblat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index 62cb7b33e4200..5cb72a84836ff 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "1.1.18" %} -{% set sha256 = "b5d0c4f3ca6e92e01aac24503212760501bd812bff7886b2a28e1219c1511f4d" %} +{% set version = "1.1.19" %} +{% set sha256 = "06a0b96ee259357dfb9838866fd528e21ce893173c26f89ded700907e6e010de" %} package: name: {{ name|lower }} From cb16ce724f4b5bb2208b2a67018b88eaecf2999f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 18:48:58 -0500 Subject: [PATCH 1858/2173] Update ncbi-datasets-pylib to 16.4.5 (#45630) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index ed48d3f17a024..1659ccf273071 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.4" %} -{% set sha256 = "34db22fd526188b0c819c1b9487a183c98c33f65ca940876b52e1debb8a8e450" %} +{% set version = "16.4.5" %} +{% set sha256 = "c7b0aaeda5327e1fccd41774c43bfa936bb176e7790b63bd9ef7d8e14bbd0e27" %} package: name: {{ name|lower }} From 89d3b78e7e82af085e4d628d9a25ca49b56fc85a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 18:49:07 -0500 Subject: [PATCH 1859/2173] Update fasten to 0.8.0 (#45628) --- recipes/fasten/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fasten/meta.yaml b/recipes/fasten/meta.yaml index dc2a8ac7831b5..f9f67c4e70b88 100644 --- a/recipes/fasten/meta.yaml +++ b/recipes/fasten/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.7.2" %} -{% set sha256 = "95e6c224c9afe30b857f002c425929f10ef022180915c0e26199cf01ca18dcab" %} +{% set version = "0.8.0" %} +{% set sha256 = "9f699b659b96d32c22f0c42e6a435b31e7ac3c4b45c8ccf8f57f7739f241e6fb" %} package: name: fasten From d4fd67ba823e038bee0942e6ec789e67f21e7ef4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 18:49:39 -0500 Subject: [PATCH 1860/2173] Update geofetch to 0.12.6 (#45619) --- recipes/geofetch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/geofetch/meta.yaml b/recipes/geofetch/meta.yaml index b98bdafa490ec..bddae8d83699a 100644 --- a/recipes/geofetch/meta.yaml +++ b/recipes/geofetch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "geofetch" %} -{% set version = "0.12.5" %} +{% set version = "0.12.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 350cad0e7117ae76087b229f1ea0191bebb3bff53d90484aa8cea117c16f812f + sha256: 7ce07c05bad3f18b6f44b79579342604c2b56890e1dec293373b462bf06690b6 build: number: 0 From d35f4c5d8b1655e830f580fe81faa0bad1fa1e7a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 18:49:48 -0500 Subject: [PATCH 1861/2173] Update pybiolib to 1.1.1745 (#45612) * Update pybiolib to 1.1.1711 * Update pybiolib to 1.1.1718 * Update pybiolib to 1.1.1734 * Update pybiolib to 1.1.1741 * Update pybiolib to 1.1.1745 --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 9676b29d9dd02..102a78061d184 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1703" %} +{% set version = "1.1.1745" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: fce4db168dccecd6500d5967d307a3fbd26bd4c4d586668a189f72103b75edbf + sha256: 3215bc496f4ddaf85d3cb327ccc19bf6a6b5f4c0edc339e0967804239dfb44e5 build: noarch: python From 93289ba8c44f36f1bbd00d52d9e3984419c5a6cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 19:19:14 -0500 Subject: [PATCH 1862/2173] Update snakemake to 8.4.4 (#45617) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index d3b7e490033f6..925989c5dbf9c 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.3" %} +{% set version = "8.4.4" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 2c1aad84792beeed8f05933978849b787409d8b96b44890fb96baee737844fbc + sha256: 03cc7383d7ab0fb5b8a18d5b842a27cb686b87c4eef1bc9922b914f405d90370 build: number: 0 From b8579eaad4bcb89ab4b7d1207605cd09e08d2f31 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 19:19:28 -0500 Subject: [PATCH 1863/2173] Update wfmash to 0.12.6 (#45629) --- recipes/wfmash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wfmash/meta.yaml b/recipes/wfmash/meta.yaml index 8ba197d1380e3..ac6ba6133b387 100644 --- a/recipes/wfmash/meta.yaml +++ b/recipes/wfmash/meta.yaml @@ -1,5 +1,5 @@ {% set name = "wfmash" %} -{% set version = "0.12.5" %} +{% set version = "0.12.6" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/waveygang/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - sha256: 797e2f968c85c631f60835ec63268fed2aba39858e7e3b30f29613b8defc40c1 + sha256: 1be1a103bf2a346b8b31aaf2a945e2477a43bb03ff4484090deedb5bb0b4e78d build: skip: True # [osx] From b6a1511119e074bcc4c213c67ffd25146e90b164 Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Mon, 5 Feb 2024 16:39:40 -0800 Subject: [PATCH 1864/2173] Update meta.yaml (#45631) --- recipes/ampliconsuite/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml index 24da7d68a4da9..84d1fa2b1de45 100644 --- a/recipes/ampliconsuite/meta.yaml +++ b/recipes/ampliconsuite/meta.yaml @@ -1,7 +1,7 @@ {% set name="ampliconsuite" %} -{% set AS_version="1.2.1" %} -{% set AA_version="1.3.r7" %} -{% set AC_version="1.1.1" %} +{% set AS_version="1.2.2" %} +{% set AA_version="1.3.r8" %} +{% set AC_version="1.1.2" %} package: name: {{ name }} @@ -11,12 +11,12 @@ source: # the sha256 sum is generated by doing # $ wget -O- [URL] | shasum -a 256 - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz - sha256: 79515b2c1a57a8ea22905737f3c02047a4319d7ab91554dff1a058ead653c720 + sha256: 40d3b4560fb2c9fd0cbc5166b9d136751ff16217a6228fb38b74e12207ef5b63 - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz - sha256: be65a0293da9ced3f6f744657db475c16dd4dcaf9f037e17ee1a19f4ceaa7430 + sha256: 44466fb4a275f5dd1a142269bb72dc53a651b9d9193e5ba799eee14f0f693f89 folder: ampliconarchitectlib - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz - sha256: 040400d2eb0b4c847245666a481de927eb0c9a368088c1e97f117e7a228c8c5d + sha256: 0f57d0775d7b68a76fab6cc375e45410fe76dd9245697855f257378bd1f21650 build: noarch: python From 7f06ba70a62cfb4113ca164e4e754347f75fde56 Mon Sep 17 00:00:00 2001 From: Kristina Gagalova Date: Tue, 6 Feb 2024 08:45:13 +0800 Subject: [PATCH 1865/2173] Add occultercut to recipe (#45510) * occultercut recepy added * updated occultercut * update for run_exports * adding gcc libs * updated meta * test with excluded prefix * lint test * clean up recipe * edit build.sh --------- Co-authored-by: mencian --- recipes/occultercut/build.sh | 17 ++++++++++++++ recipes/occultercut/meta.yaml | 44 +++++++++++++++++++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 recipes/occultercut/build.sh create mode 100644 recipes/occultercut/meta.yaml diff --git a/recipes/occultercut/build.sh b/recipes/occultercut/build.sh new file mode 100644 index 0000000000000..9e2e9cc3758cf --- /dev/null +++ b/recipes/occultercut/build.sh @@ -0,0 +1,17 @@ +#!/bin/bash +set -eu -o pipefail +# +# CONDA build script variables +# +# $PREFIX The install prefix +# + +mkdir -p "${PREFIX}/bin" + +export CPLUS_INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + +make CC="${GXX} ${LDFLAGS}" CFLAGS="${CFLAGS}" + +cp OcculterCut "${PREFIX}/bin" diff --git a/recipes/occultercut/meta.yaml b/recipes/occultercut/meta.yaml new file mode 100644 index 0000000000000..9cee221adf90c --- /dev/null +++ b/recipes/occultercut/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "occultercut" %} +{% set version = "1.1" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: "https://downloads.sourceforge.net/project/{{ name }}/OcculterCut_v{{ version }}.tar.gz" + sha256: 34aa8c3ef4c216435b4f722ea25f9dc431ef6937e47cfeb5afa323d451cc06ae + +build: + number: 0 + skip: True # [osx] + run_exports: + - {{ pin_subpackage('occultercut', max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: + - libgomp # [linux] + - llvm-openmp # [osx] + run: + - gnuplot + +test: + commands: + - OcculterCut | grep "OcculterCut" + +about: + license: GPL-3.0-or-later + license_family: GPL3 + license_file: COPYING + summary: 'A package for measuring the local GC-content bias in genomes and fungal species' + home: https://sourceforge.net/projects/occultercut + +extra: + identifiers: + - doi:10.1093/gbe/evw121 + recipe-maintainers: + - KristinaGagalova From 8fbf8ea0cb0730eb6405333d8dad72c5ec31de17 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 20:02:16 -0500 Subject: [PATCH 1866/2173] Update viralmsa to 1.1.43 (#45635) --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index 51aad2edd4c70..8c476c2293244 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.42" %} +{% set version = "1.1.43" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: dd4ba1779681479f86c3fa38c486ee36ee8f2ca5d66301e583125dc9767d1171 + sha256: 15adaed42f65e2b6a0ba7e6db498fd67f3227b4658f555313194d5b73234ed89 requirements: run: From b0e0b1b392dddf45385b80a0c701df0e6af40ebf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 20:52:32 -0500 Subject: [PATCH 1867/2173] Update last to 1541 (#45638) --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 0bb421e9f8b58..9298623f84248 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1540" %} +{% set version = "1541" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: 047d5ec2f3745f14e29de72c606fa9e74393723ebac9286584435650201de0cf + sha256: 80165ad97bd651b038ca187cc990c930ec96a0a9f5715a2179b5b75304ed64f9 build: number: 0 From aabf5e1d4cffaf1cf5febeaabfb40d93550aa5c5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 20:55:58 -0500 Subject: [PATCH 1868/2173] Update dnaapler to 0.7.0 (#45637) --- recipes/dnaapler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dnaapler/meta.yaml b/recipes/dnaapler/meta.yaml index 3417697c03deb..afdd8db8dc58a 100644 --- a/recipes/dnaapler/meta.yaml +++ b/recipes/dnaapler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dnaapler" %} -{% set version = "0.6.0" %} +{% set version = "0.7.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: b68c138bf11285f5f09add09ae44e5342c8809ce349a1bce6446d8e64f06510d + sha256: 1ae921824055e8c4e9f7651ddd4d4011612f863f17cb95b496849de03560304f build: number: 0 From a1d7a0c671da389c48e1005ba8e402213910de4e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 5 Feb 2024 22:05:13 -0500 Subject: [PATCH 1869/2173] Update ontime to 0.3.0 (#45647) --- recipes/ontime/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ontime/meta.yaml b/recipes/ontime/meta.yaml index 84e0131fe612f..1528ba3889c8a 100644 --- a/recipes/ontime/meta.yaml +++ b/recipes/ontime/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.3" %} +{% set version = "0.3.0" %} {% set name = "ontime" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz - sha256: 6ac4f5e76cb01c16e306661d865a11918604873b5d057afa1a8a37dc4829e682 + sha256: 808833ade04fa7fb318e37b2f0aad2f19a46ba678decdd34e208bf3042050ee1 build: number: 0 From fec354b339dc38ad89a114c854d366d8086429fa Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Tue, 6 Feb 2024 13:39:02 +0100 Subject: [PATCH 1870/2173] Fix deeptoolsintervals license (#45655) Co-authored-by: Devon Ryan --- recipes/deeptoolsintervals/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/deeptoolsintervals/meta.yaml b/recipes/deeptoolsintervals/meta.yaml index 592130b2c9fbe..c5b740e31279a 100644 --- a/recipes/deeptoolsintervals/meta.yaml +++ b/recipes/deeptoolsintervals/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6 build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage("deeptoolsintervals", max_pin="x.x") }} From 26b6671ca090dbd0217bae4a64db47b09832bd33 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 10:38:00 -0500 Subject: [PATCH 1871/2173] Update orthanq to 1.2.0 (#45656) --- recipes/orthanq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/orthanq/meta.yaml b/recipes/orthanq/meta.yaml index 946b26b7f0fd4..fcd3ab4b27ca6 100644 --- a/recipes/orthanq/meta.yaml +++ b/recipes/orthanq/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.0" %} +{% set version = "1.2.0" %} package: name: orthanq @@ -11,7 +11,7 @@ build: source: url: https://github.com/orthanq/orthanq/archive/v{{ version }}.tar.gz - sha256: 5ce1d2826404c04f1de8e5c543c0e23cc23b693f5d190c2602e654d510375bbd + sha256: dbb7e68ef2c16d23aad479978b5403ae652e05a0b37635f55b59c61e08197477 requirements: build: From 43718712f4664eb87f8426ef53ab970f26deed6c Mon Sep 17 00:00:00 2001 From: Tim15-tech <116898385+Tim15-tech@users.noreply.github.com> Date: Tue, 6 Feb 2024 17:08:49 +0100 Subject: [PATCH 1872/2173] Add neat (#45517) Authored-by: Tim15-tech --- recipes/neat/meta.yaml | 49 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/neat/meta.yaml diff --git a/recipes/neat/meta.yaml b/recipes/neat/meta.yaml new file mode 100644 index 0000000000000..e302227fc03b2 --- /dev/null +++ b/recipes/neat/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "NEAT" %} +{% set version = "4.0" %} + +package: + name: '{{ name|lower }}' + version: '{{ version }}' + +source: + url: https://github.com/ncsa/{{ name }}/archive/{{ version }}.tar.gz + sha256: 89abf23f202e4e93fc333a2b6f2a7c7b63ef3db691f8372b659d8627df3616c3 + + +build: + run_exports: + - {{ pin_subpackage('neat', max_pin="x") }} + script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed --no-cache-dir -vvv ." + number: 0 + noarch: python + +requirements: + host: + - python >=3.10 + - poetry-core >=1.0.0 + - pip + run: + - python >=3.10 + - biopython =1.79 + - pkginfo + - matplotlib-base + - numpy + - seaborn + - pyyaml + - scipy + - bedtools + - pybedtools >=0.9.0 + - htslib + - pysam + - frozendict + +test: + commands: + - neat -h | grep read-simulator + +about: + home: https://github.com/ncsa/NEAT/ + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE.md + summary: Toolset for generating synthethic FASTQ, VCF and BAM files. From 091174b7f3d67f958dd0e63be9bc899e224cc180 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 11:21:26 -0500 Subject: [PATCH 1873/2173] Update recentrifuge to 1.14.0 (#45650) --- recipes/recentrifuge/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/recentrifuge/meta.yaml b/recipes/recentrifuge/meta.yaml index 8f89c36bb4498..792c16374b7da 100644 --- a/recipes/recentrifuge/meta.yaml +++ b/recipes/recentrifuge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "recentrifuge" %} -{% set version = "1.13.2" %} +{% set version = "1.14.0" %} package: name: {{ name }} @@ -14,7 +14,7 @@ build: source: url: https://github.com/khyox/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 548cfe12d075e3d9e9c01e380891acc5278eae20e075818d7863136e7cf20b81 + sha256: 8151fe3f7d6581f487eb10fab61ef211b132b0774128ed7d060b5fe389d69674 requirements: host: From a25abdca18f0db70e2ab2a86bf37b50b462168de Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 11:58:28 -0500 Subject: [PATCH 1874/2173] Update phylophlan to 3.1 (#45652) * Update phylophlan to 3.1 --------- Co-authored-by: Francesco Asnicar --- recipes/phylophlan/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/phylophlan/meta.yaml b/recipes/phylophlan/meta.yaml index e5e40d9312b5b..30b9723246e4e 100644 --- a/recipes/phylophlan/meta.yaml +++ b/recipes/phylophlan/meta.yaml @@ -1,6 +1,6 @@ {% set name = "phylophlan" %} -{% set version = "3.0.3" %} -{% set sha256 = "d8d0082c95d58d7b11a60c1e2214b35c1a23a65675005f1393e7647d76c6a054" %} +{% set version = "3.1" %} +{% set sha256 = "9428a8fceb2626325fb6b93cc47143b100183c314f50eb96b32467e42a5bc4ad" %} package: name: "{{ name|lower }}" @@ -15,6 +15,8 @@ build: noarch: python number: 0 script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + run_exports: + - {{ pin_subpackage('phylophlan', max_pin='x.x') }} requirements: host: @@ -39,13 +41,14 @@ requirements: - raxml >=8.2.10 - iqtree >=1.6.6 - mash + - requests test: commands: - phylophlan --version - phylophlan_draw_metagenomic --version - phylophlan_get_reference --version - - phylophlan_metagenomic --version + - phylophlan_assign_sgbs --version - phylophlan_setup_database --version - phylophlan_strain_finder --version - phylophlan_write_config_file --version From ff6a478bbdec09e1d19dbdaf9abebed53bc5749f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 12:40:41 -0500 Subject: [PATCH 1875/2173] Update thapbi-pict to 1.0.8 (#45660) --- recipes/thapbi-pict/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 176bda0e09969..9ea4719fe92bd 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.7" %} +{% set version = "1.0.8" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: 30381e97d0af98fd4d0924130f4efaa722e8e5a3cc7a4719c7bc597d87d9e5fa + sha256: 3e0eac668b35351ea5588b0e1890ccf2e10e7aa847efd7777fd5eca497f4eef0 build: noarch: python From eac2d04d9a4313839714a6e6cecda2ddd58f260b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 13:53:10 -0500 Subject: [PATCH 1876/2173] Update lusstr to 0.9 (#45659) --- recipes/lusstr/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/lusstr/meta.yaml b/recipes/lusstr/meta.yaml index 53b7162c304b2..58fb667975528 100644 --- a/recipes/lusstr/meta.yaml +++ b/recipes/lusstr/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8" %} -{% set sha256 = "3da4c843744c84ac4bc3057b84783cbd95062df05565a66a868541e1170506ca" %} +{% set version = "0.9" %} +{% set sha256 = "abb32bac6d4fd86fbbcd630ef2b254ff66a5658bb3ef6efeb014c7304118561e" %} package: name: lusstr @@ -14,7 +14,7 @@ build: entry_points: - lusstr = lusSTR.cli:main script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv - number: 1 + number: 0 run_exports: - {{ pin_subpackage('lusstr', max_pin="x.x") }} From 950923e8962b0833b4916d4e79859880635cdb49 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Loraine=20Brillet-Gu=C3=A9guen?= Date: Tue, 6 Feb 2024 20:52:31 +0100 Subject: [PATCH 1877/2173] Update kmer-jellyfish to 2.3.1 (#45651) * update to 2.3.1 * Remove from blasklist. Bump version. Add run_exports * fix run_exports location * fix paxkage name in run_exports * following jellyfish installation doc from tar ball --- build-fail-blacklist | 1 - recipes/kmer-jellyfish/build.sh | 3 +-- recipes/kmer-jellyfish/meta.yaml | 14 +++++--------- 3 files changed, 6 insertions(+), 12 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index 743eb04f0d076..e6c6649ef9f6f 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1044,7 +1044,6 @@ recipes/sweepfinder2 # syntax error in configure script recipes/kat -recipes/kmer-jellyfish # unicode error when packaging license file recipes/mapseq diff --git a/recipes/kmer-jellyfish/build.sh b/recipes/kmer-jellyfish/build.sh index c10cb1869a9c5..071a68120b44c 100644 --- a/recipes/kmer-jellyfish/build.sh +++ b/recipes/kmer-jellyfish/build.sh @@ -1,6 +1,5 @@ #!/bin/bash -autoreconf -fi ./configure --prefix=$PREFIX -make +make -j 4 make install diff --git a/recipes/kmer-jellyfish/meta.yaml b/recipes/kmer-jellyfish/meta.yaml index 14cf2981e3866..9d58c7c727f83 100644 --- a/recipes/kmer-jellyfish/meta.yaml +++ b/recipes/kmer-jellyfish/meta.yaml @@ -1,26 +1,22 @@ -{% set version = "2.3.0" %} +{% set version = "2.3.1" %} package: name: kmer-jellyfish version: {{ version }} build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage("kmer-jellyfish", max_pin="2.3.1") }} source: url: https://github.com/gmarcais/Jellyfish/releases/download/v{{ version }}/jellyfish-{{ version }}.tar.gz - sha256: e195b7cf7ba42a90e5e112c0ed27894cd7ac864476dc5fb45ab169f5b930ea5a + sha256: ee032b57257948ca0f0610883099267572c91a635eecbd88ae5d8974c2430fcd requirements: build: - make - {{ compiler('cxx') }} - - autoconf <2.7 # configure script has a problem with later autoconf - - automake - - gettext - - libtool - - pkg-config - - yaggo >=1.5.8 test: commands: From 8440b70f5b0cb6a001b36e203468a6e66c333df0 Mon Sep 17 00:00:00 2001 From: Jaebeom Kim <68528165+jaebeom-kim@users.noreply.github.com> Date: Wed, 7 Feb 2024 05:14:58 +0900 Subject: [PATCH 1878/2173] metabuli1.0.3 (#45648) --- recipes/metabuli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metabuli/meta.yaml b/recipes/metabuli/meta.yaml index 3c74fd689a9fd..f096860d05815 100644 --- a/recipes/metabuli/meta.yaml +++ b/recipes/metabuli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.0.2" %} -{% set sha256 = "cf5c74a7aa585457c0014614e59cf850aaacfab03f326e6113466fa2b436d2c2" %} +{% set version = "1.0.3" %} +{% set sha256 = "facfc3c411b4732e80ac4dfaccf1057cf8b86da4a8d4f05667b1f07dbb18077d" %} package: name: metabuli From a3ecb0f32d1bcca964f4a0f3a5d6b7e09a3b94ea Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:37:19 -0500 Subject: [PATCH 1879/2173] Update earlgrey to 4.0.7 (#45654) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index 19c3246edd5ab..c9c4b8f190d19 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.6" %} -{% set sha256 = "bc4ba13a2f7cf10ef6eedec17529bf8e191ecdd81d85d9db8a788467e282d655" %} +{% set version = "4.0.7" %} +{% set sha256 = "d986ede4ffd3f06c5ea6ac3578c656942214031786b7e7e462b4b0ed4dbec6bd" %} package: name: {{ name|lower }} From 68a74b8a864b7edfc9d5777c753853c09f410c0f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:37:34 -0500 Subject: [PATCH 1880/2173] Update fasten to 0.8.1 (#45658) --- recipes/fasten/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fasten/meta.yaml b/recipes/fasten/meta.yaml index f9f67c4e70b88..79537796084c4 100644 --- a/recipes/fasten/meta.yaml +++ b/recipes/fasten/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.0" %} -{% set sha256 = "9f699b659b96d32c22f0c42e6a435b31e7ac3c4b45c8ccf8f57f7739f241e6fb" %} +{% set version = "0.8.1" %} +{% set sha256 = "35314fa8b6c8d2139338ed070f1c171b06bb7760efecf3e06064bc521399e2cd" %} package: name: fasten From 5ea57c34a2d1a53265d1506f2aca24efd61e6345 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:38:09 -0500 Subject: [PATCH 1881/2173] Update clipkit to 2.1.2 (#45661) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index 561c6ffd1651e..5f005ed5c3b4f 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.1.1" %} +{% set version = "2.1.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 21120216b1211db5dfbd97e575af882072e90065872aefdf1b34d55544ea881c + sha256: 37d1c5a877174048dc78e6a658dc2879e3385d054dbbc6fba0f336e457146a16 build: number: 0 From e0a171a644f74d608e315ac4993ce9fa4ae1b3b1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:41:14 -0500 Subject: [PATCH 1882/2173] Update snakemake to 8.4.6 (#45662) * Update snakemake to 8.4.5 * Update snakemake to 8.4.6 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 925989c5dbf9c..4a8831860540c 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.4" %} +{% set version = "8.4.6" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 03cc7383d7ab0fb5b8a18d5b842a27cb686b87c4eef1bc9922b914f405d90370 + sha256: 173df5ef2674191fe61c67f9a9e13fc7cbcca318d470a1d8e652f556ce706545 build: number: 0 From 86b75966040c1d33a4077b0d560ca5e1fec3982a Mon Sep 17 00:00:00 2001 From: Leonid Kostrykin Date: Wed, 7 Feb 2024 00:04:58 +0100 Subject: [PATCH 1883/2173] Update superdsm to 0.2.0 (#45664) * Update superdsm to 0.2.0 * Fix `missing_run_exports` --------- Co-authored-by: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> --- recipes/superdsm/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/superdsm/meta.yaml b/recipes/superdsm/meta.yaml index 12aa1e1c73a4d..2cd31150b245f 100644 --- a/recipes/superdsm/meta.yaml +++ b/recipes/superdsm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SuperDSM" %} -{% set version = "0.1.3" %} +{% set version = "0.2.0" %} {% set repo_url = "https://github.com/BMCV/SuperDSM" %} {% set docs_url = "https://superdsm.readthedocs.io" %} @@ -9,12 +9,14 @@ package: source: url: "{{ repo_url }}/archive/refs/tags/v{{ version }}.zip" - sha256: f55abbd6818a66886ddfe3f7fd9c5dd93c63ed2b6e3179552106e560a000ad5f + sha256: 9e9365f8df6e925851dd2bf2adeb71cdb52a6d20c775b1da4c7d8e641a02f8d7 build: - number: 1 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv " + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} requirements: host: From 64f28841d6989e165a3e960f61231e15767df143 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 10:33:31 +1100 Subject: [PATCH 1884/2173] Add hmftools-bam-tools 1.2 (#45642) --- recipes/hmftools-bam-tools/bamtools.sh | 69 ++++++++++++++++++++++++++ recipes/hmftools-bam-tools/build.sh | 12 +++++ recipes/hmftools-bam-tools/meta.yaml | 30 +++++++++++ 3 files changed, 111 insertions(+) create mode 100755 recipes/hmftools-bam-tools/bamtools.sh create mode 100644 recipes/hmftools-bam-tools/build.sh create mode 100644 recipes/hmftools-bam-tools/meta.yaml diff --git a/recipes/hmftools-bam-tools/bamtools.sh b/recipes/hmftools-bam-tools/bamtools.sh new file mode 100755 index 0000000000000..bee5781030da9 --- /dev/null +++ b/recipes/hmftools-bam-tools/bamtools.sh @@ -0,0 +1,69 @@ +#!/bin/bash +# hmftools BamTools executable shell script +# https://github.com/hartwigmedical/hmftools/tree/master/bam-tools +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' + then + pass_args="$arg" + else + pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg + fi + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/bamtools.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/bamtools.jar" $pass_args +fi +exit diff --git a/recipes/hmftools-bam-tools/build.sh b/recipes/hmftools-bam-tools/build.sh new file mode 100644 index 0000000000000..4f02d98736648 --- /dev/null +++ b/recipes/hmftools-bam-tools/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p "$TGT" +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cd "${SRC_DIR}" +mv bam-tools*.jar $TGT/bamtools.jar + +cp $RECIPE_DIR/bamtools.sh $TGT/bamtools +ln -s $TGT/bamtools $PREFIX/bin +chmod 0755 "${PREFIX}/bin/bamtools" diff --git a/recipes/hmftools-bam-tools/meta.yaml b/recipes/hmftools-bam-tools/meta.yaml new file mode 100644 index 0000000000000..138a0147d66af --- /dev/null +++ b/recipes/hmftools-bam-tools/meta.yaml @@ -0,0 +1,30 @@ +{% set version = "1.2" %} +{% set sha256 = "552f157861c22a0af22ce19400e6771a8034bdbfedbc760f287a30ac794d36c8" %} + +package: + name: hmftools-bam-tools + version: '{{ version }}' + +source: + url: https://github.com/hartwigmedical/hmftools/releases/download/bam-tools-v{{ version }}/bam-tools_v{{ version }}.jar + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("hmftools-bam-tools", max_pin="x.x") }} + +requirements: + run: + - openjdk >=8 + +test: + commands: + - 'bamtools -version | grep BamTools' + +about: + home: https://github.com/hartwigmedical/hmftools/blob/master/bam-tools/README.md + license: GPL-3.0-only + license_family: GPL3 + summary: Rapidly process BAMs for various tasks. From effdccf37b5bd9494cbd63dcd791448f878509e0 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 10:36:26 +1100 Subject: [PATCH 1885/2173] Add hmftools-virus-interpreter 1.3 (#45644) --- recipes/hmftools-virus-interpreter/build.sh | 12 ++++ recipes/hmftools-virus-interpreter/meta.yaml | 30 ++++++++ .../virusinterpreter.sh | 69 +++++++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 recipes/hmftools-virus-interpreter/build.sh create mode 100644 recipes/hmftools-virus-interpreter/meta.yaml create mode 100755 recipes/hmftools-virus-interpreter/virusinterpreter.sh diff --git a/recipes/hmftools-virus-interpreter/build.sh b/recipes/hmftools-virus-interpreter/build.sh new file mode 100644 index 0000000000000..9016c03d49166 --- /dev/null +++ b/recipes/hmftools-virus-interpreter/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p "$TGT" +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cd "${SRC_DIR}" +mv virus-interpreter*.jar $TGT/virusinterpreter.jar + +cp $RECIPE_DIR/virusinterpreter.sh $TGT/virusinterpreter +ln -s $TGT/virusinterpreter $PREFIX/bin +chmod 0755 "${PREFIX}/bin/virusinterpreter" diff --git a/recipes/hmftools-virus-interpreter/meta.yaml b/recipes/hmftools-virus-interpreter/meta.yaml new file mode 100644 index 0000000000000..d667dc1e799d2 --- /dev/null +++ b/recipes/hmftools-virus-interpreter/meta.yaml @@ -0,0 +1,30 @@ +{% set version = "1.3" %} +{% set sha256 = "b2abfcd2526e0de335455fa687fae0bfeda2f9358c53c7aa0a07bb765ea50545" %} + +package: + name: hmftools-virus-interpreter + version: '{{ version }}' + +source: + url: https://github.com/hartwigmedical/hmftools/releases/download/virus-interpreter-v{{ version }}/virus-interpreter_v{{ version }}.jar + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("hmftools-virus-interpreter", max_pin="x.x") }} + +requirements: + run: + - openjdk >=8 + +test: + commands: + - 'virusinterpreter | grep "Virus Interpreter"' + +about: + home: https://github.com/hartwigmedical/hmftools/blob/master/virus-interpreter/README.md + license: GPL-3.0-only + license_family: GPL3 + summary: Post-process VIRUSBreakend summary results. diff --git a/recipes/hmftools-virus-interpreter/virusinterpreter.sh b/recipes/hmftools-virus-interpreter/virusinterpreter.sh new file mode 100755 index 0000000000000..7ee6eced678ff --- /dev/null +++ b/recipes/hmftools-virus-interpreter/virusinterpreter.sh @@ -0,0 +1,69 @@ +#!/bin/bash +# hmftools Virus Interpreter executable shell script +# https://github.com/hartwigmedical/hmftools/tree/master/virus-interpreter +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' + then + pass_args="$arg" + else + pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg + fi + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/virusinterpreter.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/virusinterpreter.jar" $pass_args +fi +exit From b52fb98d2221bbce3f9e09a2f96ad7dc3ca6be7e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 18:41:33 -0500 Subject: [PATCH 1886/2173] Update pxblat to 1.1.20 (#45666) --- recipes/pxblat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml index 5cb72a84836ff..d3b6b59fc8765 100644 --- a/recipes/pxblat/meta.yaml +++ b/recipes/pxblat/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PxBLAT" %} -{% set version = "1.1.19" %} -{% set sha256 = "06a0b96ee259357dfb9838866fd528e21ce893173c26f89ded700907e6e010de" %} +{% set version = "1.1.20" %} +{% set sha256 = "38820df0fc8ae988446b0d69ab75ff93250e02c603c5a529d23e7b1debc34749" %} package: name: {{ name|lower }} From b065b6136ea05ee8d8489552cd68494789f2403e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 18:42:25 -0500 Subject: [PATCH 1887/2173] Update mass2chem to 0.5.0 (#45668) --- recipes/mass2chem/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mass2chem/meta.yaml b/recipes/mass2chem/meta.yaml index 7f7f765b95914..c5a5ce11d8bf2 100644 --- a/recipes/mass2chem/meta.yaml +++ b/recipes/mass2chem/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mass2chem" %} -{% set version = "0.4.9" %} +{% set version = "0.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mass2chem-{{ version }}.tar.gz - sha256: 5f570440aa217f2f2847f8b2d7cba06c2b46a4088921079db1ed0941b30c1e4b + sha256: 0ef8a49e9ae7e39502edf881249bbdeb445225ae91e6b96da3828a3793f0f8f5 build: noarch: python From 2b97a73ee28ca1db75268eac38e646d9c608ae95 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 11:36:52 +1100 Subject: [PATCH 1888/2173] Add r-mutsigextractor 1.14 (#45646) --- recipes/r-mutsigextractor/build.sh | 2 ++ recipes/r-mutsigextractor/meta.yaml | 40 +++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 recipes/r-mutsigextractor/build.sh create mode 100644 recipes/r-mutsigextractor/meta.yaml diff --git a/recipes/r-mutsigextractor/build.sh b/recipes/r-mutsigextractor/build.sh new file mode 100644 index 0000000000000..af6547bf3c22e --- /dev/null +++ b/recipes/r-mutsigextractor/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +$R CMD INSTALL --build . diff --git a/recipes/r-mutsigextractor/meta.yaml b/recipes/r-mutsigextractor/meta.yaml new file mode 100644 index 0000000000000..69edb0f20c627 --- /dev/null +++ b/recipes/r-mutsigextractor/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.14" %} +{% set sha256 = "96b5b7071209e8cf973b3147866f41d4e51c941c6a469be87f953deacfc3b1a6" %} + +package: + name: r-mutsigextractor + version: '{{ version }}' + +source: + url: https://github.com/UMCUGenetics/mutSigExtractor/archive/refs/tags/{{ version }}.tar.gz + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("r-mutsigextractor", max_pin="x.x") }} + +requirements: + host: + - r-base + - bioconductor-genomeinfodb + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 + run: + - r-base + - bioconductor-genomeinfodb + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 + +test: + commands: + - $R -e "library('mutSigExtractor')" + +about: + home: https://github.com/UMCUGenetics/mutSigExtractor + license: GPL-3.0-only + license_family: GPL3 + summary: Extract mutational signatures from VCF files From 4a4707ee565fc5ebf3d00b122eff61d42a53910a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:04:42 -0500 Subject: [PATCH 1889/2173] Update r-mutsigextractor to 1.28 (#45670) --- recipes/r-mutsigextractor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-mutsigextractor/meta.yaml b/recipes/r-mutsigextractor/meta.yaml index 69edb0f20c627..43ca06abbf2c8 100644 --- a/recipes/r-mutsigextractor/meta.yaml +++ b/recipes/r-mutsigextractor/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.14" %} -{% set sha256 = "96b5b7071209e8cf973b3147866f41d4e51c941c6a469be87f953deacfc3b1a6" %} +{% set version = "1.28" %} +{% set sha256 = "395d89050444f87babf22e3341d4898e3b0d283462ffb1f161da3b8bdc975aee" %} package: name: r-mutsigextractor From 91b6a3a5f8e4e7d85f253d5a2c5bc8d5295eaf49 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 13:05:37 +1100 Subject: [PATCH 1890/2173] Add r-chord 2.02 (#45645) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/r-chord/build.sh | 2 ++ recipes/r-chord/meta.yaml | 42 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 recipes/r-chord/build.sh create mode 100644 recipes/r-chord/meta.yaml diff --git a/recipes/r-chord/build.sh b/recipes/r-chord/build.sh new file mode 100644 index 0000000000000..af6547bf3c22e --- /dev/null +++ b/recipes/r-chord/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +$R CMD INSTALL --build . diff --git a/recipes/r-chord/meta.yaml b/recipes/r-chord/meta.yaml new file mode 100644 index 0000000000000..1053fe03cb7e8 --- /dev/null +++ b/recipes/r-chord/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "2.02" %} +{% set sha256 = "9db52b2d01ddea7d8b97c530683296988e98003a5ee859ae03503666a9013f9f" %} + +package: + name: r-chord + version: '{{ version }}' + +source: + url: https://github.com/UMCUGenetics/CHORD/archive/refs/tags/{{ version }}.tar.gz + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("r-chord", max_pin="x.x") }} + +requirements: + host: + - r-base + - r-mutsigextractor ==1.14 + - r-randomforest + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 + run: + - r-base + - r-mutsigextractor ==1.14 + - r-randomforest + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 + +test: + commands: + - $R -e "library('CHORD')" + +about: + home: https://github.com/UMCUGenetics/CHORD + license: GPL-3.0-only + license_family: GPL3 + summary: Predict HRD using somatic mutations contexts From cad4ebacaa82cf3f3f23bc6264bfd87f5865e33b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:06:54 -0500 Subject: [PATCH 1891/2173] Update hmftools-gripss to 2.4 (#45610) * Update hmftools-gripss to 2.4 * Update descriptions * Update test command --------- Co-authored-by: Stephen Watts --- recipes/hmftools-gripss/gripss.sh | 2 +- recipes/hmftools-gripss/meta.yaml | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/hmftools-gripss/gripss.sh b/recipes/hmftools-gripss/gripss.sh index fe4779d219887..4798d83fbba05 100755 --- a/recipes/hmftools-gripss/gripss.sh +++ b/recipes/hmftools-gripss/gripss.sh @@ -1,5 +1,5 @@ #!/bin/bash -# hmftools gripss executable shell script +# hmftools GRIPSS executable shell script # https://github.com/hartwigmedical/hmftools/tree/master/gripss set -eu -o pipefail diff --git a/recipes/hmftools-gripss/meta.yaml b/recipes/hmftools-gripss/meta.yaml index a0aab8147d630..60be672c9e61f 100644 --- a/recipes/hmftools-gripss/meta.yaml +++ b/recipes/hmftools-gripss/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.3.5" %} -{% set sha256 = "7df02379f416c6131de5f81ad062ab253277b68d7eb71eae0dc9e9bfe34f3bc6" %} +{% set version = "2.4" %} +{% set sha256 = "7e8fb3631c8bb410650e9d84d43d40c85322e0f73e537feae4d186d54d412411" %} package: name: hmftools-gripss @@ -21,10 +21,10 @@ requirements: test: commands: - - 'gripss 2>&1 | grep -q "loading reference data"' + - 'gripss -version | grep Gripss' about: home: https://github.com/hartwigmedical/hmftools/tree/master/gripss license: GPL-3.0-only license_family: GPL - summary: 'GRIPSS applies a set of filtering and post processing steps on GRIDSS paired tumor-normal output to produce a high confidence set of somatic SV for a tumor sample.' + summary: GRIPSS applies a set of filtering and post processing steps on GRIDSS paired tumor-normal output to produce a high confidence set of somatic SV for a tumor sample. From 6711a3fc42e619e947eb6c1cc57494c8f60225f1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:07:44 -0500 Subject: [PATCH 1892/2173] Update hmftools-sage to 3.4 (#43438) * Update hmftools-sage to 3.3 * Update hmftools-sage to 3.3.1 * add run_exports * Update hmftools-sage to 3.4 * Use lowercasing for BASH script for consistency * Update source URL * Update descriptions * Update test command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Stephen Watts --- recipes/hmftools-sage/build.sh | 6 +++--- recipes/hmftools-sage/meta.yaml | 12 +++++++----- recipes/hmftools-sage/{SAGE.sh => sage.sh} | 2 +- 3 files changed, 11 insertions(+), 9 deletions(-) rename recipes/hmftools-sage/{SAGE.sh => sage.sh} (97%) diff --git a/recipes/hmftools-sage/build.sh b/recipes/hmftools-sage/build.sh index 2763b3328ad10..d7f5400c6ef21 100644 --- a/recipes/hmftools-sage/build.sh +++ b/recipes/hmftools-sage/build.sh @@ -7,6 +7,6 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" cd "${SRC_DIR}" mv sage*.jar $TGT/sage.jar -cp $RECIPE_DIR/SAGE.sh $TGT/SAGE -ln -s $TGT/SAGE $PREFIX/bin -chmod 0755 "${PREFIX}/bin/SAGE" +cp $RECIPE_DIR/sage.sh $TGT/sage +ln -s $TGT/sage $PREFIX/bin +chmod 0755 "${PREFIX}/bin/sage" diff --git a/recipes/hmftools-sage/meta.yaml b/recipes/hmftools-sage/meta.yaml index 04abf8dab70df..8f31690dab7d3 100644 --- a/recipes/hmftools-sage/meta.yaml +++ b/recipes/hmftools-sage/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "3.2.3" %} -{% set sha256 = "a49438afee0f7595ff13f7d44e5ae08edc785dc8f04ef605482d9af59ae940f9" %} +{% set version = "3.4" %} +{% set sha256 = "f4fa9788cd3492a612fafaeb8ea1748c549a644fa4e45b98e6cb19f316793467" %} package: name: hmftools-sage version: '{{ version }}' source: - url: 'https://github.com/hartwigmedical/hmftools/releases/download/sage-v{{ version }}/sage_v{{ version }}.jar' + url: https://github.com/hartwigmedical/hmftools/releases/download/sage-v{{ version }}/sage_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-sage', max_pin="x") }} requirements: run: @@ -27,10 +29,10 @@ requirements: test: commands: - - 'SAGE 2>&1 | grep -q "Sage version"' + - 'sage -version | grep Sage' about: home: https://github.com/hartwigmedical/hmftools/tree/master/sage license: GPL-3.0-only license_family: GPL - summary: SAGE is a somatic SNV, MNV and small INDEL caller optimised to call narrow regions of the genome with high prior chance of a variant with very high sensitivity. + summary: SAGE is a somatic SNV, MNV and small INDEL caller optimised 100x tumor / 40x normal coverage, but has a flexible set of filters that can be adapted to lower or higher depth coverage. diff --git a/recipes/hmftools-sage/SAGE.sh b/recipes/hmftools-sage/sage.sh similarity index 97% rename from recipes/hmftools-sage/SAGE.sh rename to recipes/hmftools-sage/sage.sh index 5e9159203c37f..d5a456e118ba2 100755 --- a/recipes/hmftools-sage/SAGE.sh +++ b/recipes/hmftools-sage/sage.sh @@ -1,6 +1,6 @@ #!/bin/bash # hmftools SAGE executable shell script -# https://github.com/hartwigmedical/hmftools/tree/master/SAGE +# https://github.com/hartwigmedical/hmftools/tree/master/sage set -eu -o pipefail export LC_ALL=en_US.UTF-8 From 41276321f6fea435afaa18416b154c2ad6387d7e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:08:21 -0500 Subject: [PATCH 1893/2173] Update hmftools-purple to 4.0 (#43445) * Update hmftools-purple to 3.8.4 * Update hmftools-purple to 3.9 * Update hmftools-purple to 3.9.1 * Update hmftools-purple to 3.9.2 * add run_exports * edit tests * Update hmftools-purple to 4.0 * Use lowercasing for BASH script for consistency * Update about section * Update test command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Stephen Watts --- recipes/hmftools-purple/build.sh | 6 +++--- recipes/hmftools-purple/meta.yaml | 16 +++++++++------- recipes/hmftools-purple/{PURPLE.sh => purple.sh} | 6 +++--- 3 files changed, 15 insertions(+), 13 deletions(-) rename recipes/hmftools-purple/{PURPLE.sh => purple.sh} (94%) diff --git a/recipes/hmftools-purple/build.sh b/recipes/hmftools-purple/build.sh index 963fc41560196..05ac0857d05be 100644 --- a/recipes/hmftools-purple/build.sh +++ b/recipes/hmftools-purple/build.sh @@ -7,6 +7,6 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" cd "${SRC_DIR}" mv purple*.jar $TGT/purple.jar -cp $RECIPE_DIR/PURPLE.sh $TGT/PURPLE -ln -s $TGT/PURPLE $PREFIX/bin -chmod 0755 "${PREFIX}/bin/PURPLE" +cp $RECIPE_DIR/purple.sh $TGT/purple +ln -s $TGT/purple $PREFIX/bin +chmod 0755 "${PREFIX}/bin/purple" diff --git a/recipes/hmftools-purple/meta.yaml b/recipes/hmftools-purple/meta.yaml index 929b228c38a8b..a5aa250c79fa7 100644 --- a/recipes/hmftools-purple/meta.yaml +++ b/recipes/hmftools-purple/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.7.1" %} -{% set sha256 = "23c5fc9832bfd5e3686c8d2ae2285aff4d6c2ac4683021ff17ec59c48d75694c" %} +{% set version = "4.0" %} +{% set sha256 = "58b2457143f77e7752a907a59f1fdd9550fae7483def373ad39ea4ac8fdbc383" %} package: name: hmftools-purple @@ -12,6 +12,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-purple', max_pin="x") }} requirements: run: @@ -28,10 +30,10 @@ requirements: test: commands: - - 'PURPLE -version' + - 'purple -version | grep Purple' about: - home: https://github.com/hartwigmedical/hmftools/tree/master/purity-ploidy-estimator - license: MIT - license_family: MIT - summary: Purity/ploidy estimator. Leverages the read depth and tumor BAF to estimate the purity of a sample and generate a copy number profile + home: https://github.com/hartwigmedical/hmftools/tree/master/purple + license: GPL-3.0-only + license_family: GPL3 + summary: PURPLE is a purity ploidy estimator for tumor samples. diff --git a/recipes/hmftools-purple/PURPLE.sh b/recipes/hmftools-purple/purple.sh similarity index 94% rename from recipes/hmftools-purple/PURPLE.sh rename to recipes/hmftools-purple/purple.sh index 72618b94ab858..68dfb735ed9b0 100755 --- a/recipes/hmftools-purple/PURPLE.sh +++ b/recipes/hmftools-purple/purple.sh @@ -1,6 +1,6 @@ #!/bin/bash # hmftools PURPLE executable shell script -# https://github.com/hartwigmedical/hmftools/tree/master/purity-ploidy-estimator +# https://github.com/hartwigmedical/hmftools/tree/master/purple set -eu -o pipefail export LC_ALL=en_US.UTF-8 @@ -46,8 +46,8 @@ for arg in "$@"; do ;; *) if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' - then - pass_args="$arg" + then + pass_args="$arg" else pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg fi From e77c715b78592bd25d870e4ac9b4c92b06d6163c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:08:38 -0500 Subject: [PATCH 1894/2173] Update hmftools-pave to 1.6 (#43447) * Update hmftools-pave to 1.4.5 * Update hmftools-pave to 1.5 * add run_exports * edit tests * edit tests against * try lowercase pave * Update hmftools-pave to 1.5.1 * Update hmftools-pave to 1.5.1 * Update hmftools-pave to 1.6 * Update descriptions and licence family * Update source URL * Update test command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Stephen Watts --- recipes/hmftools-pave/meta.yaml | 12 +++++++----- recipes/hmftools-pave/pave.sh | 2 +- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/hmftools-pave/meta.yaml b/recipes/hmftools-pave/meta.yaml index 8bb0808513d02..84156f65d0e6f 100644 --- a/recipes/hmftools-pave/meta.yaml +++ b/recipes/hmftools-pave/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "1.4.1" %} -{% set sha256 = "eb6dbf7ff5d2729807e5a33709b256fa1537235eb263c1f0b34fba45e60fc4b3" %} +{% set version = "1.6" %} +{% set sha256 = "c553b5224dae4f61958030d2b544ad990aca6fde145ee03f43214856f3dbf634" %} package: name: hmftools-pave version: '{{ version }}' source: - url: 'https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}.jar' + url: https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-pave', max_pin="x.x") }} requirements: run: @@ -20,10 +22,10 @@ requirements: test: commands: - - 'pave 2>&1 | grep -q "Pave version"' + - 'pave -version | grep Pave' about: home: https://github.com/hartwigmedical/hmftools/tree/master/pave license: GPL-3.0-only license_family: GPL - summary: Pave annotates a somatic variant VCF with gene and transcript coding and protein effects. + summary: PAVE annotates SNV/MNV/INDEL calls with consequence on corresponding genes, transcripts, and proteins. diff --git a/recipes/hmftools-pave/pave.sh b/recipes/hmftools-pave/pave.sh index 73ae4b947b422..d3108a6244903 100755 --- a/recipes/hmftools-pave/pave.sh +++ b/recipes/hmftools-pave/pave.sh @@ -1,5 +1,5 @@ #!/bin/bash -# hmftools pave executable shell script +# hmftools PAVE executable shell script # https://github.com/hartwigmedical/hmftools/tree/master/pave set -eu -o pipefail From a3c9d0317c974265a7911f4c34f720b80a7e72ad Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:09:29 -0500 Subject: [PATCH 1895/2173] Update hmftools-linx to 1.25 (#43443) * Update hmftools-linx to 1.24 * Update hmftools-linx to 1.24.1 * add run_exports * Update hmftools-linx to 1.25 * Update descriptions * Update test command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Stephen Watts --- recipes/hmftools-linx/linx.sh | 2 +- recipes/hmftools-linx/meta.yaml | 10 ++++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/hmftools-linx/linx.sh b/recipes/hmftools-linx/linx.sh index 7fe7ef75a7882..7bc92d4b403cb 100755 --- a/recipes/hmftools-linx/linx.sh +++ b/recipes/hmftools-linx/linx.sh @@ -1,5 +1,5 @@ #!/bin/bash -# hmftools linx executable shell script +# hmftools LINX executable shell script # https://github.com/hartwigmedical/hmftools/tree/master/linx set -eu -o pipefail diff --git a/recipes/hmftools-linx/meta.yaml b/recipes/hmftools-linx/meta.yaml index bf53e28de0d52..b7d512fde85ad 100644 --- a/recipes/hmftools-linx/meta.yaml +++ b/recipes/hmftools-linx/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.23.6" %} -{% set sha256 = "6dfeb9c15369d33953193e65db8454e678772c79218643bd122293e59288d297" %} +{% set version = "1.25" %} +{% set sha256 = "2fa9a91801239ded3e82fcd0ee9987e6181d0e400855420ef7f5000f3b4a96da" %} package: name: hmftools-linx @@ -12,6 +12,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-linx', max_pin="x") }} requirements: run: @@ -27,10 +29,10 @@ requirements: test: commands: - - 'linx 2>&1 | grep -q "LINX version"' + - 'linx -version | grep Linx' about: home: https://github.com/hartwigmedical/hmftools/tree/master/linx license: GPL-3.0-only license_family: GPL - summary: Linx is an annotation, interpretation and visualisation tool for structural variants + summary: LINX is an annotation, interpretation and visualisation tool for structural variants. From 14d0aa2957a14473de048c7e45bbaa6df558ab65 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:09:42 -0500 Subject: [PATCH 1896/2173] Update hmftools-lilac to 1.6 (#43421) * Update hmftools-lilac to 1.5 * Update hmftools-lilac to 1.5.1 * Update hmftools-lilac to 1.5.2 * add run_exports * Update hmftools-lilac to 1.5.2 * Update hmftools-lilac to 1.6 * Use lowercasing for BASH script for consistency * Update source URL * Update test command * Use consistent license details, update home URL * Correct malformed build command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Stephen Watts --- recipes/hmftools-lilac/build.sh | 6 +++--- recipes/hmftools-lilac/{LILAC.sh => lilac.sh} | 0 recipes/hmftools-lilac/meta.yaml | 12 +++++++----- 3 files changed, 10 insertions(+), 8 deletions(-) rename recipes/hmftools-lilac/{LILAC.sh => lilac.sh} (100%) diff --git a/recipes/hmftools-lilac/build.sh b/recipes/hmftools-lilac/build.sh index a90fcee0b3303..a65c6f98505e2 100644 --- a/recipes/hmftools-lilac/build.sh +++ b/recipes/hmftools-lilac/build.sh @@ -7,6 +7,6 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" cd "${SRC_DIR}" mv lilac*.jar $TGT/lilac.jar -cp $RECIPE_DIR/LILAC.sh $TGT/LILAC -ln -s $TGT/LILAC $PREFIX/bin -chmod 0755 "${PREFIX}/bin/LILAC" +cp $RECIPE_DIR/lilac.sh $TGT/lilac +ln -s $TGT/lilac $PREFIX/bin +chmod 0755 "${PREFIX}/bin/lilac" diff --git a/recipes/hmftools-lilac/LILAC.sh b/recipes/hmftools-lilac/lilac.sh similarity index 100% rename from recipes/hmftools-lilac/LILAC.sh rename to recipes/hmftools-lilac/lilac.sh diff --git a/recipes/hmftools-lilac/meta.yaml b/recipes/hmftools-lilac/meta.yaml index 0ca7fb2315494..c444f5345d0a3 100644 --- a/recipes/hmftools-lilac/meta.yaml +++ b/recipes/hmftools-lilac/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "1.4.2" %} -{% set sha256 = "1df4a34f3ea777db8da21cd9eaeca19a30795e5eb0bb44c5b38cd705df5c82fe" %} +{% set version = "1.6" %} +{% set sha256 = "d5f5fc5c2fb047fdbc6292a36dc3a164f5bbf820f87ceebafecf1412c41632f6" %} package: name: hmftools-lilac version: '{{ version }}' source: - url: 'https://github.com/hartwigmedical/hmftools/releases/download/lilac-v{{ version }}/lilac_v{{ version }}.jar' + url: https://github.com/hartwigmedical/hmftools/releases/download/lilac-v{{ version }}/lilac_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-lilac', max_pin="x") }} requirements: run: @@ -20,10 +22,10 @@ requirements: test: commands: - - 'LILAC 2>&1 | grep -q "LilacApplication"' + - 'lilac -version | grep Lilac' about: home: https://github.com/hartwigmedical/hmftools/blob/master/lilac/README.md - license: "GNU General Public v3 (GPLv3)" + license: GPL-3.0-only license_family: GPL3 summary: LILAC is a WGS tool to determine HLA Class I types. From 09cdf8d945199dbf69d18430d146a16bd452b6ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:10:41 -0500 Subject: [PATCH 1897/2173] Update hmftools-isofox to 1.7.1 (#43433) * Update hmftools-isofox to 1.7 * add run_exports * Update hmftools-isofox to 1.7.1 * Update descriptions * Update test command --------- Co-authored-by: joshuazhuang7 Co-authored-by: Thanh Lee Co-authored-by: Stephen Watts --- recipes/hmftools-isofox/isofox.sh | 2 +- recipes/hmftools-isofox/meta.yaml | 10 ++++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/hmftools-isofox/isofox.sh b/recipes/hmftools-isofox/isofox.sh index 91bb67218a3dc..1c57bf313dfd7 100755 --- a/recipes/hmftools-isofox/isofox.sh +++ b/recipes/hmftools-isofox/isofox.sh @@ -1,5 +1,5 @@ #!/bin/bash -# hmftools isofox executable shell script +# hmftools Isofox executable shell script # https://github.com/hartwigmedical/hmftools/tree/master/isofox set -eu -o pipefail diff --git a/recipes/hmftools-isofox/meta.yaml b/recipes/hmftools-isofox/meta.yaml index 9cc47f9fe3d22..e3cd0ebf68cfd 100644 --- a/recipes/hmftools-isofox/meta.yaml +++ b/recipes/hmftools-isofox/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.6.2" %} -{% set sha256 = "b681b48f0a0fc31de30a0721c0094f294b1e8fe1fb567447b7bf153120981cd2" %} +{% set version = "1.7.1" %} +{% set sha256 = "978db2ea04f4b8ba07910ad01c145bb23f57c279608b9bd7f27447403a5e25ae" %} package: name: hmftools-isofox @@ -12,6 +12,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-isofox', max_pin="x.x") }} requirements: run: @@ -19,10 +21,10 @@ requirements: test: commands: - - 'isofox 2>&1 | grep -q "Isofox version"' + - 'isofox -version | grep Isofox' about: home: https://github.com/hartwigmedical/hmftools/tree/master/isofox license: GPL-3.0-only license_family: GPL - summary: 'Isofox is a tool for counting fragment support for identifying and counting gene and transcript features using genome aligned RNASeq data in tumor samples.' + summary: Isofox is a tool for counting fragment support for identifying and counting gene and transcript features using genome aligned RNASeq data in tumor samples. From 31cfa234209fb51647733377e7bfd624ee171a06 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:14:07 -0500 Subject: [PATCH 1898/2173] Update clipkit to 2.1.3 (#45669) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index 5f005ed5c3b4f..f2d9cc734178e 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.1.2" %} +{% set version = "2.1.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 37d1c5a877174048dc78e6a658dc2879e3385d054dbbc6fba0f336e457146a16 + sha256: e56e6c2c3a0c938f5026151ea191ff8fc2df7822d4aaf6487a65e9357c292487 build: number: 0 From cbac384f72fb6e00284c82ec132fae0230c142a9 Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren <78838419+alejandrogzi@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:16:05 -0500 Subject: [PATCH 1899/2173] Add gxf2bed (#45665) * new: gtfsort recipe * new: bed2gtf recipe * new: bed2gff recipe * fix: clean recipe * feat: add build.sh * fix: clean recipe; add build.sh * fix: delete other recipes already in PRs * gxt2bed! * fix: typo * gxf2bed recipe! * fix: sha256 * fix: delete other recipes already in PRs --- recipes/gxf2bed/build.sh | 9 +++++++++ recipes/gxf2bed/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 recipes/gxf2bed/build.sh create mode 100644 recipes/gxf2bed/meta.yaml diff --git a/recipes/gxf2bed/build.sh b/recipes/gxf2bed/build.sh new file mode 100644 index 0000000000000..8e10cdc3e3237 --- /dev/null +++ b/recipes/gxf2bed/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 +cargo install --verbose --path . --root ${PREFIX} diff --git a/recipes/gxf2bed/meta.yaml b/recipes/gxf2bed/meta.yaml new file mode 100644 index 0000000000000..0104d86e074a6 --- /dev/null +++ b/recipes/gxf2bed/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "gxf2bed" %} +{% set version = "0.1.0" %} + +package: + name: gxf2bed + version: {{ version }} + +source: + url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 75aa006736b7e03a16bf7cb1dd1e2a7fef87a5cc9d114b2ea603df79042cd2a9 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('gxf2bed', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("cxx") }} + - rust >=1.39 + - pkg-config + +test: + commands: + - gxf2bed --help + - gxf2bed --version + +about: + home: https://github.com/alejandrogzi/gxf2bed + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Fastest GTF/GFF-to-BED converter chilling around" + +extra: + recipe-maintainers: + - alejandrogzi From ac1b560d615adf96bc03ce8086b6e5c5aa91f1ff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:25:43 -0500 Subject: [PATCH 1900/2173] Update nextstrain-cli to 8.2.0 (#45671) --- recipes/nextstrain-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nextstrain-cli/meta.yaml b/recipes/nextstrain-cli/meta.yaml index e0bbbca25862b..1cef58d2d3db1 100644 --- a/recipes/nextstrain-cli/meta.yaml +++ b/recipes/nextstrain-cli/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.0.1" %} +{% set version = "8.2.0" %} package: name: nextstrain-cli @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain-cli-{{ version }}.tar.gz - sha256: b552463d4c4195c9b2e57cf20bfc72e9e6927231715d88ebaec13481328fb080 + sha256: 9b48dd8f32416d43b5f7db8a4a5ca045913a41a4967a5ae189240cbd67c285a2 build: number: 0 From b56e1db8d32d996ffa2b43d1df2c94dc2c6e9dd2 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 13:26:30 +1100 Subject: [PATCH 1901/2173] Apply patches to GRIDSS 2.13.2 (#45641) * Add patches * Bump build number * Add run exports --- recipes/gridss/0001-fix-samtools-version-check.patch | 11 +++++++++++ ...-set-gridssargs-for-virusbreakend-annotation.patch | 10 ++++++++++ recipes/gridss/meta.yaml | 7 ++++++- 3 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 recipes/gridss/0001-fix-samtools-version-check.patch create mode 100644 recipes/gridss/0002-set-gridssargs-for-virusbreakend-annotation.patch diff --git a/recipes/gridss/0001-fix-samtools-version-check.patch b/recipes/gridss/0001-fix-samtools-version-check.patch new file mode 100644 index 0000000000000..7111cf0e23670 --- /dev/null +++ b/recipes/gridss/0001-fix-samtools-version-check.patch @@ -0,0 +1,11 @@ +--- a/gridss_extract_overlapping_fragments ++++ b/gridss_extract_overlapping_fragments +@@ -206,7 +206,7 @@ for tool in gridsstools samtools ; do + fi + write_status "Found $(which $tool)" + done +-samtools_version=$(samtools --version | grep samtools | cut -b 10-) ++samtools_version=$(samtools --version | head -n1 | grep samtools | cut -b 10-) + write_status "samtools version: $samtools_version" + samtools_major_version=$(echo $samtools_version | cut -f 1 -d ".") + samtools_minor_version=$(echo $samtools_version | cut -f 2 -d ".") diff --git a/recipes/gridss/0002-set-gridssargs-for-virusbreakend-annotation.patch b/recipes/gridss/0002-set-gridssargs-for-virusbreakend-annotation.patch new file mode 100644 index 0000000000000..0cab94a467907 --- /dev/null +++ b/recipes/gridss/0002-set-gridssargs-for-virusbreakend-annotation.patch @@ -0,0 +1,10 @@ +--- a/virusbreakend ++++ b/virusbreakend +@@ -777,6 +777,7 @@ if [[ ! -f $file_host_annotated_vcf ]] ; then + -t $threads \ + -r $reference \ + -j $gridss_jar \ ++ $gridssargs \ + -s setupreference \ + 1>&2 2>> $logfile + $timecmd java -Xmx4g $jvm_args \ diff --git a/recipes/gridss/meta.yaml b/recipes/gridss/meta.yaml index 68671af6301ce..478a47b6b0629 100644 --- a/recipes/gridss/meta.yaml +++ b/recipes/gridss/meta.yaml @@ -8,9 +8,14 @@ package: source: url: https://github.com/PapenfussLab/gridss/releases/download/v{{ version }}/gridss-{{ version }}.tar.gz sha256: '{{ sha256 }}' + patches: + - 0001-fix-samtools-version-check.patch + - 0002-set-gridssargs-for-virusbreakend-annotation.patch build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage('gridss', max_pin="x.x.x") }} skip: True # [osx] requirements: From 19cd2610c88b1001a4572e60a69743652164dc09 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:28:38 -0500 Subject: [PATCH 1902/2173] Update phykit to 1.13.0 (#45672) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index 65ffccc3794fc..fdbe8d3ddefe3 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.12.5" %} +{% set version = "1.13.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1a1b33a683663a6fb8be56e00a41803b7e7d09183fc46d7c3a0e193a79e7584b + sha256: 22d074a5862dc6ee8402eaae9202d49d7c38e1ca15f4b55188ad14a99c292aaa build: noarch: python From 1c26b969c27a144f9685dc7700c52474ac970812 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:35:17 -0500 Subject: [PATCH 1903/2173] Update hmftools-sigs to 1.2.1 (#45609) * Update hmftools-sigs to 1.2 * Update meta.yaml * Adjust for consistency with other hmftools recipes * Update hmftools-sigs to 1.2.1 --------- Co-authored-by: Christian Brueffer Co-authored-by: Stephen Watts --- recipes/hmftools-sigs/meta.yaml | 12 +++++++----- recipes/hmftools-sigs/sigs.sh | 2 +- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/hmftools-sigs/meta.yaml b/recipes/hmftools-sigs/meta.yaml index 2a510330aeb72..386cadd737c51 100644 --- a/recipes/hmftools-sigs/meta.yaml +++ b/recipes/hmftools-sigs/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "1.1" %} -{% set sha256 = "ef38b1d36e6c326ff06e71f0d690b7503fe38efc91b1e4c4b170277f83093276" %} +{% set version = "1.2.1" %} +{% set sha256 = "b2af1ce3ac401adb145d77b031deb0edcc1d1a5257686cb67a1fc3355a7820e5" %} package: name: hmftools-sigs version: '{{ version }}' source: - url: 'https://github.com/hartwigmedical/hmftools/releases/download/sigs-v{{ version }}/sigs_v{{ version }}.jar' + url: https://github.com/hartwigmedical/hmftools/releases/download/sigs-v{{ version }}/sigs_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('hmftools-sigs', max_pin='x') }} requirements: run: @@ -20,10 +22,10 @@ requirements: test: commands: - - 'sigs 2>&1 | grep -q "running sample signature fit"' + - 'sigs -version | grep -o Sigs' about: home: https://github.com/hartwigmedical/hmftools/blob/master/sigs/README.md - license: "GNU General Public v3 (GPLv3)" + license: GPL-3.0-only license_family: GPL3 summary: Fits sample SNV counts to trinucleotide signature definitions. diff --git a/recipes/hmftools-sigs/sigs.sh b/recipes/hmftools-sigs/sigs.sh index 85cccef267a09..14bd78f53b009 100755 --- a/recipes/hmftools-sigs/sigs.sh +++ b/recipes/hmftools-sigs/sigs.sh @@ -1,5 +1,5 @@ #!/bin/bash -# hmftools sigs executable shell script +# hmftools Sigs executable shell script # https://github.com/hartwigmedical/hmftools/tree/master/sigs set -eu -o pipefail From ad7d3846395f49b412055121ebdfcfad8f829074 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 13:39:14 +1100 Subject: [PATCH 1904/2173] Update hmftools-amber to 4.0 (#45639) * Use lowercasing for BASH script for consistency * Update hmftools-amber to 4.0 * Update source URL * Update test command * Update about section --- recipes/hmftools-amber/{AMBER.sh => amber.sh} | 0 recipes/hmftools-amber/build.sh | 6 +++--- recipes/hmftools-amber/meta.yaml | 14 +++++++------- 3 files changed, 10 insertions(+), 10 deletions(-) rename recipes/hmftools-amber/{AMBER.sh => amber.sh} (100%) diff --git a/recipes/hmftools-amber/AMBER.sh b/recipes/hmftools-amber/amber.sh similarity index 100% rename from recipes/hmftools-amber/AMBER.sh rename to recipes/hmftools-amber/amber.sh diff --git a/recipes/hmftools-amber/build.sh b/recipes/hmftools-amber/build.sh index 60125bce3446e..b6c245c28bb8e 100644 --- a/recipes/hmftools-amber/build.sh +++ b/recipes/hmftools-amber/build.sh @@ -7,6 +7,6 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" cd "${SRC_DIR}" mv amber*.jar $TGT/amber.jar -cp $RECIPE_DIR/AMBER.sh $TGT/AMBER -ln -s $TGT/AMBER $PREFIX/bin -chmod 0755 "${PREFIX}/bin/AMBER" +cp $RECIPE_DIR/amber.sh $TGT/amber +ln -s $TGT/amber $PREFIX/bin +chmod 0755 "${PREFIX}/bin/amber" diff --git a/recipes/hmftools-amber/meta.yaml b/recipes/hmftools-amber/meta.yaml index 0b7a3cc9085f9..d9db37e2a08f3 100644 --- a/recipes/hmftools-amber/meta.yaml +++ b/recipes/hmftools-amber/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "3.9.1" %} -{% set sha256 = "47d2dba76b56252bd0f3a21f535096a97e2d51bc66c087f4f975272c4aaf92ef" %} +{% set version = "4.0" %} +{% set sha256 = "9fad1e78b4f177a8d2a9b6e29a34e86b82ec1239959b1f68c8f9c279fe21dc13" %} package: name: hmftools-amber version: '{{ version }}' source: - url: https://github.com/hartwigmedical/hmftools/releases/download/amber-v{{ version }}/amber-{{ version }}.jar + url: https://github.com/hartwigmedical/hmftools/releases/download/amber-v{{ version }}/amber_v{{ version }}.jar sha256: '{{ sha256 }}' build: @@ -24,10 +24,10 @@ requirements: test: commands: - - 'AMBER 2>&1 | grep -q "tumor_bam"' + - 'amber -version | grep Amber' about: home: https://github.com/hartwigmedical/hmftools/blob/master/amber/README.md - license: MIT - license_family: MIT - summary: Generates a tumor BAF file for use in PURPLE + license: GPL-3.0-only + license_family: GPL3 + summary: Generates a tumor BAF file for use in PURPLE. From cd073e71831b06263e48278336164811cc9caf07 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Wed, 7 Feb 2024 13:39:38 +1100 Subject: [PATCH 1905/2173] Update hmftools-cobalt to 1.16 (#45640) * Use lowercasing for BASH script for consistency * Update hmftools-cobalt to 1.16 * Update source URL * Update test command * Update about section * Add run exports --- recipes/hmftools-cobalt/build.sh | 8 ++++---- .../hmftools-cobalt/{COBALT.sh => cobalt.sh} | 0 recipes/hmftools-cobalt/meta.yaml | 18 ++++++++++-------- 3 files changed, 14 insertions(+), 12 deletions(-) rename recipes/hmftools-cobalt/{COBALT.sh => cobalt.sh} (100%) diff --git a/recipes/hmftools-cobalt/build.sh b/recipes/hmftools-cobalt/build.sh index 990ea8634c707..092a2525d3136 100644 --- a/recipes/hmftools-cobalt/build.sh +++ b/recipes/hmftools-cobalt/build.sh @@ -5,8 +5,8 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" [ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" cd "${SRC_DIR}" -mv *.jar $TGT/cobalt.jar +mv cobalt*.jar $TGT/cobalt.jar -cp $RECIPE_DIR/COBALT.sh $TGT/COBALT -ln -s $TGT/COBALT $PREFIX/bin -chmod 0755 "${PREFIX}/bin/COBALT" +cp $RECIPE_DIR/cobalt.sh $TGT/cobalt +ln -s $TGT/cobalt $PREFIX/bin +chmod 0755 "${PREFIX}/bin/cobalt" diff --git a/recipes/hmftools-cobalt/COBALT.sh b/recipes/hmftools-cobalt/cobalt.sh similarity index 100% rename from recipes/hmftools-cobalt/COBALT.sh rename to recipes/hmftools-cobalt/cobalt.sh diff --git a/recipes/hmftools-cobalt/meta.yaml b/recipes/hmftools-cobalt/meta.yaml index 9a4418e1c2878..1819596469f37 100644 --- a/recipes/hmftools-cobalt/meta.yaml +++ b/recipes/hmftools-cobalt/meta.yaml @@ -1,17 +1,19 @@ -{% set version = "1.13" %} -{% set sha256 = "d70a6bc73da518d159525caa5186551a771c88441efe1103a3425befd2445215" %} +{% set version = "1.16" %} +{% set sha256 = "9fe1d0f3a1f4270d354b6d3e4a6fa7a556dfbcb2e06775cd6328e1f5dba7a77c" %} package: name: hmftools-cobalt version: '{{ version }}' source: - url: https://github.com/hartwigmedical/hmftools/releases/download/cobalt-v{{ version }}/cobalt-{{ version }}.jar + url: https://github.com/hartwigmedical/hmftools/releases/download/cobalt-v{{ version }}/cobalt_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage("hmftools-cobalt", max_pin="x.x") }} requirements: run: @@ -21,10 +23,10 @@ requirements: test: commands: - - 'COBALT 2>&1 | grep -q "tumor_bam"' + - 'cobalt -version | grep Cobalt' about: home: https://github.com/hartwigmedical/hmftools/blob/master/cobalt/README.md - license: MIT - license_family: MIT - summary: Counts read starts within each 1000 base window to use in PURPLE + license: GPL-3.0-only + license_family: GPL3 + summary: Calculate read-depth counts and GC ratios to use in PURPLE. From 55e3047de465d6fdd2ad6aee2c9d68b5f36c714a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 21:40:00 -0500 Subject: [PATCH 1906/2173] Update chromap to 0.2.6 (#45657) * Update chromap to 0.2.6 * add run_exports --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/chromap/meta.yaml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/recipes/chromap/meta.yaml b/recipes/chromap/meta.yaml index 1805040802a97..05010a6f787c2 100644 --- a/recipes/chromap/meta.yaml +++ b/recipes/chromap/meta.yaml @@ -1,15 +1,17 @@ -{% set version = "0.2.5" %} +{% set version = "0.2.6" %} package: name: chromap version: {{ version }} build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('chromap', max_pin="x.x") }} source: url: https://github.com/haowenz/chromap/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9cc77d7412304d41a0a419ba1da11e6794c1dab73cee2e2d71957376b1ddbc7a + sha256: bea2fc76bd7d8931f69db0b63aef19e50070b24c0ab1415569b59d490fff42e8 requirements: build: @@ -28,6 +30,8 @@ test: about: home: https://github.com/haowenz/chromap - license: GPL-3.0 + license: MIT + license_family: MIT license_file: LICENSE summary: Fast alignment and preprocessing of chromatin profiles + doc_url: https://zhanghaowen.com/chromap/ From 6ad62555b17da53addbb9ea18c5e87911a53caa6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 23:37:21 -0500 Subject: [PATCH 1907/2173] Update planemo to 0.75.20 (#45491) * Update planemo to 0.75.20 * bump galaxy-tool version --------- Co-authored-by: mencian --- recipes/planemo/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 344b78da1932e..2fa68f4e4e03e 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "planemo" %} -{% set version = "0.75.19" %} -{% set sha256 = "4e935cc359071c0aea4a65c965eb96cb5330a33e3dcf66e1a7ad937d72a36083" %} +{% set version = "0.75.20" %} +{% set sha256 = "de61edcb2496c9301b751ac12d0c83441dfcb36cff3a279db3e7942e3fc4b873" %} package: name: {{ name|lower }} @@ -15,7 +15,7 @@ build: noarch: python run_exports: - {{ pin_subpackage('planemo', max_pin='x.x') }} - script: {{ PYTHON }} -m pip install . --no-deps -vvv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - planemo = planemo.cli:planemo @@ -33,8 +33,8 @@ requirements: - docutils - ephemeris >=0.10.3 - galaxy-containers - - galaxy-tool-util >=23.0,<23.1 - - galaxy-util >=23.0,<23.1 + - galaxy-tool-util >=23.1,<24.0 + - galaxy-util >=23.1,<24.0 - glob2 - gxformat2 >=0.14.0 - h5py From 94d1a5e66546e000140f7963778dad4ee3cd20b2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 6 Feb 2024 23:37:37 -0500 Subject: [PATCH 1908/2173] Update r-chord to 2.03 (#45673) --- recipes/r-chord/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-chord/meta.yaml b/recipes/r-chord/meta.yaml index 1053fe03cb7e8..112ef12290bf6 100644 --- a/recipes/r-chord/meta.yaml +++ b/recipes/r-chord/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.02" %} -{% set sha256 = "9db52b2d01ddea7d8b97c530683296988e98003a5ee859ae03503666a9013f9f" %} +{% set version = "2.03" %} +{% set sha256 = "def578e8e3764231d0711d0fb2542862c064fe9e355fbc6c5b61da153f50e7bc" %} package: name: r-chord From 6f49065987cde56e12be605bb27f9d68a09c9647 Mon Sep 17 00:00:00 2001 From: Travis Wrightsman Date: Tue, 6 Feb 2024 23:39:08 -0500 Subject: [PATCH 1909/2173] Update sonlib (#45415) * Fix segfault in sonLib phylogeny tests * Update sonLib to ~2.0 * Remove commit from version string --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/quicktree/meta.yaml | 4 +- ...001-Add-rule-to-build-shared-library.patch | 4 +- ...x-segfault-in-sonLib-phylogeny-tests.patch | 34 +++ recipes/sonlib/build.sh | 11 + recipes/sonlib/meta.yaml | 55 +++- ...-Add-devendored-shared-library-build.patch | 247 ++++++++++++++++++ ...-Remove-need-for-CuTest-during-build.patch | 24 ++ recipes/sonlib/run_test.sh | 7 + 8 files changed, 372 insertions(+), 14 deletions(-) create mode 100644 recipes/quicktree/patches/0002-Fix-segfault-in-sonLib-phylogeny-tests.patch create mode 100644 recipes/sonlib/patches/0001-Add-devendored-shared-library-build.patch create mode 100644 recipes/sonlib/patches/0002-Remove-need-for-CuTest-during-build.patch create mode 100644 recipes/sonlib/run_test.sh diff --git a/recipes/quicktree/meta.yaml b/recipes/quicktree/meta.yaml index 5c6cb7814f9f8..8e9fe92a91c7a 100644 --- a/recipes/quicktree/meta.yaml +++ b/recipes/quicktree/meta.yaml @@ -10,13 +10,13 @@ source: sha256: 731aa845ce3f1f0645bd0df2b54df75f78fce065d6a3ddc47fedf4bdcb11c248 patches: - patches/0001-Add-rule-to-build-shared-library.patch + - patches/0002-Fix-segfault-in-sonLib-phylogeny-tests.patch build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage(name, max_pin="x") }} - requirements: build: - make diff --git a/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch b/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch index 509748c0811eb..37c17acd29c9b 100644 --- a/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch +++ b/recipes/quicktree/patches/0001-Add-rule-to-build-shared-library.patch @@ -1,6 +1,6 @@ -From 390c2db84a0fd0ff3a05d77407d18da3b9c26d63 Mon Sep 17 00:00:00 2001 +From 6c92fb5efd973d1fa6a7ae05515ba54302be95c5 Mon Sep 17 00:00:00 2001 From: Travis Wrightsman -Date: Sat, 20 Jan 2024 17:46:20 -0500 +Date: Tue, 23 Jan 2024 23:01:04 -0500 Subject: [PATCH] Add rule to build shared library --- diff --git a/recipes/quicktree/patches/0002-Fix-segfault-in-sonLib-phylogeny-tests.patch b/recipes/quicktree/patches/0002-Fix-segfault-in-sonLib-phylogeny-tests.patch new file mode 100644 index 0000000000000..0e3f87c7aac7e --- /dev/null +++ b/recipes/quicktree/patches/0002-Fix-segfault-in-sonLib-phylogeny-tests.patch @@ -0,0 +1,34 @@ +From c4470daeed25f720de4376a5f43820ba32c2cf61 Mon Sep 17 00:00:00 2001 +From: Travis Wrightsman +Date: Tue, 23 Jan 2024 23:02:51 -0500 +Subject: [PATCH] Fix segfault in sonLib phylogeny tests + +--- + src/tree.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/tree.c b/src/tree.c +index 5b5187f..3bd8626 100644 +--- a/src/tree.c ++++ b/src/tree.c +@@ -60,7 +60,7 @@ struct Tnode *clone_Tnode( struct Tnode *source) { + struct Tnode *dest = NULL; + + if (source != NULL) { +- dest = (struct Tnode *) malloc_util( sizeof( struct Tnode ) ); ++ dest = (struct Tnode *) calloc_util(1, sizeof( struct Tnode ) ); + + dest->distance = source->distance; + dest->nodenumber = source->nodenumber; +@@ -334,7 +334,7 @@ struct Tree *get_root_Tnode( struct Tree *source ) { + struct Tnode *new_interior_Tnode( unsigned int label ) { + struct Tnode *newNode; + +- newNode = (struct Tnode *) malloc_util(sizeof(struct Tnode)); ++ newNode = (struct Tnode *) calloc_util(1, sizeof(struct Tnode)); + newNode->left = NULL; + newNode->right = NULL; + newNode->parent = NULL; +-- +2.39.2 + diff --git a/recipes/sonlib/build.sh b/recipes/sonlib/build.sh index 3786386a73c83..79758c33af1fb 100644 --- a/recipes/sonlib/build.sh +++ b/recipes/sonlib/build.sh @@ -1,3 +1,14 @@ #!/bin/bash +set -eux + +# prevent header contamination +rm -rf externalTools/ + +make -j $CPU_COUNT shlib +mkdir -p "$PREFIX"/{bin,lib,include/sonLib} +install sonLib_daemonize.py "${PREFIX}/bin/" +# some header files are named generic enough to warrant namespacing +cp lib/*.h "${PREFIX}/include/sonLib/" +cp lib/*.so "${PREFIX}/lib/" $PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/sonlib/meta.yaml b/recipes/sonlib/meta.yaml index 73ab7fdf6ae2d..21f47d0c439bb 100644 --- a/recipes/sonlib/meta.yaml +++ b/recipes/sonlib/meta.yaml @@ -1,27 +1,62 @@ +{% set name = "sonlib" %} +# No version is tagged upstream yet, but commit e25181b changes the setup.py version to 2.0 +# For now, set the .dev version to number of commits on master since then: +# git tag v2.0 e25181b && git describe --tags +{% set version = "2.0.dev88" %} +{% set commit = "9734083dffb180e3d76c323609c082b401336c0a" %} + package: - name: sonlib - version: "1.1.0" + name: {{ name }} + version: {{ version }} source: - url: https://pypi.python.org/packages/c5/63/5c597eb4895ad59e6b57050de0dbc579b400e9e2bfc7a698d6b19d91caaf/sonLib-1.1.0.tar.gz - md5: b6051a1c664ad51f8620d80a3652aa05 + url: https://github.com/ComparativeGenomicsToolkit/sonLib/archive/{{ commit }}.tar.gz + sha256: 6669056081bc96205de14b3c59c70c379dd57ab031d630480e8110e3d448628b + patches: + - patches/0001-Add-devendored-shared-library-build.patch + - patches/0002-Remove-need-for-CuTest-during-build.patch build: - noarch: python - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: + build: + - {{ compiler('c') }} + - make + - pkg-config host: - - python <3 - - pip + - python + - zlib + - quicktree run: - - python <3 + - python + - networkx test: imports: - sonLib + - sonLib.bioio + - sonLib.misc + - sonLib.nxnewick + - sonLib.nxtree + - sonLib.tree + requires: + - {{ compiler('c') }} + - make + - zlib + - cutest + source_files: + - Makefile + - include.mk + - allTests.py + - bioioTest.py + - cigarsTest.py + - C/Makefile + - C/tests/* about: - home: https://github.com/benedictpaten/sonLib + home: https://github.com/ComparativeGenomicsToolkit/sonLib license: MIT summary: 'Small general purpose library for C and Python with focus on bioinformatics.' diff --git a/recipes/sonlib/patches/0001-Add-devendored-shared-library-build.patch b/recipes/sonlib/patches/0001-Add-devendored-shared-library-build.patch new file mode 100644 index 0000000000000..3de5a2a9f3c45 --- /dev/null +++ b/recipes/sonlib/patches/0001-Add-devendored-shared-library-build.patch @@ -0,0 +1,247 @@ +From 1e06372425d4492bc943b34ade7a9ef443cb1bec Mon Sep 17 00:00:00 2001 +From: Travis Wrightsman +Date: Tue, 23 Jan 2024 21:04:37 -0500 +Subject: [PATCH] Add devendored shared library build + +--- + C/Makefile | 14 ++++++++++++++ + C/impl/stPhylogeny.c | 6 +++--- + C/tests/cigarsTest.c | 10 +++++----- + C/tests/fastaCTest.c | 6 +++--- + C/tests/kvDatabaseTestCommon.c | 2 +- + C/tests/sonLibCommonTest.c | 2 +- + C/tests/sonLibExceptTest.c | 6 +++--- + C/tests/sonLibGlobalsTest.h | 2 +- + C/tests/stPhylogenyTest.c | 4 ++-- + C/tests/stThreadPoolTest.c | 2 +- + C/tests/stUnionFindTest.c | 2 +- + Makefile | 6 ++++++ + setup.py | 2 +- + 13 files changed, 42 insertions(+), 22 deletions(-) + +diff --git a/C/Makefile b/C/Makefile +index fcb627a..92856ac 100644 +--- a/C/Makefile ++++ b/C/Makefile +@@ -1,4 +1,6 @@ + rootPath = .. ++BINDIR = ../bin ++LIBDIR = ../lib + + include ../include.mk + +@@ -23,6 +25,13 @@ LDLIBS = ${LIBDIR}/sonLib.a ${dblibs} ${LIBS} + + all : ${LIBDIR}/sonLib.a ${testProgs} ${libHeadersDep} + ++shlib : ${LIBDIR}/libsonLib.so ++ ++tests-shlib: ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -o ${rootPath}/sonLibTests tests/allTests.c ${libTests} -lsonLib -lcutest -lz -lm -lpthread ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -o ${rootPath}/sonLib_cigarTest tests/cigarsTest.c -l sonLib -lz -lpthread ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -o ${rootPath}/sonLib_fastaCTest tests/fastaCTest.c -l sonLib -lz -lpthread ++ + # note: old Makefile put .o files in this directory, clean if for now (FIXME: remove soon) + clean : + rm -rf ${BINDIR} ${LIBDIR} ${libObjs} *.o +@@ -62,5 +71,10 @@ ${LIBDIR}/sonLib.a : ${libObjs} + ${RANLIB} sonLib.a + mv sonLib.a ${LIBDIR}/ + ++${LIBDIR}/libsonLib.so : ${libObjs} ++ @mkdir -p $(dir $@) ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -shared -fPIC ${libObjs} -lquicktree -lz -o libsonLib.so ++ mv libsonLib.so ${LIBDIR}/ ++ + test: + ${PYTHON} allTests.py --testLength=SHORT --logLevel CRITICAL +diff --git a/C/impl/stPhylogeny.c b/C/impl/stPhylogeny.c +index fd0fcf4..33b594d 100644 +--- a/C/impl/stPhylogeny.c ++++ b/C/impl/stPhylogeny.c +@@ -2,9 +2,9 @@ + #include "sonLib.h" + #include "stPhylogeny.h" + // QuickTree includes +-#include "cluster.h" +-#include "tree.h" +-#include "buildtree.h" ++#include "quicktree/cluster.h" ++#include "quicktree/tree.h" ++#include "quicktree/buildtree.h" + // Spimap C/C++ translation layer include + #include "stSpimapLayer.h" + +diff --git a/C/tests/cigarsTest.c b/C/tests/cigarsTest.c +index 5189f69..a4547ba 100644 +--- a/C/tests/cigarsTest.c ++++ b/C/tests/cigarsTest.c +@@ -9,11 +9,11 @@ + #include + #include + +-#include "fastCMaths.h" +-#include "avl.h" +-#include "commonC.h" +-#include "bioioC.h" +-#include "pairwiseAlignment.h" ++#include "sonLib/fastCMaths.h" ++#include "sonLib/avl.h" ++#include "sonLib/commonC.h" ++#include "sonLib/bioioC.h" ++#include "sonLib/pairwiseAlignment.h" + + int main(int argc, char *argv[]) { + int64_t i; +diff --git a/C/tests/fastaCTest.c b/C/tests/fastaCTest.c +index 9cc81db..4d41ca4 100644 +--- a/C/tests/fastaCTest.c ++++ b/C/tests/fastaCTest.c +@@ -9,9 +9,9 @@ + #include + #include + +-#include "fastCMaths.h" +-#include "commonC.h" +-#include "bioioC.h" ++#include "sonLib/fastCMaths.h" ++#include "sonLib/commonC.h" ++#include "sonLib/bioioC.h" + + int main(int argc, char *argv[]) { + FILE *fileHandle; +diff --git a/C/tests/kvDatabaseTestCommon.c b/C/tests/kvDatabaseTestCommon.c +index eccf3c3..b5a9b21 100644 +--- a/C/tests/kvDatabaseTestCommon.c ++++ b/C/tests/kvDatabaseTestCommon.c +@@ -9,7 +9,7 @@ + */ + #include "sonLibGlobalsTest.h" + #include "kvDatabaseTestCommon.h" +-#include "stSafeC.h" ++#include "sonLib/stSafeC.h" + #include + + /* usage message and exit */ +diff --git a/C/tests/sonLibCommonTest.c b/C/tests/sonLibCommonTest.c +index 1c208fc..6924ffa 100644 +--- a/C/tests/sonLibCommonTest.c ++++ b/C/tests/sonLibCommonTest.c +@@ -11,7 +11,7 @@ + * Author: benedictpaten + */ + #include "sonLibGlobalsTest.h" +-#include "bioioC.h" ++#include "sonLib/bioioC.h" + + static void test_st_logging(CuTest *testCase) { + /* +diff --git a/C/tests/sonLibExceptTest.c b/C/tests/sonLibExceptTest.c +index db00120..4d3f1cf 100644 +--- a/C/tests/sonLibExceptTest.c ++++ b/C/tests/sonLibExceptTest.c +@@ -7,12 +7,12 @@ + /* + * basic tests of stExcept. + */ +-#include "sonLibExcept.h" ++#include "sonLib/sonLibExcept.h" + #include "sonLibGlobalsTest.h" +-#include "sonLibCommon.h" ++#include "sonLib/sonLibCommon.h" + #include + #include +-#include "stSafeC.h" ++#include "sonLib/stSafeC.h" + + /* test throwing through two levels */ + static const char *const ERR1 = "err1"; +diff --git a/C/tests/sonLibGlobalsTest.h b/C/tests/sonLibGlobalsTest.h +index ddb1293..a704b99 100644 +--- a/C/tests/sonLibGlobalsTest.h ++++ b/C/tests/sonLibGlobalsTest.h +@@ -28,6 +28,6 @@ + #include + + #include "CuTest.h" +-#include "sonLib.h" ++#include "sonLib/sonLib.h" + + #endif // SONLIB_GLOBALS_TEST_H_ +diff --git a/C/tests/stPhylogenyTest.c b/C/tests/stPhylogenyTest.c +index ea4c84b..93c3f1d 100644 +--- a/C/tests/stPhylogenyTest.c ++++ b/C/tests/stPhylogenyTest.c +@@ -1,8 +1,8 @@ + #include + #include + #include "CuTest.h" +-#include "sonLib.h" +-#include "stPhylogeny.h" ++#include "sonLib/sonLib.h" ++#include "sonLib/stPhylogeny.h" + + static stIndexedTreeInfo *getIndex(stTree *node) { + assert(node != NULL); +diff --git a/C/tests/stThreadPoolTest.c b/C/tests/stThreadPoolTest.c +index 8a456a6..a3f3128 100644 +--- a/C/tests/stThreadPoolTest.c ++++ b/C/tests/stThreadPoolTest.c +@@ -1,5 +1,5 @@ + #include "CuTest.h" +-#include "sonLib.h" ++#include "sonLib/sonLib.h" + + // Test sorting a few sublists into a larger list to try to catch out + // any race conditions. +diff --git a/C/tests/stUnionFindTest.c b/C/tests/stUnionFindTest.c +index c39826d..b7caf53 100644 +--- a/C/tests/stUnionFindTest.c ++++ b/C/tests/stUnionFindTest.c +@@ -1,5 +1,5 @@ + #include "CuTest.h" +-#include "sonLib.h" ++#include "sonLib/sonLib.h" + + // Simple static test. + static void stUnionFind_staticTest(CuTest *testCase) { +diff --git a/Makefile b/Makefile +index b244b55..e04e298 100644 +--- a/Makefile ++++ b/Makefile +@@ -5,6 +5,9 @@ BINDIR = ./bin + + all : cP ${BINDIR}/sonLib_daemonize.py + ++shlib: ++ cd C && ${MAKE} shlib ++ + clean : cP.clean externalToolsP.clean + rm -f ${BINDIR}/sonLib_daemonize.py + +@@ -23,6 +26,9 @@ externalToolsP.clean : + test : all + PYTHONPATH=src:. PATH=$$(pwd)/bin:$$PATH ${PYTHON} allTests.py --testLength=SHORT --logLevel=WARN + ++tests-shlib: ++ cd C && ${MAKE} tests-shlib ++ + ${BINDIR}/sonLib_daemonize.py : sonLib_daemonize.py cP + cp sonLib_daemonize.py ${BINDIR}/sonLib_daemonize.py + chmod +x ${BINDIR}/sonLib_daemonize.py +diff --git a/setup.py b/setup.py +index 9d96fd0..7db446e 100755 +--- a/setup.py ++++ b/setup.py +@@ -12,7 +12,7 @@ class BuildWithMake(distutils.command.build_py.build_py): + """ + def run(self): + # Call make. +- subprocess.check_call(["make"]) ++ #subprocess.check_call(["make"]) + + # Keep building the Python stuff + distutils.command.build_py.build_py.run(self) +-- +2.39.2 + diff --git a/recipes/sonlib/patches/0002-Remove-need-for-CuTest-during-build.patch b/recipes/sonlib/patches/0002-Remove-need-for-CuTest-during-build.patch new file mode 100644 index 0000000000000..bdb17a155cc5d --- /dev/null +++ b/recipes/sonlib/patches/0002-Remove-need-for-CuTest-during-build.patch @@ -0,0 +1,24 @@ +From 9852a11e4c38f92725f72eefc041cfe5fadc2ea6 Mon Sep 17 00:00:00 2001 +From: Travis Wrightsman +Date: Tue, 23 Jan 2024 22:18:44 -0500 +Subject: [PATCH] Remove need for CuTest during build + +--- + C/impl/sonLibGlobalsInternal.h | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/C/impl/sonLibGlobalsInternal.h b/C/impl/sonLibGlobalsInternal.h +index f8542a0..9a2e51d 100644 +--- a/C/impl/sonLibGlobalsInternal.h ++++ b/C/impl/sonLibGlobalsInternal.h +@@ -29,7 +29,6 @@ + #include + #include + +-#include "CuTest.h" + #include "sonLib.h" + #include "sonLibListPrivate.h" + +-- +2.39.2 + diff --git a/recipes/sonlib/run_test.sh b/recipes/sonlib/run_test.sh new file mode 100644 index 0000000000000..21a8a0e080ad4 --- /dev/null +++ b/recipes/sonlib/run_test.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +set -eux + +make tests-shlib + +PATH="$PWD:$PATH" python allTests.py From de4b3f025fa89b08cbd780ffe131ab559c82c32c Mon Sep 17 00:00:00 2001 From: msantorsola Date: Wed, 7 Feb 2024 11:07:47 +0100 Subject: [PATCH 1910/2173] Add gametes new recipe (#43783) * building gametes recipe * fixing linting errors * fixed run_exports * fixing gametes yaml * fixed gametes jar path * fixing path error * fixing path * fixing path * fixing meta.yaml * fixing path * fixing path * fixing path * fixing path * fixing path * fixing path * fixing path * fixing path * fixing path error * fixing gametes build file * fixing gametes test * check paths * fixing exit grep error * set java home * fixing tests --------- Co-authored-by: Mariangela Santorsola --- recipes/gametes/LICENSE | 362 +++++++++++++++++++++++++++++++++++++ recipes/gametes/build.sh | 24 +++ recipes/gametes/gametes.py | 88 +++++++++ recipes/gametes/meta.yaml | 38 ++++ 4 files changed, 512 insertions(+) create mode 100644 recipes/gametes/LICENSE create mode 100644 recipes/gametes/build.sh create mode 100644 recipes/gametes/gametes.py create mode 100644 recipes/gametes/meta.yaml diff --git a/recipes/gametes/LICENSE b/recipes/gametes/LICENSE new file mode 100644 index 0000000000000..8a8f06b2d908f --- /dev/null +++ b/recipes/gametes/LICENSE @@ -0,0 +1,362 @@ +# GNU GENERAL PUBLIC LICENSE + +Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc. + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + +## Preamble + +The licenses for most software are designed to take away your freedom +to share and change it. 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For software which is copyrighted by +the Free Software Foundation, write to the Free Software Foundation; +we sometimes make exceptions for this. Our decision will be guided by +the two goals of preserving the free status of all derivatives of our +free software and of promoting the sharing and reuse of software +generally. + +**NO WARRANTY** + +**11.** BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO +WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. +EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR +OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY +KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE +PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME +THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + +**12.** IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN +WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY +AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU +FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR +CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE +PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING +RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A +FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF +SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH +DAMAGES. + +END OF TERMS AND CONDITIONS + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these +terms. + +To do so, attach the following notices to the program. It is safest to +attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + one line to give the program's name and an idea of what it does. + Copyright (C) yyyy name of author + + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License + as published by the Free Software Foundation; either version 2 + of the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +Also add information on how to contact you by electronic and paper +mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details + type `show w'. This is free software, and you are welcome + to redistribute it under certain conditions; type `show c' + for details. + +The hypothetical commands \`show w' and \`show c' should show the +appropriate parts of the General Public License. Of course, the +commands you use may be called something other than \`show w' and +\`show c'; they could even be mouse-clicks or menu items--whatever +suits your program. + +You should also get your employer (if you work as a programmer) or +your school, if any, to sign a "copyright disclaimer" for the program, +if necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright + interest in the program `Gnomovision' + (which makes passes at compilers) written + by James Hacker. + + signature of Ty Coon, 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, +you may consider it more useful to permit linking proprietary +applications with the library. If this is what you want to do, use the +[GNU Lesser General Public +License](https://www.gnu.org/licenses/lgpl.html) instead of this +License. + diff --git a/recipes/gametes/build.sh b/recipes/gametes/build.sh new file mode 100644 index 0000000000000..89d67ad13e340 --- /dev/null +++ b/recipes/gametes/build.sh @@ -0,0 +1,24 @@ +#create target directory +PACKAGE_HOME=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $PACKAGE_HOME + +#create bin +BINARY_HOME=$PREFIX/bin +mkdir -p $BINARY_HOME + +cd $SRC_DIR + +JAR_NAME=GAMETES_2.1.jar + +cp $JAR_NAME $PACKAGE_HOME/gametes.jar + +#mv wrapper script to package home +cp $RECIPE_DIR/gametes.py $PACKAGE_HOME + +#and symlink to $PREFIX/bin +#ln -s $PACKAGE_HOME/gametes.py ${BINARY_HOME} +ln -s $PACKAGE_HOME/gametes.py $BINARY_HOME/gametes + +#chmod +x ${BINARY_HOME} +chmod +x ${BINARY_HOME}/gametes + diff --git a/recipes/gametes/gametes.py b/recipes/gametes/gametes.py new file mode 100644 index 0000000000000..99dc779a47f50 --- /dev/null +++ b/recipes/gametes/gametes.py @@ -0,0 +1,88 @@ +#!/usr/bin/env python + +import os +import subprocess +import sys +from os import access, getenv, path, X_OK + + +# jar file +JAR_NAME = 'gametes.jar' +PKG_NAME = 'gametes' +PKG_VERSION = '2.1' +PKG_BUILDNUM = '0' + + +default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] + + + +def real_dirname(in_path): + """Return the path to the JAR file""" + #realPath = os.path.dirname(os.path.realpath(in_path)) + realPath = os.path.dirname(os.path.dirname(os.path.realpath(in_path))) + newPath = os.path.realpath(os.path.join(realPath, "..", "share", "{}-{}-{}".format(PKG_NAME, PKG_VERSION, PKG_BUILDNUM))) + return newPath + + + +def java_executable(): + """Returns the name of the Java executable.""" + java_home = getenv('JAVA_HOME') + java_bin = path.join('bin', 'java') + if java_home and access(os.path.join(java_home, java_bin), X_OK): + return os.path.join(java_home, java_bin) + else: + return "java" # Default to using 'java' command directly + + + +def jvm_opts(argv): + """Construct list of Java arguments based on our argument list. + + The argument list passed in argv must not include the script name. + The return value is a 3-tuple lists of strings of the form: + (memory_options, prop_options, passthrough_options) + """ + + + mem_opts, prop_opts, pass_args = [], [], [] + + for arg in argv: + if arg.startswith('-D') or arg.startswith('-XX'): + opts_list = prop_opts + elif arg.startswith('-Xm'): + opts_list = mem_opts + else: + opts_list = pass_args + opts_list.append(arg) + + if mem_opts == [] and getenv('_JAVA_OPTIONS') is None: + mem_opts = default_jvm_mem_opts + + return (mem_opts, prop_opts, pass_args) + +def main(): + java = java_executable() + jar_dir = real_dirname(sys.argv[0]) + (mem_opts, prop_opts, pass_args) = jvm_opts(sys.argv[1:]) + + if pass_args != [] and pass_args[0].startswith('org'): + jar_arg = '-cp' + else: + jar_arg = '-jar' + + jar_path = os.path.join(jar_dir, JAR_NAME) + + if not os.path.isfile(jar_path): + sys.stderr.write('GAMETES jar file not found\n') + sys.exit(1) + + java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args + sys.exit(subprocess.call(java_args)) + + +if __name__ == '__main__': + main() + + diff --git a/recipes/gametes/meta.yaml b/recipes/gametes/meta.yaml new file mode 100644 index 0000000000000..6f6daf12580f6 --- /dev/null +++ b/recipes/gametes/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "gametes" %} +{% set version = "2.1" %} + +package: + name: {{ name }} + version: {{ version }} + +about: + home: https://sourceforge.net/projects/gametes/ + license: GPL-2.0-only + summary: Tool for the generation of complex single SNP models + license_file: LICENSE + + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("gametes", max_pin="x") }} + +source: + url: https://sourceforge.net/projects/gametes/files/GAMETES_2.1.jar + sha256: 5e38b0993f8915e3e3e4c225ce6b684455d02c6189877d6ae219d24ad69e27d7 + +requirements: + run: + - openjdk >=17 + - python + host: + - openjdk >=17 + - python + +test: + commands: + - $(echo $(gametes -h | grep Usage)) + + + From a9ca5e6281364b70f899123c391103a4a395e17c Mon Sep 17 00:00:00 2001 From: Jeremy Volkening Date: Wed, 7 Feb 2024 04:08:07 -0600 Subject: [PATCH 1911/2173] Update perl-ms: add run_exports, bump version (#45116) * add run_exports to perl-ms; bump version * use SPDX version string --- recipes/perl-ms/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/perl-ms/meta.yaml b/recipes/perl-ms/meta.yaml index 818495bdd9743..8a00985087dc2 100644 --- a/recipes/perl-ms/meta.yaml +++ b/recipes/perl-ms/meta.yaml @@ -1,6 +1,6 @@ {% set name = "perl-ms" %} -{% set version = "0.207002" %} -{% set sha256 = "86676202c44908eee77a7697a8ec73908707f3e5b68ba74932a375196850f1ad" %} +{% set version = "0.207003" %} +{% set sha256 = "29f1eb57200286c9e95b7f7251a3a3c7db9caf63eccdc7450467d8b77362c797" %} package: name: {{ name }} @@ -15,6 +15,8 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: @@ -90,6 +92,6 @@ test: about: home: http://metacpan.org/pod/MS - license: gpl_3 + license: GPL-3.0-or-later license_file: LICENSE summary: 'Namespace for mass spectrometry-related libraries' From 752fdf1867d9b03efcafd366d7f2da14ab3d87b5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 07:04:42 -0500 Subject: [PATCH 1912/2173] Update nanomotif to 0.1.14 (#45678) --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index a9d41641151cb..6c85011e7505b 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.13" %} +{% set version = "0.1.14" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: 97a236a5f8d56f7150292c043af057e44c8625ab92cef5e1046f3ba40a84b5d7 + sha256: f8278b9102267bdb9e4f3e2aa46d6e9f4fb9a655525766b1bc31f6cf67f2e609 build: entry_points: From f6d0cf2ed4aa32bf967bc06fde8bd2c21fe407a9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 07:05:09 -0500 Subject: [PATCH 1913/2173] Update htsinfer to 0.11.0 (#45677) --- recipes/htsinfer/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/htsinfer/meta.yaml b/recipes/htsinfer/meta.yaml index 1a4e250b5331b..df57b6f70efa5 100644 --- a/recipes/htsinfer/meta.yaml +++ b/recipes/htsinfer/meta.yaml @@ -1,13 +1,13 @@ {% set name = "HTSinfer" %} -{% set version = "0.10.0" %} +{% set version = "0.11.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/zavolanlab/htsinfer/archive/refs/tags/v0.10.0.tar.gz - sha256: a851d00a47ef5a47e9c2540599ff2c16723dfac95c12ac85f7152b0ad4c295a7 + url: https://github.com/zavolanlab/htsinfer/archive/refs/tags/v0.11.0.tar.gz + sha256: f7225290e12bf129bdb654f06f1cb98da577be81d35f7d17844447fcdf058618 build: number: 0 From 2f2916b918c4adcbca6da0771095bbcf44f36691 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 07:05:17 -0500 Subject: [PATCH 1914/2173] Update ena-webin-cli to 7.0.0 (#45676) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index aa7f4b8f4abec..b76445e0d12fe 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.10.0" %} -{% set sha256 = "3fd887d5fc5a1fbb28060f55e3903051aa9b15cc85cafd5bedb6e2c2645df1c4" %} +{% set version = "7.0.0" %} +{% set sha256 = "8b372aa08fe3e039f6d47d546ca18a20cbfcb1feb64748ea5a00527d81c7a418" %} package: name: ena-webin-cli From c8e29eb6787b306f399808f54b5b559fd6abaf6a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 07:06:14 -0500 Subject: [PATCH 1915/2173] Update gimbleprep to 0.0.2b6 (#45667) * Update gimbleprep to 0.0.2b6 * Update gimbleprep to 0.0.2b6 --- recipes/gimbleprep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gimbleprep/meta.yaml b/recipes/gimbleprep/meta.yaml index dc28547728e74..1b3c4a90144e5 100644 --- a/recipes/gimbleprep/meta.yaml +++ b/recipes/gimbleprep/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gimbleprep" %} -{% set version = "0.0.2b5" %} +{% set version = "0.0.2b6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/LohseLab/gimbleprep/archive/refs/tags/v{{ version }}.tar.gz - sha256: 6b9f893ba61fbd27577f87b561b7e2dad609589edfa62e63b6d2517b468bd953 + sha256: 5988eeb374d408f17b23cd3185e25e588c099e257357806979bea8e11e3ed272 build: noarch: python From 368340331844d21d708e6326aba5b8a058d8ac9b Mon Sep 17 00:00:00 2001 From: Travis Wrightsman Date: Wed, 7 Feb 2024 07:11:28 -0500 Subject: [PATCH 1916/2173] Add peer (#45622) * Add peer * Add license for peer itself * Add make as dependency --- recipes/peer/build.sh | 10 +++++ recipes/peer/meta.yaml | 38 +++++++++++++++++++ ...0001-Comment-out-SWIG-package-search.patch | 31 +++++++++++++++ 3 files changed, 79 insertions(+) create mode 100644 recipes/peer/build.sh create mode 100644 recipes/peer/meta.yaml create mode 100644 recipes/peer/patches/0001-Comment-out-SWIG-package-search.patch diff --git a/recipes/peer/build.sh b/recipes/peer/build.sh new file mode 100644 index 0000000000000..1f1932d3cfc51 --- /dev/null +++ b/recipes/peer/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +set -eux + +mkdir build +cd build +cmake ../ -DBUILD_PYTHON_PACKAGE=OFF -DBUILD_PEERTOOL=ON +make -j $CPU_COUNT +mkdir -p "${PREFIX}/bin" +install src/peertool "${PREFIX}/bin" diff --git a/recipes/peer/meta.yaml b/recipes/peer/meta.yaml new file mode 100644 index 0000000000000..b24994dc6127a --- /dev/null +++ b/recipes/peer/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "peer" %} +{% set version = "1.3" %} +# no tags in upstream repository yet +{% set commit = "40bc4b2cd92459ce42f44dfe279717436395f3f6" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/PMBio/peer/archive/{{ commit }}.tar.gz + sha256: 80a549354569ae5ec7d4d92c78e7f8fa72da08fcd11322611f737044c34861ed + patches: + - patches/0001-Comment-out-SWIG-package-search.patch + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - cmake + - make + +test: + commands: + - peertool --help | grep -q USAGE + +about: + home: https://github.com/PMBio/peer + license: GPL-2.0-or-later + license_file: + - LICENSE + - External/yaml-cpp/license.txt + summary: 'A collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods' diff --git a/recipes/peer/patches/0001-Comment-out-SWIG-package-search.patch b/recipes/peer/patches/0001-Comment-out-SWIG-package-search.patch new file mode 100644 index 0000000000000..6628b8077e44a --- /dev/null +++ b/recipes/peer/patches/0001-Comment-out-SWIG-package-search.patch @@ -0,0 +1,31 @@ +From a66ffa0d4b5e0aca5a1de1ffad387eadef49447f Mon Sep 17 00:00:00 2001 +From: Travis Wrightsman +Date: Mon, 5 Feb 2024 12:21:17 -0500 +Subject: [PATCH] Comment out SWIG package search + +--- + CMakeLists.txt | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 80455af..0e0c66c 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -71,11 +71,11 @@ endif (BUILD_UNIVERSAL) + #for finding external libraries. + #see /usr/local/share/cmake-2.6/Modules/Find*.cmake for more examples + +-find_package(SWIG REQUIRED) +-include(${SWIG_USE_FILE}) ++#find_package(SWIG REQUIRED) ++#include(${SWIG_USE_FILE}) + + include_directories(${CMAKE_CURRENT_SOURCE_DIR}) +-set(CMAKE_SWIG_FLAGS "") ++#set(CMAKE_SWIG_FLAGS "") + + set(CMAKE_MODULE_PATH "${PEER_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH}) + include_directories(./include) +-- +2.39.2 + From 866f79b921f82d1076470720cee84ab1e5588a95 Mon Sep 17 00:00:00 2001 From: Ryan James Kennedy <67742838+ryanjameskennedy@users.noreply.github.com> Date: Wed, 7 Feb 2024 15:02:34 +0100 Subject: [PATCH 1917/2173] Add git to virulencefinder (#45682) --- recipes/virulencefinder/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/virulencefinder/meta.yaml b/recipes/virulencefinder/meta.yaml index 0393ba33a0f8d..e57a9257fee59 100644 --- a/recipes/virulencefinder/meta.yaml +++ b/recipes/virulencefinder/meta.yaml @@ -11,8 +11,10 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic + run_exports: + - {{ pin_subpackage('virulencefinder', max_pin="x") }} requirements: run: @@ -22,10 +24,12 @@ requirements: - tabulate - cgecore - blast + - git test: commands: - virulencefinder.py --help + - git --help about: home: https://bitbucket.org/genomicepidemiology/virulencefinder From bd54c9e5f4bad7e2d7dbda19926df4a8515636d3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 12:16:17 -0500 Subject: [PATCH 1918/2173] Update hmftools-sv-prep to 1.2.3 (#43434) * Update hmftools-sv-prep to 1.2 * Update hmftools-sv-prep to 1.2.1 * Update hmftools-sv-prep to 1.2.2 * add run_exports * Update hmftools-sv-prep to 1.2.3 * Use lowercasing for BASH script for consistency * Add required GRIDSS components, dependencies * Update test command * Update license family for consistency * Set correct GRIDSS package build * Remove quotes preventing BASH brace expansion --------- Co-authored-by: joshuazhuang7 Co-authored-by: Thanh Lee Co-authored-by: Stephen Watts Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/hmftools-sv-prep/build.sh | 10 +- .../gridss_shell_with_jar_entrypoint | 18 + recipes/hmftools-sv-prep/gridss_svprep.sh | 832 ++++++++++++++++++ recipes/hmftools-sv-prep/meta.yaml | 14 +- .../hmftools-sv-prep/{SvPrep.sh => svprep.sh} | 0 5 files changed, 865 insertions(+), 9 deletions(-) create mode 100644 recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint create mode 100755 recipes/hmftools-sv-prep/gridss_svprep.sh rename recipes/hmftools-sv-prep/{SvPrep.sh => svprep.sh} (100%) diff --git a/recipes/hmftools-sv-prep/build.sh b/recipes/hmftools-sv-prep/build.sh index 2089a1b4204e8..5b0bbef52c376 100644 --- a/recipes/hmftools-sv-prep/build.sh +++ b/recipes/hmftools-sv-prep/build.sh @@ -7,6 +7,10 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" cd "${SRC_DIR}" mv sv-prep*.jar $TGT/sv-prep.jar -cp $RECIPE_DIR/SvPrep.sh $TGT/SvPrep -ln -s $TGT/SvPrep $PREFIX/bin -chmod 0755 "${PREFIX}/bin/SvPrep" +cp $RECIPE_DIR/svprep.sh $TGT/svprep +cp $RECIPE_DIR/gridss_shell_with_jar_entrypoint $TGT/ +cp $RECIPE_DIR/gridss_svprep.sh $TGT/gridss_svprep + +ln -s $TGT/svprep $PREFIX/bin/ +ln -s $TGT/gridss_shell_with_jar_entrypoint $PREFIX/bin/gridss_svprep +chmod 0755 ${PREFIX}/bin/{gridss_,}svprep diff --git a/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint b/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint new file mode 100644 index 0000000000000..d9183aebce48e --- /dev/null +++ b/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint @@ -0,0 +1,18 @@ +#!/bin/bash +# Wrapper scripts that sets --jar gridss.jar command line argument +# so users don't need to know the path to the GRIDSS jar + +# Adapted from bioconda-recipes/picard/picard.sh +set -o pipefail +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +$DIR/$(basename $0) --jar "$DIR/gridss.jar" "$@" + diff --git a/recipes/hmftools-sv-prep/gridss_svprep.sh b/recipes/hmftools-sv-prep/gridss_svprep.sh new file mode 100755 index 0000000000000..9e0f9f0d519a4 --- /dev/null +++ b/recipes/hmftools-sv-prep/gridss_svprep.sh @@ -0,0 +1,832 @@ +#!/bin/bash +# GRIDSS execution script using SvPrep BAMs + +getopt --test +if [[ ${PIPESTATUS[0]} -ne 4 ]]; then + echo 'WARNING: "getopt --test"` failed in this environment.' 1>&2 + echo "WARNING: The version of getopt(1) installed on this system might not be compatible with the GRIDSS driver script." 1>&2 +fi +unset DISPLAY # Prevents errors attempting to connecting to an X server when starting the R plotting device +ulimit -n $(ulimit -Hn 2>/dev/null) 2>/dev/null # Reduce likelihood of running out of open file handles +set -o errexit -o pipefail -o noclobber -o nounset +last_command="" +current_command="" +trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG +trap 'echo "\"${last_command}\" command completed with exit code $?."' EXIT +#253 forcing C locale for everything +export LC_ALL=C + +EX_USAGE=64 +EX_NOINPUT=66 +EX_CANTCREAT=73 +EX_CONFIG=78 + +workingdir="." +reference="" +output_vcf="" +assembly="" +threads=8 +jvmheap="30g" +otherjvmheap="4g" +blacklist="" +metricsrecords=10000000 +maxcoverage=50000 +config_file="" +labels="" +bams="" +filtered_bams="" +full_bams="" +keepTempFiles="false" + +steps="all" +do_preprocess=false +do_assemble=false +do_call=false + +USAGE_MESSAGE=" +Usage: gridss [options] -r -o -a input1.bam [input2.bam [...]] + + -r/--reference: reference genome to use. + -o/--output: output VCF. + -a/--assembly: location of the GRIDSS assembly BAM. This file will be + created by GRIDSS. + -t/--threads: number of threads to use. (Default: $threads) + -j/--jar: location of GRIDSS jar + -w/--workingdir: directory to place GRIDSS intermediate and temporary files + .gridss.working subdirectories will be created. (Default: $workingdir) + -s/--steps: processing steps to run. Defaults to all steps. + Multiple steps are specified using comma separators. Possible steps are: + preprocess, assemble, call, all + -e/--blacklist: BED file containing regions to ignore + -c/--configuration: configuration file use to override default GRIDSS + settings. + -l/--labels: comma separated labels to use in the output VCF for the input + files. Supporting read counts for input files with the same label are + aggregated (useful for multiple sequencing runs of the same sample). + Labels default to input filenames, unless a single read group with a + non-empty sample name exists in which case the read group sample name + is used (which can be disabled by \"useReadGroupSampleNameCategoryLabel=false\" + in the configuration file). If labels are specified, they must be + specified for all input files. + -b/bams: comma separated full-path BAM files + -f/filtered_bams: comma separated full-path filtered BAM files + --jvmheap: size of JVM heap for the high-memory component of assembly and variant calling. (Default: $jvmheap) + --otherjvmheap: size of JVM heap for everything else. Useful to prevent + java out of memory errors when using large (>4Gb) reference genomes. + Note that some parts of assembly and variant calling use this heap + size. (Default: $otherjvmheap) + " + +OPTIONS=r:o:a:t:j:w:e:s:c:l:b:f: +LONGOPTS=reference:,output:,assembly:,threads:,jar:,workingdir:,jvmheap:,otherjvmheap:,blacklist:,steps:,configuration:,labels:,bams:,filtered_bams: +! PARSED=$(getopt --options=$OPTIONS --longoptions=$LONGOPTS --name "$0" -- "$@") +if [[ ${PIPESTATUS[0]} -ne 0 ]]; then + # e.g. return value is 1 + # then getopt has complained about wrong arguments to stdout + echo "$USAGE_MESSAGE" 1>&2 + exit $EX_USAGE +fi +eval set -- "$PARSED" + +POSITIONAL_ARGS=() + +#while true; do +while [[ $# -gt 0 ]]; do + case "$1" in + -r|--reference) + reference="$2" + shift 2 + ;; + -l|--labels) + labels="$2" + shift 2 + ;; + -b|--bams) + bams="$2" + shift 2 + ;; + -f|--filtered_bams) + filtered_bams="$2" + shift 2 + ;; + -s|--steps) + steps="$2" + shift 2 + ;; + -w|--workingdir) + workingdir="$2" + shift 2 + ;; + -o|--output) + output_vcf="$2" + shift 2 + ;; + -a|--assembly) + if [[ "$assembly" == "" ]] ; then + assembly="$2" + else + assembly="$assembly $2" + fi + # TODO: support multiple assembly files + shift 2 + ;; + -e|--blacklist) + blacklist="$2" + shift 2 + ;; + -j|--jar) + GRIDSS_JAR="$2" + shift 2 + ;; + --jvmheap) + jvmheap="$2" + shift 2 + ;; + --otherjvmheap) + otherjvmheap="$2" + shift 2 + ;; + -t|--threads) + printf -v threads '%d\n' "$2" 2>/dev/null + printf -v threads '%d' "$2" 2>/dev/null + shift 2 + ;; + -c|--configuration) + config_file=$2 + shift 2 + ;; + *) + POSITIONAL_ARGS+=("$1") # save positional arg + # echo "Unparsed param" + shift + ;; + esac +done + +##### --workingdir +echo "Using working directory \"$workingdir\"" 1>&2 +if [[ "$workingdir" == "" ]] ; then + echo "$USAGE_MESSAGE" 1>&2 + echo "Working directory must be specified. Specify using the --workingdir command line argument" 1>&2 + exit $EX_USAGE +fi +if [[ "$(tr -d ' \n' <<< "$workingdir")" != "$workingdir" ]] ; then + echo "workingdir cannot contain whitespace" 1>&2 + exit $EX_USAGE + fi +if [[ ! -d $workingdir ]] ; then + mkdir -p $workingdir + if [[ ! -d $workingdir ]] ; then + echo Unable to create working directory $workingdir 1>&2 + exit $EX_CANTCREAT + fi +fi +workingdir=$(dirname $workingdir/placeholder) +timestamp=$(date +%Y%m%d_%H%M%S) +# Logging +logfile=$workingdir/gridss.full.$timestamp.$HOSTNAME.$$.log +# $1 is message to write +write_status() { + echo "$(date): $1" | tee -a $logfile 1>&2 +} +write_status "Full log file is: $logfile" +trap 'echo "\"${last_command}\" command completed with exit code $?. +***** +The underlying error message can be found in $logfile +*****"' EXIT +# Timing instrumentation +timinglogfile=$workingdir/gridss.timing.$timestamp.$HOSTNAME.$$.log +if which /usr/bin/time >/dev/null ; then + timecmd="/usr/bin/time" + write_status "Found /usr/bin/time" +else + timecmd="" + write_status "Not found /usr/bin/time" +fi +if [[ "$timecmd" != "" ]] ; then + timecmd="/usr/bin/time --verbose -a -o $timinglogfile" + if ! $timecmd echo 2>&1 > /dev/null; then + timecmd="/usr/bin/time -a -o $timinglogfile" + fi + if ! $timecmd echo 2>&1 > /dev/null ; then + timecmd="" + write_status "Unexpected /usr/bin/time version. Not logging timing information." + fi + # We don't need timing info of the echo + rm -f $timinglogfile +fi + +### Find the jars +find_jar() { + env_name=$1 + if [[ -f "${!env_name:-}" ]] ; then + echo "${!env_name}" + else + write_status "Unable to find $2 jar. Specify using the environment variant $env_name, or the --jar command line parameter." + exit $EX_NOINPUT + fi +} +gridss_jar=$(find_jar GRIDSS_JAR gridss) +write_status "Using GRIDSS jar $gridss_jar" + +# Check all key inputs: + +if [[ "$labels" == "" ]] ; then + write_status "Labels must be specified" + exit $EX_USAGE +fi + +if [[ "$bams" == "" ]] ; then + write_status "Full BAMs must be specified" + exit $EX_USAGE +fi + +if [[ "$filtered_bams" == "" ]] ; then + write_status "Filtered BAMs must be specified" + exit $EX_USAGE +fi + +##### --reference +if [[ "$reference" == "" ]] ; then + write_status "$USAGE_MESSAGE" + write_status "Reference genome must be specified. Specify using the --reference command line argument" + exit $EX_USAGE +fi + +if [ ! -f $reference ] ; then + write_status "$USAGE_MESSAGE" + write_status "Missing reference genome $reference. Specify reference location using the --reference command line argument" + exit $EX_USAGE +fi +write_status "Using reference genome \"$reference\"" + +##### --output +if [[ $do_call == "true" ]] ; then + if [[ "$output_vcf" == "" ]] ; then + write_status "$USAGE_MESSAGE" + write_status "Output VCF not specified. Use --output to specify output file." + exit $EX_USAGE + fi + mkdir -p $(dirname $output_vcf) + if [[ ! -d $(dirname $output_vcf) ]] ; then + write_status "Unable to create directory for $output_vcf for output VCF." + exit $EX_CANTCREAT + fi + write_status "Using output VCF $output_vcf" +fi + +##### --assembly +if [[ $do_assemble == "true" ]] || [[ $do_call == "true" ]]; then + if [[ "$assembly" == "" ]] ; then + if [[ "$output_vcf" == "" ]] ; then + write_status "Either the assembly output file must explicitly specified with -a, or the output VCF specified with -o" + exit $EX_USAGE + fi + assembly=$output_vcf.assembly.bam + fi + write_status "Using assembly bam $assembly" + if [[ $do_assemble == "true" ]] ; then + mkdir -p $(dirname $assembly) + if [[ ! -d $(dirname $assembly) ]] ; then + write_status "Unable to parent create directory for $assembly" + exit $EX_CANTCREAT + fi + else + if [[ ! -f $assembly ]] ; then + write_status "Missing assembly file $assembly" + write_status "Ensure the GRIDSS assembly step has been run" + exit $EX_NOINPUT + fi + fi +fi + +##### --threads +if [[ "$threads" -lt 1 ]] ; then + write_status "$USAGE_MESSAGE" + write_status "Illegal thread count: $threads. Specify an integer thread count using the --threads command line argument" + exit $EX_USAGE +fi +if [[ "$threads" -gt 8 ]] ; then + write_status "WARNING: GRIDSS scales sub-linearly at high thread count. Up to 8 threads is the recommended level of parallelism." +fi +write_status "Using $threads worker threads." + +if [[ "$blacklist" == "" ]] ; then + blacklist_arg="" + write_status "Using no blacklist bed. The encode DAC blacklist is recommended for hg19." +elif [[ ! -f $blacklist ]] ; then + write_status "$USAGE_MESSAGE" + write_status "Missing blacklist file $blacklist" + exit $EX_NOINPUT +else + blacklist_arg="BLACKLIST=$blacklist" + write_status "Using blacklist $blacklist" + if [[ "$(tr -d ' \n' <<< "$blacklist_arg")" != "$blacklist_arg" ]] ; then + write_status "blacklist cannot contain whitespace" + exit $EX_USAGE + fi +fi + +if [[ "$jvmheap" == "" ]] ; then + if [[ $threads -gt 8 ]] ; then + write_status "Warning: GRIDSS assembly may stall and run out of memory. with $threads and $jvmheap heap size." + fi +fi + +write_status "Using JVM maximum heap size of $jvmheap for assembly and variant calling." + +config_args="" +if [[ "$config_file" != "" ]] ; then + if [[ ! -f $config_file ]] ; then + write_status "Configuration file $config_file does not exist" + exit $EX_NOINPUT + fi + config_args="CONFIGURATION_FILE=$config_file" +fi + +input_args="" +input_filtered_args="" + +# no longer read in the BAM file list from the end of the arguments list + +nows_labels=$(tr -d ' \n' <<< "$labels") +if [[ "$nows_labels" != "$labels" ]] ; then + write_status "input labels cannot contain whitespace" + exit $EX_USAGE +fi +IFS=',' read -ra LABEL_ARRAY <<< "$nows_labels" +label_count=${#LABEL_ARRAY[@]} + +for label in "${LABEL_ARRAY[@]}" ; do + input_args="$input_args INPUT_LABEL=$label" + input_filtered_args="$input_filtered_args INPUT_LABEL=$label" + #write_status "label is $label" +done + +nows_bams=$(tr -d ' \n' <<< "$bams") +if [[ "$nows_bams" != "$bams" ]] ; then + write_status "input filtered BAMs cannot contain whitespace" + exit $EX_USAGE +fi +IFS=',' read -ra BAM_ARRAY <<< "$nows_bams" +for bam_file in "${BAM_ARRAY[@]}" ; do + + if [[ "$(basename $bam_file)" == "$(basename $assembly)" ]] ; then + write_status "assembly and input filtered bam files must have different filenames" + exit $EX_USAGE + fi + + input_args="$input_args INPUT=$bam_file" + # write_status "full bam file is $bam_file" +done + +nows_bams=$(tr -d ' \n' <<< "$filtered_bams") +if [[ "$nows_bams" != "$filtered_bams" ]] ; then + write_status "input filtered BAMs cannot contain whitespace" + exit $EX_USAGE +fi +IFS=',' read -ra FILT_BAM_ARRAY <<< "$nows_bams" +for filtered_bam_file in "${FILT_BAM_ARRAY[@]}" ; do + + if [[ "$(basename $filtered_bam_file)" == "$(basename $assembly)" ]] ; then + write_status "assembly and input filtered bam files must have different filenames" + exit $EX_USAGE + fi + + input_filtered_args="$input_filtered_args INPUT=$filtered_bam_file" + # write_status "filtered bam file is $filtered_bam_file" +done + +for (( i=0; i < $label_count; ++i )) +do + write_status "Label $i: name=${LABEL_ARRAY[$i]} full-bam=${BAM_ARRAY[$i]} filtered-bam=${FILT_BAM_ARRAY[$i]}" +done + +write_status "Full BAM args: $input_args" +write_status "Filtered BAM args: $input_filtered_args" + + +# Validate tools exist on path +for tool in Rscript samtools java bwa ; do #minimap2 + if ! which $tool >/dev/null; then + write_status "Error: unable to find $tool on \$PATH" + exit $EX_CONFIG + fi + write_status "Found $(which $tool)" +done +if $(samtools --version-only >/dev/null) ; then + write_status "samtools version: $(samtools --version-only 2>&1)" +else + write_status "Your samtools version does not support --version-only. Update samtools." + exit $EX_CONFIG +fi +if [[ "$(samtools --version-only)" =~ ^([0-9]+)[.]([0-9]+) ]] ; then + samtools_major_version=${BASH_REMATCH[1]} + samtools_minor_version=${BASH_REMATCH[2]} + if [[ "$samtools_major_version" -le 1 ]] && [[ "$samtools_minor_version" -lt 10 ]] ; then + write_status "samtools 1.13 or later is required." + exit $EX_CONFIG + fi +else + write_status "Unable to determine samtools version" + exit $EX_CONFIG +fi + +# write_status "R version: $(Rscript --version 2>&1)" + +write_status "bwa $(bwa 2>&1 | grep Version || echo -n)" + +if [[ "$timecmd" != "" ]] ; then + if which /usr/bin/time >/dev/null ; then + write_status "time version: $(/usr/bin/time --version 2>&1)" + fi +fi +write_status "bash version: $(/bin/bash --version 2>&1 | head -1)" + +# check java version is ok using the gridss.Echo entry point +if java -cp $gridss_jar gridss.Echo ; then + write_status "java version: $(java -version 2>&1 | tr '\n' '\t')" +else + write_status "Unable to run GRIDSS jar - requires java 1.8 or later" + write_status "java version: $(java -version 2>&1)" + exit $EX_CONFIG +fi + +if ! java -Xms$jvmheap -cp $gridss_jar gridss.Echo ; then + write_status "Failure invoking java with --jvmheap parameter of \"$jvmheap\". Specify a JVM heap size (e.g. \"31g\") that is valid for this machine." + exit 1 +fi + +write_status "Max file handles: $(ulimit -n)" 1>&2 + +steps_message="Running GRIDSS steps:" + +for step in $(echo $steps | tr ',' ' ' ) ; do + if [[ "$step" == "all" ]] ; then + do_preprocess=true + do_assemble=true + do_call=true + steps_message="$steps_message all" + elif [[ "$step" == "preprocess" ]] ; then + do_preprocess=true + steps_message="$steps_message pre-process" + elif [[ "$step" == "assemble" ]] ; then + do_assemble=true + steps_message="$steps_message assembly" + elif [[ "$step" == "call" ]] ; then + do_call=true + steps_message="$steps_message call" + else + write_status "Unknown step \"$step\"" + exit $EX_USAGE + fi +done + +write_status "$steps_message" + +# don't keep files +if [[ $keepTempFiles == "true" ]] ; then + rmcmd="echo rm disabled:" + jvm_args="-Dgridss.keepTempFiles=true" +else + rmcmd="rm" + jvm_args="" +fi + +jvm_args="$jvm_args \ + -XX:ParallelGCThreads=$threads \ + -Dsamjdk.reference_fasta=$reference \ + -Dsamjdk.use_async_io_read_samtools=true \ + -Dsamjdk.use_async_io_write_samtools=true \ + -Dsamjdk.use_async_io_write_tribble=true \ + -Dsamjdk.buffer_size=4194304 \ + -Dsamjdk.async_io_read_threads=$threads" + +aligner_args=' + ALIGNER_COMMAND_LINE=null + ALIGNER_COMMAND_LINE=bwa + ALIGNER_COMMAND_LINE=mem + ALIGNER_COMMAND_LINE=-K + ALIGNER_COMMAND_LINE=10000000 + ALIGNER_COMMAND_LINE=-L + ALIGNER_COMMAND_LINE=0,0 + ALIGNER_COMMAND_LINE=-t + ALIGNER_COMMAND_LINE=%3$d + ALIGNER_COMMAND_LINE=%2$s + ALIGNER_COMMAND_LINE=%1$s' + +samtools_sort="samtools sort --no-PG -@ $threads" + +readpairing_args="READ_PAIR_CONCORDANT_PERCENT=null" + + +# set-up reference has been removed since can assume to exist + +#### +# Pre-process for each filtered BAM file +#### + +if [[ $do_preprocess == true ]] ; then + write_status "*** PRE-PROCESS ***" + + for (( i=0; i < $label_count; ++i )) + do + label=${LABEL_ARRAY[$i]} + bam_file=${FILT_BAM_ARRAY[$i]} + write_status "Processing: sample ${LABEL_ARRAY[$i]}, filtered-bam ${FILT_BAM_ARRAY[$i]}" + + dir=$workingdir/$(basename $bam_file).gridss.working + prefix=$dir/$(basename $bam_file) + write_status "Start pre-processing: $bam_file, working dir: $dir, prefix: $prefix" + + tmp_prefix=$workingdir/$(basename $bam_file).gridss.working/tmp.$(basename $bam_file) + mkdir -p $dir + if [[ ! -d $dir ]] ; then + write_status "Unable to create directory $dir" + exit $EX_CANTCREAT + fi + + name_sorted_bam=$tmp_prefix.namedsorted.bam + write_status "Creating name-sorted BAM from $bam_file, writing to $name_sorted_bam" + + $timecmd $samtools_sort -l 1 -n \ + -T $tmp_prefix.namedsorted-tmp \ + -Obam \ + -o ${name_sorted_bam} \ + ${bam_file} + + write_status "Running ComputeSamTags|samtools: $bam_file" + + rm -f $tmp_prefix.coordinate-tmp* + + { $timecmd java -Xmx$otherjvmheap $jvm_args \ + -cp $gridss_jar gridss.ComputeSamTags \ + TMP_DIR=$dir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + COMPRESSION_LEVEL=0 \ + I=$name_sorted_bam \ + O=/dev/stdout \ + WORKER_THREADS=$threads \ + ASSUME_SORTED=true \ + REMOVE_TAGS=aa \ + MODIFICATION_SUMMARY_FILE=$prefix.computesamtags.changes.tsv \ + | $timecmd $samtools_sort \ + -l 1 \ + -T $tmp_prefix.coordinate-tmp \ + -Obam \ + -o $tmp_prefix.coordinate.bam \ + /dev/stdin \ + ; } 1>&2 2>> $logfile + + write_status "Removing name-sorted bam: $tmp_prefix.namedsorted.bam" + $rmcmd $tmp_prefix.namedsorted.bam + + write_status "Running SoftClipsToSplitReads: sample $label, input: $tmp_prefix.coordinate.bam, output: $tmp_prefix.sc2sr.primary.sv.bam" + rm -f $tmp_prefix.sc2sr.suppsorted.sv-tmp* + { $timecmd java -Xmx$otherjvmheap $jvm_args \ + -Dsamjdk.create_index=false \ + -cp $gridss_jar gridss.SoftClipsToSplitReads \ + TMP_DIR=$workingdir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + I=$tmp_prefix.coordinate.bam \ + O=$tmp_prefix.sc2sr.primary.sv.bam \ + COMPRESSION_LEVEL=1 \ + OUTPUT_UNORDERED_RECORDS=$tmp_prefix.sc2sr.supp.sv.bam \ + WORKER_THREADS=$threads \ + $aligner_args \ + && $rmcmd $tmp_prefix.coordinate.bam \ + && $timecmd $samtools_sort \ + -l 1 \ + -T $tmp_prefix.sc2sr.suppsorted.sv-tmp \ + -Obam \ + -o $tmp_prefix.sc2sr.suppsorted.sv.bam \ + $tmp_prefix.sc2sr.supp.sv.bam \ + && $rmcmd $tmp_prefix.sc2sr.supp.sv.bam \ + && $rmcmd -f $prefix.sv.tmp.bam $prefix.sv.tmp.bam.bai \ + && $timecmd samtools merge \ + -c \ + -p \ + --write-index \ + -@ $threads \ + $prefix.sv.tmp.bam \ + $tmp_prefix.sc2sr.primary.sv.bam \ + $tmp_prefix.sc2sr.suppsorted.sv.bam \ + && $rmcmd $tmp_prefix.sc2sr.primary.sv.bam \ + && $rmcmd $tmp_prefix.sc2sr.suppsorted.sv.bam \ + && mv $prefix.sv.tmp.bam $prefix.sv.bam \ + && mv $prefix.sv.tmp.bam.csi $prefix.sv.bam.csi \ + ; } 1>&2 2>> $logfile + + write_status "Produced SV bam:: $prefix.sv.bam" + + # create metrics on the full BAM and then copy these over the metrics made from the filtered BAMs + full_bam_file=${BAM_ARRAY[$i]} + write_status "Running CollectGridssMetrics on $label full BAM $full_bam_file" + + # test_prefix=$prefix.cp + + { $timecmd java -Xmx$otherjvmheap $jvm_args \ + -cp $gridss_jar gridss.analysis.CollectGridssMetrics \ + REFERENCE_SEQUENCE=$reference \ + TMP_DIR=$dir \ + ASSUME_SORTED=true \ + I=$full_bam_file \ + O=$prefix \ + THRESHOLD_COVERAGE=$maxcoverage \ + FILE_EXTENSION=null \ + GRIDSS_PROGRAM=null \ + GRIDSS_PROGRAM=CollectCigarMetrics \ + GRIDSS_PROGRAM=CollectMapqMetrics \ + GRIDSS_PROGRAM=CollectTagMetrics \ + GRIDSS_PROGRAM=CollectIdsvMetrics \ + PROGRAM=null \ + PROGRAM=CollectInsertSizeMetrics \ + STOP_AFTER=$metricsrecords \ + ; } 1>&2 2>> $logfile + + write_status "Complete pre-processing sample: $label" + done + + write_status "*** PRE-PROCESS COMPLETE ***" +fi + +##### +# ASSEMBLY +#### + +assembly_args="ASSEMBLY=$assembly" + +if [[ $do_assemble == true ]] ; then + + write_status "*** ASSEMBLY ***" + write_status "Running AssembleBreakends: writing output to dir $assembly" + { $timecmd java -Xmx$jvmheap $jvm_args \ + -Dgridss.output_to_temp_file=true \ + -cp $gridss_jar gridss.AssembleBreakends \ + JOB_INDEX=0 \ + JOB_NODES=1 \ + TMP_DIR=$workingdir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + WORKER_THREADS=$threads \ + $input_filtered_args \ + $blacklist_arg \ + $config_args \ + $readpairing_args \ + O=$assembly \ + ; } 1>&2 2>> $logfile + + write_status "AssemblyBreakends complete" + + dir=$workingdir/$(basename $assembly).gridss.working/ + prefix=$dir/$(basename $assembly) + tmp_prefix=$dir/tmp.$(basename $assembly) + + write_status "RunningSoftClipsToSplitReads: running on assembly output dir $assembly" + rm -f $tmp_prefix.sc2sr.suppsorted.sv-tmp* + { $timecmd java -Xmx$otherjvmheap $jvm_args \ + -Dgridss.async.buffersize=16 \ + -Dsamjdk.create_index=false \ + -Dgridss.output_to_temp_file=true \ + -cp $gridss_jar gridss.SoftClipsToSplitReads \ + TMP_DIR=$dir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + WORKER_THREADS=$threads \ + I=$assembly \ + O=$tmp_prefix.sc2sr.primary.sv.bam \ + OUTPUT_UNORDERED_RECORDS=$tmp_prefix.sc2sr.supp.sv.bam \ + REALIGN_ENTIRE_READ=true \ + READJUST_PRIMARY_ALIGNMENT_POSITION=true \ + $aligner_args \ + && $timecmd $samtools_sort \ + -T $tmp_prefix.sc2sr.suppsorted.sv-tmp \ + -Obam \ + -o $tmp_prefix.sc2sr.suppsorted.sv.bam \ + $tmp_prefix.sc2sr.supp.sv.bam \ + && $rmcmd $tmp_prefix.sc2sr.supp.sv.bam \ + && $rmcmd -f $prefix.sv.tmp.bam $prefix.sv.tmp.bam.bai \ + && $timecmd samtools merge \ + -c \ + -p \ + -@ $threads \ + $prefix.sv.tmp.bam \ + $tmp_prefix.sc2sr.primary.sv.bam \ + $tmp_prefix.sc2sr.suppsorted.sv.bam \ + && $timecmd samtools index $prefix.sv.tmp.bam \ + && $rmcmd $tmp_prefix.sc2sr.primary.sv.bam \ + && $rmcmd $tmp_prefix.sc2sr.suppsorted.sv.bam \ + && mv $prefix.sv.tmp.bam $prefix.sv.bam \ + && mv $prefix.sv.tmp.bam.bai $prefix.sv.bam.bai \ + ; } 1>&2 2>> $logfile + + write_status "Produced assembly BAM: $prefix.sv.bam" + + write_status "Complete Assembly" + + # no idea why this is a for loop, could just be: ASSEMBLY=$assembly + #assembly_args="" + #for ass in $assembly ; do + # assembly_args="$assembly_args ASSEMBLY=$ass" + #done + write_status "Assembly args: $assembly_args" + + write_status "*** ASSEMBLY COMPLETE ***" +fi + +#### +# VARIANT CALLING +#### + +if [[ $do_call == true ]] ; then + write_status "*** VARIANT CALLING ***" + + write_status "Creating variant VCF: $output_vcf" + + dir=$workingdir/$(basename $output_vcf).gridss.working + prefix=$dir/$(basename $output_vcf) + mkdir -p $dir + if [[ ! -d $dir ]] ; then + write_status "Unable to create directory $dir" + exit $EX_CANTCREAT + fi + + # create symbolic links to the full BAM as though they were produced by the pre-process step + # eg: ./gridss_02/COLO829R.bam.gridss.working/COLO829R.bam.sv.bam + for (( i=0; i < $label_count; ++i )) + do + bam_file=${BAM_ARRAY[$i]} + bam_dir=$workingdir/$(basename $bam_file).gridss.working + + if [[ ! -d $bam_dir ]] ; then + mkdir -p $bam_dir + fi + + sv_bam_file=$bam_dir/$(basename $bam_file).sv.bam + # write_status "Making soft-link to ${sv_bam_file}" + #ln -sfr ${bam_file} ${sv_bam_file} + #ln -sfr ${bam_file}.bai ${sv_bam_file}.bai + done + + write_status "Running IdentifyVariants" + { $timecmd java -Xmx$jvmheap $jvm_args \ + -Dgridss.output_to_temp_file=true \ + -cp $gridss_jar gridss.IdentifyVariants \ + TMP_DIR=$workingdir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + WORKER_THREADS=$threads \ + $input_filtered_args \ + $blacklist_arg \ + $config_args \ + $assembly_args \ + OUTPUT_VCF=$prefix.unallocated.vcf \ + $readpairing_args \ + ; } 1>&2 2>> $logfile + write_status "IdentifyVariants complete, produced $prefix.unallocated.vcf" + + write_status "Running AnnotateVariants" + { $timecmd java -Xmx$jvmheap $jvm_args \ + -Dgridss.output_to_temp_file=true \ + -Dgridss.async.buffersize=2048 \ + -cp $gridss_jar gridss.AnnotateVariants \ + TMP_DIR=$workingdir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + WORKER_THREADS=$threads \ + $input_filtered_args \ + $blacklist_arg \ + $config_args \ + $assembly_args \ + INPUT_VCF=$prefix.unallocated.vcf \ + OUTPUT_VCF=$prefix.allocated.vcf \ + $readpairing_args \ + ; } 1>&2 2>> $logfile + $rmcmd $prefix.unallocated.vcf + write_status "AnnotateVariants complete, produced $prefix.allocated.vcf" + + write_status "Running AnnotateInsertedSequence" + + { $timecmd java -Xmx$otherjvmheap $jvm_args \ + -Dgridss.output_to_temp_file=true \ + -cp $gridss_jar gridss.AnnotateInsertedSequence \ + TMP_DIR=$workingdir \ + WORKING_DIR=$workingdir \ + REFERENCE_SEQUENCE=$reference \ + WORKER_THREADS=$threads \ + INPUT=$prefix.allocated.vcf \ + OUTPUT=$output_vcf \ + && $rmcmd $prefix.allocated.vcf \ + ; } 1>&2 2>> $logfile + write_status "AnnotateInsertedSequence complete, produced $output_vcf" + + write_status "*** VARIANT CALLING COMPLETE ***" +fi + +if [[ -f $logfile ]] ; then + write_status "Run complete with $(grep WARNING $logfile | wc -l) warnings and $(grep ERROR $logfile | wc -l) errors." +fi +trap - EXIT +exit 0 # success! diff --git a/recipes/hmftools-sv-prep/meta.yaml b/recipes/hmftools-sv-prep/meta.yaml index c81ed9c3f6a43..2af81c748ca39 100644 --- a/recipes/hmftools-sv-prep/meta.yaml +++ b/recipes/hmftools-sv-prep/meta.yaml @@ -1,27 +1,29 @@ -{% set version = "1.1" %} -{% set sha256 = "e7487a16c609ad4d9f3b2d29ebada02b04fbd3bef3dacd26f228bb1928d5606e" %} +{% set version = "1.2.3" %} +{% set sha256 = "8f42be297e1ece6d070324f8b12b0a30106291731ac89f5d3c0fc2d82fd887ab" %} package: name: hmftools-sv-prep version: '{{ version }}' source: - url: 'https://github.com/hartwigmedical/hmftools/releases/download/sv-prep-v{{ version }}/sv-prep_v{{ version }}.jar' + url: https://github.com/hartwigmedical/hmftools/releases/download/sv-prep-v{{ version }}/sv-prep_v{{ version }}.jar sha256: '{{ sha256 }}' build: noarch: generic - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage('hmftools-sv-prep', max_pin="x") }} requirements: run: - zlib - openjdk >=8 - - samtools + - gridss =2.13.2=h50ea8bc_3 test: commands: - - 'SvPrep 2>&1 | grep -q "SvPrep version"' + - 'svprep -version | grep SvPrep' about: home: https://github.com/hartwigmedical/hmftools/tree/master/sv-prep diff --git a/recipes/hmftools-sv-prep/SvPrep.sh b/recipes/hmftools-sv-prep/svprep.sh similarity index 100% rename from recipes/hmftools-sv-prep/SvPrep.sh rename to recipes/hmftools-sv-prep/svprep.sh From 12a6a10e57cf73ce8ef627f2483be2ebe96ac18e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 12:22:43 -0500 Subject: [PATCH 1919/2173] Update capcruncher to 0.3.12 (#45679) --- recipes/capcruncher/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/capcruncher/meta.yaml b/recipes/capcruncher/meta.yaml index 39a98b445fdb9..f65c123600dbe 100644 --- a/recipes/capcruncher/meta.yaml +++ b/recipes/capcruncher/meta.yaml @@ -1,5 +1,5 @@ {% set name = "capcruncher" %} -{% set version = "0.3.11" %} +{% set version = "0.3.12" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/capcruncher-{{ version }}.tar.gz - sha256: 1baee46dc9eaab97125796292bc7d6a24821c69538d43f205a344f550db14a7a + sha256: 43b1e634dac4eee5f801b69b2adafb07b61c72556cc32b1cd5e03518ed2e407b build: number: 0 From 1e53680bdbf17e351f39fef567435696b74fd534 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 12:23:28 -0500 Subject: [PATCH 1920/2173] Update hmftools-purple to 4.0.1 (#45685) --- recipes/hmftools-purple/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-purple/meta.yaml b/recipes/hmftools-purple/meta.yaml index a5aa250c79fa7..ec2fb71d6ffb2 100644 --- a/recipes/hmftools-purple/meta.yaml +++ b/recipes/hmftools-purple/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "4.0" %} -{% set sha256 = "58b2457143f77e7752a907a59f1fdd9550fae7483def373ad39ea4ac8fdbc383" %} +{% set version = "4.0.1" %} +{% set sha256 = "e52e98b04dd22ae5b785257f9decb16d4ea270a8de7aaa124ad07e5653b4713c" %} package: name: hmftools-purple From c7db36fb950d4cd5ac6d98bf97f936c4ad08c8f3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 12:23:55 -0500 Subject: [PATCH 1921/2173] Update nanomotif to 0.1.15 (#45688) --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index 6c85011e7505b..300d48d2bebe0 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.14" %} +{% set version = "0.1.15" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: f8278b9102267bdb9e4f3e2aa46d6e9f4fb9a655525766b1bc31f6cf67f2e609 + sha256: d218e3ea6822891c17225800849944ba87b64da3dff75526aa0c5f09d43f2234 build: entry_points: From e670c5f1c08801603117a44411a3441771d072c1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 15:50:36 -0500 Subject: [PATCH 1922/2173] Update snakemake to 8.4.7 (#45684) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 4a8831860540c..c1aeb3dbbadc4 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.6" %} +{% set version = "8.4.7" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 173df5ef2674191fe61c67f9a9e13fc7cbcca318d470a1d8e652f556ce706545 + sha256: 030f299937a09d328254a0705b87b91ecaf7d3bce51f3c4cee16df2a3718158f build: number: 0 From 6845dee9718ffa42f9af21e484b2011e1e6e6cc5 Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Wed, 7 Feb 2024 15:51:06 -0500 Subject: [PATCH 1923/2173] Update gsearch v0.1.9 (#45690) * Update annembed v0.1.4 * Update gsearch v0.1.9 --- recipes/gsearch/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/gsearch/meta.yaml b/recipes/gsearch/meta.yaml index b378ec2e3aee7..3149d4081ee0d 100644 --- a/recipes/gsearch/meta.yaml +++ b/recipes/gsearch/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.8" %} +{% set version = "0.1.9" %} package: name: gsearch @@ -11,7 +11,7 @@ build: skip: True # [osx] source: url: https://github.com/jianshu93/gsearch/archive/v{{ version }}.tar.gz - sha256: bdb954e52c61baf94f7de574b4a578df19f12508af89996d461aeebb43a39a8f + sha256: 21d87192f55a0826744e474c5e22add204b7d2b634bdc692d29ab88175a34c36 requirements: build: @@ -23,7 +23,7 @@ requirements: test: commands: - - gsearchbin -h + - gsearch -h about: home: https://github.com/jean-pierreBoth/gsearch From 1f304b1561dbc81e5036ab10e4a8db4f23963bc8 Mon Sep 17 00:00:00 2001 From: Andrea Guarracino <62253982+AndreaGuarracino@users.noreply.github.com> Date: Wed, 7 Feb 2024 21:51:40 +0100 Subject: [PATCH 1924/2173] add pyhon3 as `run` requirement to `wfmash` recipe (#45687) * add pyhon3 as `run` requirement * increment number --- recipes/wfmash/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/wfmash/meta.yaml b/recipes/wfmash/meta.yaml index ac6ba6133b387..c01b522985de1 100644 --- a/recipes/wfmash/meta.yaml +++ b/recipes/wfmash/meta.yaml @@ -13,7 +13,7 @@ build: skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} - number: 0 + number: 1 requirements: build: @@ -30,6 +30,7 @@ requirements: - libblas run: - llvm-openmp # [osx] + - python >=3.7 test: commands: From 5ef65fc9d405f0eee305877cdc3a4272f6bc307f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 7 Feb 2024 21:53:07 -0500 Subject: [PATCH 1925/2173] Update snaketool-utils to 0.0.5 (#45695) --- recipes/snaketool-utils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snaketool-utils/meta.yaml b/recipes/snaketool-utils/meta.yaml index 36bc8b6314b9f..2d9130b89bfb3 100644 --- a/recipes/snaketool-utils/meta.yaml +++ b/recipes/snaketool-utils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snaketool-utils" %} -{% set version = "0.0.4" %} +{% set version = "0.0.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snaketool_utils-{{ version }}.tar.gz - sha256: 75a35ba887be3ead290087241d1222dc8ef79e36cb3ccb395d9c7059b72cbe06 + sha256: a686300efcec715fba806479b10dde0f98781a90600c7bf7cadcca1ebb655305 build: noarch: python From b141b9c8b16523ef53f4cd820129b5096b071d7d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 00:16:32 -0500 Subject: [PATCH 1926/2173] Update koverage to 0.1.11 (#45697) --- recipes/koverage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/koverage/meta.yaml b/recipes/koverage/meta.yaml index d7047f608650d..fb97ab5265ccd 100644 --- a/recipes/koverage/meta.yaml +++ b/recipes/koverage/meta.yaml @@ -1,5 +1,5 @@ {% set name = "koverage" %} -{% set version = "0.1.10" %} +{% set version = "0.1.11" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 46d7d444350932a88f6d0158c946671f2f0a6b4769f3c9c68e4b13fa76ecefc2 + sha256: 24d785d654524a59c109f6fb3b3f6fc211b5f7177d643597f144fc6954a74d57 build: noarch: python From 87bdc097f64f6087ac2e2929fccd7a02d9ef912b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 00:16:56 -0500 Subject: [PATCH 1927/2173] Update trimnami to 0.1.3 (#45698) --- recipes/trimnami/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/trimnami/meta.yaml b/recipes/trimnami/meta.yaml index 74c441bf5757e..f1153c947bca4 100644 --- a/recipes/trimnami/meta.yaml +++ b/recipes/trimnami/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trimnami" %} -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 5a045d74b3a3e388d32ef2b43429f3742adaa90566d44a52f7cd9bb70d428e69 + sha256: 37e15eec675d7cc65d75b49e0d6151ceceee53ea043f854ffad05b5895ce8d78 build: noarch: python From 04a385c5eb851022a97a0fb33b879d2653cf3e71 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 05:39:21 -0500 Subject: [PATCH 1928/2173] Update nanomotif to 0.1.17 (#45699) * Update nanomotif to 0.1.16 * Update nanomotif to 0.1.17 --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index 300d48d2bebe0..8bf32fe611950 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.15" %} +{% set version = "0.1.17" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: d218e3ea6822891c17225800849944ba87b64da3dff75526aa0c5f09d43f2234 + sha256: 48bd357472e36ed6336ff555fc55a81779d05ea3cf0e1b25f6a5d1cadf0763f5 build: entry_points: From 4445fa1cca4be1f3481571f29e84491e0566781c Mon Sep 17 00:00:00 2001 From: Ryan James Kennedy <67742838+ryanjameskennedy@users.noreply.github.com> Date: Thu, 8 Feb 2024 14:44:57 +0100 Subject: [PATCH 1929/2173] Add git to resfinder (#45686) --- recipes/resfinder/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/resfinder/meta.yaml b/recipes/resfinder/meta.yaml index 53c3e5a68befa..4f4e2bcf04abe 100644 --- a/recipes/resfinder/meta.yaml +++ b/recipes/resfinder/meta.yaml @@ -12,7 +12,7 @@ source: - python_path.patch build: - number: 0 + number: 1 noarch: python run_exports: - {{ pin_subpackage('resfinder', max_pin="x") }} @@ -33,10 +33,13 @@ requirements: - python-dateutil - kma - blast >=2.8.1 + - git test: imports: - resfinder + commands: + - python -m resfinder --help about: home: https://bitbucket.org/genomicepidemiology/resfinder From 8d6f2a7987b96ac68c5b546f574bc794a1144226 Mon Sep 17 00:00:00 2001 From: Andrei Prodan Date: Thu, 8 Feb 2024 15:29:56 +0100 Subject: [PATCH 1930/2173] Add Scevan R package recipe (#45649) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * receipt for SCEVAN R package * add LICENSE and fix linting errors * fix build errors * fix linting error * add devtools and other dependencies as conda installs * add tag for SCEVAN; use "host" instead of "build" requirements * Update recipes/scevan/meta.yaml Co-authored-by: Pablo Moreno * bump rename to r-scevan; bump version to v1.0.1 * rename recipe subfolder to r-scevan * fix typo in tag URL * fix type in SCEVAN devtools::install_github() command * Update recipes/r-scevan/meta.yaml Co-authored-by: Björn Grüning * Update recipes/r-scevan/meta.yaml Co-authored-by: Björn Grüning * update license identifier * Update recipes/r-scevan/meta.yaml Co-authored-by: Christian Brueffer * solve conflict * edit "script:" * re-add yaGST installation * re-add ${R} CMD INSTALL --build . * fix order in "script:" * build using a build.sh file and devtools * fix dependencies --------- Co-authored-by: Pablo Moreno Co-authored-by: Björn Grüning Co-authored-by: Christian Brueffer --- recipes/r-scevan/build.sh | 4 +++ recipes/r-scevan/meta.yaml | 64 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 recipes/r-scevan/build.sh create mode 100644 recipes/r-scevan/meta.yaml diff --git a/recipes/r-scevan/build.sh b/recipes/r-scevan/build.sh new file mode 100644 index 0000000000000..c3ea0d7102a89 --- /dev/null +++ b/recipes/r-scevan/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +R -e "library(devtools)" +R -e "devtools::install_github('miccec/yaGST')" +R CMD INSTALL --build . diff --git a/recipes/r-scevan/meta.yaml b/recipes/r-scevan/meta.yaml new file mode 100644 index 0000000000000..bb1703e201397 --- /dev/null +++ b/recipes/r-scevan/meta.yaml @@ -0,0 +1,64 @@ +package: + name: r-scevan + version: 1.0.1 + +source: + url: https://github.com/AntonioDeFalco/SCEVAN/archive/refs/tags/v1.0.1.tar.gz + sha256: 7558d31282c36418db3960b3edb9cb9815db14b0a48d8882287e11f752dfeab1 + +build: + number: 0 + noarch: generic # Specify that the package is noarch + run_exports: '{{ pin_compatible("r-scevan", max_pin="x.x") }}' + rpaths: + - lib/R/lib + - lib + +requirements: + host: + - r-base + - r-remotes + - r-devtools + - r-rcpp + - r-paralleldist + - r-pheatmap + - r-forcats + - r-dplyr + - bioconductor-fgsea + - r-cluster + - r-ggplot2 + - r-Rtsne + - bioconductor-scran + - r-ape + - bioconductor-ggtree + - r-tidytree + - r-ggrepel + - r-optparse + run: + - r-base + - r-devtools + - r-paralleldist + - r-pheatmap + - r-forcats + - r-dplyr + - bioconductor-fgsea + - r-cluster + - r-ggplot2 + - r-Rtsne + - bioconductor-scran + - r-ape + - bioconductor-ggtree + - r-tidytree + - r-ggrepel + - r-optparse + +test: + commands: + - $R -e "library(SCEVAN)" + +about: + home: https://github.com/AntonioDeFalco/SCEVAN/ + license: GPL-3.0-only + license_family: GPL3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single CEll Variational Aneuploidy aNalysis From fc9275a8b401ee13182ab386afa833ef0930dcc3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ozan=20=C3=96z=C4=B1=C5=9F=C4=B1k?= Date: Thu, 8 Feb 2024 16:59:45 +0100 Subject: [PATCH 1931/2173] Update orsum (#45701) --- recipes/orsum/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/orsum/meta.yaml b/recipes/orsum/meta.yaml index 3591a34be072a..914af7c1fb195 100644 --- a/recipes/orsum/meta.yaml +++ b/recipes/orsum/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.6.0" %} -{% set sha256hash = "b44f9d5a68e4983da93c41cf5e4053c77ac550e0482601c1da6a83b039328da9" %} +{% set version = "1.7.0" %} +{% set sha256hash = "ba228a3d1ca6aa6269a624ab109c1a6c41c58dd392abcf46f8edc2e52760c1a8" %} package: name: orsum version: {{ version }} @@ -11,6 +11,8 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('orsum', max_pin="x.x") }} requirements: run: From a18569923db4c332ad20f157b1eeb2aaaf97726b Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Thu, 8 Feb 2024 08:00:21 -0800 Subject: [PATCH 1932/2173] Add ntsynt (#45692) --- recipes/ntsynt/build.sh | 9 ++++++++ recipes/ntsynt/meta.yaml | 49 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 recipes/ntsynt/build.sh create mode 100644 recipes/ntsynt/meta.yaml diff --git a/recipes/ntsynt/build.sh b/recipes/ntsynt/build.sh new file mode 100644 index 0000000000000..c0ea64c9342bc --- /dev/null +++ b/recipes/ntsynt/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" + +# Build ntSynt +mkdir -p ${PREFIX}/bin +meson setup build --prefix ${PREFIX} +cd build +ninja install diff --git a/recipes/ntsynt/meta.yaml b/recipes/ntsynt/meta.yaml new file mode 100644 index 0000000000000..0fa8488dc1a91 --- /dev/null +++ b/recipes/ntsynt/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "ntSynt" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/bcgsc/ntSynt/releases/download/v{{ version }}/{{ name }}-{{ version }}.tar.gz + sha256: db3fe491233d93967120d091a19abbef1fa5dfa637814bb617814a1b3e3f1331 + +build: + number: 0 + run_exports: + - {{ pin_subpackage("ntsynt", max_pin="x") }} + +requirements: + build: + - {{ compiler('cxx') }} + - cmake + host: + - python + - meson + - ninja + - llvm-openmp # [osx] + - libgomp # [linux] + - btllib + run: + - python + - btllib + - intervaltree + - pybedtools + - ncls + - python-igraph + - snakemake + - samtools + - seqtk + +test: + commands: + - ntSynt -h + imports: + - btllib + +about: + home: https://github.com/bcgsc/ntsynt + license: GPL-3.0 + license_file: LICENSE + summary: 'Detecting multi-genome synteny blocks using minimizer graph mapping' From e9d741f5fa10ae49f1d9df236f6d5fadd36eea2e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:16:29 -0500 Subject: [PATCH 1933/2173] Update pango-designation to 1.25 (#45717) --- recipes/pango-designation/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pango-designation/meta.yaml b/recipes/pango-designation/meta.yaml index 3c559b4e5981f..7dcdda6f72e20 100644 --- a/recipes/pango-designation/meta.yaml +++ b/recipes/pango-designation/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.24" %} +{% set version = "1.25" %} package: name: pango-designation @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pango-designation/archive/refs/tags/v{{ version }}.tar.gz - sha256: 9b84365c503a71ac5aadf47b977aa022450457492b24955149f26469f733f898 + sha256: f57bc2dee34d39ac73d27782357a4332f899bf45a495c8c279c6905c8b0130be build: number: 0 From ed8e6329943d83e1a4d0166b3f78cbb75fef279f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:18:56 -0500 Subject: [PATCH 1934/2173] Update planemo to 0.75.21 (#45713) --- recipes/planemo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 2fa68f4e4e03e..6ac4349111683 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "planemo" %} -{% set version = "0.75.20" %} -{% set sha256 = "de61edcb2496c9301b751ac12d0c83441dfcb36cff3a279db3e7942e3fc4b873" %} +{% set version = "0.75.21" %} +{% set sha256 = "c8b238d258ee85244a2a7d067452ef14f191c78e1e0923945bdd5e759682716e" %} package: name: {{ name|lower }} From a3dcc9c3cf714ecc514406f7ffbdfabb54d2ff80 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:19:32 -0500 Subject: [PATCH 1935/2173] Update annonars to 0.35.0 (#45712) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 49388dd1ed49a..7cfa355bc6dbb 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.34.1" %} +{% set version = "0.35.0" %} package: name: annonars @@ -12,7 +12,7 @@ build: source: url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 55f4d7fff2f94eaf94e7752a426ee2532f88ffb25a0d2bb0cf0b4127212bf3e1 + sha256: cdea1de0bdcc1d223093fcf8d629af5c24bc788900a0cc47256e42fba587c2c8 requirements: build: From b91f4aca703cc2fd3e0369a83c60e17c58fd3e91 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:49:36 -0500 Subject: [PATCH 1936/2173] Update cramino to 0.14.1 (#45710) * Update cramino to 0.14.0 * Update cramino to 0.14.1 --------- Co-authored-by: Wouter De Coster --- recipes/cramino/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cramino/meta.yaml b/recipes/cramino/meta.yaml index 0d07842df6aad..5647f84ea1049 100644 --- a/recipes/cramino/meta.yaml +++ b/recipes/cramino/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.13.1" %} +{% set version = "0.14.1" %} package: name: cramino @@ -12,7 +12,7 @@ build: source: url: https://github.com/wdecoster/cramino/archive/v{{ version }}.tar.gz - sha256: 92e60915b2fccacb21f2c5b71253b667615e1a99f964f232569122458cf64c40 + sha256: 57e15afb113808c327a4ec843ae1677f37c35f692e04927cfcc3823affac6cff requirements: build: From 13394e59ef54c179e3540d4e799c77b02681532d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 15:50:45 -0500 Subject: [PATCH 1937/2173] Update vcfsim to 1.0.9.alpha (#45719) --- recipes/vcfsim/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vcfsim/meta.yaml b/recipes/vcfsim/meta.yaml index 96d58274dcb6d..5883749ef127a 100644 --- a/recipes/vcfsim/meta.yaml +++ b/recipes/vcfsim/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vcfsim" %} -{% set version = "1.0.8.alpha" %} +{% set version = "1.0.9.alpha" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Pie115/VCFSimulator-SamukLab/archive/{{ version }}.tar.gz - sha256: 67a2be52bb06b44dfb3cb96cff766cae866181b0b1e136d1d8737a229438068c + sha256: 364eb81f21b5071450b553649c5be1e2c273a63bb04e9a6e4af2e1455bb8c48e build: noarch: python From 389f9e14394ddc6e6aff433d896d41fabd5349dd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:16:10 -0500 Subject: [PATCH 1938/2173] Update dfast to 1.2.21 (#45702) * Update dfast to 1.2.21 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/dfast/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/dfast/meta.yaml b/recipes/dfast/meta.yaml index bee44b4572a7a..b57da8b83f70f 100644 --- a/recipes/dfast/meta.yaml +++ b/recipes/dfast/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.20" %} +{% set version = "1.2.21" %} package: name: dfast @@ -6,11 +6,13 @@ package: source: url: https://github.com/nigyta/dfast_core/archive/{{ version }}.tar.gz - sha256: 57f24e8bc20f412b73612ba710e14a009f77381f415f3ee47d69b5c7411ef71d + sha256: 70283cbfc756f5033cc92d1c721b9f7b5d5ba521a6da6e36e2bed794267c8a7b build: number: 0 binary_relocation: False # [osx] + run_exports: + - {{ pin_subpackage("dfast", max_pin="x.x") }} requirements: build: From 4eafef2b2723b5c36dbc4688edf0d1861b9ece5e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:16:18 -0500 Subject: [PATCH 1939/2173] Update oakvar to 2.9.87 (#45696) * Update oakvar to 2.9.86 * Update oakvar to 2.9.87 --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 15f40af72b4d6..2054f16001ab9 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.85" %} -{% set sha256 = "ff8f8f8a6ab8cd9c9307edf2cb710a9ccdb9649f3c46ff656f336678419e514b" %} +{% set version = "2.9.87" %} +{% set sha256 = "3ee4c24b0d1f8995b7f41ec2ba2c6948c9bd6bed4166715a1fe3b0e4436fba44" %} package: name: {{ name|lower }} From d8eae6f11a813361323ecf193dbbe98194cbbd0a Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Fri, 9 Feb 2024 01:16:43 +0100 Subject: [PATCH 1940/2173] Fix pydantic dependency of varfish-cli more strictly. (#45703) --- recipes/varfish-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varfish-cli/meta.yaml b/recipes/varfish-cli/meta.yaml index f65d88b9dd723..909078b89013b 100644 --- a/recipes/varfish-cli/meta.yaml +++ b/recipes/varfish-cli/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - varfish-cli = varfish_cli.__main__:main @@ -33,7 +33,7 @@ requirements: - tqdm - tabulate - polyleven - - pydantic + - pydantic >=2.0,<3.0 - python-dateutil - simplejson - typeguard From 27e54d99e2c6b409a6cbba4d17f6103b1ad640b4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:17:31 -0500 Subject: [PATCH 1941/2173] Update assemblycomparator2 to 2.5.18 (#45706) --- recipes/assemblycomparator2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml index 6c929a7075290..1558758fef16b 100644 --- a/recipes/assemblycomparator2/meta.yaml +++ b/recipes/assemblycomparator2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5.17" %} +{% set version = "2.5.18" %} package: name: assemblycomparator2 @@ -6,7 +6,7 @@ package: source: url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5c15c4882529d33d56678eb3b710e243e3f5adc49b7d0ad1871f26ecab69d97e + sha256: 74d1f4959405c8ad01dd2cb2ad842c8ac71211b9ae8a125f4e58e44016cfd4a6 build: From 7e01903bae3b27bbe769e5ae22e5e3bfbd2bd0a1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:17:44 -0500 Subject: [PATCH 1942/2173] Update centrifuger to 1.0.1 (#45711) --- recipes/centrifuger/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/centrifuger/meta.yaml b/recipes/centrifuger/meta.yaml index a25ea6d2ebf32..dbb8ff62c7d69 100644 --- a/recipes/centrifuger/meta.yaml +++ b/recipes/centrifuger/meta.yaml @@ -1,5 +1,5 @@ {% set name = "centrifuger" %} -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ build: source: url: https://github.com/mourisl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 88d8e9031caa9298a2ea0c3a7a4d4a8a2a569dcc32cf6f795a13cdf03612aa49 + sha256: 4ce9a20d786a39ef26b1ef31851c180e0b1baae1efc2d9ad8442bec6203d04bb requirements: build: From edbc6a89073ac7558cbf5e26cf2004a70e77e8bf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:18:04 -0500 Subject: [PATCH 1943/2173] Update igv-reports to 1.12.0 (#45720) --- recipes/igv-reports/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/igv-reports/meta.yaml b/recipes/igv-reports/meta.yaml index 8b464c54de237..1e69cef3c08a1 100644 --- a/recipes/igv-reports/meta.yaml +++ b/recipes/igv-reports/meta.yaml @@ -1,5 +1,5 @@ {% set name = "igv-reports" %} -{% set version = "1.11.0" %} +{% set version = "1.12.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 8a524c53f4bbcf93d58a2b2246d8473b22bea1955a492f81365c4c27164efe86 + sha256: 2a4bb08945e7872108a83037468249581b2fb42b2934cf33446971443175611d build: noarch: python From 952ae2132661c9e0d30abc91b374bc3fbcff5232 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:18:17 -0500 Subject: [PATCH 1944/2173] Update ndex2 to 3.8.0 (#45721) --- recipes/ndex2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ndex2/meta.yaml b/recipes/ndex2/meta.yaml index 223be915ae200..b3b3536e16221 100644 --- a/recipes/ndex2/meta.yaml +++ b/recipes/ndex2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ndex2" %} -{% set version = "3.7.0" %} +{% set version = "3.8.0" %} package: @@ -8,7 +8,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ndex2-{{ version }}.tar.gz" - sha256: "5fed3b6c204275fd75724f7d609823f9f6e249b3d468fdd8b0a1f7a9be7a294f" + sha256: "9f4d7f4b9594664191fba5c6512e315ed47b13bc416df5769802f87a7c22d1c8" build: noarch: python From 5143486201359a6b46e8f4f020365a0357a85b74 Mon Sep 17 00:00:00 2001 From: Catherine Chahrour <74187550+CChahrour@users.noreply.github.com> Date: Fri, 9 Feb 2024 00:23:39 +0000 Subject: [PATCH 1945/2173] Add seqnado (#45705) * add seqnado * add seqnado * add alsmith as maintainer * edit recipe * add singularity * require wget for testing * update recipe * fix license SPDX identifier --- recipes/seqnado/meta.yaml | 66 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 recipes/seqnado/meta.yaml diff --git a/recipes/seqnado/meta.yaml b/recipes/seqnado/meta.yaml new file mode 100644 index 0000000000000..c9914ff336c16 --- /dev/null +++ b/recipes/seqnado/meta.yaml @@ -0,0 +1,66 @@ +{% set name = "seqnado" %} +{% set version = "0.4.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/seqnado-{{ version }}.tar.gz + sha256: 171d551baf6eb3e6b7402510826688804f9fab0d3dba0db9907da92a1059dc47 + +build: + number: 0 + noarch: python + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} + script: {{ PYTHON }} -m pip install . --no-deps -vvv + entry_points: + - seqnado = seqnado.cli:cli_pipeline + - seqnado-design = seqnado.cli:cli_design + - seqnado-config = seqnado.cli:cli_config + run_exports: + - {{ pin_subpackage('seqnado', max_pin="x.x") }} + +requirements: + host: + - python >=3.10 + - setuptools >=61.0 + - wheel + - setuptools-scm >=6.2 + - pip + run: + - click + - cookiecutter + - drmaa + - pandas + - pulp <=2.7.0 + - pydantic + - python >=3.10 + - pyyaml + - seaborn + - setuptools-scm + - singularity + - snakemake <=7.3.2 + - snakemake-wrapper-utils + - tracknado + - wget + +test: + imports: + - seqnado + commands: + - seqnado --help + - seqnado-design --help + - seqnado-config --help + +about: + home: https://alsmith151.github.io/SeqNado/ + summary: Pipelines for genomics analysis + license: GPL-3.0-or-later + license_file: LICENSE + +extra: + recipe-maintainers: + - alsmith151 + - CChahrour From 98fa66e9c88f54a9591e27d6fbfaa8bc8083b257 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 19:24:32 -0500 Subject: [PATCH 1946/2173] Update pangu to 0.2.4 (#45496) * Update pangu to 0.2.3 * add run_exports * Update pangu to 0.2.4 --------- Co-authored-by: mencian --- recipes/pangu/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/pangu/meta.yaml b/recipes/pangu/meta.yaml index cabad42e5e79a..dbf8e578c4815 100644 --- a/recipes/pangu/meta.yaml +++ b/recipes/pangu/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.2" %} -{% set sha256 = "91133019717eb8becc6f9345257891206bea57c5b3706b18440cfe3c393fd07c" %} +{% set version = "0.2.4" %} +{% set sha256 = "1437175d891a76f71a19dc86121c08b19d81a61273cbbd09bbab6e090c42e3f2" %} package: name: pangu @@ -14,7 +14,9 @@ build: noarch: python entry_points: - pangu = pangu.__main__:main_cli - script: python -m pip install --no-deps -vv . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation -vvv . + run_exports: + - {{ pin_subpackage('pangu', max_pin="x.x") }} requirements: host: From 61438c4133787ccd8d5bfd325e65d19b49408020 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= <51365402+balajtimate@users.noreply.github.com> Date: Fri, 9 Feb 2024 01:25:28 +0100 Subject: [PATCH 1947/2173] Update htsinfer (#45633) * update htsinfer * update sha256 * update tests * update version and sha * reset build number * increase build number --- recipes/htsinfer/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/htsinfer/meta.yaml b/recipes/htsinfer/meta.yaml index df57b6f70efa5..b853db128b352 100644 --- a/recipes/htsinfer/meta.yaml +++ b/recipes/htsinfer/meta.yaml @@ -10,7 +10,7 @@ source: sha256: f7225290e12bf129bdb654f06f1cb98da577be81d35f7d17844447fcdf058618 build: - number: 0 + number: 1 noarch: python entry_points: - htsinfer = htsinfer.cli:main @@ -26,7 +26,7 @@ requirements: - numpy >=1.22, <1.25 - pandas >=1.3.5, <1.4.0 - biopython >=1.78 - - pydantic >=1.8.1, <2 + - pydantic >=2, <3 - pysam >=0.16.0 - pyahocorasick >=1.4.0 run: @@ -36,7 +36,7 @@ requirements: - numpy >=1.22, <1.25 - pandas >=1.3.5, <1.4.0 - pyahocorasick >=1.4.0 - - pydantic >=1.8.1, <2 + - pydantic >=2, <3 - pysam >=0.16.0 - python >=3.8, <=3.10 - star >=2.7.6 From e719b532b605326654de08d9781d72fdffa48765 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Fri, 9 Feb 2024 11:27:42 +1100 Subject: [PATCH 1948/2173] Patch hmftools-sv-prep 1.2.3 (#45694) * Enable SvPrep to discover GRIDSS JAR * Bump build number * Fix class-path detection in BASH script --- .../gridss_shell_with_jar_entrypoint | 32 +++++++++++++------ recipes/hmftools-sv-prep/meta.yaml | 2 +- recipes/hmftools-sv-prep/svprep.sh | 2 +- 3 files changed, 24 insertions(+), 12 deletions(-) diff --git a/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint b/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint index d9183aebce48e..1b8d632b76499 100644 --- a/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint +++ b/recipes/hmftools-sv-prep/gridss_shell_with_jar_entrypoint @@ -4,15 +4,27 @@ # Adapted from bioconda-recipes/picard/picard.sh set -o pipefail -# Find original directory of bash script, resolving symlinks -# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 -SOURCE="${BASH_SOURCE[0]}" -while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink - DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located -done -DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" -$DIR/$(basename $0) --jar "$DIR/gridss.jar" "$@" +resolve_source_directory() { + # Find original directory of bash script, resolving symlinks + # http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 + local SOURCE="${1}" + while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located + done + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + echo $DIR +} +# Sanity check for GRIDSS dependency +if ! hash gridss 2>/dev/null; then + echo "Could not find 'gridss' in PATH, exiting"; + exit 1; +fi + +SCRIPT_DIR=$(resolve_source_directory ${BASH_SOURCE[0]}) +JAR_DIR=$(resolve_source_directory $(which gridss)) + +$SCRIPT_DIR/$(basename $0) --jar "$JAR_DIR/gridss.jar" "$@" diff --git a/recipes/hmftools-sv-prep/meta.yaml b/recipes/hmftools-sv-prep/meta.yaml index 2af81c748ca39..17301d9a6a0ec 100644 --- a/recipes/hmftools-sv-prep/meta.yaml +++ b/recipes/hmftools-sv-prep/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('hmftools-sv-prep', max_pin="x") }} diff --git a/recipes/hmftools-sv-prep/svprep.sh b/recipes/hmftools-sv-prep/svprep.sh index 053fdd8f1f5e2..6cd23a12769db 100755 --- a/recipes/hmftools-sv-prep/svprep.sh +++ b/recipes/hmftools-sv-prep/svprep.sh @@ -60,7 +60,7 @@ if [ "$jvm_mem_opts" == "" ]; then fi pass_arr=($pass_args) -if [[ ${pass_arr[0]:=} == org* ]] +if [[ ${pass_arr[0]:=} == com.hartwig.* ]] then eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/sv-prep.jar" $pass_args else From df056b733ca1307a748fc6bd59d3e0e18e51a332 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 9 Feb 2024 01:53:31 +0100 Subject: [PATCH 1949/2173] Update sepp (#44721) * using latest release of upstream * use recent gapc update with hopes to compile on OSX * add subrecipe for older version 4.3.10 (pinned in qiime2) which shall additionally expose upp.config * fix breaking changes in recipe, no changes in upstream * remove sub-recipe (for now) --- recipes/sepp/build.sh | 15 ++++++++++++++- recipes/sepp/meta.yaml | 6 +++--- 2 files changed, 17 insertions(+), 4 deletions(-) diff --git a/recipes/sepp/build.sh b/recipes/sepp/build.sh index 679123229a05e..925564b6363c6 100644 --- a/recipes/sepp/build.sh +++ b/recipes/sepp/build.sh @@ -5,13 +5,26 @@ python setup.py upp -c # ensure SEPP's configuration file is at the correct location ... echo "${PREFIX}/share/sepp/sepp" > home.path -cp home.path ${PREFIX}/lib/python*/site-packages/ +# ensure directory is created ... ($SP_DIR = Python's site-packages location, see https://docs.conda.io/projects/conda-build/en/stable/user-guide/environment-variables.html#environment-variables-set-during-the-build-process) +mkdir -p $SP_DIR/ +# ... before we copy content into it +cp -rv home.path $SP_DIR/ mkdir -p $PREFIX/share/sepp/sepp # ... and holds correct path names mv -v sepp-package/sepp/default.main.config $PREFIX/share/sepp/sepp/main.config # copy upp config, as it's still needed cp ./.sepp/upp.config $PREFIX/share/sepp/sepp/upp.config +# replace $PREFIX with /opt/anaconda1anaconda2anaconda3 for later replacement of concrete build PREFIX +# note: can't apply a patch here, as upp.config is not part of upstream but gets generated during python setup +if [ $unamestr == 'Linux' ]; +then + sed -i 's@'"$PREFIX"'@/opt/anaconda1anaconda2anaconda3@g' $PREFIX/share/sepp/sepp/upp.config +elif [ $unamestr == 'Darwin' ]; +then + gsed -i 's@'"$PREFIX"'@/opt/anaconda1anaconda2anaconda3@g' $PREFIX/share/sepp/sepp/upp.config +fi + $PYTHON -m pip install . --ignore-installed --no-deps -vv # copy bundled binaries, but hmmer which should be provided by conda, into $PREFIX/bin/ diff --git a/recipes/sepp/meta.yaml b/recipes/sepp/meta.yaml index 731db6eeaceb8..980e754e11f8c 100644 --- a/recipes/sepp/meta.yaml +++ b/recipes/sepp/meta.yaml @@ -15,13 +15,13 @@ source: - nodeps.setup.py.patch build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('sepp', max_pin="x") }} requirements: host: - - python 3.7 + - python <=3.9 - setuptools - pip - dendropy <=4.5.1 @@ -29,7 +29,7 @@ requirements: - hmmer ==3.1b2 run: - - python 3.7 + - python <=3.9 - dendropy <=4.5.1 - openjdk - hmmer ==3.1b2 From b03b752c1912b8d74fd3fac9665182e4c8314113 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 20:16:48 -0500 Subject: [PATCH 1950/2173] Update r-jackstraw to 1.3.9 (#45683) * Update r-jackstraw to 1.3.9 * add run_exports --------- Co-authored-by: mencian --- recipes/r-jackstraw/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/r-jackstraw/meta.yaml b/recipes/r-jackstraw/meta.yaml index 5bb00456a1c3e..87c8d069725c3 100644 --- a/recipes/r-jackstraw/meta.yaml +++ b/recipes/r-jackstraw/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.3.8' %} +{% set version = '1.3.9' %} package: name: r-jackstraw @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/jackstraw_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/jackstraw/jackstraw_{{ version }}.tar.gz - sha256: 897146888be7f7962a038939fa88005de729f4fcbf4291f6577d59f456cca011 + sha256: 6a599ec3803c64884973eeab44aaf5a78ec44406ef4f536993406e4b6c90f871 build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-jackstraw', max_pin="x") }} requirements: host: From 6361b1e22bb3a057f784076426059ed51c4bd328 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Fri, 9 Feb 2024 01:17:44 +0000 Subject: [PATCH 1951/2173] Re-points LD_LIBRARY_PATH to dynamically linked library when loading environment (#45716) * Re-points LD_LIBRARY_PATH to static library when loading environment * Bump aster build number --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/aster/activate.sh | 3 +++ recipes/aster/build.sh | 6 ++++++ recipes/aster/deactivate.sh | 3 +++ recipes/aster/meta.yaml | 2 +- 4 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 recipes/aster/activate.sh create mode 100644 recipes/aster/deactivate.sh diff --git a/recipes/aster/activate.sh b/recipes/aster/activate.sh new file mode 100644 index 0000000000000..8b7e185b7e5ce --- /dev/null +++ b/recipes/aster/activate.sh @@ -0,0 +1,3 @@ +export OLD_LD_LIBRARY_PATH=${LD_LIBRARY_PATH} +export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib/:${LD_LIBRARY_PATH} +export SINGULARITYENV_LD_LIBRARY_PATH=${LD_LIBRARY_PATH} \ No newline at end of file diff --git a/recipes/aster/build.sh b/recipes/aster/build.sh index 786e3a99cae85..ef017cb87c7ae 100644 --- a/recipes/aster/build.sh +++ b/recipes/aster/build.sh @@ -1,5 +1,11 @@ #!/bin/bash +for CHANGE in "activate" "deactivate" +do + mkdir -p "${PREFIX}/etc/conda/${CHANGE}.d" + cp "${RECIPE_DIR}/${CHANGE}.sh" "${PREFIX}/etc/conda/${CHANGE}.d/${PKG_NAME}_${CHANGE}.sh" +done + sed -i.bak1 's/-march=native/-march=x86-64 -mtune=generic/g' makefile if [ "$(uname)" == "Darwin" ]; then diff --git a/recipes/aster/deactivate.sh b/recipes/aster/deactivate.sh new file mode 100644 index 0000000000000..3b8e36f330814 --- /dev/null +++ b/recipes/aster/deactivate.sh @@ -0,0 +1,3 @@ +export LD_LIBRARY_PATH=${OLD_LD_LIBRARY_PATH} +unset OLD_LD_LIBRARY_PATH +unset SINGULARITYENV_LD_LIBRARY_PATH \ No newline at end of file diff --git a/recipes/aster/meta.yaml b/recipes/aster/meta.yaml index 30d17f22be13c..261c0d86b4a8b 100644 --- a/recipes/aster/meta.yaml +++ b/recipes/aster/meta.yaml @@ -7,7 +7,7 @@ package: version: "{{ version }}" build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('aster', max_pin="x") }} From b31d260a5283f37645ab883b61ea5f72f0f14aad Mon Sep 17 00:00:00 2001 From: Jens-Uwe Ulrich <46562264+JensUweUlrich@users.noreply.github.com> Date: Fri, 9 Feb 2024 02:29:29 +0100 Subject: [PATCH 1952/2173] Add taxor (#45392) * initial taxor commit * skip osx build * add requirement libgomp * build taxor instead of using prebuild binary * md5sum correction * change cmake minimum version to 3.28 * use taxor version 0.1.1 * removed chopper tests * add requirement cxxopts * remove chopper install command * update seqan3 platform.hpp * upgrade to seqan 3.3 * change build directories * change source directories * removed seqan dependencies * use dynamic zlib and bzip2 * libdirsuffix for ankerl * check existing libdir for ankerl * add requirement sdsl-lite * try again with precompiled binary * rollback * syncmer preprocessor directive added * preprocessor directive added to insert_into_ixf * preprocessor directive added to ixf * updated IXF code in seqan3 * updated xxhash.h * updated xxhash.h and release * edit dependencies and use SPDX identifier --------- Co-authored-by: Jens-Uwe Ulrich Co-authored-by: mencian --- recipes/taxor/build.sh | 10 +++++++++ recipes/taxor/meta.yaml | 47 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100755 recipes/taxor/build.sh create mode 100755 recipes/taxor/meta.yaml diff --git a/recipes/taxor/build.sh b/recipes/taxor/build.sh new file mode 100755 index 0000000000000..92946f0a50a31 --- /dev/null +++ b/recipes/taxor/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +mkdir ${SRC_DIR}/build/ +cd ${SRC_DIR}/build/ +cmake ${SRC_DIR}/src +cmake --build . --config Release + +cp ${SRC_DIR}/build/main/taxor $PREFIX/bin +chmod +x $PREFIX/bin/taxor + diff --git a/recipes/taxor/meta.yaml b/recipes/taxor/meta.yaml new file mode 100755 index 0000000000000..cc994c4012da7 --- /dev/null +++ b/recipes/taxor/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "0.1.1" %} + +package: + name: taxor + version: {{ version }} + +source: + url: https://github.com/JensUweUlrich/Taxor/archive/refs/tags/{{ version }}.tar.gz # [linux] + md5: ad6a34b6c3d2c114bed5181af8f69ad3 # [linux] + +build: + number: 0 + run_exports: + - {{ pin_subpackage('taxor', max_pin='x.x.x') }} + skip: true # [osx] + +requirements: + build: + - make + - {{ compiler('cxx') }} + - {{ compiler('c') }} + - cmake >=3.21 + host: + - zlib + - bzip2 + - libgomp # [linux] + - cxxopts >=2.2.0 + - grep + - coreutils + - curl + - diffutils + run: + - grep + - coreutils + - curl + - diffutils + +test: + commands: + - taxor --help + +about: + home: https://github.com/JensUweUlrich/Taxor + summary: Fast and space-efficient taxonomic classification of long reads + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE.md From fbc456e62020224065d9d571654efbaa28336918 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 8 Feb 2024 21:17:23 -0600 Subject: [PATCH 1953/2173] Add recipe for gffpandas v1.2.2 (#45724) * Add recipe for gffpandas v1.2.2 * add summary --- recipes/gffpandas/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 recipes/gffpandas/meta.yaml diff --git a/recipes/gffpandas/meta.yaml b/recipes/gffpandas/meta.yaml new file mode 100644 index 0000000000000..0d3f2ead2c06e --- /dev/null +++ b/recipes/gffpandas/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "gffpandas" %} +{% set version = "1.2.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/foerstner-lab/gffpandas/archive/v{{ version }}.tar.gz + sha256: bf58757e8d0eb4c2aa800864d2ab6e8ee3d499862473417435b57a05d9bf00b2 + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('gffpandas', max_pin="x") }} + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - pandas + +test: + imports: + - gffpandas + +about: + home: https://github.com/foerstner-lab/gffpandas + summary: "Parse GFF3 into Pandas dataframes" + license: MIT + license_family: MIT + license_file: LICENSE + doc_url: https://gffpandas.readthedocs.io/en/latest/ From 6faeb4d7aa75f5c46fc5cace813c8ec2f43476df Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 8 Feb 2024 22:17:45 -0500 Subject: [PATCH 1954/2173] Update liftover to 1.1.18 (#45723) --- recipes/liftover/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/liftover/meta.yaml b/recipes/liftover/meta.yaml index 8c82c1069fba5..13f38da8679fa 100644 --- a/recipes/liftover/meta.yaml +++ b/recipes/liftover/meta.yaml @@ -1,6 +1,6 @@ {% set name = "liftover" %} -{% set version = "1.1.17" %} -{% set sha256 = "cb06a3843b570ec554fbc0dd871c0b87d3645200e2c65f6cc97cd4b6146efaf9" %} +{% set version = "1.1.18" %} +{% set sha256 = "a4bf896c5dd59a284929d68f446a78c426827efbec430d35da1ec7bcd29eac44" %} package: name: {{ name|lower }} From f1a1021e076a9bdc3aaca793cfcfe467c55fb62e Mon Sep 17 00:00:00 2001 From: Michael Roach Date: Fri, 9 Feb 2024 15:40:43 +1030 Subject: [PATCH 1955/2173] Update purge_haplotigs to 1.1.3 (#45726) * Update purge_haplotigs to 1.1.3 * Update maintainer information --- recipes/purge_haplotigs/meta.yaml | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/recipes/purge_haplotigs/meta.yaml b/recipes/purge_haplotigs/meta.yaml index c8cde29e6dec1..583dc731bed0f 100644 --- a/recipes/purge_haplotigs/meta.yaml +++ b/recipes/purge_haplotigs/meta.yaml @@ -1,15 +1,18 @@ -{% set version = "1.1.2" %} +{% set name = "purge_haplotigs" %} +{% set version = "1.1.3" %} package: - name: purge_haplotigs - version: '{{ version }}' + name: {{ name }} + version: {{ version }} source: - url: https://bitbucket.org/mroachawri/purge_haplotigs/get/v{{ version }}.tar.gz - sha256: 14daf0454606232c5adbc5ca42cd873a0c4eb8b7f52d22edd434027d5e8fdca0 + url: https://bitbucket.org/mroachawri/{{ name }}/get/v{{ version }}.tar.gz + sha256: 68d9bc8464f6d53281127576eab67068fbc1c45d37a60dffdc344b2c0be4ff84 build: number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} noarch: generic requirements: @@ -40,3 +43,7 @@ about: license_family: MIT license_file: LICENSE summary: Pipeline to help with curating heterozygous diploid genome assemblies. + +extra: + recipe-maintainers: + - beardymcjohnface From 619e346893aa896f376e3f6a7c1ad56a25f885d3 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 9 Feb 2024 01:27:30 -0600 Subject: [PATCH 1956/2173] Update taxonomy to 0.10.0 (#45674) * Update taxonomy to 0.10.0 * remove python pinning * move rust and maturin to build dependencies and fix PATH * move maturin back to host section --- build-fail-blacklist | 3 --- recipes/taxonomy/LICENSE | 21 --------------------- recipes/taxonomy/build.sh | 21 +++++++++++---------- recipes/taxonomy/meta.yaml | 19 +++++++++++-------- recipes/taxonomy/pyproject.patch | 9 +++++++++ 5 files changed, 31 insertions(+), 42 deletions(-) delete mode 100644 recipes/taxonomy/LICENSE create mode 100644 recipes/taxonomy/pyproject.patch diff --git a/build-fail-blacklist b/build-fail-blacklist index e6c6649ef9f6f..f3f7e72ee6305 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1057,9 +1057,6 @@ recipes/fmlrc2 # tries to download zlib itself, which fails recipes/d4binding -# maturin build fails -recipes/taxonomy - # no matching package named `quickersort` found recipes/mudskipper diff --git a/recipes/taxonomy/LICENSE b/recipes/taxonomy/LICENSE deleted file mode 100644 index 2cdd581feedab..0000000000000 --- a/recipes/taxonomy/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2019 One Codex - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/recipes/taxonomy/build.sh b/recipes/taxonomy/build.sh index 9a5673054d7ff..e7403810f522a 100644 --- a/recipes/taxonomy/build.sh +++ b/recipes/taxonomy/build.sh @@ -1,17 +1,18 @@ #!/bin/bash -set -ex +set -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" if [ `uname` == Darwin ]; then - export HOME=`mktemp -d` + export HOME=`mktemp -d` + export PATH="$CARGO_HOME/bin:$PATH" fi -curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y - -export PATH="$HOME/.cargo/bin:$PATH" - -export CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER="$CC" - -maturin build --interpreter python --release #--cargo-extra-args="--features=python" +# build statically linked binary with Rust +RUST_BACKTRACE=1 +maturin build -b cffi --interpreter "${PYTHON}" --release --strip #--cargo-extra-args="--features=python" -$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv +${PYTHON} -m pip install . --no-deps --no-build-isolation -vvv diff --git a/recipes/taxonomy/meta.yaml b/recipes/taxonomy/meta.yaml index 793be03563091..10c7fb6a093ab 100644 --- a/recipes/taxonomy/meta.yaml +++ b/recipes/taxonomy/meta.yaml @@ -1,26 +1,30 @@ {% set name = "taxonomy" %} -{% set version = "0.9.0" %} +{% set version = "0.10.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/onecodex/taxonomy/archive/v{{ version }}.tar.gz - sha256: 3d9fb6604ce119bd46635eb1ab43212f9da591f0b6fc53cfcd8c97598025d159 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/taxonomy-{{ version }}.tar.gz + sha256: 3ff7e2299c9554b8b8be2f00bb4cd9722d0ae820e8a271aaf1390a7e790c3f51 + patches: + - pyproject.patch build: - number: 1 - skip: True # [py < 37] + number: 0 + run_exports: + - {{ pin_subpackage('taxonomy', max_pin="x.x") }} requirements: build: - {{ compiler('c') }} + - {{ compiler('rust') }} host: + - python - pip - cffi - maturin - - python run: - python - cffi @@ -31,8 +35,7 @@ test: about: home: https://github.com/onecodex/taxonomy/ - license: MIT License + license: MIT license_family: MIT license_file: LICENSE summary: "Python and Rust library for loading, saving, and manipulating taxonomic trees" - diff --git a/recipes/taxonomy/pyproject.patch b/recipes/taxonomy/pyproject.patch new file mode 100644 index 0000000000000..7d6fc2b1b3235 --- /dev/null +++ b/recipes/taxonomy/pyproject.patch @@ -0,0 +1,9 @@ +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -1,5 +1,5 @@ + [build-system] +-requires = ["maturin>=0.14,<0.15"] ++requires = ["maturin>=1.0,<2.0"] + build-backend = "maturin" + + [project] From 231ac53be055fdabe9a49c8a95fe77ecfb573ebe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 9 Feb 2024 02:27:46 -0500 Subject: [PATCH 1957/2173] Update hecatomb to 1.3.2 (#45729) --- recipes/hecatomb/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hecatomb/meta.yaml b/recipes/hecatomb/meta.yaml index 6793fb605bf02..3aa74512cf22e 100644 --- a/recipes/hecatomb/meta.yaml +++ b/recipes/hecatomb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "Hecatomb" %} -{% set version = "1.3.1" %} +{% set version = "1.3.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/shandley/{{ name|lower }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: ce078b0d8327e07ba2a814d054b3f7b8c09ec76ad8dd421549676c792ff35ab1 + sha256: d1699d80bef234c6815333d468721a6c57c24697a26d6e26ab9e0a3167373ff8 build: number: 0 From fc8475f9c484b953df5e066ea2d4704fa0baff47 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 9 Feb 2024 12:07:00 -0500 Subject: [PATCH 1958/2173] Update primer3-py to 2.0.2 (#45738) --- recipes/primer3-py/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/primer3-py/meta.yaml b/recipes/primer3-py/meta.yaml index dd28aab34137d..f9a31011d0db2 100644 --- a/recipes/primer3-py/meta.yaml +++ b/recipes/primer3-py/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primer3-py" %} -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/primer3-py-{{ version }}.tar.gz - sha256: 30b549c568ae5712e3e6cde6c1f5b243f328247ec8d6ec89d4b705873a44e772 + sha256: 1fa140cab651a2841ec71f3e29ef347e6546f644884e3cac1fe536c4feb8eb5c build: - number: 1 + number: 0 skip: True # [py < 38] run_exports: - {{ pin_subpackage('primer3-py', max_pin="x") }} From 2cfa2bab74d0c387d4d6665798fa80b0ade87aef Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Fri, 9 Feb 2024 15:10:04 -0800 Subject: [PATCH 1959/2173] Update auspice to 2.52.0 (#45745) --- recipes/auspice/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/auspice/meta.yaml b/recipes/auspice/meta.yaml index 32592ef4fcbe1..2be485192dd3a 100644 --- a/recipes/auspice/meta.yaml +++ b/recipes/auspice/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.50.0" %} +{% set version = "2.52.0" %} package: name: auspice @@ -6,7 +6,7 @@ package: source: url: https://registry.npmjs.org/auspice/-/auspice-{{ version }}.tgz - sha256: 60642de3c9cbbce388a81668f1d116ca8c28520abe5770298dd51aebd94660b0 + sha256: c23a411c10066d173ed2c4b687e3f60429b3ef4cf16cc6e13d79766bafba28df build: number: 0 From f204d2a9593f19ce67fe61cc0359ac5621d76327 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Fri, 9 Feb 2024 15:11:10 -0800 Subject: [PATCH 1960/2173] Update evofr to 0.1.22 (#45744) Includes dependency changes https://github.com/blab/evofr/commit/4b64dfc5cb14620021835aaee41337affcd3a3a4 --- recipes/evofr/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/evofr/meta.yaml b/recipes/evofr/meta.yaml index a5eae9189357a..e874ecf75867f 100644 --- a/recipes/evofr/meta.yaml +++ b/recipes/evofr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.21" %} +{% set version = "0.1.22" %} package: name: evofr @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/e/evofr/evofr-{{ version }}.tar.gz - sha256: 0ec5329a19087992e14e8c5a5b969b6069308f287595125b67574176c73532c0 + sha256: 8643b54c985dd01ce915c1cf4f475d4f29370166ad62cde7619f66c9f50890e6 build: number: 0 @@ -24,9 +24,9 @@ requirements: - python >=3.9,<4 - numpy >=1.22.4 - pandas >=1.4.2 - - jax >=0.4.1,<0.5.0 + - jax >=0.4.14,<0.5.0 - jaxlib >=0.4.1,<0.5.0 - - numpyro >=0.12.0,<0.13.0 + - numpyro >=0.13.2,<0.14.0 - blackjax >=0.9.6,<0.10.0 test: From f35c61b8f1719d6cdd5210a49a807b0c561f7b61 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 9 Feb 2024 18:23:55 -0500 Subject: [PATCH 1961/2173] Update aletsch to 1.1.1 (#45736) --- recipes/aletsch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/aletsch/meta.yaml b/recipes/aletsch/meta.yaml index f97373d1f61d4..1abc848d3520a 100644 --- a/recipes/aletsch/meta.yaml +++ b/recipes/aletsch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "aletsch" %} -{% set version = "1.1.0" %} +{% set version = "1.1.1" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/Shao-Group/aletsch/releases/download/v{{ version }}/aletsch-{{ version }}.tar.gz" - sha256: "075e514da0b8e264fb7822d065061f406d5f73bea95c60ab31f08d2c498010a2" + sha256: "3537e90213baa7ea132b1648f4687780537999f3796711cf7398f9168d72f027" build: number: 0 From e0c01e2c030a02c54ae2ad541f85449181d18082 Mon Sep 17 00:00:00 2001 From: Sergey Koren Date: Sat, 10 Feb 2024 03:19:07 -0500 Subject: [PATCH 1962/2173] update verkko to v2.0 (#45708) * update verkko to v2.0 * try fix osx build * fix --- recipes/verkko/meta.yaml | 15 ++++---- recipes/verkko/osx_availability.patch | 52 +++++++++++++++++++++++++++ recipes/verkko/run_test.sh | 29 +++++++++------ recipes/verkko/version.patch | 2 +- 4 files changed, 80 insertions(+), 18 deletions(-) create mode 100644 recipes/verkko/osx_availability.patch diff --git a/recipes/verkko/meta.yaml b/recipes/verkko/meta.yaml index 5f622352244e0..247baef98498b 100644 --- a/recipes/verkko/meta.yaml +++ b/recipes/verkko/meta.yaml @@ -1,5 +1,5 @@ {% set name = "verkko" %} -{% set version = "1.4.1" %} +{% set version = "2.0" %} package: name: {{ name|lower }} @@ -7,14 +7,16 @@ package: source: url: https://github.com/marbl/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz - md5: 37299a7938c9806763586c2d386f38e8 + md5: be5b322b2fcfcee07c0d64fa49c6a9b4 patches: - version.patch - - tips.patch + - osx_availability.patch # [osx] build: number: 0 + run_exports: + - {{ pin_subpackage('verkko', max_pin="x.x") }} requirements: build: @@ -25,15 +27,16 @@ requirements: - rust >=1.66 host: - gsl + - zlib run: - python >=3.7 - perl >=5.6 + - seqtk - parasail-python >=1.3.3 - networkx >=2.6.3 - biopython - - snakemake-minimal >=7.8.0 - - graphaligner >=1.0.17b - - mbg >=1.0.15 + - snakemake-minimal >=7.8.0,<8.0 + - graphaligner >=1.0.19 - findutils >=4.6.0 - mashmap >=3.0.6 - winnowmap >=2.0 diff --git a/recipes/verkko/osx_availability.patch b/recipes/verkko/osx_availability.patch new file mode 100644 index 0000000000000..69344ea5b476f --- /dev/null +++ b/recipes/verkko/osx_availability.patch @@ -0,0 +1,52 @@ +diff --git a/src/MBG/makefile b/src/MBG/makefile +index 0c0113b..c6fd847 100644 +--- a/src/MBG/makefile ++++ b/src/MBG/makefile +@@ -1,7 +1,7 @@ + PLATFORM=$(shell uname -s) + + GPP=$(CXX) +-CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Wno-unused-parameter -Icxxopts/include -Iconcurrentqueue `pkg-config --cflags zlib` ++CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Wno-unused-parameter -Icxxopts/include -Iconcurrentqueue `pkg-config --cflags zlib` -D_LIBCPP_DISABLE_AVAILABILITY + + ODIR=obj + BINDIR=bin +diff --git a/src/hifioverlapper/MBG/makefile b/src/hifioverlapper/MBG/makefile +index 0c0113b..c6fd847 100644 +--- a/src/hifioverlapper/MBG/makefile ++++ b/src/hifioverlapper/MBG/makefile +@@ -1,7 +1,7 @@ + PLATFORM=$(shell uname -s) + + GPP=$(CXX) +-CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Wno-unused-parameter -Icxxopts/include -Iconcurrentqueue `pkg-config --cflags zlib` ++CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Wno-unused-parameter -Icxxopts/include -Iconcurrentqueue `pkg-config --cflags zlib` -D_LIBCPP_DISABLE_AVAILABILITY + + ODIR=obj + BINDIR=bin +diff --git a/src/hifioverlapper/makefile b/src/hifioverlapper/makefile +index 0bc9ee7..0f53de7 100644 +--- a/src/hifioverlapper/makefile ++++ b/src/hifioverlapper/makefile +@@ -1,5 +1,7 @@ ++PLATFORM=$(shell uname -s) ++ + GPP=$(CXX) +-CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Icxxopts/include -Wno-unused-parameter `pkg-config --cflags zlib` -IMBG/src -Iconcurrentqueue ++CPPFLAGS=-Wall -Wextra -std=c++17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Icxxopts/include -Wno-unused-parameter `pkg-config --cflags zlib` -IMBG/src -Iconcurrentqueue -D_LIBCPP_DISABLE_AVAILABILITY + + ODIR=obj + BINDIR=bin +@@ -14,7 +16,11 @@ DEPS = $(patsubst %, $(SRCDIR)/%, $(_DEPS)) + _OBJ = MatchIndex.o MinimizerIterator.o TwobitString.o ReadStorage.o UnitigKmerCorrector.o UnitigStorage.o ReadMatchposStorage.o + OBJ = $(patsubst %, $(ODIR)/%, $(_OBJ)) + +-LINKFLAGS = $(CPPFLAGS) -Wl,-Bstatic $(LIBS) -Wl,-Bdynamic -Wl,--as-needed -lpthread -pthread -static-libstdc++ ++ifeq ($(PLATFORM),Linux) ++ LINKFLAGS = $(CPPFLAGS) -Wl,-Bstatic $(LIBS) -Wl,-Bdynamic -Wl,--as-needed -lpthread -pthread -static-libstdc++ ++else ++ LINKFLAGS = $(CPPFLAGS) $(LIBS) -lpthread -pthread -static-libstdc++ ++endif + + VERSION := Branch $(shell git rev-parse --abbrev-ref HEAD) commit $(shell git rev-parse HEAD) $(shell git show -s --format=%ci) + diff --git a/recipes/verkko/run_test.sh b/recipes/verkko/run_test.sh index 69595121dea11..05ab448c0a670 100644 --- a/recipes/verkko/run_test.sh +++ b/recipes/verkko/run_test.sh @@ -6,6 +6,8 @@ if [ ! -n "${PREFIX-}" -a "${PREFIX+defined}" != defined ]; then echo "Prefix undefined, setting it to be path to script" PREFIX=$(dirname "$0") PREFIX=$(dirname "$PREFIX") + + export PATH=$PREFIX/bin:$PATH fi # taken from yacrd recipe, see: https://github.com/bioconda/bioconda-recipes/blob/2b02c3db6400499d910bc5f297d23cb20c9db4f8/recipes/yacrd/build.sh @@ -18,20 +20,25 @@ if [ "$(uname)" == "Darwin" ]; then fi # download and run a small assembly, skip alignment of ONT on OSX to save time -rm -f ./hifi.fastq.gz ./ont.fastq.gz +rm -f ./subset.ids ./hifi.fastq.gz ./ont.fastq.gz curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_hifi_subset24x.fastq.gz -o hifi.fastq.gz curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_ont_subset50x.fastq.gz -o ont.fastq.gz +curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_hifi_subset.ids -o subset.ids + +seqtk sample hifi.fastq.gz 0.5 |seqtk subseq - subset.ids > hifi_lowcov.fastq +seqtk sample ont.fastq.gz 0.10 > ont_lowcov.fastq +touch empty.fasta # now start tests -ONT="--nano ./ont.fastq.gz" -if [ "$(uname)" == "Darwin" ]; then - ONT="" -fi +ONT="--nano ./ont_lowcov.fastq" +#if [ "$(uname)" == "Darwin" ]; then +# ONT="" +#fi -verkko -d asm --no-correction --hifi ./hifi.fastq.gz $ONT +verkko -d asm --hifi ./hifi_lowcov.fastq $ONT > run.out 2>&1 if [ -s asm/assembly.fasta ]; then - python $PREFIX/lib/verkko/scripts/circularize_ctgs.py -p 10 -f 0.01 -o asm/assembly_circular.fasta --min-ovl 1000 asm/assembly.fasta + python $PREFIX/lib/verkko/scripts/circularize_ctgs.py -p 5 -f 0.01 -o asm/assembly_circular.fasta --min-ovl 1 asm/assembly.fasta fi if [ ! -s asm/assembly_circular.fasta ]; then @@ -46,9 +53,9 @@ if [ "$(uname)" == "Darwin" ]; then exit 0 fi -verkko -d asm --hifi hifi.fastq.gz $ONT --hic1 hifi.fastq.gz --hic2 hifi.fastq.gz +verkko -d asm --hifi hifi_lowcov.fastq $ONT --hic1 empty.fasta --hic2 empty.fasta > run.out 2>&1 -if [ ! -e asm/assembly.haplotype1.fasta ]; then +if [[ ! -s asm/assembly.unassigned.fasta || -s asm/assembly.haplotype1.fasta || -s asm/assembly.haplotype2.fasta ]]; then echo "Error: verkko hic assembly test failed!" tail -n +1 `find asm -name *.err` exit 1 @@ -56,9 +63,9 @@ fi #now test trio rm -rf asm/8-* asm/6-layoutContigs/ asm/7-consensus/ asm/assembly.* asm/6-rukki/ -$PREFIX/lib/verkko/bin/meryl count compress k=21 memory=4 threads=8 output empty1.meryl hifi.fastq.gz +$PREFIX/lib/verkko/bin/meryl count compress k=21 memory=4 threads=8 output empty1.meryl hifi_lowcov.fastq $PREFIX/lib/verkko/bin/meryl greater-than 100 empty1.meryl/ output empty2.meryl -verkko -d asm --hifi hifi.fastq.gz $ONT --hap-kmers empty1.meryl empty2.meryl trio +verkko -d asm --hifi hifi_lowcov.fastq $ONT --hap-kmers empty1.meryl empty2.meryl trio > run.out 2>&1 if [ ! -s asm/assembly.haplotype1.fasta ]; then echo "Error: verkko trio assembly test failed!" diff --git a/recipes/verkko/version.patch b/recipes/verkko/version.patch index 9566555502810..9a05bb37485c1 100644 --- a/recipes/verkko/version.patch +++ b/recipes/verkko/version.patch @@ -25,7 +25,7 @@ index 5f33ff4..25c2285 100644 # Perform post-processing on global variables as needed. DEFS := $(addprefix -D,${DEFS}) -INCDIRS := $(addprefix -I,$(call CANONICAL_PATH,${INCDIRS})) --VERSION := verkko release v1.4.1 +-VERSION := verkko release v2.0 +INCDIRS := $(addprefix -isystem,$(call CANONICAL_PATH,${INCDIRS})) +VERSION := bioconda $(PKG_NAME) bioconda $(PKG_VERSION) From 1326a94275b0e0c7b315d3ac204355330c8d0abc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 05:11:46 -0500 Subject: [PATCH 1963/2173] Update snakemake to 8.4.8 (#45739) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index c1aeb3dbbadc4..9fc08ce4c7cbd 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.7" %} +{% set version = "8.4.8" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 030f299937a09d328254a0705b87b91ecaf7d3bce51f3c4cee16df2a3718158f + sha256: ab64a4f402f78ec252f211d9cc900344fdc2a000dadcec91833efb5fd0f275e7 build: number: 0 From 67974cba373a1f781725543f0e2952b34ab2cc05 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 05:12:46 -0500 Subject: [PATCH 1964/2173] Update trgt to 0.8.0 (#45740) --- recipes/trgt/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/trgt/meta.yaml b/recipes/trgt/meta.yaml index e56dd01517b57..686a008743d0f 100644 --- a/recipes/trgt/meta.yaml +++ b/recipes/trgt/meta.yaml @@ -1,7 +1,7 @@ {% set name = "trgt" %} -{% set version = "0.7.0" %} -{% set trgt_sha256 = "09ea997ffd90e1c9aba0a25a38eaa70a95d0d4c365518003b6f340b6f6b9e186" %} -{% set trvz_sha256 = "4b7a642dc69093d68eb8d68a10c49749c382f0db8f71131ce703687438b69b13" %} +{% set version = "0.8.0" %} +{% set trgt_sha256 = "1e927aa3befb6e4973798c742747a88e804ff39f34c6d1c9184b2fecf0f23757" %} +{% set trvz_sha256 = "fce346185d15809a5d1b72ca0c01521d5cdefd3fc924ad4682d0398129eb99e1" %} package: name: {{ name }} From 662b3f66e67ac5d2e44c9767a91b519a94d01a68 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Sat, 10 Feb 2024 21:13:26 +1100 Subject: [PATCH 1965/2173] Add hmftools-mark-dups 1.1 (#45728) --- recipes/hmftools-mark-dups/build.sh | 12 +++++ recipes/hmftools-mark-dups/markdups.sh | 69 ++++++++++++++++++++++++++ recipes/hmftools-mark-dups/meta.yaml | 32 ++++++++++++ 3 files changed, 113 insertions(+) create mode 100644 recipes/hmftools-mark-dups/build.sh create mode 100755 recipes/hmftools-mark-dups/markdups.sh create mode 100644 recipes/hmftools-mark-dups/meta.yaml diff --git a/recipes/hmftools-mark-dups/build.sh b/recipes/hmftools-mark-dups/build.sh new file mode 100644 index 0000000000000..55784e8b35b79 --- /dev/null +++ b/recipes/hmftools-mark-dups/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p "$TGT" +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cd "${SRC_DIR}" +mv mark-dups*.jar $TGT/markdups.jar + +cp $RECIPE_DIR/markdups.sh $TGT/markdups +ln -s $TGT/markdups $PREFIX/bin +chmod 0755 "${PREFIX}/bin/markdups" diff --git a/recipes/hmftools-mark-dups/markdups.sh b/recipes/hmftools-mark-dups/markdups.sh new file mode 100755 index 0000000000000..c69115b6bee1d --- /dev/null +++ b/recipes/hmftools-mark-dups/markdups.sh @@ -0,0 +1,69 @@ +#!/bin/bash +# hmftools MarkDups executable shell script +# https://github.com/hartwigmedical/hmftools/tree/master/mark-dups +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' + then + pass_args="$arg" + else + pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg + fi + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == com.hartwig.* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/markdups.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/markdups.jar" $pass_args +fi +exit diff --git a/recipes/hmftools-mark-dups/meta.yaml b/recipes/hmftools-mark-dups/meta.yaml new file mode 100644 index 0000000000000..c1fc3b06c02b4 --- /dev/null +++ b/recipes/hmftools-mark-dups/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.1" %} +{% set sha256 = "f2939d64ef5d96c638264074cf28eaf140d85ff5a21b537dbb156b54ab142047" %} + +package: + name: hmftools-mark-dups + version: '{{ version }}' + +source: + url: https://github.com/hartwigmedical/hmftools/releases/download/mark-dups-v{{ version }}/mark-dups_v{{ version }}.jar + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('hmftools-mark-dups', max_pin="x.x") }} + +requirements: + run: + - openjdk >=8 + - sambamba >=1.0 + - samtools >=1.17 + +test: + commands: + - 'markdups -version | grep MarkDups' + +about: + home: https://github.com/hartwigmedical/hmftools/tree/master/mark-dups + license: GPL-3.0-only + license_family: GPL + summary: Mark read duplicates and form consenus sequences From 1e5cb52afb6a4a28a11e25d128472f9bcb91076c Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Sat, 10 Feb 2024 21:16:13 +1100 Subject: [PATCH 1966/2173] Add r-linxreport 1.0.0 (#45727) --- recipes/r-linxreport/build.sh | 6 ++++ recipes/r-linxreport/meta.yaml | 56 ++++++++++++++++++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 recipes/r-linxreport/build.sh create mode 100644 recipes/r-linxreport/meta.yaml diff --git a/recipes/r-linxreport/build.sh b/recipes/r-linxreport/build.sh new file mode 100644 index 0000000000000..6fd1541af9a34 --- /dev/null +++ b/recipes/r-linxreport/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash +$R CMD INSTALL --build . + +mkdir -p ${PREFIX}/bin +cp ${SRC_DIR}/inst/cli/linxreport.R ${PREFIX}/bin +chmod +x ${PREFIX}/bin/linxreport.R diff --git a/recipes/r-linxreport/meta.yaml b/recipes/r-linxreport/meta.yaml new file mode 100644 index 0000000000000..a7ac9a43641e4 --- /dev/null +++ b/recipes/r-linxreport/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.0.0" %} +{% set sha256 = "447658b9ac5974f696c6b2c0fce59fc846d7419da8fc79aa81109630701cef55" %} + +package: + name: r-linxreport + version: '{{ version }}' + +source: + url: https://github.com/umccr/linxreport/archive/refs/tags/v{{ version }}.tar.gz + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("r-linxreport", max_pin="x.x") }} + +requirements: + host: + - r-base >=4 + - r-assertthat + - r-details + - r-dplyr + - r-dt + - r-fs + - r-gtools + - r-optparse + - r-readr + - r-rlang + - r-rmarkdown + - r-sessioninfo + - r-stringr + run: + - r-base >=4 + - r-assertthat + - r-details + - r-dplyr + - r-dt + - r-fs + - r-gtools + - r-optparse + - r-readr + - r-rlang + - r-rmarkdown + - r-sessioninfo + - r-stringr + +test: + commands: + - $R -e "library('linxreport')" + +about: + home: https://github.com/umccr/linxreport + license: MIT + file LICENSE + license_family: MIT + summary: LINX Result Reporter From 7599d499f958950918b497ec1fa623dcdce44666 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 05:20:55 -0500 Subject: [PATCH 1967/2173] Update freyja to 1.4.9 (#45742) --- recipes/freyja/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/freyja/meta.yaml b/recipes/freyja/meta.yaml index 41ae8a92a8758..6c3686a0eef7c 100644 --- a/recipes/freyja/meta.yaml +++ b/recipes/freyja/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.8" %} +{% set version = "1.4.9" %} {% set name = "Freyja" %} package: @@ -16,7 +16,7 @@ build: source: url: https://github.com/andersen-lab/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 4534bf227fc58317c535c2c5d0d031816c8a5b1ae0968175a97cd02cb3530672 + sha256: aeaa1697d7e12386e50c96880ab976e2cc68989bd7fdf4bfe802cb02bb3982ba requirements: host: From e3417bf5e18e6e297d43ded3bb6d4f88d4ff0a5b Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Sat, 10 Feb 2024 15:26:16 +0100 Subject: [PATCH 1968/2173] require python >=3.9 for varfish-cli (#45731) --- recipes/varfish-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varfish-cli/meta.yaml b/recipes/varfish-cli/meta.yaml index 909078b89013b..6baa90f445ec8 100644 --- a/recipes/varfish-cli/meta.yaml +++ b/recipes/varfish-cli/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - varfish-cli = varfish_cli.__main__:main @@ -23,7 +23,7 @@ requirements: - python >=3 - pip run: - - python >=3 + - python >=3.9 - attrs - cattrs - jsonschema From 066a5a600a5afee0918f5a13f9d660954800824a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:01:11 -0500 Subject: [PATCH 1969/2173] Update pymzml to 2.5.4 (#45735) --- recipes/pymzml/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pymzml/meta.yaml b/recipes/pymzml/meta.yaml index a0256bea1be73..626e6ccb8c945 100644 --- a/recipes/pymzml/meta.yaml +++ b/recipes/pymzml/meta.yaml @@ -1,10 +1,10 @@ package: name: pymzml - version: "2.5.3" + version: "2.5.4" source: - url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.3.tar.gz - sha256: 3578da1962670ef90027cb2944ad64dc39a4457cd93a637bbd2655a7f074a2ee + url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.4.tar.gz + sha256: f3da945e09f4b7b091feaf5b168c3543b3489bc8adf0bac48029f8d70b22de7f build: number: 0 From 9c38600a2d68d89ddbe574d27f7945b088060f46 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:01:27 -0500 Subject: [PATCH 1970/2173] Update nanomotif to 0.1.18 (#45734) --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index 8bf32fe611950..afe275f534641 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.17" %} +{% set version = "0.1.18" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: 48bd357472e36ed6336ff555fc55a81779d05ea3cf0e1b25f6a5d1cadf0763f5 + sha256: a8a4e7bfe21617c51003ae9d0ed056b1a5380d7df83b3d115cd079d06e8cd116 build: entry_points: From fbe2febbf92e17bea52854d82df8a844b0c4c7b6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:01:39 -0500 Subject: [PATCH 1971/2173] Update tissuumaps to 3.2.0.4 (#45733) --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index 8555dcfae9eba..5f81144cf6ced 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.0.3" %} +{% set version = "3.2.0.4" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: 372a92e7aa8fb5f6149bac1133aae6d04653c87ba3048af9ed95da84a64f2592 + sha256: 02ce7e575075fd5b401c322ade25ed9f52cc4b7af944a9c29441c1784506a1ed build: number: 0 From 4a1fb373f7cf46afb834c6f2de9556e38c29b05d Mon Sep 17 00:00:00 2001 From: Brandon Seah Date: Sat, 10 Feb 2024 19:01:53 +0100 Subject: [PATCH 1972/2173] Add recipe pytransaln v0.2.1 (#45732) * Add recipe pytransaln from PyPI package Generated by grayskull * Add homepage URL * Add run_exports statement --- recipes/pytransaln/meta.yaml | 50 ++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 recipes/pytransaln/meta.yaml diff --git a/recipes/pytransaln/meta.yaml b/recipes/pytransaln/meta.yaml new file mode 100644 index 0000000000000..d3c02cd1a111b --- /dev/null +++ b/recipes/pytransaln/meta.yaml @@ -0,0 +1,50 @@ +{% set name = "pytransaln" %} +{% set version = "0.2.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pytransaln-{{ version }}.tar.gz + sha256: 280a035573dc2e709d226b628fbee41d1ee6afcff5f7a7185aac05135314a2e2 + +build: + entry_points: + - pytransaln = pytransaln.pytransaln:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('pytransaln', max_pin="x.x") }} + +requirements: + host: + - python + - setuptools >=61.0.0 + - pip + run: + - python + - biopython >=1.80,<2 + - pandas >=1.3,<3 + - matplotlib-base >=3.6,<4 + - pyhmmer ==0.10 + +test: + imports: + - pytransaln + commands: + - pip check + - pytransaln --help + requires: + - pip + +about: + home: https://github.com/monagrland/pytransaln + summary: Translation-guided nucleotide alignment for coding sequences + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - kbseah From ddefda81cc1d464233f38a27ec059fca96529df6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:02:03 -0500 Subject: [PATCH 1973/2173] Update mehari to 0.22.0 (#45730) * Update mehari to 0.22.0 * Update homepage URL --------- Co-authored-by: Brandon Seah --- recipes/mehari/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 91cc370330ddc..e410ddacac824 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.21.2" %} -{% set sha256 = "37fc1ef33d8d7f49886312283ac1e4009fba92db40e254cb03356e0e6f643774" %} +{% set version = "0.22.0" %} +{% set sha256 = "1240ac7d026eebfa6a4396548f748848501fd0128e3ca81cc890ee70faf33fac" %} package: name: mehari @@ -38,6 +38,6 @@ test: - mehari -h about: - home: https://github.com/bihealth/varfish-org + home: https://github.com/varfish-org/mehari license: MIT summary: VEP-like tool for sequence ontology and HGVS annotation of VCF files written in Rust. From a06525bd636223042ec845e75a653249534103dd Mon Sep 17 00:00:00 2001 From: Jianshu_Zhao <38149286+jianshu93@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:02:44 -0500 Subject: [PATCH 1974/2173] Add new graph embedding software for large-scale biological network (#45725) * Update annembed v0.1.4 * Update gsearch v0.1.9 * Add graphembed v0.1.0 --- recipes/graphembed/build.sh | 8 ++++++++ recipes/graphembed/meta.yaml | 35 +++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 recipes/graphembed/build.sh create mode 100644 recipes/graphembed/meta.yaml diff --git a/recipes/graphembed/build.sh b/recipes/graphembed/build.sh new file mode 100644 index 0000000000000..f4634f476014f --- /dev/null +++ b/recipes/graphembed/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -euo + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --features intel-mkl-static --verbose --path . --root $PREFIX diff --git a/recipes/graphembed/meta.yaml b/recipes/graphembed/meta.yaml new file mode 100644 index 0000000000000..99a1ca4a5f0bc --- /dev/null +++ b/recipes/graphembed/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.1.0" %} + +package: + name: graphembed + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('graphembed', max_pin="x.x") }} + skip: True # [osx] +source: + url: https://github.com/jianshu93/graphembed/archive/v{{ version }}.tar.gz + sha256: 5c38244781574c2dd1aa1c20e1b2b5ea181f3ffab42ea47a014be0de28810210 + +requirements: + build: + - {{ compiler("cxx") }} + - {{ compiler('c') }} + - rust >=1.39 + - make + - cmake + +test: + commands: + - graphembed -h + +about: + home: https://github.com/jean-pierreBoth/graphembed + license: MIT + summary: Efficient Graph Embedding via Recursive Sketching or High-order Transitivity Preserving +extra: + maintainers: + - Jean Pierre-Both + - Jianshu Zhao From ed91eb2e3c4346a34c71a6c1d144e5fb74a1081c Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Sun, 11 Feb 2024 05:09:38 +1100 Subject: [PATCH 1975/2173] Add hmftools-cuppa 1.8.1 (#45643) * Add hmftools-cuppa 1.8.1 * Replace matplotlib with matplotlib-base * Create target subdirectory for cuppa-chart * Remove quotes preventing BASH brace expansion * Pin r-base to minor version only * Fix empty comment line * Set correct path for passthrough BASH script * Further relax r-base version dependency --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/hmftools-cuppa/build.sh | 14 ++++++ recipes/hmftools-cuppa/cuppa-chart.sh | 23 +++++++++ recipes/hmftools-cuppa/cuppa.sh | 69 +++++++++++++++++++++++++++ recipes/hmftools-cuppa/meta.yaml | 46 ++++++++++++++++++ 4 files changed, 152 insertions(+) create mode 100644 recipes/hmftools-cuppa/build.sh create mode 100755 recipes/hmftools-cuppa/cuppa-chart.sh create mode 100755 recipes/hmftools-cuppa/cuppa.sh create mode 100644 recipes/hmftools-cuppa/meta.yaml diff --git a/recipes/hmftools-cuppa/build.sh b/recipes/hmftools-cuppa/build.sh new file mode 100644 index 0000000000000..a11f515c544f5 --- /dev/null +++ b/recipes/hmftools-cuppa/build.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p $TGT/{,chart/} +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cd "${SRC_DIR}" +mv jar/cuppa*.jar $TGT/cuppa.jar +mv src/cuppa/src/main/resources/cuppa-chart/* $TGT/chart/ + +cp $RECIPE_DIR/cuppa.sh $TGT/cuppa +cp $RECIPE_DIR/cuppa-chart.sh $TGT/cuppa-chart +ln -s $TGT/cuppa{,-chart} ${PREFIX}/bin/ +chmod 0755 ${PREFIX}/bin/cuppa{,-chart} diff --git a/recipes/hmftools-cuppa/cuppa-chart.sh b/recipes/hmftools-cuppa/cuppa-chart.sh new file mode 100755 index 0000000000000..98ffa9f9ad790 --- /dev/null +++ b/recipes/hmftools-cuppa/cuppa-chart.sh @@ -0,0 +1,23 @@ +#!/bin/bash +# hmftools CUPPA chart executable shell script +# https://github.com/hartwigmedical/hmftools/tree/master/cuppa +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Python installed with Anaconda to ensure correct version +python="$ENV_PREFIX/bin/python" + +# Run with argument passthrough +eval ${python} ${DIR}/chart/cuppa-chart.py ${@} diff --git a/recipes/hmftools-cuppa/cuppa.sh b/recipes/hmftools-cuppa/cuppa.sh new file mode 100755 index 0000000000000..33e257cb82296 --- /dev/null +++ b/recipes/hmftools-cuppa/cuppa.sh @@ -0,0 +1,69 @@ +#!/bin/bash +# hmftools CUPPA executable shell script +# https://github.com/hartwigmedical/hmftools/tree/master/cuppa +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' + then + pass_args="$arg" + else + pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg + fi + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/cuppa.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/cuppa.jar" $pass_args +fi +exit diff --git a/recipes/hmftools-cuppa/meta.yaml b/recipes/hmftools-cuppa/meta.yaml new file mode 100644 index 0000000000000..4c09d7747c28f --- /dev/null +++ b/recipes/hmftools-cuppa/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.8.1" %} +{% set sha256_jar = "595cf6ba5a60a23cf18005cdc2aed18b3f48470f5479aa4e5ee6f386d23e00bb" %} +{% set sha256_src = "39bb318f590ba905c18c0ed42411c97ba482ed98059e456a0f5ec42ad915c8e1" %} + +package: + name: hmftools-cuppa + version: '{{ version }}' + +source: + - folder: jar + url: https://github.com/hartwigmedical/hmftools/releases/download/cuppa-v{{ version }}/cuppa_v{{ version }}.jar + sha256: '{{ sha256_jar }}' + - folder: src + url: https://github.com/hartwigmedical/hmftools/archive/refs/tags/cuppa-v{{ version }}.tar.gz + sha256: '{{ sha256_src }}' + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage("hmftools-cuppa", max_pin="x.x") }} + +requirements: + run: + - openjdk >=8 + - r-base >=4 + - r-cowplot + - r-ggplot2 + - r-gridextra + - r-stringi + - r-tidyr + - matplotlib-base >=3.3,<4 + - numpy >=1.19,<2 + - pandas >=1.1,<2 + - scipy >=1,<2 + - seaborn >=0.11,<1 + +test: + commands: + - 'cuppa | grep Cuppa' + +about: + home: https://github.com/hartwigmedical/hmftools/blob/master/cuppa/README.md + license: GPL-3.0-only + license_family: GPL3 + summary: Predict tissue of origin for tumor samples from WGTS data. From cce88a3cea810fd582e8cc46813501d6afd75039 Mon Sep 17 00:00:00 2001 From: Jack Huey <31162821+jackh726@users.noreply.github.com> Date: Sat, 10 Feb 2024 13:10:25 -0500 Subject: [PATCH 1976/2173] Add recipes for `bigtools` and `pybigtools` (#45634) * Add bigtools and pybigtools recipes bigtools: Fix urls and sha bigtools: specify pybigtools cargo.toml bigtools: Fix typo bigtools: Add bigtools build bigtools: Point cargo to bigtools dir * MIT License -> MIT --- recipes/bigtools/build.sh | 10 +++++++++ recipes/bigtools/meta.yaml | 35 +++++++++++++++++++++++++++++++ recipes/pybigtools/build.sh | 17 +++++++++++++++ recipes/pybigtools/meta.yaml | 40 ++++++++++++++++++++++++++++++++++++ 4 files changed, 102 insertions(+) create mode 100644 recipes/bigtools/build.sh create mode 100644 recipes/bigtools/meta.yaml create mode 100644 recipes/pybigtools/build.sh create mode 100644 recipes/pybigtools/meta.yaml diff --git a/recipes/bigtools/build.sh b/recipes/bigtools/build.sh new file mode 100644 index 0000000000000..cd115956df52e --- /dev/null +++ b/recipes/bigtools/build.sh @@ -0,0 +1,10 @@ +#!/bin/bash +set -ex + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" +export RUST_BACKTRACE=full + +cargo install --verbose --path ./bigtools --root $PREFIX --locked + diff --git a/recipes/bigtools/meta.yaml b/recipes/bigtools/meta.yaml new file mode 100644 index 0000000000000..72e92841c1718 --- /dev/null +++ b/recipes/bigtools/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.4.1" %} + +package: + name: bigtools + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('bigtools', max_pin="x.x") }} + +source: + url: https://github.com/jackh726/bigtools/archive/refs/tags/v{{ version }}.tar.gz + sha256: "92b9ea165adb1f9b13222d6c78e12148d9ba04a0d6ae96001820d43d9af7b39e" + +requirements: + build: + - {{ compiler('c') }} + - rust >=1.70 + +test: + commands: + - bigtools --help | grep Usage + +about: + home: https://github.com/jackh726/bigtools/ + license: MIT + doc_url: https://docs.rs/bigtools/latest/bigtools/ + summary: 'Bigtools provides a high-level, performant API for reading and writing bigWig and bigBed files.' + license_family: MIT + license_file: LICENSE + +extra: + identifiers: + - doi:10.5281/zenodo.10606493 diff --git a/recipes/pybigtools/build.sh b/recipes/pybigtools/build.sh new file mode 100644 index 0000000000000..d9c921719d1d8 --- /dev/null +++ b/recipes/pybigtools/build.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +# -e = exit on first error +# -x = print every executed command +set -ex + +# Use a custom temporary directory as home on macOS. +# (not sure why this is useful, but people use it in bioconda recipes) +if [ `uname` == Darwin ]; then + export HOME=`mktemp -d` +fi + +# Build the package using maturin - should produce *.whl files. +maturin build -m pybigtools/Cargo.toml --interpreter $PYTHON --release + +# Install *.whl files using pip +$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv diff --git a/recipes/pybigtools/meta.yaml b/recipes/pybigtools/meta.yaml new file mode 100644 index 0000000000000..fb3f24390e236 --- /dev/null +++ b/recipes/pybigtools/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "0.1.0" %} + +package: + name: pybigtools + version: {{ version }} + +source: + url: https://github.com/jackh726/bigtools/archive/refs/tags/pybigtools@v{{ version }}.tar.gz + sha256: "bb1a1f1d1f39ce0b73eafb40e291b1ded26fbb283898371ade3414c008b80cdf" + +build: + number: 0 + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('rust') }} + - maturin + host: + - pip + - python + run: + - python + - numpy + +test: + imports: + - pybigtools + +about: + home: https://github.com/jackh726/bigtools/ + license: MIT + summary: 'pybigtools: Python bindings to the Bigtools Rust library for high-performance BigWig and BigBed I/O' + license_family: MIT + license_file: LICENSE + doc_url: https://bigtools.readthedocs.io + +extra: + identifiers: + - doi:10.5281/zenodo.10606493 From efe8e263c7c03b3b06669474f96b2085e151eb07 Mon Sep 17 00:00:00 2001 From: Marco Matthies <71844+marcom@users.noreply.github.com> Date: Sat, 10 Feb 2024 19:11:54 +0100 Subject: [PATCH 1977/2173] Update linearpartition to 1.0.1.dev20240123 (#45593) * Update linearpartition to 1.0.1.dev20240123 This updates linearpartition to git-sha1 fa953f6323274eeadd92cc1f4e5535417f3fb821 from 2024-01-23. The main reason for the update to an unreleased version is that all releases by the upstream repo require python2. Changes to 1.0 (my summary): - driver script uses python3 - support for SHAPE chemical probing data - FASTA file input - dangles -d0 mode support * Retry build --- ...IX-command-broken-with-symbolic-link.patch | 22 +++++-------------- recipes/linearpartition/meta.yaml | 14 +++++++----- 2 files changed, 14 insertions(+), 22 deletions(-) diff --git a/recipes/linearpartition/0001-FIX-command-broken-with-symbolic-link.patch b/recipes/linearpartition/0001-FIX-command-broken-with-symbolic-link.patch index 95a8be08c0583..53c9c754a9810 100644 --- a/recipes/linearpartition/0001-FIX-command-broken-with-symbolic-link.patch +++ b/recipes/linearpartition/0001-FIX-command-broken-with-symbolic-link.patch @@ -1,25 +1,13 @@ -From 7413bfa18dddf47924be0839df0147045db0d045 Mon Sep 17 00:00:00 2001 -From: Fabien Pertuy -Date: Fri, 21 May 2021 10:39:10 +0000 -Subject: [PATCH] FIX command broken with symbolic link - ---- - linearpartition | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - diff --git a/linearpartition b/linearpartition -index 6c9d877..9d8a5b6 100755 +index f6c2a4e..7b0fe1d 100755 --- a/linearpartition +++ b/linearpartition -@@ -87,7 +87,7 @@ def main(): - # if os.path.exists(ThreshKnot_output): os.remove(ThreshKnot_output) - +@@ -80,7 +80,7 @@ def main(): + print("Exit!\n"); + exit(); - path = os.path.dirname(os.path.abspath(__file__)) + path = os.path.dirname(os.path.realpath(__file__)) - cmd = ["%s/%s" % (path, ('bin/linearpartition_v' if use_vienna else 'bin/linearpartition_c')), beamsize, is_sharpturn, is_verbose, bpp_file, bpp_prefix, pf_only, bpp_cutoff, forest_file, mea, gamma, TK, threshold, ThreshKnot_prefix, MEA_prefix, MEA_bpseq] + cmd = ["%s/%s" % (path, ('bin/linearpartition_v' if use_vienna else 'bin/linearpartition_c')), beamsize, is_sharpturn, is_verbose, bpp_file, bpp_prefix, pf_only, bpp_cutoff, forest_file, mea, gamma, TK, threshold, ThreshKnot_prefix, MEA_prefix, MEA_bpseq, shape_file_path, is_fasta, dangles] subprocess.call(cmd, stdin=sys.stdin) --- -2.30.2 - diff --git a/recipes/linearpartition/meta.yaml b/recipes/linearpartition/meta.yaml index eaa4d137d8ee7..7a42168cc778e 100644 --- a/recipes/linearpartition/meta.yaml +++ b/recipes/linearpartition/meta.yaml @@ -1,17 +1,20 @@ {% set name = "LinearPartition" %} -{% set version = "1.0" %} -{% set sha256 = "4fdea96f7ffbd4804d9308ddb46db5f96d1abc4b7bd737725f9bedcae3c88178" %} +{% set version = "1.0.1.dev20240123" %} +{% set git_sha1 = "fa953f6323274eeadd92cc1f4e5535417f3fb821" %} +{% set sha256 = "e93c6a26c246c2e0927592052516d6fb15e7e1e8a378f74474136ba85746be58" %} package: name: {{ name | lower }} version: {{ version }} build: - number: 3 + number: 0 skip: True # [osx] + run_exports: + - {{ pin_subpackage(name | lower, max_pin="x.x.x") }} source: - url: https://github.com/LinearFold/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + url: https://github.com/LinearFold/{{ name }}/archive/{{ git_sha1 }}.tar.gz sha256: {{ sha256 }} patches: - 0001-FIX-command-broken-with-symbolic-link.patch @@ -25,7 +28,7 @@ requirements: - matplotlib-base - numpy - pandas - - python=2.7 + - python >=3,<4 - python-gflags - seaborn @@ -41,3 +44,4 @@ about: license: custom license_file: LICENSE summary: 'Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities' + From 1047d9379b2c6416746c203214d6f5f78aa827e8 Mon Sep 17 00:00:00 2001 From: Marco Matthies <71844+marcom@users.noreply.github.com> Date: Sat, 10 Feb 2024 19:12:49 +0100 Subject: [PATCH 1978/2173] Add recipe for MultiRNAFold v2.1 (#45623) * Add recipe for MultiRNAFold v2.1 http://www.rnasoft.ca/download/README.html http://www.rnasoft.ca/download.html The MultiRNAFold package contains software for secondary structure prediction of one, two, or many interacting RNA or DNA molecules. It is composed of three pieces of software: SimFold, PairFold and MultiFold. The programs are also known in the literature as the RNAsoft suite. * Improve description * Fix summary, add run_exports * Shorter summary line * Fix run_exports * Skip osx build * Use SPDX license identifier, add comment on osx build fail * Try and fix OSX build --- recipes/multirnafold/0001-FIX-Makefile.patch | 925 ++++++++++++++++++ .../0002-FIX-printf-missing-arg.patch | 26 + .../0003-FIX-remove-unneeded-include.patch | 126 +++ recipes/multirnafold/build.sh | 13 + recipes/multirnafold/meta.yaml | 43 + 5 files changed, 1133 insertions(+) create mode 100644 recipes/multirnafold/0001-FIX-Makefile.patch create mode 100644 recipes/multirnafold/0002-FIX-printf-missing-arg.patch create mode 100644 recipes/multirnafold/0003-FIX-remove-unneeded-include.patch create mode 100644 recipes/multirnafold/build.sh create mode 100644 recipes/multirnafold/meta.yaml diff --git a/recipes/multirnafold/0001-FIX-Makefile.patch b/recipes/multirnafold/0001-FIX-Makefile.patch new file mode 100644 index 0000000000000..ff8e6c124469c --- /dev/null +++ b/recipes/multirnafold/0001-FIX-Makefile.patch @@ -0,0 +1,925 @@ +diff --git a/Makefile b/Makefile +index 6e3f2fe..28bb7e7 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,7 +1,7 @@ + # makefile for the MultiRNAFold package + +-CC = g++ +-CFLAGS = -g -I./include -I./src/common -I./src/simfold -I./src/pairfold -I./src/multifold -w -Wno-deprecated ++CXX = g++ ++CXXFLAGS = -O2 -ggdb -I./include -I./src/common -I./src/simfold -I./src/pairfold -I./src/multifold -Wno-deprecated + # -pg for profiling + #-O3 + # -p is for profiler +@@ -101,7 +101,7 @@ L_C_OBJS = $(L_C_SRCS:.cpp=.o) + L_S_OBJS = $(L_S_SRCS:.cpp=.o) + L_P_OBJS = $(L_P_SRCS:.cpp=.o) + L_M_OBJS = $(L_M_SRCS:.cpp=.o) +- ++ + AR = ar + ARFLAGS = rv + RANLIB = ranlib +@@ -114,78 +114,64 @@ default: $(LIB) $(SIMFOLD) $(SIMFOLD_PF) $(PAIRFOLD) $(PAIRFOLD_WEB) $(MULTIFOL + $(LIB): $(L_C_OBJS) $(L_S_OBJS) $(L_P_OBJS) $(L_M_OBJS) + $(RM) $@ + $(AR) $(ARFLAGS) $@ $(L_C_OBJS) $(L_S_OBJS) $(L_P_OBJS) $(L_M_OBJS) +- $(RANLIB) $@ +- ++ $(RANLIB) $@ ++ + $(SIMFOLD): $(S_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) +- ++ $(CXX) -o $@ $@.o $(LFLAGS) ++ + $(SIMFOLD_PF): $(S2_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) +- ++ $(CXX) -o $@ $@.o $(LFLAGS) ++ + $(PAIRFOLD): $(P_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) +- ++ $(CXX) -o $@ $@.o $(LFLAGS) ++ + $(PAIRFOLD_WEB): $(P2_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) +- ++ $(CXX) -o $@ $@.o $(LFLAGS) ++ + $(MULTIFOLD): $(M_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) +- ++ $(CXX) -o $@ $@.o $(LFLAGS) ++ + $(DRIVER): $(D_OBJS) $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) ++ $(CXX) -o $@ $@.o $(LFLAGS) + + $(PARTITION): $(PARTITION).o $(LIB) +- $(CC) -o $@ $@.o $(LFLAGS) ++ $(CXX) -o $@ $@.o $(LFLAGS) + + $(DRIVER1): $(DRIVER1).o $(LIB) + mpiCC -o $(DRIVER1) $(DRIVER1).o $(LFLAGS) -L$(LAMDIR)/lib + + $(DRIVER1).o: $(DRIVER1).cpp +- mpiCC -c $(DRIVER1).cpp $(CFLAGS) -I$(LAMDIR)/include -o $(DRIVER1).o ++ mpiCC -c $(DRIVER1).cpp $(CXXFLAGS) -I$(LAMDIR)/include -o $(DRIVER1).o + + $(DRIVER2): $(DRIVER2).o $(LIB) +- mpiCC -o $(DRIVER2) $(DRIVER2).o $(LFLAGS) -L$(LAMDIR)/lib ++ mpiCC -o $(DRIVER2) $(DRIVER2).o $(LFLAGS) -L$(LAMDIR)/lib + + $(DRIVER2).o: $(DRIVER2).cpp +- mpiCC -c $(DRIVER2).cpp $(CFLAGS) -I$(LAMDIR)/include -o $(DRIVER2).o ++ mpiCC -c $(DRIVER2).cpp $(CXXFLAGS) -I$(LAMDIR)/include -o $(DRIVER2).o + +- + $(RUNTIMEV): $(RUNTIMEV).o +- $(CC) -o $@ $@.o -L$(VIENNADIR)/lib -lviennapp $(LFLAGS) ++ $(CXX) -o $@ $@.o -L$(VIENNADIR)/lib -lviennapp $(LFLAGS) + + $(RUNTIMEV).o: $(RUNTIMEV).cpp +- $(CC) -c $(RUNTIMEV).cpp -I$(VIENNADIR)/include $(CFLAGS) +- +- ++ $(CXX) -c $(RUNTIMEV).cpp -I$(VIENNADIR)/include $(CXXFLAGS) ++ + .SUFFIXES: .cpp + .cpp.o: +- $(CC) -c $*.cpp $(CFLAGS) -o $*.o ++ $(CXX) -c $*.cpp $(CXXFLAGS) -o $*.o + + clean: + rm -f $(L_C_OBJS) $(L_S_OBJS) $(L_P_OBJS) $(L_M_OBJS) +- rm -f $(S_OBJS) $(S2_OBJS) $(P_OBJS) $(P2_OBJS) $(M_OBJS) $(D_OBJS) ++ rm -f $(S_OBJS) $(S2_OBJS) $(P_OBJS) $(P2_OBJS) $(M_OBJS) $(D_OBJS) + # $(SIMFOLD) $(SIMFOLD_PF) $(PAIRFOLD) $(MULTIFOLD) $(DRIVER) *~ core + rm -f $(SRC_C)/*~ $(SRC_S)/*~ $(SRC_P)/*~ $(SRC_M)/*~ include/*~ *.a *.bak + + depend: +- makedepend -- $(CFLAGS) -- $(L_C_SRCS) $(L_S_SRCS) $(L_P_SRCS) $(L_M_SRCS) $(S_SRCS) $(S2_SRCS) $(P_SRCS) $(M_SRCS) $(D_SRCS) +- +- ++ makedepend -Y $(CXXFLAGS) -- $(L_C_SRCS) $(L_S_SRCS) $(L_P_SRCS) $(L_M_SRCS) $(S_SRCS) $(S2_SRCS) $(P_SRCS) $(M_SRCS) $(D_SRCS) ++ + # end of makefile + + # DO NOT DELETE + +-src/common/common.o: /usr/include/stdio.h /usr/include/features.h +-src/common/common.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-src/common/common.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-src/common/common.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-src/common/common.o: /usr/include/libio.h /usr/include/_G_config.h +-src/common/common.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/common/common.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-src/common/common.o: /usr/include/bits/sys_errlist.h /usr/include/stdlib.h +-src/common/common.o: /usr/include/math.h /usr/include/bits/huge_val.h +-src/common/common.o: /usr/include/bits/mathdef.h +-src/common/common.o: /usr/include/bits/mathcalls.h /usr/include/string.h + src/common/common.o: ./include/constants.h ./include/structs.h + src/common/common.o: ./include/externs.h src/common/common.h + src/common/common.o: ./src/simfold/s_partition_function.h +@@ -195,16 +181,6 @@ src/common/common.o: ./src/simfold/s_energy_matrix.h + src/common/common.o: ./src/simfold/s_stacked_pair.h + src/common/common.o: ./src/simfold/s_multi_loop.h + src/common/common.o: ./src/simfold/s_multi_loop_sub.h +-src/common/params.o: /usr/include/stdio.h /usr/include/features.h +-src/common/params.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-src/common/params.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-src/common/params.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-src/common/params.o: /usr/include/libio.h /usr/include/_G_config.h +-src/common/params.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/common/params.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-src/common/params.o: /usr/include/bits/sys_errlist.h /usr/include/math.h +-src/common/params.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h +-src/common/params.o: /usr/include/bits/mathcalls.h /usr/include/stdlib.h + src/common/params.o: src/common/params.h ./include/constants.h + src/common/params.o: src/common/common.h ./include/structs.h + src/common/params.o: ./src/simfold/s_partition_function.h +@@ -214,60 +190,20 @@ src/common/params.o: ./src/simfold/s_energy_matrix.h + src/common/params.o: ./src/simfold/s_stacked_pair.h + src/common/params.o: ./src/simfold/s_multi_loop.h + src/common/params.o: ./src/simfold/s_multi_loop_sub.h ./include/externs.h +-src/common/params.o: /usr/include/string.h + src/common/params.o: ./src/simfold/s_specific_functions.h + src/common/params.o: ./src/simfold/s_min_folding.h + src/common/params.o: ./src/simfold/s_sub_folding.h ./include/simfold.h + src/common/params.o: ./include/init.h +-src/common/init.o: /usr/include/stdio.h /usr/include/features.h +-src/common/init.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-src/common/init.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-src/common/init.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-src/common/init.o: /usr/include/libio.h /usr/include/_G_config.h +-src/common/init.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/common/init.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-src/common/init.o: /usr/include/bits/sys_errlist.h /usr/include/stdlib.h +-src/common/init.o: /usr/include/string.h /usr/include/math.h +-src/common/init.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h +-src/common/init.o: /usr/include/bits/mathcalls.h ./include/constants.h +-src/common/init.o: ./include/structs.h ./include/globals.h +-src/common/init.o: src/common/common.h ./src/simfold/s_partition_function.h ++src/common/init.o: ./include/constants.h ./include/structs.h ++src/common/init.o: ./include/globals.h src/common/common.h ++src/common/init.o: ./src/simfold/s_partition_function.h + src/common/init.o: ./src/simfold/s_hairpin_loop.h + src/common/init.o: ./src/simfold/s_internal_loop.h + src/common/init.o: ./src/simfold/s_energy_matrix.h + src/common/init.o: ./src/simfold/s_stacked_pair.h + src/common/init.o: ./src/simfold/s_multi_loop.h +-src/common/init.o: ./src/simfold/s_multi_loop_sub.h +-src/common/timer.o: /usr/include/math.h /usr/include/features.h +-src/common/timer.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-src/common/timer.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-src/common/timer.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h +-src/common/timer.o: /usr/include/bits/mathcalls.h /usr/include/ctype.h +-src/common/timer.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-src/common/timer.o: /usr/include/endian.h /usr/include/bits/endian.h +-src/common/timer.o: /usr/include/time.h /usr/include/bits/time.h +-src/common/timer.o: /usr/include/string.h /usr/include/sys/times.h +-src/common/timer.o: /usr/include/limits.h src/common/timer.h +-src/simfold/s_specific_functions.o: /usr/include/stdio.h +-src/simfold/s_specific_functions.o: /usr/include/features.h +-src/simfold/s_specific_functions.o: /usr/include/sys/cdefs.h +-src/simfold/s_specific_functions.o: /usr/include/bits/wordsize.h +-src/simfold/s_specific_functions.o: /usr/include/gnu/stubs.h +-src/simfold/s_specific_functions.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_specific_functions.o: /usr/include/bits/types.h +-src/simfold/s_specific_functions.o: /usr/include/bits/typesizes.h +-src/simfold/s_specific_functions.o: /usr/include/libio.h +-src/simfold/s_specific_functions.o: /usr/include/_G_config.h +-src/simfold/s_specific_functions.o: /usr/include/wchar.h +-src/simfold/s_specific_functions.o: /usr/include/bits/wchar.h +-src/simfold/s_specific_functions.o: /usr/include/gconv.h +-src/simfold/s_specific_functions.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_specific_functions.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_specific_functions.o: /usr/include/stdlib.h /usr/include/math.h +-src/simfold/s_specific_functions.o: /usr/include/bits/huge_val.h +-src/simfold/s_specific_functions.o: /usr/include/bits/mathdef.h +-src/simfold/s_specific_functions.o: /usr/include/bits/mathcalls.h +-src/simfold/s_specific_functions.o: /usr/include/string.h ++src/common/init.o: ./src/simfold/s_multi_loop_sub.h src/common/params.h ++src/common/timer.o: src/common/timer.h + src/simfold/s_specific_functions.o: ./include/constants.h ./include/structs.h + src/simfold/s_specific_functions.o: ./include/externs.h src/common/common.h + src/simfold/s_specific_functions.o: ./src/simfold/s_partition_function.h +@@ -281,22 +217,6 @@ src/simfold/s_specific_functions.o: ./include/simfold.h ./include/init.h + src/simfold/s_specific_functions.o: ./src/simfold/s_specific_functions.h + src/simfold/s_specific_functions.o: ./src/simfold/s_min_folding.h + src/simfold/s_specific_functions.o: ./src/simfold/s_sub_folding.h +-src/simfold/s_specific_functions.o: src/simfold/s_partition_function_complex.h +-src/simfold/s_specific_functions.o: /usr/include/complex.h +-src/simfold/s_specific_functions.o: /usr/include/bits/cmathcalls.h +-src/simfold/s_min_folding.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_min_folding.o: /usr/include/sys/cdefs.h +-src/simfold/s_min_folding.o: /usr/include/bits/wordsize.h +-src/simfold/s_min_folding.o: /usr/include/gnu/stubs.h +-src/simfold/s_min_folding.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_min_folding.o: /usr/include/bits/types.h +-src/simfold/s_min_folding.o: /usr/include/bits/typesizes.h +-src/simfold/s_min_folding.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_min_folding.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_min_folding.o: /usr/include/gconv.h +-src/simfold/s_min_folding.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_min_folding.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_min_folding.o: /usr/include/string.h /usr/include/stdlib.h + src/simfold/s_min_folding.o: ./include/constants.h ./include/structs.h + src/simfold/s_min_folding.o: ./include/externs.h src/common/common.h + src/simfold/s_min_folding.o: ./src/simfold/s_partition_function.h +@@ -309,22 +229,8 @@ src/simfold/s_min_folding.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_min_folding.o: ./include/simfold.h ./include/init.h + src/simfold/s_min_folding.o: ./src/simfold/s_specific_functions.h + src/simfold/s_min_folding.o: ./src/simfold/s_min_folding.h +-src/simfold/s_hairpin_loop.o: /usr/include/string.h /usr/include/features.h +-src/simfold/s_hairpin_loop.o: /usr/include/sys/cdefs.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/wordsize.h +-src/simfold/s_hairpin_loop.o: /usr/include/gnu/stubs.h +-src/simfold/s_hairpin_loop.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_hairpin_loop.o: /usr/include/ctype.h /usr/include/bits/types.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/typesizes.h +-src/simfold/s_hairpin_loop.o: /usr/include/endian.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/endian.h + src/simfold/s_hairpin_loop.o: ./include/constants.h ./include/structs.h + src/simfold/s_hairpin_loop.o: ./include/externs.h src/common/common.h +-src/simfold/s_hairpin_loop.o: /usr/include/stdio.h /usr/include/libio.h +-src/simfold/s_hairpin_loop.o: /usr/include/_G_config.h /usr/include/wchar.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/wchar.h /usr/include/gconv.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_hairpin_loop.o: /usr/include/bits/sys_errlist.h + src/simfold/s_hairpin_loop.o: ./src/simfold/s_partition_function.h + src/simfold/s_hairpin_loop.o: ./src/simfold/s_hairpin_loop.h + src/simfold/s_hairpin_loop.o: ./src/simfold/s_internal_loop.h +@@ -334,20 +240,8 @@ src/simfold/s_hairpin_loop.o: ./src/simfold/s_multi_loop.h + src/simfold/s_hairpin_loop.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_hairpin_loop.o: ./include/simfold.h ./include/init.h + src/simfold/s_hairpin_loop.o: src/common/params.h +-src/simfold/s_stacked_pair.o: /usr/include/string.h /usr/include/features.h +-src/simfold/s_stacked_pair.o: /usr/include/sys/cdefs.h +-src/simfold/s_stacked_pair.o: /usr/include/bits/wordsize.h +-src/simfold/s_stacked_pair.o: /usr/include/gnu/stubs.h +-src/simfold/s_stacked_pair.o: /usr/include/gnu/stubs-32.h + src/simfold/s_stacked_pair.o: ./include/constants.h ./include/structs.h + src/simfold/s_stacked_pair.o: ./include/externs.h src/common/common.h +-src/simfold/s_stacked_pair.o: /usr/include/stdio.h /usr/include/bits/types.h +-src/simfold/s_stacked_pair.o: /usr/include/bits/typesizes.h +-src/simfold/s_stacked_pair.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_stacked_pair.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_stacked_pair.o: /usr/include/gconv.h +-src/simfold/s_stacked_pair.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_stacked_pair.o: /usr/include/bits/sys_errlist.h + src/simfold/s_stacked_pair.o: ./src/simfold/s_partition_function.h + src/simfold/s_stacked_pair.o: ./src/simfold/s_hairpin_loop.h + src/simfold/s_stacked_pair.o: ./src/simfold/s_internal_loop.h +@@ -357,22 +251,8 @@ src/simfold/s_stacked_pair.o: ./src/simfold/s_multi_loop.h + src/simfold/s_stacked_pair.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_stacked_pair.o: ./include/simfold.h ./include/init.h + src/simfold/s_stacked_pair.o: src/common/params.h +-src/simfold/s_energy_matrix.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_energy_matrix.o: /usr/include/sys/cdefs.h +-src/simfold/s_energy_matrix.o: /usr/include/bits/wordsize.h +-src/simfold/s_energy_matrix.o: /usr/include/gnu/stubs.h +-src/simfold/s_energy_matrix.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_energy_matrix.o: /usr/include/bits/types.h +-src/simfold/s_energy_matrix.o: /usr/include/bits/typesizes.h +-src/simfold/s_energy_matrix.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_energy_matrix.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_energy_matrix.o: /usr/include/gconv.h +-src/simfold/s_energy_matrix.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_energy_matrix.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_energy_matrix.o: /usr/include/string.h /usr/include/stdlib.h +-src/simfold/s_energy_matrix.o: /usr/include/malloc.h ./include/constants.h +-src/simfold/s_energy_matrix.o: ./include/structs.h ./include/externs.h +-src/simfold/s_energy_matrix.o: src/common/common.h ++src/simfold/s_energy_matrix.o: ./include/constants.h ./include/structs.h ++src/simfold/s_energy_matrix.o: ./include/externs.h src/common/common.h + src/simfold/s_energy_matrix.o: ./src/simfold/s_partition_function.h + src/simfold/s_energy_matrix.o: ./src/simfold/s_hairpin_loop.h + src/simfold/s_energy_matrix.o: ./src/simfold/s_internal_loop.h +@@ -381,19 +261,6 @@ src/simfold/s_energy_matrix.o: ./src/simfold/s_stacked_pair.h + src/simfold/s_energy_matrix.o: ./src/simfold/s_multi_loop.h + src/simfold/s_energy_matrix.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_energy_matrix.o: ./include/simfold.h ./include/init.h +-src/simfold/s_internal_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_internal_loop.o: /usr/include/sys/cdefs.h +-src/simfold/s_internal_loop.o: /usr/include/bits/wordsize.h +-src/simfold/s_internal_loop.o: /usr/include/gnu/stubs.h +-src/simfold/s_internal_loop.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_internal_loop.o: /usr/include/bits/types.h +-src/simfold/s_internal_loop.o: /usr/include/bits/typesizes.h +-src/simfold/s_internal_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_internal_loop.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_internal_loop.o: /usr/include/gconv.h +-src/simfold/s_internal_loop.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_internal_loop.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_internal_loop.o: /usr/include/string.h /usr/include/stdlib.h + src/simfold/s_internal_loop.o: ./src/simfold/s_internal_loop.h + src/simfold/s_internal_loop.o: ./include/constants.h ./include/structs.h + src/simfold/s_internal_loop.o: ./src/simfold/s_energy_matrix.h +@@ -405,21 +272,8 @@ src/simfold/s_internal_loop.o: ./include/externs.h src/common/common.h + src/simfold/s_internal_loop.o: ./src/simfold/s_partition_function.h + src/simfold/s_internal_loop.o: ./include/simfold.h ./include/init.h + src/simfold/s_internal_loop.o: src/common/params.h +-src/simfold/s_multi_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_multi_loop.o: /usr/include/sys/cdefs.h +-src/simfold/s_multi_loop.o: /usr/include/bits/wordsize.h +-src/simfold/s_multi_loop.o: /usr/include/gnu/stubs.h +-src/simfold/s_multi_loop.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_multi_loop.o: /usr/include/bits/types.h +-src/simfold/s_multi_loop.o: /usr/include/bits/typesizes.h +-src/simfold/s_multi_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_multi_loop.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_multi_loop.o: /usr/include/gconv.h +-src/simfold/s_multi_loop.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_multi_loop.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_multi_loop.o: /usr/include/malloc.h ./include/externs.h +-src/simfold/s_multi_loop.o: ./include/structs.h ./include/constants.h +-src/simfold/s_multi_loop.o: src/common/common.h ++src/simfold/s_multi_loop.o: ./include/externs.h ./include/structs.h ++src/simfold/s_multi_loop.o: ./include/constants.h src/common/common.h + src/simfold/s_multi_loop.o: ./src/simfold/s_partition_function.h + src/simfold/s_multi_loop.o: ./src/simfold/s_hairpin_loop.h + src/simfold/s_multi_loop.o: ./src/simfold/s_internal_loop.h +@@ -428,22 +282,8 @@ src/simfold/s_multi_loop.o: ./src/simfold/s_stacked_pair.h + src/simfold/s_multi_loop.o: ./src/simfold/s_multi_loop.h + src/simfold/s_multi_loop.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_multi_loop.o: ./include/simfold.h ./include/init.h +-src/simfold/s_multi_loop_sub.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_multi_loop_sub.o: /usr/include/sys/cdefs.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/wordsize.h +-src/simfold/s_multi_loop_sub.o: /usr/include/gnu/stubs.h +-src/simfold/s_multi_loop_sub.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/types.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/typesizes.h +-src/simfold/s_multi_loop_sub.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_multi_loop_sub.o: /usr/include/wchar.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/wchar.h +-src/simfold/s_multi_loop_sub.o: /usr/include/gconv.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_multi_loop_sub.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_multi_loop_sub.o: /usr/include/malloc.h ./include/externs.h +-src/simfold/s_multi_loop_sub.o: ./include/structs.h ./include/constants.h +-src/simfold/s_multi_loop_sub.o: src/common/common.h ++src/simfold/s_multi_loop_sub.o: ./include/externs.h ./include/structs.h ++src/simfold/s_multi_loop_sub.o: ./include/constants.h src/common/common.h + src/simfold/s_multi_loop_sub.o: ./src/simfold/s_partition_function.h + src/simfold/s_multi_loop_sub.o: ./src/simfold/s_hairpin_loop.h + src/simfold/s_multi_loop_sub.o: ./src/simfold/s_internal_loop.h +@@ -452,20 +292,7 @@ src/simfold/s_multi_loop_sub.o: ./src/simfold/s_stacked_pair.h + src/simfold/s_multi_loop_sub.o: ./src/simfold/s_multi_loop.h + src/simfold/s_multi_loop_sub.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_sub_folding.o: ./src/simfold/s_sub_folding.h +-src/simfold/s_sub_folding.o: /usr/include/stdio.h /usr/include/features.h +-src/simfold/s_sub_folding.o: /usr/include/sys/cdefs.h +-src/simfold/s_sub_folding.o: /usr/include/bits/wordsize.h +-src/simfold/s_sub_folding.o: /usr/include/gnu/stubs.h +-src/simfold/s_sub_folding.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_sub_folding.o: /usr/include/bits/types.h +-src/simfold/s_sub_folding.o: /usr/include/bits/typesizes.h +-src/simfold/s_sub_folding.o: /usr/include/libio.h /usr/include/_G_config.h +-src/simfold/s_sub_folding.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/simfold/s_sub_folding.o: /usr/include/gconv.h +-src/simfold/s_sub_folding.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_sub_folding.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_sub_folding.o: /usr/include/string.h ./include/structs.h +-src/simfold/s_sub_folding.o: ./include/constants.h ++src/simfold/s_sub_folding.o: ./include/structs.h ./include/constants.h + src/simfold/s_sub_folding.o: ./src/simfold/s_energy_matrix.h + src/simfold/s_sub_folding.o: ./src/simfold/s_stacked_pair.h + src/simfold/s_sub_folding.o: ./src/simfold/s_hairpin_loop.h +@@ -475,30 +302,6 @@ src/simfold/s_sub_folding.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_sub_folding.o: ./include/externs.h src/common/common.h + src/simfold/s_sub_folding.o: ./src/simfold/s_partition_function.h + src/simfold/s_sub_folding.o: ./include/simfold.h ./include/init.h +-src/simfold/s_partition_function.o: /usr/include/stdio.h +-src/simfold/s_partition_function.o: /usr/include/features.h +-src/simfold/s_partition_function.o: /usr/include/sys/cdefs.h +-src/simfold/s_partition_function.o: /usr/include/bits/wordsize.h +-src/simfold/s_partition_function.o: /usr/include/gnu/stubs.h +-src/simfold/s_partition_function.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_partition_function.o: /usr/include/bits/types.h +-src/simfold/s_partition_function.o: /usr/include/bits/typesizes.h +-src/simfold/s_partition_function.o: /usr/include/libio.h +-src/simfold/s_partition_function.o: /usr/include/_G_config.h +-src/simfold/s_partition_function.o: /usr/include/wchar.h +-src/simfold/s_partition_function.o: /usr/include/bits/wchar.h +-src/simfold/s_partition_function.o: /usr/include/gconv.h +-src/simfold/s_partition_function.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_partition_function.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_partition_function.o: /usr/include/string.h +-src/simfold/s_partition_function.o: /usr/include/stdlib.h +-src/simfold/s_partition_function.o: /usr/include/malloc.h /usr/include/math.h +-src/simfold/s_partition_function.o: /usr/include/bits/huge_val.h +-src/simfold/s_partition_function.o: /usr/include/bits/mathdef.h +-src/simfold/s_partition_function.o: /usr/include/bits/mathcalls.h +-src/simfold/s_partition_function.o: /usr/include/ctype.h +-src/simfold/s_partition_function.o: /usr/include/endian.h +-src/simfold/s_partition_function.o: /usr/include/bits/endian.h + src/simfold/s_partition_function.o: ./include/constants.h ./include/structs.h + src/simfold/s_partition_function.o: ./include/externs.h src/common/common.h + src/simfold/s_partition_function.o: ./src/simfold/s_partition_function.h +@@ -512,31 +315,6 @@ src/simfold/s_partition_function.o: ./include/simfold.h ./include/init.h + src/simfold/s_partition_function.o: ./src/simfold/s_min_folding.h + src/simfold/s_partition_function.o: ./src/simfold/s_sub_folding.h + src/simfold/s_partition_function.o: src/common/params.h +-src/simfold/s_partition_function_complex.o: /usr/include/stdio.h +-src/simfold/s_partition_function_complex.o: /usr/include/features.h +-src/simfold/s_partition_function_complex.o: /usr/include/sys/cdefs.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/wordsize.h +-src/simfold/s_partition_function_complex.o: /usr/include/gnu/stubs.h +-src/simfold/s_partition_function_complex.o: /usr/include/gnu/stubs-32.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/types.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/typesizes.h +-src/simfold/s_partition_function_complex.o: /usr/include/libio.h +-src/simfold/s_partition_function_complex.o: /usr/include/_G_config.h +-src/simfold/s_partition_function_complex.o: /usr/include/wchar.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/wchar.h +-src/simfold/s_partition_function_complex.o: /usr/include/gconv.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/stdio_lim.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/sys_errlist.h +-src/simfold/s_partition_function_complex.o: /usr/include/string.h +-src/simfold/s_partition_function_complex.o: /usr/include/stdlib.h +-src/simfold/s_partition_function_complex.o: /usr/include/malloc.h +-src/simfold/s_partition_function_complex.o: /usr/include/math.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/huge_val.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/mathdef.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/mathcalls.h +-src/simfold/s_partition_function_complex.o: /usr/include/ctype.h +-src/simfold/s_partition_function_complex.o: /usr/include/endian.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/endian.h + src/simfold/s_partition_function_complex.o: ./include/constants.h + src/simfold/s_partition_function_complex.o: ./include/structs.h + src/simfold/s_partition_function_complex.o: ./include/externs.h +@@ -551,32 +329,9 @@ src/simfold/s_partition_function_complex.o: ./src/simfold/s_multi_loop_sub.h + src/simfold/s_partition_function_complex.o: ./include/simfold.h + src/simfold/s_partition_function_complex.o: ./include/init.h + src/simfold/s_partition_function_complex.o: src/simfold/s_partition_function_complex.h +-src/simfold/s_partition_function_complex.o: /usr/include/complex.h +-src/simfold/s_partition_function_complex.o: /usr/include/bits/cmathcalls.h + src/simfold/s_partition_function_complex.o: ./src/simfold/s_min_folding.h + src/simfold/s_partition_function_complex.o: ./src/simfold/s_sub_folding.h + src/simfold/s_partition_function_complex.o: src/common/params.h +-src/pairfold/p_specific_functions.o: /usr/include/stdio.h +-src/pairfold/p_specific_functions.o: /usr/include/features.h +-src/pairfold/p_specific_functions.o: /usr/include/sys/cdefs.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/wordsize.h +-src/pairfold/p_specific_functions.o: /usr/include/gnu/stubs.h +-src/pairfold/p_specific_functions.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/types.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/typesizes.h +-src/pairfold/p_specific_functions.o: /usr/include/libio.h +-src/pairfold/p_specific_functions.o: /usr/include/_G_config.h +-src/pairfold/p_specific_functions.o: /usr/include/wchar.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/wchar.h +-src/pairfold/p_specific_functions.o: /usr/include/gconv.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_specific_functions.o: /usr/include/stdlib.h +-src/pairfold/p_specific_functions.o: /usr/include/math.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/huge_val.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/mathdef.h +-src/pairfold/p_specific_functions.o: /usr/include/bits/mathcalls.h +-src/pairfold/p_specific_functions.o: /usr/include/string.h + src/pairfold/p_specific_functions.o: ./include/constants.h + src/pairfold/p_specific_functions.o: ./include/structs.h ./include/externs.h + src/pairfold/p_specific_functions.o: src/common/common.h +@@ -597,19 +352,6 @@ src/pairfold/p_specific_functions.o: src/pairfold/p_multi_loop.h + src/pairfold/p_specific_functions.o: src/pairfold/p_multi_loop_sub.h + src/pairfold/p_specific_functions.o: src/pairfold/p_sub_folding.h + src/pairfold/p_specific_functions.o: src/pairfold/p_specific_functions.h +-src/pairfold/p_min_folding.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_min_folding.o: /usr/include/sys/cdefs.h +-src/pairfold/p_min_folding.o: /usr/include/bits/wordsize.h +-src/pairfold/p_min_folding.o: /usr/include/gnu/stubs.h +-src/pairfold/p_min_folding.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_min_folding.o: /usr/include/bits/types.h +-src/pairfold/p_min_folding.o: /usr/include/bits/typesizes.h +-src/pairfold/p_min_folding.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_min_folding.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/pairfold/p_min_folding.o: /usr/include/gconv.h +-src/pairfold/p_min_folding.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_min_folding.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_min_folding.o: /usr/include/string.h + src/pairfold/p_min_folding.o: src/pairfold/p_min_folding.h + src/pairfold/p_min_folding.o: ./include/structs.h ./include/constants.h + src/pairfold/p_min_folding.o: src/pairfold/p_energy_matrix.h +@@ -627,20 +369,8 @@ src/pairfold/p_min_folding.o: ./src/simfold/s_stacked_pair.h + src/pairfold/p_min_folding.o: ./src/simfold/s_multi_loop.h + src/pairfold/p_min_folding.o: ./src/simfold/s_multi_loop_sub.h + src/pairfold/p_min_folding.o: ./include/pairfold.h ./include/init.h +-src/pairfold/p_hairpin_loop.o: /usr/include/string.h /usr/include/features.h +-src/pairfold/p_hairpin_loop.o: /usr/include/sys/cdefs.h +-src/pairfold/p_hairpin_loop.o: /usr/include/bits/wordsize.h +-src/pairfold/p_hairpin_loop.o: /usr/include/gnu/stubs.h +-src/pairfold/p_hairpin_loop.o: /usr/include/gnu/stubs-32.h + src/pairfold/p_hairpin_loop.o: ./include/constants.h ./include/structs.h + src/pairfold/p_hairpin_loop.o: ./include/externs.h src/common/common.h +-src/pairfold/p_hairpin_loop.o: /usr/include/stdio.h /usr/include/bits/types.h +-src/pairfold/p_hairpin_loop.o: /usr/include/bits/typesizes.h +-src/pairfold/p_hairpin_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_hairpin_loop.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/pairfold/p_hairpin_loop.o: /usr/include/gconv.h +-src/pairfold/p_hairpin_loop.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_hairpin_loop.o: /usr/include/bits/sys_errlist.h + src/pairfold/p_hairpin_loop.o: ./src/simfold/s_partition_function.h + src/pairfold/p_hairpin_loop.o: ./src/simfold/s_hairpin_loop.h + src/pairfold/p_hairpin_loop.o: ./src/simfold/s_internal_loop.h +@@ -650,20 +380,8 @@ src/pairfold/p_hairpin_loop.o: ./src/simfold/s_multi_loop.h + src/pairfold/p_hairpin_loop.o: ./src/simfold/s_multi_loop_sub.h + src/pairfold/p_hairpin_loop.o: ./include/pairfold.h ./include/init.h + src/pairfold/p_hairpin_loop.o: src/pairfold/p_hairpin_loop.h +-src/pairfold/p_stacked_pair.o: /usr/include/string.h /usr/include/features.h +-src/pairfold/p_stacked_pair.o: /usr/include/sys/cdefs.h +-src/pairfold/p_stacked_pair.o: /usr/include/bits/wordsize.h +-src/pairfold/p_stacked_pair.o: /usr/include/gnu/stubs.h +-src/pairfold/p_stacked_pair.o: /usr/include/gnu/stubs-32.h + src/pairfold/p_stacked_pair.o: ./include/constants.h ./include/structs.h + src/pairfold/p_stacked_pair.o: ./include/externs.h src/common/common.h +-src/pairfold/p_stacked_pair.o: /usr/include/stdio.h /usr/include/bits/types.h +-src/pairfold/p_stacked_pair.o: /usr/include/bits/typesizes.h +-src/pairfold/p_stacked_pair.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_stacked_pair.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/pairfold/p_stacked_pair.o: /usr/include/gconv.h +-src/pairfold/p_stacked_pair.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_stacked_pair.o: /usr/include/bits/sys_errlist.h + src/pairfold/p_stacked_pair.o: ./src/simfold/s_partition_function.h + src/pairfold/p_stacked_pair.o: ./src/simfold/s_hairpin_loop.h + src/pairfold/p_stacked_pair.o: ./src/simfold/s_internal_loop.h +@@ -678,23 +396,8 @@ src/pairfold/p_stacked_pair.o: src/pairfold/p_hairpin_loop.h + src/pairfold/p_stacked_pair.o: src/pairfold/p_internal_loop.h + src/pairfold/p_stacked_pair.o: src/pairfold/p_multi_loop.h + src/pairfold/p_stacked_pair.o: src/pairfold/p_multi_loop_sub.h +-src/pairfold/p_energy_matrix.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_energy_matrix.o: /usr/include/sys/cdefs.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/wordsize.h +-src/pairfold/p_energy_matrix.o: /usr/include/gnu/stubs.h +-src/pairfold/p_energy_matrix.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/types.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/typesizes.h +-src/pairfold/p_energy_matrix.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_energy_matrix.o: /usr/include/wchar.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/wchar.h +-src/pairfold/p_energy_matrix.o: /usr/include/gconv.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_energy_matrix.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_energy_matrix.o: /usr/include/string.h /usr/include/stdlib.h +-src/pairfold/p_energy_matrix.o: /usr/include/malloc.h ./include/constants.h +-src/pairfold/p_energy_matrix.o: ./include/structs.h ./include/externs.h +-src/pairfold/p_energy_matrix.o: src/common/common.h ++src/pairfold/p_energy_matrix.o: ./include/constants.h ./include/structs.h ++src/pairfold/p_energy_matrix.o: ./include/externs.h src/common/common.h + src/pairfold/p_energy_matrix.o: ./src/simfold/s_partition_function.h + src/pairfold/p_energy_matrix.o: ./src/simfold/s_hairpin_loop.h + src/pairfold/p_energy_matrix.o: ./src/simfold/s_internal_loop.h +@@ -709,20 +412,6 @@ src/pairfold/p_energy_matrix.o: src/pairfold/p_hairpin_loop.h + src/pairfold/p_energy_matrix.o: src/pairfold/p_internal_loop.h + src/pairfold/p_energy_matrix.o: src/pairfold/p_multi_loop.h + src/pairfold/p_energy_matrix.o: src/pairfold/p_multi_loop_sub.h +-src/pairfold/p_internal_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_internal_loop.o: /usr/include/sys/cdefs.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/wordsize.h +-src/pairfold/p_internal_loop.o: /usr/include/gnu/stubs.h +-src/pairfold/p_internal_loop.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/types.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/typesizes.h +-src/pairfold/p_internal_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_internal_loop.o: /usr/include/wchar.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/wchar.h +-src/pairfold/p_internal_loop.o: /usr/include/gconv.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_internal_loop.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_internal_loop.o: /usr/include/string.h /usr/include/stdlib.h + src/pairfold/p_internal_loop.o: src/pairfold/p_internal_loop.h + src/pairfold/p_internal_loop.o: ./include/constants.h ./include/structs.h + src/pairfold/p_internal_loop.o: src/pairfold/p_energy_matrix.h +@@ -740,21 +429,8 @@ src/pairfold/p_internal_loop.o: ./src/simfold/s_multi_loop.h + src/pairfold/p_internal_loop.o: ./src/simfold/s_multi_loop_sub.h + src/pairfold/p_internal_loop.o: ./include/pairfold.h ./include/init.h + src/pairfold/p_internal_loop.o: src/pairfold/p_specific_functions.h +-src/pairfold/p_multi_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_multi_loop.o: /usr/include/sys/cdefs.h +-src/pairfold/p_multi_loop.o: /usr/include/bits/wordsize.h +-src/pairfold/p_multi_loop.o: /usr/include/gnu/stubs.h +-src/pairfold/p_multi_loop.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_multi_loop.o: /usr/include/bits/types.h +-src/pairfold/p_multi_loop.o: /usr/include/bits/typesizes.h +-src/pairfold/p_multi_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_multi_loop.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/pairfold/p_multi_loop.o: /usr/include/gconv.h +-src/pairfold/p_multi_loop.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_multi_loop.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_multi_loop.o: /usr/include/malloc.h ./include/externs.h +-src/pairfold/p_multi_loop.o: ./include/structs.h ./include/constants.h +-src/pairfold/p_multi_loop.o: src/common/common.h ++src/pairfold/p_multi_loop.o: ./include/externs.h ./include/structs.h ++src/pairfold/p_multi_loop.o: ./include/constants.h src/common/common.h + src/pairfold/p_multi_loop.o: ./src/simfold/s_partition_function.h + src/pairfold/p_multi_loop.o: ./src/simfold/s_hairpin_loop.h + src/pairfold/p_multi_loop.o: ./src/simfold/s_internal_loop.h +@@ -769,23 +445,8 @@ src/pairfold/p_multi_loop.o: src/pairfold/p_hairpin_loop.h + src/pairfold/p_multi_loop.o: src/pairfold/p_internal_loop.h + src/pairfold/p_multi_loop.o: src/pairfold/p_multi_loop_sub.h + src/pairfold/p_multi_loop.o: ./include/pairfold.h ./include/init.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/sys/cdefs.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/wordsize.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/gnu/stubs.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/types.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/typesizes.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/libio.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/_G_config.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/wchar.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/wchar.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/gconv.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_multi_loop_sub.o: /usr/include/malloc.h ./include/externs.h +-src/pairfold/p_multi_loop_sub.o: ./include/structs.h ./include/constants.h +-src/pairfold/p_multi_loop_sub.o: src/common/common.h ++src/pairfold/p_multi_loop_sub.o: ./include/externs.h ./include/structs.h ++src/pairfold/p_multi_loop_sub.o: ./include/constants.h src/common/common.h + src/pairfold/p_multi_loop_sub.o: ./src/simfold/s_partition_function.h + src/pairfold/p_multi_loop_sub.o: ./src/simfold/s_hairpin_loop.h + src/pairfold/p_multi_loop_sub.o: ./src/simfold/s_internal_loop.h +@@ -801,20 +462,7 @@ src/pairfold/p_multi_loop_sub.o: src/pairfold/p_internal_loop.h + src/pairfold/p_multi_loop_sub.o: src/pairfold/p_multi_loop.h + src/pairfold/p_multi_loop_sub.o: ./include/pairfold.h ./include/init.h + src/pairfold/p_sub_folding.o: src/pairfold/p_sub_folding.h +-src/pairfold/p_sub_folding.o: /usr/include/stdio.h /usr/include/features.h +-src/pairfold/p_sub_folding.o: /usr/include/sys/cdefs.h +-src/pairfold/p_sub_folding.o: /usr/include/bits/wordsize.h +-src/pairfold/p_sub_folding.o: /usr/include/gnu/stubs.h +-src/pairfold/p_sub_folding.o: /usr/include/gnu/stubs-32.h +-src/pairfold/p_sub_folding.o: /usr/include/bits/types.h +-src/pairfold/p_sub_folding.o: /usr/include/bits/typesizes.h +-src/pairfold/p_sub_folding.o: /usr/include/libio.h /usr/include/_G_config.h +-src/pairfold/p_sub_folding.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/pairfold/p_sub_folding.o: /usr/include/gconv.h +-src/pairfold/p_sub_folding.o: /usr/include/bits/stdio_lim.h +-src/pairfold/p_sub_folding.o: /usr/include/bits/sys_errlist.h +-src/pairfold/p_sub_folding.o: /usr/include/string.h ./include/structs.h +-src/pairfold/p_sub_folding.o: ./include/constants.h ++src/pairfold/p_sub_folding.o: ./include/structs.h ./include/constants.h + src/pairfold/p_sub_folding.o: src/pairfold/p_energy_matrix.h + src/pairfold/p_sub_folding.o: src/pairfold/p_stacked_pair.h + src/pairfold/p_sub_folding.o: src/pairfold/p_hairpin_loop.h +@@ -830,27 +478,6 @@ src/pairfold/p_sub_folding.o: ./src/simfold/s_stacked_pair.h + src/pairfold/p_sub_folding.o: ./src/simfold/s_multi_loop.h + src/pairfold/p_sub_folding.o: ./src/simfold/s_multi_loop_sub.h + src/pairfold/p_sub_folding.o: ./include/pairfold.h ./include/init.h +-src/multifold/m_specific_functions.o: /usr/include/stdio.h +-src/multifold/m_specific_functions.o: /usr/include/features.h +-src/multifold/m_specific_functions.o: /usr/include/sys/cdefs.h +-src/multifold/m_specific_functions.o: /usr/include/bits/wordsize.h +-src/multifold/m_specific_functions.o: /usr/include/gnu/stubs.h +-src/multifold/m_specific_functions.o: /usr/include/gnu/stubs-32.h +-src/multifold/m_specific_functions.o: /usr/include/bits/types.h +-src/multifold/m_specific_functions.o: /usr/include/bits/typesizes.h +-src/multifold/m_specific_functions.o: /usr/include/libio.h +-src/multifold/m_specific_functions.o: /usr/include/_G_config.h +-src/multifold/m_specific_functions.o: /usr/include/wchar.h +-src/multifold/m_specific_functions.o: /usr/include/bits/wchar.h +-src/multifold/m_specific_functions.o: /usr/include/gconv.h +-src/multifold/m_specific_functions.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_specific_functions.o: /usr/include/bits/sys_errlist.h +-src/multifold/m_specific_functions.o: /usr/include/stdlib.h +-src/multifold/m_specific_functions.o: /usr/include/math.h +-src/multifold/m_specific_functions.o: /usr/include/bits/huge_val.h +-src/multifold/m_specific_functions.o: /usr/include/bits/mathdef.h +-src/multifold/m_specific_functions.o: /usr/include/bits/mathcalls.h +-src/multifold/m_specific_functions.o: /usr/include/string.h + src/multifold/m_specific_functions.o: ./include/constants.h + src/multifold/m_specific_functions.o: ./include/structs.h ./include/externs.h + src/multifold/m_specific_functions.o: src/common/common.h +@@ -869,19 +496,6 @@ src/multifold/m_specific_functions.o: src/multifold/m_hairpin_loop.h + src/multifold/m_specific_functions.o: src/multifold/m_internal_loop.h + src/multifold/m_specific_functions.o: src/multifold/m_multi_loop.h + src/multifold/m_specific_functions.o: src/multifold/m_specific_functions.h +-src/multifold/m_min_folding.o: /usr/include/stdio.h /usr/include/features.h +-src/multifold/m_min_folding.o: /usr/include/sys/cdefs.h +-src/multifold/m_min_folding.o: /usr/include/bits/wordsize.h +-src/multifold/m_min_folding.o: /usr/include/gnu/stubs.h +-src/multifold/m_min_folding.o: /usr/include/gnu/stubs-32.h +-src/multifold/m_min_folding.o: /usr/include/bits/types.h +-src/multifold/m_min_folding.o: /usr/include/bits/typesizes.h +-src/multifold/m_min_folding.o: /usr/include/libio.h /usr/include/_G_config.h +-src/multifold/m_min_folding.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/multifold/m_min_folding.o: /usr/include/gconv.h +-src/multifold/m_min_folding.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_min_folding.o: /usr/include/bits/sys_errlist.h +-src/multifold/m_min_folding.o: /usr/include/string.h + src/multifold/m_min_folding.o: src/multifold/m_min_folding.h + src/multifold/m_min_folding.o: ./include/structs.h ./include/constants.h + src/multifold/m_min_folding.o: src/multifold/m_energy_matrix.h +@@ -899,22 +513,8 @@ src/multifold/m_min_folding.o: ./src/simfold/s_multi_loop.h + src/multifold/m_min_folding.o: ./src/simfold/s_multi_loop_sub.h + src/multifold/m_min_folding.o: ./include/multifold.h ./include/init.h + src/multifold/m_min_folding.o: src/multifold/m_specific_functions.h +-src/multifold/m_hairpin_loop.o: /usr/include/string.h /usr/include/features.h +-src/multifold/m_hairpin_loop.o: /usr/include/sys/cdefs.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/wordsize.h +-src/multifold/m_hairpin_loop.o: /usr/include/gnu/stubs.h +-src/multifold/m_hairpin_loop.o: /usr/include/gnu/stubs-32.h + src/multifold/m_hairpin_loop.o: ./include/constants.h ./include/structs.h + src/multifold/m_hairpin_loop.o: ./include/externs.h src/common/common.h +-src/multifold/m_hairpin_loop.o: /usr/include/stdio.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/types.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/typesizes.h +-src/multifold/m_hairpin_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/multifold/m_hairpin_loop.o: /usr/include/wchar.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/wchar.h +-src/multifold/m_hairpin_loop.o: /usr/include/gconv.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_hairpin_loop.o: /usr/include/bits/sys_errlist.h + src/multifold/m_hairpin_loop.o: ./src/simfold/s_partition_function.h + src/multifold/m_hairpin_loop.o: ./src/simfold/s_hairpin_loop.h + src/multifold/m_hairpin_loop.o: ./src/simfold/s_internal_loop.h +@@ -925,22 +525,8 @@ src/multifold/m_hairpin_loop.o: ./src/simfold/s_multi_loop_sub.h + src/multifold/m_hairpin_loop.o: ./include/multifold.h ./include/init.h + src/multifold/m_hairpin_loop.o: src/multifold/m_hairpin_loop.h + src/multifold/m_hairpin_loop.o: src/multifold/m_specific_functions.h +-src/multifold/m_stacked_pair.o: /usr/include/string.h /usr/include/features.h +-src/multifold/m_stacked_pair.o: /usr/include/sys/cdefs.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/wordsize.h +-src/multifold/m_stacked_pair.o: /usr/include/gnu/stubs.h +-src/multifold/m_stacked_pair.o: /usr/include/gnu/stubs-32.h + src/multifold/m_stacked_pair.o: ./include/constants.h ./include/structs.h + src/multifold/m_stacked_pair.o: ./include/externs.h src/common/common.h +-src/multifold/m_stacked_pair.o: /usr/include/stdio.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/types.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/typesizes.h +-src/multifold/m_stacked_pair.o: /usr/include/libio.h /usr/include/_G_config.h +-src/multifold/m_stacked_pair.o: /usr/include/wchar.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/wchar.h +-src/multifold/m_stacked_pair.o: /usr/include/gconv.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_stacked_pair.o: /usr/include/bits/sys_errlist.h + src/multifold/m_stacked_pair.o: ./src/simfold/s_partition_function.h + src/multifold/m_stacked_pair.o: ./src/simfold/s_hairpin_loop.h + src/multifold/m_stacked_pair.o: ./src/simfold/s_internal_loop.h +@@ -955,24 +541,8 @@ src/multifold/m_stacked_pair.o: src/multifold/m_hairpin_loop.h + src/multifold/m_stacked_pair.o: src/multifold/m_internal_loop.h + src/multifold/m_stacked_pair.o: src/multifold/m_multi_loop.h + src/multifold/m_stacked_pair.o: src/multifold/m_specific_functions.h +-src/multifold/m_energy_matrix.o: /usr/include/stdio.h /usr/include/features.h +-src/multifold/m_energy_matrix.o: /usr/include/sys/cdefs.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/wordsize.h +-src/multifold/m_energy_matrix.o: /usr/include/gnu/stubs.h +-src/multifold/m_energy_matrix.o: /usr/include/gnu/stubs-32.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/types.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/typesizes.h +-src/multifold/m_energy_matrix.o: /usr/include/libio.h +-src/multifold/m_energy_matrix.o: /usr/include/_G_config.h +-src/multifold/m_energy_matrix.o: /usr/include/wchar.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/wchar.h +-src/multifold/m_energy_matrix.o: /usr/include/gconv.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_energy_matrix.o: /usr/include/bits/sys_errlist.h +-src/multifold/m_energy_matrix.o: /usr/include/string.h /usr/include/stdlib.h +-src/multifold/m_energy_matrix.o: /usr/include/malloc.h ./include/constants.h +-src/multifold/m_energy_matrix.o: ./include/structs.h ./include/externs.h +-src/multifold/m_energy_matrix.o: src/common/common.h ++src/multifold/m_energy_matrix.o: ./include/constants.h ./include/structs.h ++src/multifold/m_energy_matrix.o: ./include/externs.h src/common/common.h + src/multifold/m_energy_matrix.o: ./src/simfold/s_partition_function.h + src/multifold/m_energy_matrix.o: ./src/simfold/s_hairpin_loop.h + src/multifold/m_energy_matrix.o: ./src/simfold/s_internal_loop.h +@@ -986,21 +556,6 @@ src/multifold/m_energy_matrix.o: src/multifold/m_stacked_pair.h + src/multifold/m_energy_matrix.o: src/multifold/m_hairpin_loop.h + src/multifold/m_energy_matrix.o: src/multifold/m_internal_loop.h + src/multifold/m_energy_matrix.o: src/multifold/m_multi_loop.h +-src/multifold/m_internal_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/multifold/m_internal_loop.o: /usr/include/sys/cdefs.h +-src/multifold/m_internal_loop.o: /usr/include/bits/wordsize.h +-src/multifold/m_internal_loop.o: /usr/include/gnu/stubs.h +-src/multifold/m_internal_loop.o: /usr/include/gnu/stubs-32.h +-src/multifold/m_internal_loop.o: /usr/include/bits/types.h +-src/multifold/m_internal_loop.o: /usr/include/bits/typesizes.h +-src/multifold/m_internal_loop.o: /usr/include/libio.h +-src/multifold/m_internal_loop.o: /usr/include/_G_config.h +-src/multifold/m_internal_loop.o: /usr/include/wchar.h +-src/multifold/m_internal_loop.o: /usr/include/bits/wchar.h +-src/multifold/m_internal_loop.o: /usr/include/gconv.h +-src/multifold/m_internal_loop.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_internal_loop.o: /usr/include/bits/sys_errlist.h +-src/multifold/m_internal_loop.o: /usr/include/string.h /usr/include/stdlib.h + src/multifold/m_internal_loop.o: src/multifold/m_internal_loop.h + src/multifold/m_internal_loop.o: ./include/constants.h ./include/structs.h + src/multifold/m_internal_loop.o: src/multifold/m_energy_matrix.h +@@ -1017,21 +572,8 @@ src/multifold/m_internal_loop.o: ./src/simfold/s_multi_loop.h + src/multifold/m_internal_loop.o: ./src/simfold/s_multi_loop_sub.h + src/multifold/m_internal_loop.o: ./include/multifold.h ./include/init.h + src/multifold/m_internal_loop.o: src/multifold/m_specific_functions.h +-src/multifold/m_multi_loop.o: /usr/include/stdio.h /usr/include/features.h +-src/multifold/m_multi_loop.o: /usr/include/sys/cdefs.h +-src/multifold/m_multi_loop.o: /usr/include/bits/wordsize.h +-src/multifold/m_multi_loop.o: /usr/include/gnu/stubs.h +-src/multifold/m_multi_loop.o: /usr/include/gnu/stubs-32.h +-src/multifold/m_multi_loop.o: /usr/include/bits/types.h +-src/multifold/m_multi_loop.o: /usr/include/bits/typesizes.h +-src/multifold/m_multi_loop.o: /usr/include/libio.h /usr/include/_G_config.h +-src/multifold/m_multi_loop.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-src/multifold/m_multi_loop.o: /usr/include/gconv.h +-src/multifold/m_multi_loop.o: /usr/include/bits/stdio_lim.h +-src/multifold/m_multi_loop.o: /usr/include/bits/sys_errlist.h +-src/multifold/m_multi_loop.o: /usr/include/malloc.h ./include/externs.h +-src/multifold/m_multi_loop.o: ./include/structs.h ./include/constants.h +-src/multifold/m_multi_loop.o: src/common/common.h ++src/multifold/m_multi_loop.o: ./include/externs.h ./include/structs.h ++src/multifold/m_multi_loop.o: ./include/constants.h src/common/common.h + src/multifold/m_multi_loop.o: ./src/simfold/s_partition_function.h + src/multifold/m_multi_loop.o: ./src/simfold/s_hairpin_loop.h + src/multifold/m_multi_loop.o: ./src/simfold/s_internal_loop.h +@@ -1046,68 +588,31 @@ src/multifold/m_multi_loop.o: src/multifold/m_hairpin_loop.h + src/multifold/m_multi_loop.o: src/multifold/m_internal_loop.h + src/multifold/m_multi_loop.o: ./include/multifold.h ./include/init.h + src/multifold/m_multi_loop.o: src/multifold/m_specific_functions.h +-simfold.o: /usr/include/stdio.h /usr/include/features.h +-simfold.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-simfold.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-simfold.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-simfold.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h +-simfold.o: /usr/include/bits/wchar.h /usr/include/gconv.h +-simfold.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h +-simfold.o: /usr/include/string.h /usr/include/stdlib.h /usr/include/time.h +-simfold.o: /usr/include/bits/time.h /usr/include/unistd.h +-simfold.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h + simfold.o: ./include/simfold.h ./include/constants.h ./include/init.h + simfold.o: ./include/externs.h ./include/structs.h src/common/params.h +-simfold_pf.o: /usr/include/stdio.h /usr/include/features.h +-simfold_pf.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-simfold_pf.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-simfold_pf.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-simfold_pf.o: /usr/include/libio.h /usr/include/_G_config.h +-simfold_pf.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-simfold_pf.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-simfold_pf.o: /usr/include/bits/sys_errlist.h /usr/include/string.h +-simfold_pf.o: /usr/include/stdlib.h /usr/include/time.h +-simfold_pf.o: /usr/include/bits/time.h /usr/include/unistd.h +-simfold_pf.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h ++simfold.o: ./src/simfold/s_partition_function.h ++simfold.o: ./src/simfold/s_hairpin_loop.h ./src/simfold/s_internal_loop.h ++simfold.o: ./src/simfold/s_energy_matrix.h ./src/simfold/s_stacked_pair.h ++simfold.o: ./src/simfold/s_multi_loop.h ./src/simfold/s_multi_loop_sub.h ++simfold.o: src/common/common.h + simfold_pf.o: ./include/simfold.h ./include/constants.h ./include/init.h + simfold_pf.o: ./include/externs.h ./include/structs.h src/common/params.h + simfold_pf.o: ./src/simfold/s_partition_function.h + simfold_pf.o: ./src/simfold/s_hairpin_loop.h ./src/simfold/s_internal_loop.h + simfold_pf.o: ./src/simfold/s_energy_matrix.h ./src/simfold/s_stacked_pair.h + simfold_pf.o: ./src/simfold/s_multi_loop.h ./src/simfold/s_multi_loop_sub.h +-pairfold.o: /usr/include/stdio.h /usr/include/features.h +-pairfold.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-pairfold.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-pairfold.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-pairfold.o: /usr/include/libio.h /usr/include/_G_config.h +-pairfold.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-pairfold.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-pairfold.o: /usr/include/bits/sys_errlist.h /usr/include/string.h +-pairfold.o: /usr/include/stdlib.h /usr/include/time.h +-pairfold.o: /usr/include/bits/time.h ./include/pairfold.h +-pairfold.o: ./include/constants.h ./include/init.h ./include/externs.h +-pairfold.o: ./include/structs.h src/common/timer.h /usr/include/sys/times.h +-pairfold.o: /usr/include/limits.h +-multifold.o: /usr/include/stdio.h /usr/include/features.h +-multifold.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-multifold.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-multifold.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-multifold.o: /usr/include/libio.h /usr/include/_G_config.h +-multifold.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-multifold.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-multifold.o: /usr/include/bits/sys_errlist.h /usr/include/string.h +-multifold.o: /usr/include/stdlib.h ./include/multifold.h +-multifold.o: ./include/constants.h ./include/init.h ./include/externs.h +-multifold.o: ./include/structs.h +-test_get_counts.o: /usr/include/stdio.h /usr/include/features.h +-test_get_counts.o: /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h +-test_get_counts.o: /usr/include/gnu/stubs.h /usr/include/gnu/stubs-32.h +-test_get_counts.o: /usr/include/bits/types.h /usr/include/bits/typesizes.h +-test_get_counts.o: /usr/include/libio.h /usr/include/_G_config.h +-test_get_counts.o: /usr/include/wchar.h /usr/include/bits/wchar.h +-test_get_counts.o: /usr/include/gconv.h /usr/include/bits/stdio_lim.h +-test_get_counts.o: /usr/include/bits/sys_errlist.h /usr/include/string.h +-test_get_counts.o: /usr/include/stdlib.h /usr/include/time.h +-test_get_counts.o: /usr/include/bits/time.h ./include/simfold.h +-test_get_counts.o: ./include/constants.h ./include/init.h ./include/externs.h +-test_get_counts.o: ./include/structs.h src/common/params.h ++pairfold.o: ./include/pairfold.h ./include/constants.h ./include/init.h ++pairfold.o: ./include/externs.h ./include/structs.h src/common/timer.h ++multifold.o: ./include/multifold.h ./include/constants.h ./include/init.h ++multifold.o: ./include/externs.h ./include/structs.h ++feature_description.o: ./include/simfold.h ./include/constants.h ++feature_description.o: ./include/init.h ./include/externs.h ++feature_description.o: ./include/structs.h src/common/params.h ++feature_description.o: src/common/common.h ++feature_description.o: ./src/simfold/s_partition_function.h ++feature_description.o: ./src/simfold/s_hairpin_loop.h ++feature_description.o: ./src/simfold/s_internal_loop.h ++feature_description.o: ./src/simfold/s_energy_matrix.h ++feature_description.o: ./src/simfold/s_stacked_pair.h ++feature_description.o: ./src/simfold/s_multi_loop.h ++feature_description.o: ./src/simfold/s_multi_loop_sub.h diff --git a/recipes/multirnafold/0002-FIX-printf-missing-arg.patch b/recipes/multirnafold/0002-FIX-printf-missing-arg.patch new file mode 100644 index 0000000000000..471631385a018 --- /dev/null +++ b/recipes/multirnafold/0002-FIX-printf-missing-arg.patch @@ -0,0 +1,26 @@ +diff --git a/simfold.cpp b/simfold.cpp +index 08cffe2..0ca03e3 100644 +--- a/simfold.cpp ++++ b/simfold.cpp +@@ -64,7 +64,7 @@ void usage (const char *prog) + printf ("Examples:\n"); + printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -n 10 \n", prog); + printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -n 10 -r \"(____________________________)\"\n", prog); +- printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -p params/CG_best_parameters_ISMB2007.txt\n"); ++ printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -p params/CG_best_parameters_ISMB2007.txt\n", prog); + exit (0); + } + +diff --git a/simfold_pf.cpp b/simfold_pf.cpp +index e3ba56e..424ee85 100644 +--- a/simfold_pf.cpp ++++ b/simfold_pf.cpp +@@ -35,7 +35,7 @@ void usage (const char *prog) + printf ("Examples:\n"); + printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\"\n", prog); + printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -t 0.5\n", prog); +- printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -p params/CG_best_parameters_ISMB2007.txt\n"); ++ printf ("\t%s -s \"GCAACGAUGACAUACAUCGCUAGUCGACGC\" -p params/CG_best_parameters_ISMB2007.txt\n", prog); + exit (0); + } + diff --git a/recipes/multirnafold/0003-FIX-remove-unneeded-include.patch b/recipes/multirnafold/0003-FIX-remove-unneeded-include.patch new file mode 100644 index 0000000000000..51509cbcf874a --- /dev/null +++ b/recipes/multirnafold/0003-FIX-remove-unneeded-include.patch @@ -0,0 +1,126 @@ +commit 625122c01dbf740131c2419a5d2bfd65d8d315d8 +Author: Marco Matthies <71844+marcom@users.noreply.github.com> +Date: Thu Feb 8 16:12:41 2024 +0100 + + Remove unneeded include of malloc.h + +diff --git a/src/multifold/m_energy_matrix.cpp b/src/multifold/m_energy_matrix.cpp +index 4d47d90..4030513 100644 +--- a/src/multifold/m_energy_matrix.cpp ++++ b/src/multifold/m_energy_matrix.cpp +@@ -18,7 +18,6 @@ + #include + #include + #include +-#include + + #include "constants.h" + #include "structs.h" +diff --git a/src/multifold/m_multi_loop.cpp b/src/multifold/m_multi_loop.cpp +index a017da8..382d57a 100644 +--- a/src/multifold/m_multi_loop.cpp ++++ b/src/multifold/m_multi_loop.cpp +@@ -16,7 +16,6 @@ + ***************************************************************************/ + + #include +-#include + + #include "externs.h" + #include "common.h" +diff --git a/src/pairfold/p_energy_matrix.cpp b/src/pairfold/p_energy_matrix.cpp +index 42c15c2..dc23e29 100644 +--- a/src/pairfold/p_energy_matrix.cpp ++++ b/src/pairfold/p_energy_matrix.cpp +@@ -18,7 +18,6 @@ + #include + #include + #include +-#include + + #include "constants.h" + #include "structs.h" +diff --git a/src/pairfold/p_multi_loop.cpp b/src/pairfold/p_multi_loop.cpp +index f562ce0..267035a 100644 +--- a/src/pairfold/p_multi_loop.cpp ++++ b/src/pairfold/p_multi_loop.cpp +@@ -16,7 +16,6 @@ + ***************************************************************************/ + + #include +-#include + + #include "externs.h" + #include "common.h" +diff --git a/src/pairfold/p_multi_loop_sub.cpp b/src/pairfold/p_multi_loop_sub.cpp +index 467fb53..a418218 100644 +--- a/src/pairfold/p_multi_loop_sub.cpp ++++ b/src/pairfold/p_multi_loop_sub.cpp +@@ -16,7 +16,6 @@ + ***************************************************************************/ + + #include +-#include + + #include "externs.h" + #include "common.h" +diff --git a/src/simfold/s_energy_matrix.cpp b/src/simfold/s_energy_matrix.cpp +index cafc1d7..ce09162 100644 +--- a/src/simfold/s_energy_matrix.cpp ++++ b/src/simfold/s_energy_matrix.cpp +@@ -20,7 +20,6 @@ + #include + #include + #include +-#include + + #include "constants.h" + #include "structs.h" +diff --git a/src/simfold/s_multi_loop.cpp b/src/simfold/s_multi_loop.cpp +index 6c5998a..de7991e 100644 +--- a/src/simfold/s_multi_loop.cpp ++++ b/src/simfold/s_multi_loop.cpp +@@ -18,7 +18,6 @@ + // The main class for multi-loop related functions, the mfe case + + #include +-#include + + #include "externs.h" + #include "common.h" +diff --git a/src/simfold/s_multi_loop_sub.cpp b/src/simfold/s_multi_loop_sub.cpp +index e8f5219..bbdeb98 100644 +--- a/src/simfold/s_multi_loop_sub.cpp ++++ b/src/simfold/s_multi_loop_sub.cpp +@@ -18,7 +18,6 @@ + // this class represents multi-loops for suboptimal pairfold, it implements the Wuchty complete suboptimal paper + + #include +-#include + + #include "externs.h" + #include "common.h" +diff --git a/src/simfold/s_partition_function.cpp b/src/simfold/s_partition_function.cpp +index c551b6d..c63e8b4 100644 +--- a/src/simfold/s_partition_function.cpp ++++ b/src/simfold/s_partition_function.cpp +@@ -18,7 +18,6 @@ + #include + #include + #include +-#include + #include + #include + +diff --git a/src/simfold/s_partition_function_complex.cpp b/src/simfold/s_partition_function_complex.cpp +index 2654f25..2fb2a00 100644 +--- a/src/simfold/s_partition_function_complex.cpp ++++ b/src/simfold/s_partition_function_complex.cpp +@@ -18,7 +18,6 @@ + #include + #include + #include +-#include + #include + #include + diff --git a/recipes/multirnafold/build.sh b/recipes/multirnafold/build.sh new file mode 100644 index 0000000000000..1a10377f73b68 --- /dev/null +++ b/recipes/multirnafold/build.sh @@ -0,0 +1,13 @@ +# build +make CC="${CC}" CXX="${CXX}" + +# install +mkdir -p "$PREFIX/bin" +mkdir -p "$PREFIX/shared/${PKG_NAME}/params" +mkdir -p "$PREFIX/include" +mkdir -p "$PREFIX/lib" + +cp feature_description multifold pairfold pairfold-web simfold simfold_pf "$PREFIX/bin/" +cp -r params/* "$PREFIX/shared/${PKG_NAME}/params/" +cp -r include/* "$PREFIX/include/" +cp libMultiRNAFold.a "$PREFIX/lib/" diff --git a/recipes/multirnafold/meta.yaml b/recipes/multirnafold/meta.yaml new file mode 100644 index 0000000000000..ad45a1c49cb85 --- /dev/null +++ b/recipes/multirnafold/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "MultiRNAFold" %} +{% set version = "2.1" %} +{% set sha256 = "cb5462e03c70da24caaa9706f493fa329b1e15f697fbffd5bf460cd873243306" %} + +package: + name: {{ name | lower }} + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name | lower, max_pin="x.x") }} + +source: + url: http://www.rnasoft.ca/download/MultiRNAFold-{{ version }}.tar.gz + sha256: {{ sha256 }} + patches: + - 0001-FIX-Makefile.patch + - 0002-FIX-printf-missing-arg.patch + - 0003-FIX-remove-unneeded-include.patch + +requirements: + build: + - make + - {{ compiler('cxx') }} + +test: + commands: + - "test -x $PREFIX/bin/feature_description" + - "test -x $PREFIX/bin/multifold" + - "test -x $PREFIX/bin/pairfold" + - "test -x $PREFIX/bin/pairfold-web" + - "test -x $PREFIX/bin/simfold" + - "test -x $PREFIX/bin/simfold_pf" + - "pairfold -h" + - "simfold -h" + - "simfold_pf -h" + - "multifold -h" + +about: + home: http://www.rnasoft.ca/download/README.html + license: GPL-2.0-or-later + summary: 'RNA/DNA secondary structure prediction for one, two, or many interacting strands' From 95f8c62050b502a756a610cbfd2528737d11f9de Mon Sep 17 00:00:00 2001 From: Reid Wagner <74672860+reid-wagner@users.noreply.github.com> Date: Sat, 10 Feb 2024 14:06:46 -0600 Subject: [PATCH 1979/2173] Add MSFragger recipe. (#45127) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- recipes/msfragger/academic_install.py | 74 +++++++++++++++++++++++ recipes/msfragger/build.sh | 33 ++++++++++ recipes/msfragger/meta.yaml | 54 +++++++++++++++++ recipes/msfragger/msfragger.py | 86 +++++++++++++++++++++++++++ 4 files changed, 247 insertions(+) create mode 100755 recipes/msfragger/academic_install.py create mode 100644 recipes/msfragger/build.sh create mode 100644 recipes/msfragger/meta.yaml create mode 100755 recipes/msfragger/msfragger.py diff --git a/recipes/msfragger/academic_install.py b/recipes/msfragger/academic_install.py new file mode 100755 index 0000000000000..2f47dc5e87cfa --- /dev/null +++ b/recipes/msfragger/academic_install.py @@ -0,0 +1,74 @@ +#!/usr/bin/env python3 + +# Automates accepting the academic license agreements in order to download MSFragger. A user of this package is then expected to accept the terms themselves when they download a license key from the MSFragger site, which is enforced by the wrapper script and MSFragger jar file. + +import argparse +import hashlib +import os +import re +import sys +import urllib.request +import urllib.parse + +MSFRAGGER_URL = 'http://msfragger-upgrader.nesvilab.org/upgrader/upgrade_download.php' +DOWNLOAD_READ_SIZE = 1000000 + +def download_url(url, post_dict, dest): + data = urllib.parse.urlencode(post_dict).encode('ascii') + with open(dest, 'wb') as wh: + size = 0 + m = hashlib.sha256() + with urllib.request.urlopen(url, data) as f: + while True: + seg = f.read(DOWNLOAD_READ_SIZE) + m.update(seg) + bytes_read = len(seg) + if bytes_read < 1: + break + size += bytes_read + wh.write(seg) + + return m.hexdigest() + +def parse_version(version_string): + version_pattern = '([\\d.]+)' + m = re.search(version_pattern, version_string.strip()) + if m: + return m.groups()[0] + return None + +parser = argparse.ArgumentParser( + description="Download MSFragger zip file." +) +parser.add_argument( + '-n', '--name', help='user name' +) +parser.add_argument( + '-e', '--email', help='email' +) +parser.add_argument( + '-o', '--organization', help='institutional organization' +) +parser.add_argument( + '-m', '--msfragger_version', help='MSFragger version', required=True +) +parser.add_argument( + '-p', '--path', default='.', help='path in which to install' +) +parser.add_argument( + '--hash', default='.', help='SHA256 hash of downloaded zip' +) + +args = parser.parse_args() +fgr_ver = parse_version(args.msfragger_version) +if fgr_ver is None: + print(f'Could not find version: {args.msfragger_version}', file=sys.stderr) + sys.exit(1) + +fgr_zip = 'Release ' + fgr_ver + '$zip' +dest = os.path.join(args.path, 'MSFragger-' + fgr_ver + '.zip') +data = {'transfer': 'academic', 'agreement1': 'true', 'agreement2': 'true','agreement3': 'true', 'name': args.name, 'email' : args.email, 'organization' : args.organization, 'download': fgr_zip} + +if download_url(MSFRAGGER_URL, data, dest) != args.hash: + print('Invalid hash calculated.', file=sys.stderr) + sys.exit(1) diff --git a/recipes/msfragger/build.sh b/recipes/msfragger/build.sh new file mode 100644 index 0000000000000..f3d467463dbdd --- /dev/null +++ b/recipes/msfragger/build.sh @@ -0,0 +1,33 @@ +#!/bin/bash + +# These values are submitted to the MSFragger site when downloading the application zip. +if [[ -z "$NAME" ]]; then + NAME="${USERNAME:-bioconda}"; +fi +if [[ -z "$EMAIL" ]]; then + EMAIL="${NAME}@${HOSTNAME:-bioconda.org}"; +fi +if [[ -z "$INSTITUTION" ]]; then + INSTITUTION="${HOSTNAME:-bioconda.org}"; +fi + +# Create directories +TARGET="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +mkdir -p "$TARGET" + +# Add wrapper python script and link to unprefixed name. +cp "$RECIPE_DIR/msfragger.py" "$TARGET" +ln -s "$TARGET/msfragger.py" "$PREFIX/bin/msfragger" +chmod 0755 "${PREFIX}/bin/msfragger" + +# This script automates accepting the academic license agreements in order to download MSFragger and build the package. A user of this package is then expected to accept the terms themselves when they download a license key from the MSFragger site, which is enforced by the wrapper script and MSFragger jar file. +"${RECIPE_DIR}/academic_install.py" -n galaxy -e "$EMAIL" -o "$INSTITUTION" -m "$PKG_VERSION" -p "$TARGET" --hash "$SHA256SUM" +if [[ $? -ne 0 ]]; then + echo "Problem downloading jar file." > /dev/stderr + exit 1; +fi + +# Unzip and link jar. +cd "$TARGET" +unzip "MSFragger-$PKG_VERSION.zip" +ln -s "MSFragger-$PKG_VERSION/MSFragger-$PKG_VERSION.jar" "MSFragger.jar" diff --git a/recipes/msfragger/meta.yaml b/recipes/msfragger/meta.yaml new file mode 100644 index 0000000000000..000aa4ee6fe93 --- /dev/null +++ b/recipes/msfragger/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "4.0" %} + +# This key was generated ONLY for the testing of this bioconda package. +# Users must generate their own key by agreeing to the terms at https://msfragger.arsci.com/upgrader/MSFragger-LICENSE.pdf. +{% set academic_use_only_key = "f28c4be2-759b0a11-6c1ea652-1240565a" %} +{% set sha256sum = "25bdab705c4ac97729d1da8d7a075e3920d8a447596fa52eff8e564606d1720e" %} + +package: + name: msfragger + version: {{ version }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('msfragger', max_pin="x.x") }} + script_env: + - SHA256SUM={{ sha256sum }} + +requirements: + host: + - python >3.9 + - unzip + run: + - openjdk >=11 + - python >=3.9 + - mono >=5, <6 + - zlib >=1.2.13 + +test: + commands: + - msfragger --key {{ academic_use_only_key }} -Xms512m -Xmx1g --help 2>&1 | grep 'MSFragger' + +about: + home: https://github.com/Nesvilab/MSFragger + license: Academic License (https://msfragger.arsci.com/upgrader/MSFragger-LICENSE.pdf) + summary: Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics + description: | + MSFragger is an ultrafast database search tool for peptide identification in mass spectrometry-based proteomics. + It has demonstrated excellent performance across a wide range of datasets and applications. + MSFragger is suitable for standard shotgun proteomics analyses as well as large datasets (including timsTOF PASEF data), + enzyme unconstrained searches (e.g., peptidome), + open database searches (e.g., precursor mass tolerance set to hundreds of Daltons) for identification + of modified peptides, and glycopeptide identification (N-linked and O-linked). + + MSFragger is available freely for academic research and educational purposes only, in accordance with the terms at https://msfragger.arsci.com/upgrader/MSFragger-LICENSE.pdf. + +extra: + notes: | + The "msfragger" command runs the MSFragger java program. + identifiers: + - doi:10.1038/nmeth.4256 + - doi:10.1038/s41467-020-17921-y + - doi:10.1038/s41592-020-0967-9 diff --git a/recipes/msfragger/msfragger.py b/recipes/msfragger/msfragger.py new file mode 100755 index 0000000000000..05d98f890af37 --- /dev/null +++ b/recipes/msfragger/msfragger.py @@ -0,0 +1,86 @@ +#!/usr/bin/env python +# +# Wrapper script for Java Conda packages that ensures that the java runtime +# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). +# + +import os +import sys +import subprocess +from os import access, getenv, X_OK + +jar_file = os.path.join(os.path.dirname(__file__), "MSFragger.jar") + +default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] + +license_agreement_text = ''' +Please provide pass a license key with the --key argument. You may obtain a key by agreeing to the terms at msfragger-upgrader.nesvilab.org/upgrader/. +''' + +def real_dirname(path): + """Return the symlink-resolved, canonicalized directory-portion of path.""" + return os.path.dirname(os.path.realpath(path)) + + +def java_executable(): + """Return the executable name of the Java interpreter.""" + java_home = getenv('JAVA_HOME') + java_bin = os.path.join('bin', 'java') + + if java_home and access(os.path.join(java_home, java_bin), X_OK): + return os.path.join(java_home, java_bin) + else: + return 'java' + + +def jvm_opts(argv): + """Construct list of Java arguments based on our argument list. + + The argument list passed in argv must not include the script name. + The return value is a 3-tuple lists of strings of the form: + (memory_options, prop_options, passthrough_options) + """ + mem_opts = [] + prop_opts = [] + pass_args = [] + + for arg in argv: + if arg.startswith('-D'): + prop_opts.append(arg) + elif arg.startswith('-XX'): + prop_opts.append(arg) + elif arg.startswith('-Xm'): + mem_opts.append(arg) + else: + pass_args.append(arg) + + # In the original shell script the test coded below read: + # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] + # To reproduce the behaviour of the above shell code fragment + # it is important to explictly check for equality with None + # in the second condition, so a null envar value counts as True! + + if mem_opts == [] and getenv('_JAVA_OPTIONS') == None: + mem_opts = default_jvm_mem_opts + + return (mem_opts, prop_opts, pass_args) + + +def main(): + java = java_executable() + jar_dir = real_dirname(sys.argv[0]) + jar_path = os.path.join(jar_dir, jar_file) + jar_arg = '-jar' + + (mem_opts, prop_opts, pass_args) = jvm_opts(sys.argv[1:]) + + if '--key' not in sys.argv: + print(license_agreement_text) + sys.exit(1) + + java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args + + sys.exit(subprocess.call(java_args)) + +if __name__ == '__main__': + main() From 441c1c7f042b62da8444484eb453b2a44aa9971b Mon Sep 17 00:00:00 2001 From: Alejandro Buendia Date: Sat, 10 Feb 2024 15:31:27 -0500 Subject: [PATCH 1980/2173] Update arcas-hla to 0.6.0 (#45718) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update arcas-hla to 0.6.0 * Linting fix * Fix run_export statement * Add extra deps * Add dep * Unpin conda-forge deps * Remove channels and unpin deps * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/arcas-hla/meta.yaml | 30 ++++++++++++++++++------------ 1 file changed, 18 insertions(+), 12 deletions(-) diff --git a/recipes/arcas-hla/meta.yaml b/recipes/arcas-hla/meta.yaml index fa98f4d095d42..9121cf059a94f 100644 --- a/recipes/arcas-hla/meta.yaml +++ b/recipes/arcas-hla/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.0" %} +{% set version = "0.6.0" %} package: name: arcas-hla @@ -6,26 +6,31 @@ package: source: url: https://github.com/RabadanLab/arcasHLA/archive/v{{ version }}.tar.gz - sha256: fb17b3ba74facf4edb3329099b158910bdc7c4e73074efab9880d4136a0d4e93 + sha256: 75bef1a5596a9dfabccb901420f5d852d6d8a15d9c676e4c94787b8d25dd708b build: - number: 3 + number: 0 noarch: generic + run_exports: + - {{ pin_subpackage("arcas-hla", max_pin="x.x") }} requirements: run: + - bedtools + - biopython - coreutils - - bedtools >=2.27.1 - - biopython <=1.77 - git - git-lfs - - kallisto ==0.44.0 + - kallisto ==0.44 - numpy - pandas - pigz - - python >=3.6.1 - - samtools >=1.9 - - scipy ==1.1.0 + - pip + - pyarrow + - pytest + - python + - samtools + - scipy test: commands: @@ -33,10 +38,11 @@ test: about: home: https://github.com/RabadanLab/arcasHLA - license: GPL-3.0 - summary: high resolution HLA typing from RNA seq + license: GPL-3.0-only + license_file: LICENSE + summary: high-resolution HLA typing from RNA seq description: | - arcasHLA performs high resolution genotyping for HLA class I and class II + arcasHLA performs high-resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples. extra: From ca684bf7afb6a80885873b68e128745932bece4f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 10 Feb 2024 17:04:09 -0500 Subject: [PATCH 1981/2173] Update phykit to 1.13.1 (#45747) --- recipes/phykit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phykit/meta.yaml b/recipes/phykit/meta.yaml index fdbe8d3ddefe3..5199781fe01be 100644 --- a/recipes/phykit/meta.yaml +++ b/recipes/phykit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phykit" %} -{% set version = "1.13.0" %} +{% set version = "1.13.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 22d074a5862dc6ee8402eaae9202d49d7c38e1ca15f4b55188ad14a99c292aaa + sha256: bd8076262d7f25f6780deed903af3d16abeb268975420e8f2fd2a3e5379e40cd build: noarch: python From 8ac2e9266636445594d92f1f53a24947e83251bb Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Sun, 11 Feb 2024 15:10:37 +0000 Subject: [PATCH 1982/2173] Update scanpy-scripts to scanpy 1.9.x (#45750) * Update scanpy-scripts to scanpy 1.9.x * Pin part * Separate package from constraints --- recipes/scanpy-scripts/meta.yaml | 68 ++++++++++++++++++++------------ 1 file changed, 43 insertions(+), 25 deletions(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index 5428c9ec3c8ab..6cad46ec670b5 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -1,23 +1,20 @@ {% set name = "scanpy-scripts" %} -{% set version = "1.1.6" %} +{% set version = "1.9.0" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 1701e35f93f5370ab451760b3892caf01b46d2898c3dd149e1dcba602e45eea1 + # - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + - url: https://github.com/ebi-gene-expression-group/scanpy-scripts/archive/refs/heads/develop.tar.gz + sha256: 669fb6f12e23a689e2e889d160c3f4f09d05d33068bef36a88bb94f9053c7b9c folder: scanpy-scripts - - url: https://pypi.io/packages/source/s/scanpy/scanpy-1.8.1.tar.gz - sha256: 1b8603a868d783bd6c18c8db763a450153feefc8daed862c440749790d47c654 - folder: scanpy - patches: - - scrublet.patch build: number: 0 noarch: python + run_exports: '{{ pin_compatible("scanpy-scripts", max_pin="x.x") }}' entry_points: - scanpy-cli=scanpy_scripts.cli:cli - scanpy-read-10x=scanpy_scripts.cmds:READ_CMD @@ -36,37 +33,57 @@ build: - scanpy-integrate=scanpy_scripts.cli:integrate - scanpy-multiplet=scanpy_scripts.cli:multiplet script: - - "{{ PYTHON }} -m pip install {{ SRC_DIR }}/scanpy --no-deps --ignore-installed -vv" - "{{ PYTHON }} -m pip install {{ SRC_DIR }}/scanpy-scripts --no-deps --ignore-installed -vv" requirements: host: - - python >=3.7 + - python <3.10 - pip + - scanpy =1.9.3 + - louvain + - igraph + - leidenalg + - loompy + - Click <8 + - harmonypy >=0.0.5 + - bbknn >=1.5.0,<1.6.0 + - mnnpy >=0.1.9.5 + - scipy <1.9.0 + - scikit-learn <1.3.0 + - scrublet + - fa2 + # for testing + - bats + - black + - pytest - flit-core - setuptools_scm - pytoml - packaging run: - - anndata - - bbknn>=1.5.0 - - click<8 - - fa2 - - h5py<3.0.0 - - harmonypy>=0.0.5 + - python <3.10 + - scanpy =1.9.3 - leidenalg - loompy - louvain - - matplotlib-base - - mnnpy>=0.1.9.5 - - packaging - - pandas - - python>=3.6 - - scanpy=1.8.1 - - scikit-misc - - scipy + - igraph + - Click <8 + - harmonypy >=0.0.5 + - bbknn >=1.5.0,<1.6.0 + - mnnpy >=0.1.9.5 + # for mnnpy using n_jobs + - scipy <1.9.0 + - scikit-learn <1.3.0 - scrublet - - umap-learn + - fa2 + # for testing + - bats + - black + - pytest + - flit-core + - setuptools_scm + - pytoml + - packaging test: imports: @@ -104,3 +121,4 @@ extra: recipe-maintainers: - nh3 - pinin4fjords + - pcm32 From 40bb118b233ac7109ad2b03e8428e0cd25ba7bc8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 11 Feb 2024 12:32:45 -0500 Subject: [PATCH 1983/2173] Update sourmash to 4.8.6 (#45749) Co-authored-by: C. Titus Brown --- recipes/sourmash/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sourmash/meta.yaml b/recipes/sourmash/meta.yaml index 4feaa4aaee077..262fde0161307 100644 --- a/recipes/sourmash/meta.yaml +++ b/recipes/sourmash/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.8.5" %} +{% set version = "4.8.6" %} package: name: sourmash @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/sourmash/sourmash-{{ version }}.tar.gz - sha256: 9016c338d6b01f152d2c7becf5631000b058ff657f4fc50daa6ef15373d8a02a + sha256: 5a09c5d12cb07f8d73eb60db8dbd30e4e74aabf53a718610ddb5e6c91b341dca build: number: 0 From 8b5a043b725b05a4d958e6a042f7aeccca2ef235 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 11 Feb 2024 16:15:43 -0500 Subject: [PATCH 1984/2173] Update bx-python to 0.11.0 (#45748) * Update bx-python to 0.11.0 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/bx-python/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/bx-python/meta.yaml b/recipes/bx-python/meta.yaml index bbf510cd6ac66..4190c732ecd3c 100644 --- a/recipes/bx-python/meta.yaml +++ b/recipes/bx-python/meta.yaml @@ -1,6 +1,6 @@ {% set name = "bx-python" %} -{% set version = "0.10.0" %} -{% set sha256 = "bfe9541d7b18a98e907b085e31f58d3989fbca4dc667c4ae48c33b753e0e2da8" %} +{% set version = "0.11.0" %} +{% set sha256 = "2cf8872572817e0d36145cc2711889df5729987ffed4e51280da1e3c2ccb9429" %} package: name: {{ name|lower }} @@ -14,6 +14,8 @@ build: number: 0 skip: True # [py < 37] script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vvv + run_exports: + - {{ pin_subpackage(name|lower, max_pin='x') }} requirements: build: From e86fca3d0ba0de4ca401211bcf96bc9c48b083fe Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Mon, 12 Feb 2024 18:53:34 +1100 Subject: [PATCH 1985/2173] Update hmftools-bam-tools 1.2 recipe (#45754) * Fix class-path detection in BASH script * Bump build number --- recipes/hmftools-bam-tools/bamtools.sh | 2 +- recipes/hmftools-bam-tools/meta.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-bam-tools/bamtools.sh b/recipes/hmftools-bam-tools/bamtools.sh index bee5781030da9..b62ff17d5670f 100755 --- a/recipes/hmftools-bam-tools/bamtools.sh +++ b/recipes/hmftools-bam-tools/bamtools.sh @@ -60,7 +60,7 @@ if [ "$jvm_mem_opts" == "" ]; then fi pass_arr=($pass_args) -if [[ ${pass_arr[0]:=} == org* ]] +if [[ ${pass_arr[0]:=} == com.hartwig.* ]] then eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/bamtools.jar" $pass_args else diff --git a/recipes/hmftools-bam-tools/meta.yaml b/recipes/hmftools-bam-tools/meta.yaml index 138a0147d66af..58f205663e016 100644 --- a/recipes/hmftools-bam-tools/meta.yaml +++ b/recipes/hmftools-bam-tools/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage("hmftools-bam-tools", max_pin="x.x") }} From eea5269acd821b41f772df497016b9c831bf8392 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Mon, 12 Feb 2024 18:53:56 +1100 Subject: [PATCH 1986/2173] Update hmftools-sage 3.4 recipe (#45755) * Fix class-path detection in BASH script * Bump build number --- recipes/hmftools-sage/meta.yaml | 2 +- recipes/hmftools-sage/sage.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-sage/meta.yaml b/recipes/hmftools-sage/meta.yaml index 8f31690dab7d3..36e0eef3e635a 100644 --- a/recipes/hmftools-sage/meta.yaml +++ b/recipes/hmftools-sage/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('hmftools-sage', max_pin="x") }} diff --git a/recipes/hmftools-sage/sage.sh b/recipes/hmftools-sage/sage.sh index d5a456e118ba2..0164c0f1b3c2c 100755 --- a/recipes/hmftools-sage/sage.sh +++ b/recipes/hmftools-sage/sage.sh @@ -60,7 +60,7 @@ if [ "$jvm_mem_opts" == "" ]; then fi pass_arr=($pass_args) -if [[ ${pass_arr[0]:=} == org* ]] +if [[ ${pass_arr[0]:=} == com.hartwig.* ]] then eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/sage.jar" $pass_args else From 3370e7f8e230d4c4870d04970735c0dd963cb18a Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Mon, 12 Feb 2024 12:43:06 +0100 Subject: [PATCH 1987/2173] Bump GATK4 gcnvkernel (#45759) Bumped underlying gatk version, relaxed some dependencies causing issues --- recipes/gcnvkernel/meta.yaml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/gcnvkernel/meta.yaml b/recipes/gcnvkernel/meta.yaml index da4ef22df24e6..f8c6448ea98bb 100644 --- a/recipes/gcnvkernel/meta.yaml +++ b/recipes/gcnvkernel/meta.yaml @@ -1,7 +1,7 @@ {% set name = "gcnvkernel" %} {% set version = "0.8" %} -{% set gatk_version = "4.3.0.0" %} -{% set gatk_sha256 = "e2c27229b34c3e22445964adf00639a0909887bbfcc040f6910079177bc6e2dd" %} +{% set gatk_version = "4.5.0.0" %} +{% set gatk_sha256 = "dc1a4471e8bb566397db9894ca18acbf8f40f3fc312c8fad9a8c5390c218e916" %} package: name: {{ name|lower }} @@ -13,7 +13,9 @@ source: build: noarch: python - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage('gcnvkernel', max_pin="x") }} requirements: build: @@ -24,17 +26,17 @@ requirements: # # https://github.com/broadinstitute/gatk/blob/master/scripts/gatkcondaenv.yml.template - conda-forge::python =3.6.10 - - pip =20.0.2 + - pip =21.3.1 - conda-forge::mkl =2019.5 - conda-forge::mkl-service =2.3.0 - conda-forge::numpy =1.17.5 - conda-forge::theano =1.0.4 - - defaults::tensorflow =1.15.0 + - tensorflow <2 - conda-forge::scipy =1.0.0 - conda-forge::pymc3 =3.1 - conda-forge::h5py =2.10.0 - conda-forge::keras =2.2.4 - - defaults::intel-openmp =2019.4 + - conda-forge::intel-openmp - conda-forge::scikit-learn =0.23.1 - conda-forge::matplotlib =3.2.1 - conda-forge::pandas =1.0.3 From 7bd086e46652c78b972e74ba685575885733edc0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 08:03:17 -0500 Subject: [PATCH 1988/2173] Update pymzml to 2.5.5 (#45761) --- recipes/pymzml/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pymzml/meta.yaml b/recipes/pymzml/meta.yaml index 626e6ccb8c945..5ac2c87b095ef 100644 --- a/recipes/pymzml/meta.yaml +++ b/recipes/pymzml/meta.yaml @@ -1,10 +1,10 @@ package: name: pymzml - version: "2.5.4" + version: "2.5.5" source: - url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.4.tar.gz - sha256: f3da945e09f4b7b091feaf5b168c3543b3489bc8adf0bac48029f8d70b22de7f + url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.5.tar.gz + sha256: ffe96ccad5bd1eb7214b4afbc8c42c07d3a1a9f8cb41bcc0bad422c71af625c4 build: number: 0 From 971c7c23376c325a55672b9c55e38c510f70a288 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 08:03:57 -0500 Subject: [PATCH 1989/2173] Update bigtools to 0.4.2 (#45756) --- recipes/bigtools/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bigtools/meta.yaml b/recipes/bigtools/meta.yaml index 72e92841c1718..ff77a44e62f1c 100644 --- a/recipes/bigtools/meta.yaml +++ b/recipes/bigtools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: bigtools @@ -11,7 +11,7 @@ build: source: url: https://github.com/jackh726/bigtools/archive/refs/tags/v{{ version }}.tar.gz - sha256: "92b9ea165adb1f9b13222d6c78e12148d9ba04a0d6ae96001820d43d9af7b39e" + sha256: "bd26a59e89cd00b1c7c82e038f03528ebf853182ae26213aeae2c936f203633e" requirements: build: From a34fec33dc3c7e43cd6748d154541cd4811de0e6 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:58:49 +0100 Subject: [PATCH 1990/2173] Update GATK4 to 4.5.0.0 (#45762) * bump gatk4 version * add run_exports * add run_exports * pin R version to agree with gcnvkernel * pin R to correct version --- recipes/gatk4/meta.yaml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/gatk4/meta.yaml b/recipes/gatk4/meta.yaml index 5e77a8f9a2ef8..f588a9884779c 100644 --- a/recipes/gatk4/meta.yaml +++ b/recipes/gatk4/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GATK4" %} -{% set version = "4.4.0.0" %} -{% set sha256 = "444600f7b38b46ad0b3606b7d40ce921e0ff1910a50165872f1c73c7c4a1a390" %} +{% set version = "4.5.0.0" %} +{% set sha256 = "dc1a4471e8bb566397db9894ca18acbf8f40f3fc312c8fad9a8c5390c218e916" %} package: name: {{ name|lower }} @@ -13,24 +13,26 @@ source: build: noarch: generic number: 0 + run_exports: + - {{ pin_subpackage('gatk4', max_pin="x") }} requirements: host: - - r-base + - r-base =3.6 - r-gplots - r-ggplot2 - r-gsalib - r-reshape - - gcnvkernel + - gcnvkernel =0.8 run: - openjdk >=17,<18 - python - - r-base + - r-base =3.6 - r-gplots - r-ggplot2 - r-gsalib - r-reshape - - gcnvkernel + - gcnvkernel =0.8 test: commands: From 02d3b390eec8a141f26304a2cf3b4ebecae8f25c Mon Sep 17 00:00:00 2001 From: Yuri Pirola Date: Mon, 12 Feb 2024 16:05:49 +0100 Subject: [PATCH 1991/2173] Add RecGraph (#45680) * Add RecGraph v1.0.0 --- recipes/recgraph/build.sh | 6 ++++++ recipes/recgraph/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 recipes/recgraph/build.sh create mode 100644 recipes/recgraph/meta.yaml diff --git a/recipes/recgraph/build.sh b/recipes/recgraph/build.sh new file mode 100644 index 0000000000000..049babcc91015 --- /dev/null +++ b/recipes/recgraph/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash -euo + +RUST_BACKTRACE=1 CARGO_HOME="${BUILD_PREFIX}/.cargo" cargo build --release + +mkdir -p $PREFIX/bin +cp target/release/recgraph $PREFIX/bin diff --git a/recipes/recgraph/meta.yaml b/recipes/recgraph/meta.yaml new file mode 100644 index 0000000000000..227ff06ebd53e --- /dev/null +++ b/recipes/recgraph/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "RecGraph" %} +{% set version = "1.0.0" %} +{% set sha256 = "a68a49ecc457f4070604244a21abde60c76b12dba03e8d4136c3fe20abae7ffc" %} + + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/AlgoLab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x") }} + +requirements: + build: + - make + - {{ compiler('c') }} + - rust =1.74 + +test: + commands: + - recgraph --help + +about: + home: https://github.com/AlgoLab/{{ name }} + license: MIT + license_file: LICENSE + summary: Optimal sequence-to-graph alignment with recombinations + +extra: + recipe-maintainers: + - yp From 4cf79cd9e8fc0a23a60fb90fead0526909680af2 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Mon, 12 Feb 2024 08:34:59 -0800 Subject: [PATCH 1992/2173] Add pass (#45722) * add pass * Add LICENSE file * Update meta.yaml * Fix LICENSE (SPDX identifier) --- recipes/pass/LICENSE | 674 +++++++++++++++++++++++++++++++++++++++++ recipes/pass/build.sh | 3 + recipes/pass/meta.yaml | 33 ++ 3 files changed, 710 insertions(+) create mode 100644 recipes/pass/LICENSE create mode 100755 recipes/pass/build.sh create mode 100644 recipes/pass/meta.yaml diff --git a/recipes/pass/LICENSE b/recipes/pass/LICENSE new file mode 100644 index 0000000000000..8f286b96aa63f --- /dev/null +++ b/recipes/pass/LICENSE @@ -0,0 +1,674 @@ +GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + ntEdit: scalable genome sequence polishing + Copyright (C) 2018-2019 BC Cancer + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + ntEdit Copyright (C) 2018-2019 Rene Warren @ BC Cancer + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/recipes/pass/build.sh b/recipes/pass/build.sh new file mode 100755 index 0000000000000..5bf1eeb9bd3a7 --- /dev/null +++ b/recipes/pass/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash +mkdir -p ${PREFIX}/bin +cp PASS ${PREFIX}/bin \ No newline at end of file diff --git a/recipes/pass/meta.yaml b/recipes/pass/meta.yaml new file mode 100644 index 0000000000000..96d7ce28ab436 --- /dev/null +++ b/recipes/pass/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "0.3.1" %} +{% set version_tar = "0-3-1" %} +{% set name = "pass" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/bcgsc/{{ name | upper }}/releases/download/v{{ version }}/pass_v{{ version_tar}}.tar.gz + sha256: 813fab567b1159c6dc32ed8ad537d19c50e70bde347b4e8b1249a4ece1de4383 + +build: + noarch: generic + number: 0 + run_exports: + - {{ pin_subpackage('pass', max_pin="x") }} + +requirements: + run: + - perl + +test: + commands: + - PASS -h | grep "Usage" + +about: + summary: Proteome Assembler with Short Sequence peptides + home: https://github.com/bcgsc/PASS + license: GPL-3.0-only + license_file: LICENSE + doc_url: https://github.com/bcgsc/PASS + From 44c4bebe1ecaa84227d9b77e825325d5d11b9771 Mon Sep 17 00:00:00 2001 From: Vlad Savelyev Date: Mon, 12 Feb 2024 17:35:24 +0100 Subject: [PATCH 1993/2173] MultiQC 1.20 (#45764) * MultiQC 1.20 * kaleido -> python-kaleido * Fix SHA --- recipes/multiqc/meta.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index 2d17086c661b8..489e083760ed5 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.19" %} +{% set version = "1.20" %} package: name: multiqc @@ -6,7 +6,7 @@ package: source: url: https://github.com/ewels/MultiQC/archive/v{{ version }}.tar.gz - sha256: 7c1501c8306f69a6f32777fe732fb4a53f71b066512a2252a8b2b4b89f994ca8 + sha256: 46e01394ee4c213eee3c14fde01afcb0da3e87a29b09a119e5aaeabf2817313d build: number: 0 @@ -33,6 +33,9 @@ requirements: - lzstring - markdown - matplotlib-base >=2.1.1 + - plotly + - python-kaleido + - pillow >=10.2.0 - networkx >=2.5.1 - numpy - packaging From 43b072008e2ebe2ccbc63dab38823ea950ed5aa6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 12:53:25 -0500 Subject: [PATCH 1994/2173] Update thapbi-pict to 1.0.9 (#45767) --- recipes/thapbi-pict/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 9ea4719fe92bd..c643e4772b02d 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.8" %} +{% set version = "1.0.9" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: 3e0eac668b35351ea5588b0e1890ccf2e10e7aa847efd7777fd5eca497f4eef0 + sha256: 2b271400901dc7378302c7279416b591f4317d6deb43ae6bb6fa3ae1ee1d1a49 build: noarch: python From 1fdaa2693ba0074f91aaeb6600f64885832279c4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:00:07 -0500 Subject: [PATCH 1995/2173] Update ska2 to 0.3.6 (#45768) --- recipes/ska2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ska2/meta.yaml b/recipes/ska2/meta.yaml index bd250923fcb6e..575802314f7b1 100644 --- a/recipes/ska2/meta.yaml +++ b/recipes/ska2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ska2" %} -{% set version = "0.3.5" %} +{% set version = "0.3.6" %} package: name: {{ name|lower}} @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/ska.rust/archive/v{{ version }}.tar.gz - sha256: 507290aef6ec268e2b5098b60a208dddfc690f1c029e50b68eb5169ba3b1c9f0 + sha256: b1f7aecec7ff50c982d4dabceeb091b4c00071bfb4385aa5ea931fdbdca32e1e build: number: 0 From 4d068c815efa32635ec150fb348e0f6898037858 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:00:17 -0500 Subject: [PATCH 1996/2173] Update integron_finder to 2.0.3 (#45766) * Update integron_finder to 2.0.3 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/integron_finder/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/integron_finder/meta.yaml b/recipes/integron_finder/meta.yaml index ddbeab522060d..6aebd892b1ec7 100644 --- a/recipes/integron_finder/meta.yaml +++ b/recipes/integron_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name="integron_finder" %} -{% set version="2.0.2" %} +{% set version="2.0.3" %} package: name: {{ name }} @@ -9,10 +9,12 @@ build: noarch: python number: 0 script: python -m pip install --no-deps --ignore-installed . + run_exports: + - {{ pin_subpackage("integron_finder", max_pin="x.x") }} source: - url: https://files.pythonhosted.org/packages/4a/39/816165ed051a41560c9167590bf974a83de34e5a43509e9501f79cdf4ba4/integron_finder-2.0.2.tar.gz - sha256: 62444c43895c2b68289bc7ceaa2da417766c82852b5ecf1c3280e41ba3beaa6f + url: https://files.pythonhosted.org/packages/e7/b0/00059b74aed8542f276cfd377c51b6cf5695d0b97fcc90dd39da9b68f552/integron_finder-2.0.3.tar.gz + sha256: 2ecc0579490daf5b75a5cedfb22b446e830a0ca547c8acae92ee2ab2a755aa01 requirements: host: From 301ddb52194560b5fe735fff0249c63bd279c3b7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:00:24 -0500 Subject: [PATCH 1997/2173] Update assembly_finder to 0.4.2 (#45765) --- recipes/assembly_finder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml index 0da7d56f0b95d..d54840930f3be 100644 --- a/recipes/assembly_finder/meta.yaml +++ b/recipes/assembly_finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "assembly_finder" %} -{% set version = "0.4.1" %} +{% set version = "0.4.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: - url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: be7b470ad55c5ca304816b7414bf6d8f50db351b92ed9c6be6842ec0ed8cee8b + sha256: 6f035d34e562c0727fa0a43172de61b879714c3a1d964b6a5952afb49301129b build: number: 0 entry_points: From 642afc8dcf9f9489ff4bdbb15c799d55fd9d4ed6 Mon Sep 17 00:00:00 2001 From: AllenWLynch Date: Mon, 12 Feb 2024 14:05:07 -0500 Subject: [PATCH 1998/2173] Update Lisa2 (#45753) * Update lisa2 to version 2.3.2 * bumped build number for lisa 2.3.2 * Update meta.yaml Added space between packages and version to pass linting --- recipes/lisa2/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/lisa2/meta.yaml b/recipes/lisa2/meta.yaml index 2725f8ee5badf..20859b72ef139 100644 --- a/recipes/lisa2/meta.yaml +++ b/recipes/lisa2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: dc9df3495322c94f93c12372fb8d88d355447f7b8b69ea639394fc6274e9affb build: - number: 0 + number: 1 noarch: python script: {{ PYTHON }} -m pip install . -vv run_exports: @@ -22,10 +22,10 @@ requirements: - python >=3.5 run: - h5py >=2 - - numpy <2,>=1.17 + - numpy >=1.17,<2 - python >=3.5 - - scikit-learn <2,>=0.22 - - scipy <2,>=1.4 + - scikit-learn >=0.22,<2 + - scipy >=1.4,<2 test: imports: From 75e0c8689723c104c29bd24a6923a21eb0b4ba3b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:50:17 -0500 Subject: [PATCH 1999/2173] Update mira-multiome to 2.1.1 (#45763) * Update mira-multiome to 2.1.1 * run_exports * clean up recipe and pin python to <3.12 --------- Co-authored-by: Thanh Lee Co-authored-by: mencian --- recipes/mira-multiome/meta.yaml | 33 +++++++++++++++------------------ 1 file changed, 15 insertions(+), 18 deletions(-) diff --git a/recipes/mira-multiome/meta.yaml b/recipes/mira-multiome/meta.yaml index d897c3b0eddf6..98ec59647c8a5 100644 --- a/recipes/mira-multiome/meta.yaml +++ b/recipes/mira-multiome/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mira-multiome" %} -{% set version = "2.1.0" %} +{% set version = "2.1.1" %} package: name: {{ name|lower }} @@ -7,42 +7,39 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mira-multiome-{{ version }}.tar.gz - sha256: c28a8fe8388f35c020815e27ad4d046a796680c4e43400decd53952e0502159d + sha256: f981bc40542097c3892cb02efca0c25766dfa0bbafcbd4e94ea18b3e5e27157b build: noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv number: 0 + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: - - python >=3.7 + - python >=3.7,<3.12 - wheel - pip - - setuptools >=35.0 - setuptools_scm run: - - python >=3.7 - - pytorch <2,>=1.8.0 - - pyro-ppl <2,>=1.5.2 - - networkx <3,>=2.3 - - optuna <3,>=2.8 - - anndata <1,>=0.7.6 + - python >=3.7,<3.12 + - pytorch >=1.8.0,<2 + - pyro-ppl >=1.5.2,<2 + - networkx >=2.3,<3 + - optuna >=2.8,<3 + - anndata >=0.7.6,<1 - moods >=1.9.4.1 - - pyfaidx <1,>=0.5 - - matplotlib-base <4,>=3.4 + - pyfaidx >=0.5,<1 + - matplotlib-base >=3.4,<4 - lisa2 >=2.3.0 - - requests <3,>=2 + - requests >=2,<3 - tqdm - tensorboard test: imports: - mira - commands: - - pip check - requires: - - pip about: home: https://mira-multiome.readthedocs.io/en/latest/ From 3000ab7bc36168842f760c6af7724ce9c60a957e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 14:50:32 -0500 Subject: [PATCH 2000/2173] Update samestr to 1.2024.2.post1 (#45737) * Update samestr to 1.2024.2.post1 * add run_exports --------- Co-authored-by: mencian --- recipes/samestr/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/samestr/meta.yaml b/recipes/samestr/meta.yaml index 36690b13adb95..54f65bf516a7c 100644 --- a/recipes/samestr/meta.yaml +++ b/recipes/samestr/meta.yaml @@ -1,5 +1,5 @@ {% set name = "samestr" %} -{% set version = "1.2023.4" %} +{% set version = "1.2024.2.post1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 268b26ea7e7225373ea35ff75f30e4f0f8840946a92469b6bf51a7433d0b7d2c + sha256: d03c5f1fd89fd018409bcf332c3a95e752aca9fb47b88c617fad702581630bdd build: number: 0 - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" noarch: python + run_exports: + - {{ pin_subpackage('samestr', max_pin=None) }} requirements: host: @@ -47,7 +49,7 @@ test: about: home: "https://github.com/danielpodlesny/samestr/" - license: "GNU Affero General Public License v3" + license: "AGPL-3.0-or-later" license_family: AGPL license_file: LICENSE summary: "SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles." From 973a75e5fb60600fd738b517ff9e9dc76d3004df Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 17:38:45 -0500 Subject: [PATCH 2001/2173] Update augur to 24.2.0 (#45771) --- recipes/augur/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index 9d585bfd5ce39..7eb5aee525913 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "24.1.0" %} +{% set version = "24.2.0" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: 22d349581fbbdfdcca0df02ce5d093965c9963931ef42c946a63b87d79a7ab08 + sha256: 965ab4808e937f5772022aa45444a42d89d293e9ed72272c639a570bc54540e2 build: number: 0 From 810e69434920f18e833b9ac9c2e9232424cb2606 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 12 Feb 2024 21:44:01 -0500 Subject: [PATCH 2002/2173] Update ontime to 0.3.1 (#45773) --- recipes/ontime/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ontime/meta.yaml b/recipes/ontime/meta.yaml index 1528ba3889c8a..b0764d525b178 100644 --- a/recipes/ontime/meta.yaml +++ b/recipes/ontime/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} {% set name = "ontime" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz - sha256: 808833ade04fa7fb318e37b2f0aad2f19a46ba678decdd34e208bf3042050ee1 + sha256: 1caee3197d1032da38c55a47c3b626fe00b07831362e734fb2174747fca17fc4 build: number: 0 From c4269e6b7a771857df0931409dac571684316f70 Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Tue, 13 Feb 2024 01:09:24 -0800 Subject: [PATCH 2003/2173] Update nextclade to 3.2.0 (#45777) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index fa81294b44098..b53743caebf7f 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "3.1.0" %} +{% set version = "3.2.0" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: 949ec8ea1eb9705529425543292347ce7fbf9c799ec9f82fb3a9dab5f9e39450 # [linux64] + sha256: 392f5b980f291f1580cfc09abc51779955c83811aa0537f6dba7d755e03c8fa9 # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: 878523f7c278c16bb19c47ab6421c63ccb876bbd2820cc997bcda62dcf3eb4d4 # [osx and x86_64] + sha256: deabdd06b1e6b6052c0ae50985b36db9839dfd8393de3a8d44b812b4b8b52cf6 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: 967ed5de693aa162ba010521d397462c7a73ff9430b2d70af42bc05b52782881 # [arm64] + sha256: 3b6185ff3741da4f15bd382f2f3c9cefb342e8add90a29be6050e20e4b3e66d2 # [arm64] build: number: 0 From 067edb8dbee2c29b3ac3bc242fa703cb019e836c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 04:48:44 -0500 Subject: [PATCH 2004/2173] Update clipkit to 2.2.0 (#45774) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index f2d9cc734178e..63fb201258cb4 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.1.3" %} +{% set version = "2.2.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e56e6c2c3a0c938f5026151ea191ff8fc2df7822d4aaf6487a65e9357c292487 + sha256: 7f973cec1842a3066c1478752b8692012174f5a58df870c1518a56cd37264605 build: number: 0 From 1f21b2540d3f593e65806c8bad851fe96c5394ae Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 04:49:22 -0500 Subject: [PATCH 2005/2173] Update dajin2 to 0.4.1 (#45776) --- recipes/dajin2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dajin2/meta.yaml b/recipes/dajin2/meta.yaml index 9c3310af914d4..2c1bd818cfbc1 100644 --- a/recipes/dajin2/meta.yaml +++ b/recipes/dajin2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "DAJIN2" %} -{% set version = "0.4.0" %} +{% set version = "0.4.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/DAJIN2-{{ version }}.zip - sha256: 0b0abcc8f40679bec605c85643b069b55914ac1ac9031f6ad73c319899abd002 + sha256: 5a0c360cf52d506c1c60ba94a13f408a2789c66443ba92f3d2a6f1a7acd0aa3e build: entry_points: From 417664e414951482a5d851571721a3607ded2c28 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 08:58:55 -0500 Subject: [PATCH 2006/2173] Update earlgrey to 4.0.8 (#45781) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index c9c4b8f190d19..e53bf3657fabd 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.7" %} -{% set sha256 = "d986ede4ffd3f06c5ea6ac3578c656942214031786b7e7e462b4b0ed4dbec6bd" %} +{% set version = "4.0.8" %} +{% set sha256 = "ae68c9bc464320d07ee026079c7fc2819d5768f29b7742224fc481fd03c46615" %} package: name: {{ name|lower }} From 9920006918f8b19f65262954de241ff58e3089a3 Mon Sep 17 00:00:00 2001 From: richard-burhans Date: Tue, 13 Feb 2024 15:44:54 -0500 Subject: [PATCH 2007/2173] recipe for segalign-full (#45783) * recipe for segalign-full * adding "noarch: generic" to the build section * removed skip from build section * changed license_file to license_url * change lastz command * user lastz --version instead of --help * changing twobit commands * changing twobit commands again --------- Co-authored-by: Richard C. Burhans --- recipes/segalign-full/meta.yaml | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 recipes/segalign-full/meta.yaml diff --git a/recipes/segalign-full/meta.yaml b/recipes/segalign-full/meta.yaml new file mode 100644 index 0000000000000..ef44b90632061 --- /dev/null +++ b/recipes/segalign-full/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "0.1.2" %} + +package: + name: segalign-full + version: {{ version }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_compatible('segalign-full', max_pin='x.x') }} + +requirements: + run: + - segalign + - lastz + - ucsc-fatotwobit + - ucsc-twobittofa + +test: + commands: + - segalign --help + - segalign_repeat_masker --help + - lastz --version 2>&1 | grep released + - which faToTwoBit + - which twoBitToFa + +about: + home: https://github.com/gsneha26/SegAlign + summary: 'SegAlign: A Scalable GPU-Based Whole Genome Aligner' + description: | + SegAlign is a Scalable GPU System for Pairwise Whole Genome + Alignments based on LASTZ's seed-filter-extend paradigm. + license: MIT + license_family: MIT + license_url: https://github.com/gsneha26/SegAlign/blob/main/LICENSE + doc_url: https://github.com/gsneha26/SegAlign/blob/main/README.md + dev_url: https://github.com/gsneha26/SegAlign + +extra: + identifiers: + - doi:10.1109/SC41405.2020.00043 + - doi:10.5281/zenodo.3880947 From 95840d0f9b4a5296344ee9e27498480fa37cb629 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 13 Feb 2024 23:52:03 +0100 Subject: [PATCH 2008/2173] Update: sepp subrecipe 4.3.10 (#44540) * using latest release of upstream * use recent gapc update with hopes to compile on OSX * add subrecipe for older version 4.3.10 (pinned in qiime2) which shall additionally expose upp.config * adding run_exports * pin dendropy * pin pymongo, a dependency of pasta * link to identically main recipe, instead of actual file copies * relax dendropy version & remove explicit pymongo dependency * looks like symlinks don't work * attempt to apply condas mechanism for PREFIX replacement for upp.config file * more explicit mechanism to copy files * use $SP_DIR to avoid issues with py >=3.1x * Update meta.yaml pin python to <=3.9 * adding info why python is pinned --- recipes/sepp/4.3.10/build.sh | 42 +++++++++++++ recipes/sepp/4.3.10/meta.yaml | 63 +++++++++++++++++++ recipes/sepp/4.3.10/nodeps.setup.py.patch | 11 ++++ .../sepp/4.3.10/relocate.run-sepp.sh.patch | 36 +++++++++++ .../sepp/4.3.10/relocate.sepp.config.patch | 28 +++++++++ 5 files changed, 180 insertions(+) create mode 100644 recipes/sepp/4.3.10/build.sh create mode 100644 recipes/sepp/4.3.10/meta.yaml create mode 100644 recipes/sepp/4.3.10/nodeps.setup.py.patch create mode 100644 recipes/sepp/4.3.10/relocate.run-sepp.sh.patch create mode 100644 recipes/sepp/4.3.10/relocate.sepp.config.patch diff --git a/recipes/sepp/4.3.10/build.sh b/recipes/sepp/4.3.10/build.sh new file mode 100644 index 0000000000000..a21681feb1e3a --- /dev/null +++ b/recipes/sepp/4.3.10/build.sh @@ -0,0 +1,42 @@ +#!/bin/bash +set -ex +python setup.py config -c +python setup.py upp -c + +# ensure SEPP's configuration file is at the correct location ... +echo "${PREFIX}/share/sepp/sepp" > home.path +# ensure directory is created ... ($SP_DIR = Python's site-packages location, see https://docs.conda.io/projects/conda-build/en/stable/user-guide/environment-variables.html#environment-variables-set-during-the-build-process) +mkdir -p $SP_DIR/ +# ... before we copy content into it +cp -rv home.path $SP_DIR/ +mkdir -p $PREFIX/share/sepp/sepp +# ... and holds correct path names +mv -v sepp-package/sepp/default.main.config $PREFIX/share/sepp/sepp/main.config +# copy upp config, as it's still needed +cp ./.sepp/upp.config $PREFIX/share/sepp/sepp/upp.config +# replace $PREFIX with /opt/anaconda1anaconda2anaconda3 for later replacement of concrete build PREFIX +# note: can't apply a patch here, as upp.config is not part of upstream but gets generated during python setup +if [ $unamestr == 'Linux' ]; +then + sed -i 's@'"$PREFIX"'@/opt/anaconda1anaconda2anaconda3@g' $PREFIX/share/sepp/sepp/upp.config +elif [ $unamestr == 'Darwin' ]; +then + gsed -i 's@'"$PREFIX"'@/opt/anaconda1anaconda2anaconda3@g' $PREFIX/share/sepp/sepp/upp.config +fi + +$PYTHON -m pip install . --ignore-installed --no-deps -vv + +# copy bundled binaries, but hmmer which should be provided by conda, into $PREFIX/bin/ +mkdir -p $PREFIX/bin/ +cp `cat $SRC_DIR/.sepp/main.config | grep "^path" -m 1 | grep -v "hmm" | cut -d "=" -f 2 | xargs dirname`/* $PREFIX/bin/ +cp `cat $SRC_DIR/.sepp/upp.config | grep "^path" -m 1 | grep -v "hmm" | cut -d "=" -f 2 | xargs dirname`/* $PREFIX/bin/ + +# configure run-sepp.sh for qiime2 fragment-insertion +mv -v sepp-package/run-sepp.sh $PREFIX/bin/run-sepp.sh + +# copy files for tests to shared conda directory +mkdir -p $PREFIX/share/sepp/ref/ +cp -v test/unittest/data/q2-fragment-insertion/input_fragments.fasta $PREFIX/share/sepp/ref/ +cp -v test/unittest/data/q2-fragment-insertion/reference_alignment_tiny.fasta $PREFIX/share/sepp/ref/ +cp -v test/unittest/data/q2-fragment-insertion/reference_phylogeny_tiny.nwk $PREFIX/share/sepp/ref/ +cp -v test/unittest/data/q2-fragment-insertion/RAxML_info-reference-gg-raxml-bl.info $PREFIX/share/sepp/ref/ diff --git a/recipes/sepp/4.3.10/meta.yaml b/recipes/sepp/4.3.10/meta.yaml new file mode 100644 index 0000000000000..74c5177ff7068 --- /dev/null +++ b/recipes/sepp/4.3.10/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "4.3.10" %} +{% set sha256 = "24d8d410138563017e6f2f1263d5e34427f5bbddb875b72a036f7c879cef203b" %} +package: + name: sepp + version: '{{version}}' + +source: + - url: https://github.com/smirarab/sepp/archive/{{version}}.tar.gz + sha256: '{{sha256}}' + patches: + - relocate.run-sepp.sh.patch + - relocate.sepp.config.patch + # prevent python's setup to search for dendropy dependency via pip. + # Instead use dendropy provided by conda: + - nodeps.setup.py.patch + +build: + number: 3 + run_exports: + - {{ pin_subpackage('sepp', max_pin="x") }} + +# upstream is not (yet) compatible with python >=3.10 +requirements: + host: + - python <=3.9 + - setuptools + - pip + - dendropy 4.4.0 + - openjdk + - hmmer ==3.1b2 + + run: + - python <=3.9 + - dendropy 4.4.0 + - openjdk + - hmmer ==3.1b2 + - pasta + # TODO: source bundled binaries as conda packages. + # But pplacer / guppy are not available for OSX. + # - pplacer + +test: + commands: + - run_sepp.py --help + - run-sepp.sh $PREFIX/share/sepp/ref/input_fragments.fasta testrun_tiny -a $PREFIX/share/sepp/ref/reference_alignment_tiny.fasta -t $PREFIX/share/sepp/ref/reference_phylogeny_tiny.nwk -r $PREFIX/share/sepp/ref/RAxML_info-reference-gg-raxml-bl.info -x 1 -b 1 + - grep "f__Halomonadaceae" testrun_tiny_placement.tog.relabelled.tre + - grep "testseqd" testrun_tiny_placement.tog.relabelled.tre + - run_upp.py --help + +about: + home: https://github.com/smirarab/sepp + license: GPLv3 + license_family: GPL3 + license_file: LICENSE + summary: SATe-enabled phylogenetic placement + +extra: + identifiers: + - biotools:sepp + skip-lints: + # necessary, because sepp is NOT platform independent: + # during build time, platform specific binaries for pplacer / guppy are copied into the PREFIX/bin dir + - should_be_noarch_generic diff --git a/recipes/sepp/4.3.10/nodeps.setup.py.patch b/recipes/sepp/4.3.10/nodeps.setup.py.patch new file mode 100644 index 0000000000000..f93b859cf421e --- /dev/null +++ b/recipes/sepp/4.3.10/nodeps.setup.py.patch @@ -0,0 +1,11 @@ +--- setup.py 2019-03-31 07:43:25.000000000 +0200 ++++ setup.py 2019-04-03 12:12:30.701516881 +0200 +@@ -219,7 +219,7 @@ + author_email="smirarab@gmail.com, namphuon@cs.utah.edu", + + license="General Public License (GPL)", +- install_requires=["dendropy >= 4.0.0"], ++ install_requires=[], + provides=["sepp"], + scripts=["run_sepp.py", 'run_tipp.py', 'run_upp.py', 'run_abundance.py', + "split_sequences.py", "run_tipp_tool.py"], diff --git a/recipes/sepp/4.3.10/relocate.run-sepp.sh.patch b/recipes/sepp/4.3.10/relocate.run-sepp.sh.patch new file mode 100644 index 0000000000000..89839cb66476f --- /dev/null +++ b/recipes/sepp/4.3.10/relocate.run-sepp.sh.patch @@ -0,0 +1,36 @@ +--- sepp/sepp-package/run-sepp.sh 2019-03-19 16:33:17.267182143 +0100 ++++ sepp-package/run-sepp.sh 2019-03-19 20:23:08.591954892 +0100 +@@ -111,7 +111,7 @@ + done + + +-DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) ++DIR=/opt/anaconda1anaconda2anaconda3/share/sepp/ + + # Reference tree + if [ -z $t ]; then +@@ -134,7 +134,7 @@ + if [ ! -z "$printDebug" ]; then + export SEPP_DEBUG=True + fi; +-python $DIR/sepp/run_sepp.py -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log ++run_sepp.py -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log + + tail sepp-$name-* + +@@ -146,13 +146,11 @@ + # we might want to split computation in two parts: a) obtaining placements and b) creation of an insertion tree. + # If -n set to something, we stop after a) and leave it to the user to compute b) afterwards. + if [ -z ${noTree+x} ]; then +- gbin=$( dirname `grep -A1 "pplacer" $DIR/sepp/.sepp/main.config |grep path|sed -e "s/^path=//g"` ) +- +- $gbin/guppy tog ${name}_placement.json ++ guppy tog ${name}_placement.json + + cat ${name}_placement.tog.tre | python ${name}_rename-json.py > ${name}_placement.tog.relabelled.tre + +- $gbin/guppy tog --xml ${name}_placement.json ++ guppy tog --xml ${name}_placement.json + + cat ${name}_placement.tog.xml | python ${name}_rename-json.py > ${name}_placement.tog.relabelled.xml + else diff --git a/recipes/sepp/4.3.10/relocate.sepp.config.patch b/recipes/sepp/4.3.10/relocate.sepp.config.patch new file mode 100644 index 0000000000000..cb5f917265157 --- /dev/null +++ b/recipes/sepp/4.3.10/relocate.sepp.config.patch @@ -0,0 +1,28 @@ +--- sepp-package/sepp/default.main.config 2019-03-18 10:14:42.363446570 +0100 ++++ sepp-package/sepp/default.main.config 2019-04-04 10:10:22.171485197 +0200 +@@ -1,20 +1,20 @@ + [pplacer] +-path=~/pplacer ++path=/opt/anaconda1anaconda2anaconda3/bin/pplacer + + [hmmalign] +-path=~/hmmalign ++path=/opt/anaconda1anaconda2anaconda3/bin/hmmalign + + [hmmsearch] +-path=~/hmmsearch ++path=/opt/anaconda1anaconda2anaconda3/bin/hmmsearch + piped=False + elim=10000 + filters=True + + [hmmbuild] +-path=~/hmmbuild ++path=/opt/anaconda1anaconda2anaconda3/bin/hmmbuild + + [jsonmerger] +-path=~/seppJsonMerger.jar ++path=/opt/anaconda1anaconda2anaconda3/bin/seppJsonMerger.jar + + [exhaustive] + strategy = centroid From 9c7399ecd5baf69c20b35bfe0df07b18858f03e8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 17:52:40 -0500 Subject: [PATCH 2009/2173] Update ncbi-datasets-pylib to 16.4.7 (#45782) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 1659ccf273071..adb9708118530 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.5" %} -{% set sha256 = "c7b0aaeda5327e1fccd41774c43bfa936bb176e7790b63bd9ef7d8e14bbd0e27" %} +{% set version = "16.4.7" %} +{% set sha256 = "6d637d0b730426a35fa89f8107ada4573abe374214a1c93f9bafdb265986c9f4" %} package: name: {{ name|lower }} From 33c9d960482960cef05b437cc9d76daea83a4bb0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 17:53:31 -0500 Subject: [PATCH 2010/2173] Update dxpy to 0.369.1 (#45785) --- recipes/dxpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index 5dd102f8d5615..e2bc358122061 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.369.0" %} +{% set version = "0.369.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: dc2f58723d70c6d02155c08d4ac65f41f63aeb05000e4782940d2196b05a962b + sha256: 6e83d6c0756ff2b6691c9b789298ef5fdbe3f3df67b8fd90beb8420782219d41 build: number: 0 From a11065f7615fa8e60eff2fe2afbe0e926e9aec92 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 17:54:12 -0500 Subject: [PATCH 2011/2173] Update panaroo to 1.4.0 (#45786) --- recipes/panaroo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/panaroo/meta.yaml b/recipes/panaroo/meta.yaml index 4a3566f47f25b..8d83ad1beb7c2 100644 --- a/recipes/panaroo/meta.yaml +++ b/recipes/panaroo/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.4" %} +{% set version = "1.4.0" %} {% set name = "panaroo" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/gtonkinhill/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 95d9b166b0f554ca9b6b9326d3a85a065edee468e7d469f77d8b5242d7f82b9b + sha256: 651a11c9326bf885709ad555722ffefc5f67a365dce8a6475c09cd8d3537a89c build: number: 0 From 570e8619ecbfae2e6f7babac5c41d8403f5f6c86 Mon Sep 17 00:00:00 2001 From: Mike Tisza Date: Tue, 13 Feb 2024 17:10:13 -0600 Subject: [PATCH 2012/2173] Update meta.yaml (#45769) --- recipes/cenote-taker3/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/cenote-taker3/meta.yaml b/recipes/cenote-taker3/meta.yaml index 6717368a52f63..8a3b8e9aadc5e 100644 --- a/recipes/cenote-taker3/meta.yaml +++ b/recipes/cenote-taker3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cenote-taker3" %} -{% set version = "3.2.0" %} +{% set version = "3.2.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/mtisza1/{{ name }}/archive/v{{ version }}.tar.gz" - sha256: fe28c66009a4b1ee6755fbabcfbe5a8d0cba985977818155d6aefd0324ea9f95 + sha256: ffda0fcc8bee4c9200e46833008664bbe9155b6aae2b62d741943f27f6532a16 build: number: 0 @@ -43,6 +43,8 @@ requirements: - sed - grep - samtools + - pandas + - pyarrow test: From 34f650f1090f366c36bd27c0e1221fca47cca4dc Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 14 Feb 2024 12:11:45 +1300 Subject: [PATCH 2013/2173] Add LTR_FINDER_parallel (#45772) * Added recipe for ltr_finder_parallel * Fixed typo * Locked version of ltr_finder to 1.07 * Replacing ltr_finder problematic line * Added a explanatory comment for the patch --- recipes/ltr_finder_parallel/build.sh | 24 +++++++++++++++++ recipes/ltr_finder_parallel/meta.yaml | 39 +++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 recipes/ltr_finder_parallel/build.sh create mode 100644 recipes/ltr_finder_parallel/meta.yaml diff --git a/recipes/ltr_finder_parallel/build.sh b/recipes/ltr_finder_parallel/build.sh new file mode 100644 index 0000000000000..5967719b8716f --- /dev/null +++ b/recipes/ltr_finder_parallel/build.sh @@ -0,0 +1,24 @@ +#!/bin/sh +set -x -e + +LTR_FINDER_PARALLEL_DIR=${PREFIX}/share/LTR_FINDER_parallel + +mkdir -p ${PREFIX}/bin +mkdir -p ${LTR_FINDER_PARALLEL_DIR} +cp -r * ${LTR_FINDER_PARALLEL_DIR} + +# LTR_FINDER_parallel creates the path to ltr_finder by using `which ltr_finder` +# `which ltr_finder` returns the path along with a newline character '\n'. +# To replace the newline character, LTR_FINDER_parallel matches regex 'ltr_finder\\n?' +# This regex logic fails in the case of this CONDA recipe because the path to +# ltr_finder includes ltr_finder_parallel which is replaced as _parallel, resulting in +# an invalid path. I have changed the regex so that ltr_finder_parallel is not replaced. +sed -i.bak 's|\$ltr_finder=~s/ltr_finder\\n?//;|\$ltr_finder=~s/\\bltr_finder\\n?\$//m;|' \ + ${LTR_FINDER_PARALLEL_DIR}/LTR_FINDER_parallel + +cat <>${PREFIX}/bin/LTR_FINDER_parallel +#!/bin/bash +perl ${LTR_FINDER_PARALLEL_DIR}/LTR_FINDER_parallel \$@ +END + +chmod a+x ${PREFIX}/bin/LTR_FINDER_parallel diff --git a/recipes/ltr_finder_parallel/meta.yaml b/recipes/ltr_finder_parallel/meta.yaml new file mode 100644 index 0000000000000..70c9f77428cf8 --- /dev/null +++ b/recipes/ltr_finder_parallel/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "LTR_FINDER_parallel" %} +{% set version = "1.1" %} +{% set sha256 = "5d1fed2a3a38c0927ccd7fc6cc38ba13ce293c5b1805299c999c5d52d085a1b9" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/oushujun/LTR_FINDER_parallel/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('ltr_finder_parallel', max_pin='x') }} + +requirements: + run: + - ltr_finder ==1.07 + +test: + commands: + - ltr_finder 2>&1 | grep -i usage + - LTR_FINDER_parallel -check_dependencies > /dev/null + +about: + home: https://github.com/oushujun/LTR_FINDER_parallel + license: MIT + license_family: MIT + license_file: LICENSE + summary: Perl wrapper to parallelize ltr_finder + dev_url: https://github.com/oushujun/LTR_FINDER_parallel + doc_url: https://github.com/oushujun/LTR_FINDER_parallel + +extra: + identifiers: + - doi:10.1186/s13100-019-0193-0 From 72afa882c3898f5b5461a7e73f5fac9ba48edde1 Mon Sep 17 00:00:00 2001 From: Ryan James Kennedy <67742838+ryanjameskennedy@users.noreply.github.com> Date: Wed, 14 Feb 2024 00:21:40 +0100 Subject: [PATCH 2014/2173] Update serotypefinder to v2.0.2 (#45770) * Update serotypefinder to v2.0.2 * Add run_exports to fix linting error * Update build script commit id re serotypefinder_db * Add python3.8 to host requirements, update build script, add download-db script * Fix mamba solver errors --- recipes/serotypefinder/build.sh | 25 ++++++++----------------- recipes/serotypefinder/download-db.sh | 21 +++++++++++++++++++++ recipes/serotypefinder/meta.yaml | 16 ++++++++++------ 3 files changed, 39 insertions(+), 23 deletions(-) create mode 100644 recipes/serotypefinder/download-db.sh diff --git a/recipes/serotypefinder/build.sh b/recipes/serotypefinder/build.sh index f86371d384563..448adcd673160 100644 --- a/recipes/serotypefinder/build.sh +++ b/recipes/serotypefinder/build.sh @@ -9,28 +9,19 @@ cp serotypefinder.py ${PREFIX}/bin/serotypefinder chmod +x ${RECIPE_DIR}/update-serotypefinder-db.sh cp ${RECIPE_DIR}/update-serotypefinder-db.sh ${PREFIX}/bin/update-serotypefinder-db -# Grab latest database -# The SerotypeFinder database is not tagged and versioned, but it's also not updated -# very often (~7 commits in 5 years). 25ddd141d245db6382ca5876f7c7ddd0288aeb30 is the -# latest commit as of 2021/07/22. A script is provided to allow users to update in the -# event an update is made. -mkdir database/ -git clone https://bitbucket.org/genomicepidemiology/serotypefinder_db.git database/ -cd database/ -git checkout 25ddd141d245db6382ca5876f7c7ddd0288aeb30 -python3 INSTALL.py -echo "25ddd141d245db6382ca5876f7c7ddd0288aeb30" > serotypefinder-db-commit.txt -cd .. +# create folder for database download +target=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION} +mkdir -p ${target}/db/ +touch ${target}/db/.empty -# Path for database -outdir=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM} -mkdir -p ${outdir}/ -mv ./database/ ${outdir}/ +# copy script to download database +cp ${RECIPE_DIR}/download-db.sh ${PREFIX}/bin +chmod +x ${PREFIX}/bin/download-db.sh # set SEROTYPEFINDER_DB variable on env activation mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d cat <> ${PREFIX}/etc/conda/activate.d/serotypefinder.sh -export SEROTYPEFINDER_DB=${outdir}/database/ +export SEROTYPEFINDER_DB=${target}/db/ EOF cat <> ${PREFIX}/etc/conda/deactivate.d/serotypefinder.sh diff --git a/recipes/serotypefinder/download-db.sh b/recipes/serotypefinder/download-db.sh new file mode 100644 index 0000000000000..74296aca0dcd7 --- /dev/null +++ b/recipes/serotypefinder/download-db.sh @@ -0,0 +1,21 @@ +#!/usr/bin/env bash + +echo "Downloading SerotypeFinder database to ${SEROTYPEFINDER_DB}..." + +# Grab latest database +# The SerotypeFinder database is not tagged and versioned, but it's also not updated +# very often (~7 commits in 5 years). ada62c62a7fa74032448bb2273d1f7045c59fdda is the +# latest commit as of 2022/05/16. A script is provided to allow users to update in the +# event an update is made. + +cd ${SEROTYPEFINDER_DB} +# download SerotypeFinder database +git clone https://bitbucket.org/genomicepidemiology/serotypefinder_db.git db_serotypefinder +cd db_serotypefinder +python3 INSTALL.py +git rev-parse HEAD > serotypefinder-db-commit.txt +cd .. + +echo "SerotypeFinder database is downloaded." + +exit 0 diff --git a/recipes/serotypefinder/meta.yaml b/recipes/serotypefinder/meta.yaml index ae555ddfebb03..6fb2ab6ca1434 100644 --- a/recipes/serotypefinder/meta.yaml +++ b/recipes/serotypefinder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SerotypeFinder" %} -{% set version = "2.0.1" %} +{% set version = "2.0.2" %} package: name: "{{ name|lower }}" @@ -7,22 +7,26 @@ package: source: url: https://bitbucket.org/genomicepidemiology/{{ name|lower }}/get/{{ version }}.tar.gz - sha256: b937c0d85085f77f750665f28181656e5fb689e0d19a920ff7064f2ab4463783 + sha256: c6e13a3ef91c2f137bad99925a6b64e31330b768a4d8214bb767a51b3ea11446 patches: - - database_path.patch + - database_path.patch build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('serotypefinder', max_pin="x") }} requirements: + host: + - python >=3.8 run: - - biopython =1.73 + - biopython >=1.79 - blast >=2.8.1 - cgecore >=1.5.5 - kma - - python >=3 - - tabulate >=0.7.7 + - python >=3.8 + - tabulate >=0.8.9 test: From 7854fe95a9f5645be371fe1b264a15e7b6fb58f2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= Date: Wed, 14 Feb 2024 00:56:56 +0100 Subject: [PATCH 2015/2173] Update Integron finder to new release 2.0.3 (#45778) * add recipe to build squizz * update version * fixtypo in test section * update integron_finder recipe for new release 2.0.3 * clean up recipe --------- Co-authored-by: mencian --- recipes/integron_finder/meta.yaml | 59 ++++++++++++++++++------------- 1 file changed, 35 insertions(+), 24 deletions(-) diff --git a/recipes/integron_finder/meta.yaml b/recipes/integron_finder/meta.yaml index 6aebd892b1ec7..7e8566ea79450 100644 --- a/recipes/integron_finder/meta.yaml +++ b/recipes/integron_finder/meta.yaml @@ -1,48 +1,59 @@ -{% set name="integron_finder" %} -{% set version="2.0.3" %} +{% set name = "integron_finder" %} +{% set version = "2.0.3" %} package: - name: {{ name }} + name: {{ name|lower }} version: {{ version }} +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/integron_finder-{{ version }}.tar.gz + sha256: 2ecc0579490daf5b75a5cedfb22b446e830a0ca547c8acae92ee2ab2a755aa01 + build: + entry_points: + - integron_finder=integron_finder.scripts.finder:main + - integron_split=integron_finder.scripts.split:main + - integron_merge=integron_finder.scripts.merge:main noarch: python - number: 0 - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + number: 1 run_exports: - - {{ pin_subpackage("integron_finder", max_pin="x.x") }} - -source: - url: https://files.pythonhosted.org/packages/e7/b0/00059b74aed8542f276cfd377c51b6cf5695d0b97fcc90dd39da9b68f552/integron_finder-2.0.3.tar.gz - sha256: 2ecc0579490daf5b75a5cedfb22b446e830a0ca547c8acae92ee2ab2a755aa01 + - {{ pin_subpackage('integron_finder', max_pin="x") }} requirements: host: - - python >=3.7,<=3.10 + - python >=3.10 - pip run: - - python >=3.7,<=3.10 - - biopython ==1.78 - - numpy ==1.19.4 - - matplotlib-base ==3.3.3 - - colorlog <=6.6.0 - - pandas ==1.1.5 + - python >=3.10 + - numpy >=1.26 + - matplotlib-base >=3.8 + - pandas >=2 + - biopython >=1.82 + - colorlog - hmmer >=3.1b2,<=3.3.2 - infernal >=1.1.2,<=1.1.4 - prodigal >=2.6.3 test: + imports: + - integron_finder commands: - - integron_finder --version + - integron_finder --help + - integron_split --help + - integron_merge --help about: - home: https://github.com/gem-pasteur/Integron_Finder - license: 'GPLv3' + home: https://github.com/gem-pasteur/Integron_Finder/ + summary: Integron Finder aims at detecting integrons in DNA sequences + license: GPL-3.0-or-later + license_family: GPL3 license_file: COPYING - summary: 'Finds integrons in DNA sequences' + doc_url: https://integronfinder.readthedocs.io/en/latest/ + dev_url: https://github.com/gem-pasteur/Integron_Finder/ extra: recipe-maintainers: - - thanhleviet - doi: - - 10.1093/nar/gkw319 + - bneron + identifiers: + - doi:10.3390/microorganisms10040700 From 68b1d89a83b102e9ee1b5c3009cd3668c4b685c8 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 13 Feb 2024 18:42:06 -0600 Subject: [PATCH 2016/2173] Update infernal to 1.1.5 (#45787) --- recipes/infernal/build.sh | 5 ++--- recipes/infernal/meta.yaml | 29 +++++++++++++++++++++-------- 2 files changed, 23 insertions(+), 11 deletions(-) diff --git a/recipes/infernal/build.sh b/recipes/infernal/build.sh index e81bb592239ce..cf8e77142882d 100644 --- a/recipes/infernal/build.sh +++ b/recipes/infernal/build.sh @@ -4,8 +4,7 @@ set -ex grep -l -r "/usr/bin/perl" . | xargs sed -i.bak -e 's/usr\/bin\/perl/usr\/bin\/env perl/g' - -./configure --prefix=$PREFIX +autoreconf -i +./configure --prefix="${PREFIX}" --enable-sse make -j 2 -make check make install diff --git a/recipes/infernal/meta.yaml b/recipes/infernal/meta.yaml index 67b3bcad6bc71..33fd6e2aa733d 100644 --- a/recipes/infernal/meta.yaml +++ b/recipes/infernal/meta.yaml @@ -1,29 +1,34 @@ -{% set version = "1.1.4" %} +{% set name = "infernal" %} +{% set version = "1.1.5" %} package: - name: infernal + name: {{ name }} version: {{ version }} source: - url: http://eddylab.org/infernal/infernal-{{ version }}.tar.gz - sha256: f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc + url: http://eddylab.org/infernal/{{ name }}-{{ version }}.tar.gz + sha256: ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage('infernal', max_pin="x") }} requirements: build: - - make - {{ compiler('c') }} + - make + - autoconf + - automake + - libtool host: - perl - run: test: commands: - cmalign -h - cmbuild -h - - cmcalibrate -h + - cmcalibrate -h - cmconvert -h - cmemit -h - cmfetch -h @@ -35,6 +40,14 @@ test: about: home: http://eddylab.org/infernal license: BSD-3-Clause + license_family: BSD license_file: LICENSE summary: Infernal is for searching DNA sequence databases for RNA structure and sequence similarities. description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. + doc_url: http://eddylab.org/infernal/Userguide.pdf + dev_url: https://github.com/EddyRivasLab/infernal + +extra: + identifiers: + - doi:10.1093/bioinformatics/btt509 + - biotools:infernal From de77ef791b979a6f6cc324415a45efcaa01b1a6f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 23:00:59 -0500 Subject: [PATCH 2017/2173] Update augur to 24.2.1 (#45788) --- recipes/augur/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index 7eb5aee525913..acab680fa5d8b 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "24.2.0" %} +{% set version = "24.2.1" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: 965ab4808e937f5772022aa45444a42d89d293e9ed72272c639a570bc54540e2 + sha256: c1fe7c357357d9b73dd614db7641695bbd780d884bebe2fb6082f19a28bb0f3b build: number: 0 From 7fa2edbb375f1bcc902099554062ab9ae2097c2e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 13 Feb 2024 23:01:14 -0500 Subject: [PATCH 2018/2173] Update submission-excel2xml to 2.6 (#45789) --- recipes/submission-excel2xml/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/submission-excel2xml/meta.yaml b/recipes/submission-excel2xml/meta.yaml index aaa47188eaa55..8a1c9a794ed3f 100644 --- a/recipes/submission-excel2xml/meta.yaml +++ b/recipes/submission-excel2xml/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.5" %} +{% set version = "2.6" %} package: name: submission-excel2xml @@ -12,7 +12,7 @@ build: source: url: https://github.com/ddbj/submission-excel2xml/archive/refs/tags/v{{ version }}.tar.gz - md5: 14369dca823b18bc4c345913d689ae64 + sha256: 50d903242184967be8a39a88bb0e0bd0cf6d0d185c89b89fe3ed9525875fe01d requirements: host: From d758b80a9bcaedf79bcbb3285bacda5872c1f6d2 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 13 Feb 2024 22:31:53 -0600 Subject: [PATCH 2019/2173] Update antismash to 7.1.0 (#45331) * Update antismash to 7.1.0 * add post-link.sh back * remove post-link.sh again * add post-link.sh message --- recipes/antismash/build.sh | 4 ++-- recipes/antismash/meta.yaml | 36 +++++++++++++++++++++------------- recipes/antismash/post-link.sh | 9 ++++++++- 3 files changed, 32 insertions(+), 17 deletions(-) diff --git a/recipes/antismash/build.sh b/recipes/antismash/build.sh index e60c5bc782d58..336e0d884c8bf 100644 --- a/recipes/antismash/build.sh +++ b/recipes/antismash/build.sh @@ -1,5 +1,5 @@ #!/bin/bash echo "include antismash/detection/genefinding/data/train_crypto" >> MANIFEST.in -df -h -$PYTHON -m pip install . --ignore-installed --no-deps -vv +df -h +${PYTHON} -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv diff --git a/recipes/antismash/meta.yaml b/recipes/antismash/meta.yaml index 6d4818140a158..c6ae23bcad79e 100644 --- a/recipes/antismash/meta.yaml +++ b/recipes/antismash/meta.yaml @@ -1,6 +1,6 @@ {% set name = "antiSMASH" %} -{% set version = "6.1.1" %} -{% set sha256 = "38c9fa8d34dea2552d3b21e3cb2ca293864f2f53d381764de9dd3d5f0b40139e" %} +{% set version = "7.1.0" %} +{% set sha256 = "5c01cce48ef5cc2bc60bfd2e185a5937e731e86a711c4c822a336640984e9b48" %} package: name: {{ name|lower }} @@ -9,6 +9,11 @@ package: build: number: 0 noarch: python + entry_points: + - download-antismash-databases=antismash.download_databases:_main + - antismash=antismash.__main__:entrypoint + run_exports: + - {{ pin_subpackage('antismash', max_pin="x") }} source: url: https://dl.secondarymetabolites.org/releases/{{ version }}/antismash-{{ version }}.tar.gz @@ -16,31 +21,33 @@ source: requirements: host: - - python >=3.7 + - python >=3.9 - pip + - pytest run: - - python >=3.7 + - python >=3.9 + - brawn >=1.0.1 - numpy - - biopython 1.78 - - helperlibs >=0.2.0 + - biopython 1.78.* + - helperlibs >=0.2.1 - jinja2 - joblib - jsonschema - markupsafe >=2.0 + - nrpys >=0.1.1 - pysvg-py3 - bcbio-gff - - pyscss + - libsass - matplotlib-base - scipy - - openjdk - - scikit-learn >=0.19 - - diamond 0.9.* + - scikit-learn >=1.3.2 + - moods >=1.9.4.2 + - diamond - fasttree 2.1.* - glimmerhmm ==3.0.* - hmmer2 - - hmmer ==3.1b2 - - meme <=4.11.2 - - muscle 3.8.* + - hmmer >=3.1b2 + - meme 4.11.2 - blast - prodigal @@ -53,7 +60,7 @@ test: about: home: https://docs.antismash.secondarymetabolites.org/intro/ - license: AGPL-3.0 + license: AGPL-3.0-or-later license_family: AGPL license_file: LICENSE.txt summary: antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell @@ -72,4 +79,5 @@ extra: - doi:10.1093/nar/gkx319 - doi:10.1093/nar/gkz310 - doi:10.1093/nar/gkab335 + - doi:10.1093/nar/gkad344 - usegalaxy-eu:antismash diff --git a/recipes/antismash/post-link.sh b/recipes/antismash/post-link.sh index 26fdad9e1d1cd..0df651f1df344 100644 --- a/recipes/antismash/post-link.sh +++ b/recipes/antismash/post-link.sh @@ -1,4 +1,11 @@ #!/bin/bash -# download the databases required by several options +cat <> ${PREFIX}/.messages.txt + + +antiSMASH databases are no longer included in the antismash conda package due to a "no space left on device" error. +Before using antiSMASH, please download the databases required by several options: download-antismash-databases + + +EOF From 2cb33b9041b5678adda05a7673908d503d9244a1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 03:42:07 -0500 Subject: [PATCH 2020/2173] Update pangolin-data to 1.25 (#45791) --- recipes/pangolin-data/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangolin-data/meta.yaml b/recipes/pangolin-data/meta.yaml index d8b1f3721fb4d..6cbc9961cc1f7 100644 --- a/recipes/pangolin-data/meta.yaml +++ b/recipes/pangolin-data/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.24" %} +{% set version = "1.25" %} package: name: pangolin-data @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pangolin-data/archive/refs/tags/v{{ version }}.tar.gz - sha256: 63e3eb2598b90d0b0c3ab6b9be34cd520c7b060751f5511e653616146407f839 + sha256: abb7a1cdd2ac9f00f33bc1158262548e9219c631d363bc83d8ba4b3d914ca910 build: number: 0 From bee25d6cf6150ed49f467120e535f196aef5c942 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 03:42:17 -0500 Subject: [PATCH 2021/2173] Update metacerberus to 1.2.1 (#45790) --- recipes/metacerberus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metacerberus/meta.yaml b/recipes/metacerberus/meta.yaml index 79300581b533d..670a203a2f29b 100644 --- a/recipes/metacerberus/meta.yaml +++ b/recipes/metacerberus/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MetaCerberus" %} -{% set version = "1.2" %} +{% set version = "1.2.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 6103002803d448df349f770a38e0da9a261a688993b5d33afbf1a9024ecbba07 + sha256: 1140732198b95c0d670fccb213c84464eb80bbe27127e4a85560de30c4873ac6 build: number: 0 From 8085b6a064520d08244e18135cc0920ba006f9d5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 04:14:49 -0500 Subject: [PATCH 2022/2173] Update riassigner to 0.4.0 (#45779) * Update riassigner to 0.4.0 * add run_exports and use pypi source --------- Co-authored-by: Helge Hecht Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/riassigner/meta.yaml | 34 +++++++++++++++++++--------------- 1 file changed, 19 insertions(+), 15 deletions(-) diff --git a/recipes/riassigner/meta.yaml b/recipes/riassigner/meta.yaml index ee61afd653b1c..25837214f09ca 100644 --- a/recipes/riassigner/meta.yaml +++ b/recipes/riassigner/meta.yaml @@ -1,32 +1,35 @@ -{% set version = "0.3.4" %} +{% set name = "riassigner" %} +{% set version = "0.4.0" %} package: - name: riassigner - version: "{{ version }}" + name: {{ name }} + version: {{ version }} source: - url: "https://github.com/RECETOX/RIAssigner/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 7a8977603e659b76e87a558add2ae7960eb7e352365c289a7a193d4d8f68da3a + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/riassigner-{{ version }}.tar.gz + sha256: 32d0306ba76feb7d470eb504b2bd382f0d78c85f7795bc275abad0c874ee7d61 build: noarch: python - preserve_egg_dir: True - number: 4 - script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv + number: 0 + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv + run_exports: + - {{ pin_subpackage('riassigner', max_pin="x.x") }} requirements: host: - - python >=3.7,<3.9 + - python >=3.10,<3.13 - pip - - pytest-runner - - setuptools + - poetry-core run: - - numpy <=1.23 - - matchms >=0.14.0,<0.18.0 - - pint >=0.17,<0.20 + - numpy + - matchms >=0.24.1,<0.25.0 + - pint >=0.23.0,<0.24.0 - pandas - - python >=3.7,<3.9 + - python >=3.10,<3.13 - scipy + - urllib3 1.26.15 + - fastparquet >=2023.10.1,<2024.0.0 test: imports: @@ -35,6 +38,7 @@ test: about: home: https://github.com/RECETOX/RIAssigner license: MIT + license_family: MIT license_file: LICENSE summary: 'GC-MS retention index calculation' description: | From 438e424deb42db3c91cd6ffd6742f75d910c8d4a Mon Sep 17 00:00:00 2001 From: Vlad Savelyev Date: Wed, 14 Feb 2024 11:17:10 +0100 Subject: [PATCH 2023/2173] MultiQC: pin plotly version (#45780) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/multiqc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index 489e083760ed5..cb8edecf3f5a4 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 46e01394ee4c213eee3c14fde01afcb0da3e87a29b09a119e5aaeabf2817313d build: - number: 0 + number: 1 entry_points: - multiqc=multiqc.__main__:run_multiqc noarch: python @@ -33,7 +33,7 @@ requirements: - lzstring - markdown - matplotlib-base >=2.1.1 - - plotly + - plotly >=5.18 - python-kaleido - pillow >=10.2.0 - networkx >=2.5.1 From 24a112f31c2466d11cbc9949d86e2524b40a0cd5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 13:30:59 -0500 Subject: [PATCH 2024/2173] Update pybiolib to 1.1.1747 (#45800) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 102a78061d184..4d20a5881de64 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1745" %} +{% set version = "1.1.1747" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 3215bc496f4ddaf85d3cb327ccc19bf6a6b5f4c0edc339e0967804239dfb44e5 + sha256: b6e014d302e0551db14697ec438ec07fecbf7bdd3634ccd22a47c4410a7a7839 build: noarch: python From ad40e0a46904fab92c8f678b4ecde26b791c8ef4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 14:53:21 -0500 Subject: [PATCH 2025/2173] Update hiphase to 1.4.0 (#45804) --- recipes/hiphase/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml index 59ee793e0ae92..92a902546ec07 100644 --- a/recipes/hiphase/meta.yaml +++ b/recipes/hiphase/meta.yaml @@ -1,6 +1,6 @@ {% set name = "hiphase" %} -{% set version = "1.3.0" %} -{% set hiphase_sha256 = "dd2708f5dd057009be555bf548aecfe30b189c4da086d026bdbb226bd4fb576e" %} +{% set version = "1.4.0" %} +{% set hiphase_sha256 = "ca38d56df8c644c3f60db26107d21dcaf58bdf53ee166c316fb51de7b8d21768" %} package: name: {{ name }} From c9d162c4484ef6b890e6002245272ea89594ffee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 15:06:32 -0500 Subject: [PATCH 2026/2173] Update biocommons.seqrepo to 0.6.7 (#45803) --- recipes/biocommons.seqrepo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biocommons.seqrepo/meta.yaml b/recipes/biocommons.seqrepo/meta.yaml index f70cee72ac83a..190a81d3545ba 100644 --- a/recipes/biocommons.seqrepo/meta.yaml +++ b/recipes/biocommons.seqrepo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biocommons.seqrepo" %} -{% set version = "0.6.6" %} +{% set version = "0.6.7" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/biocommons.seqrepo-{{ version }}.tar.gz - sha256: 655eb8a2b6e3d4564ef2cbfaa2db6415ccb066f9fd786bd4b3303bbba00e752a + sha256: 2c3f982c1ed3adb1971a0dd2e7a554d096a1c5801075e384a62dd3f73d5e8c81 build: number: 0 From d922222454bf7cda4eae563877808d9d2243e7ee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 15:06:52 -0500 Subject: [PATCH 2027/2173] Update ena-webin-cli to 7.0.1 (#45802) --- recipes/ena-webin-cli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ena-webin-cli/meta.yaml b/recipes/ena-webin-cli/meta.yaml index b76445e0d12fe..2046d32218378 100644 --- a/recipes/ena-webin-cli/meta.yaml +++ b/recipes/ena-webin-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "7.0.0" %} -{% set sha256 = "8b372aa08fe3e039f6d47d546ca18a20cbfcb1feb64748ea5a00527d81c7a418" %} +{% set version = "7.0.1" %} +{% set sha256 = "7adf27f5d333045a3a960b0cb6342e2facc082239ee815ba446d6c8f51492184" %} package: name: ena-webin-cli From eb8f485718673b253bbffe244397cac4f82692af Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 15:07:01 -0500 Subject: [PATCH 2028/2173] Update pyteomics to 4.7.1 (#45801) --- recipes/pyteomics/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyteomics/meta.yaml b/recipes/pyteomics/meta.yaml index 3a7d5dfd42122..feb0274d684e9 100644 --- a/recipes/pyteomics/meta.yaml +++ b/recipes/pyteomics/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.7" %} +{% set version = "4.7.1" %} package: name: pyteomics @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/p/pyteomics/pyteomics-{{ version }}.tar.gz - sha256: 9f3f83da617c9e7576a927f1dd668f0725789384545e3bc1fd53401d829534c2 + sha256: e5e5d3204af3050b9bf95bb64941b6156331335216e125ac253e7c8dfb1cf0ab build: noarch: python From 4e9bc0ca301fd6baa11b4e219cee4b1d2ccdfece Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 15:07:06 -0500 Subject: [PATCH 2029/2173] Update savana to 1.0.5 (#45796) --- recipes/savana/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/savana/meta.yaml b/recipes/savana/meta.yaml index 1e02c7e699603..346e21295480e 100644 --- a/recipes/savana/meta.yaml +++ b/recipes/savana/meta.yaml @@ -1,5 +1,5 @@ {% set name = "savana" %} -{% set version = "1.0.4" %} +{% set version = "1.0.5" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/cortes-ciriano-lab/{{ name }}/archive/{{ version }}.tar.gz" - sha256: f870ec9d36b20c1caf7849a4bff7af8cc984cd076b2f4d39153661e15776c644 + sha256: 987cf91c355f98e45b29fbca32d7766284eea98d63333ed34f60885d8234510e build: number: 0 From 87d0796ae84891ff83247e21567a2f49fe32f7b3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 14 Feb 2024 17:19:54 -0500 Subject: [PATCH 2030/2173] Update hmftools-bam-tools to 1.2.1 (#45805) --- recipes/hmftools-bam-tools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hmftools-bam-tools/meta.yaml b/recipes/hmftools-bam-tools/meta.yaml index 58f205663e016..68e1d104b1102 100644 --- a/recipes/hmftools-bam-tools/meta.yaml +++ b/recipes/hmftools-bam-tools/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.2" %} -{% set sha256 = "552f157861c22a0af22ce19400e6771a8034bdbfedbc760f287a30ac794d36c8" %} +{% set version = "1.2.1" %} +{% set sha256 = "3be174019a397a0ff7049be60c9abf8826c59b58b0a3b416fce26cf2a8c12695" %} package: name: hmftools-bam-tools @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 1 + number: 0 run_exports: - {{ pin_subpackage("hmftools-bam-tools", max_pin="x.x") }} From 4ec92e1858290c38764923847bcc838c4042f4bb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 05:32:37 -0500 Subject: [PATCH 2031/2173] Update umi_tools to 1.1.5 (#45795) * Update umi_tools to 1.1.5 * Add run_exports --------- Co-authored-by: Jonathan Manning --- recipes/umi_tools/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/umi_tools/meta.yaml b/recipes/umi_tools/meta.yaml index 1dfa3b6caa4b6..8a309583a61c8 100644 --- a/recipes/umi_tools/meta.yaml +++ b/recipes/umi_tools/meta.yaml @@ -1,6 +1,6 @@ {% set name = "umi_tools" %} -{% set version = "1.1.4" %} -{% set sha256hash = "945c4c98e2007369c301a7a009c6f9deb0fda74b0117cd14e14bd134164a4ff6" %} +{% set version = "1.1.5" %} +{% set sha256hash = "2a87b75364ebe3e6ccf467d3b6d0501c458a48f3e6c8ab8b7c4dfb3fd7627fab" %} package: name: {{ name }} @@ -11,11 +11,13 @@ source: sha256: {{ sha256hash }} build: - number: 2 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" skip: True # [py27] entry_points: - umi_tools = umi_tools.umi_tools:main + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: From 90e15f0667967650647a109e454246538472972b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 11:10:37 -0500 Subject: [PATCH 2032/2173] Update pangolin-data to 1.25.1 (#45806) --- recipes/pangolin-data/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pangolin-data/meta.yaml b/recipes/pangolin-data/meta.yaml index 6cbc9961cc1f7..172b1dbf9901b 100644 --- a/recipes/pangolin-data/meta.yaml +++ b/recipes/pangolin-data/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.25" %} +{% set version = "1.25.1" %} package: name: pangolin-data @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pangolin-data/archive/refs/tags/v{{ version }}.tar.gz - sha256: abb7a1cdd2ac9f00f33bc1158262548e9219c631d363bc83d8ba4b3d914ca910 + sha256: d92af7f5563cf8b3c0db4fa16748476d0033153865d75711a2dec46039c2473a build: number: 0 From 919e57f96db8f6925cd2d335d633f1c73cd27060 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 11:10:45 -0500 Subject: [PATCH 2033/2173] Update hicstuff to 3.2.2 (#45811) --- recipes/hicstuff/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hicstuff/meta.yaml b/recipes/hicstuff/meta.yaml index e0c50b567fcdf..fe9ff01dcad2e 100644 --- a/recipes/hicstuff/meta.yaml +++ b/recipes/hicstuff/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "3.2.1" %} +{% set version = "3.2.2" %} package: name: hicstuff @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/h/hicstuff/hicstuff-{{ version }}.tar.gz - sha256: cfea38c69d2594168d734f8e292a84b1f4d2135a31dd877fb175fad0aac4bdf4 + sha256: 8d1dc203fa5352e9b0014ec29d03dc796f2dbc0d51fef1a9b0df4c3aedb4065d build: number: 0 From bc8d25ea71aa24d0e40a5c94e7c6601736f5ea4f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 12:25:39 -0500 Subject: [PATCH 2034/2173] Update defense-finder to 1.2.1 (#45817) --- recipes/defense-finder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/defense-finder/meta.yaml b/recipes/defense-finder/meta.yaml index 91d9f8225e58c..3bb41bf1ac853 100644 --- a/recipes/defense-finder/meta.yaml +++ b/recipes/defense-finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "defense-finder" %} -{% set version = "1.2.0" %} +{% set version = "1.2.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/mdmparis/defense-finder/archive/v{{ version }}.tar.gz - sha256: 79547704ebe5d758b7692c2a9bdd1c4ccd6084a35ee18201dabb2e494da3ec36 + sha256: bff50fce7442e1bcc7fb7dd9ed202176662e5e02205551eee5ca05e4172cd2cd # patches: 0001-fix-no-results.patch build: From 4a76e8712b71365184849df2c54ed157277f1449 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:28:13 -0500 Subject: [PATCH 2035/2173] Update terrace to 1.1.2 (#45818) --- recipes/terrace/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/terrace/meta.yaml b/recipes/terrace/meta.yaml index 136afdf510081..6def5bd34e555 100644 --- a/recipes/terrace/meta.yaml +++ b/recipes/terrace/meta.yaml @@ -1,5 +1,5 @@ {% set name = "terrace" %} -{% set version = "1.1.1" %} +{% set version = "1.1.2" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/Shao-Group/TERRACE/releases/download/v{{ version }}/terrace-{{ version }}.tar.gz" - sha256: "2014bce67e6d05cf7c71ba16033f044c7043dc60217ca390741cff8818538664" + sha256: "cac4e9ae9ec61f49089c898f8c9484057ff16534fa1b12b02a5a06346dc56e8c" build: number: 0 From 5ff3914c14dee0d9325379e9373210442fbf7e28 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:29:42 -0500 Subject: [PATCH 2036/2173] Update snakemake-executor-plugin-slurm to 0.3.1 (#45797) --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 3d08d331ed1ed..38c4d83d70a5c 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 0200006e4860d4966ed092e0b2d335068a2b0aef33f8938bca435890b790e5fa + sha256: 3c45605515f73020d437872e6003de661ddd17a09e2e60780b2d19a5668f0eb5 build: noarch: python From ba52aa39ab7bd505b4bc4991b4234d6c69d1cef7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:30:02 -0500 Subject: [PATCH 2037/2173] Update snakemake-interface-common to 1.16.0 (#45798) * Update snakemake-interface-common to 1.15.4 * Update snakemake-interface-common to 1.16.0 --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 525b28533b34c..f7298deb2e3a2 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.15.3" %} +{% set version = "1.16.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: 7587c5e553c6ddaf0e2542bad1ffda55c3adf5b8ca651f4bc359a17d3f747ceb + sha256: b0780b9c3525435031815fd1f01079828d55c83fef18b5a0b05caa965408046b build: noarch: python From 89ae2e1c31adfdbfe455f15b1a30fd526d2d46bb Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" <19176506+pdimens@users.noreply.github.com> Date: Thu, 15 Feb 2024 13:46:12 -0500 Subject: [PATCH 2038/2173] Update harpy to 0.5.0 (#45714) * update to 0.5.0 * fix and add description * fix typo * clean up recipe * revert to noarch:generic * rm entry point * add pandas * rm no build isolation * fix build? * rm entrypoint * return build to what it was * add missing dso * fix python version and add DSO * add libcc/libz * restore the OSX skip --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/harpy/build.sh | 17 +++++------- recipes/harpy/meta.yaml | 59 ++++++++++++++++------------------------- 2 files changed, 30 insertions(+), 46 deletions(-) diff --git a/recipes/harpy/build.sh b/recipes/harpy/build.sh index 535a622944105..dacb8c084c852 100644 --- a/recipes/harpy/build.sh +++ b/recipes/harpy/build.sh @@ -1,19 +1,16 @@ -#!/bin/bash +#!/usr/bin/env bash mkdir -p ${PREFIX}/bin -# Harpy executable -#cp harpy ${PREFIX}/bin/ - -# build harpy -${PREFIX}/bin/python -m pip install . --ignore-installed --no-deps -vv +# install harpy proper +${PYTHON} -m pip install . --no-deps -vv # rules -cp rules/*.smk ${PREFIX}/bin/ +cp workflow/rules/*.smk ${PREFIX}/bin/ # associated scripts -chmod +x utilities/* -cp utilities/* ${PREFIX}/bin/ +chmod +x workflow/scripts/* +cp workflow/scripts/* ${PREFIX}/bin/ # reports -cp reports/*.Rmd ${PREFIX}/bin/ \ No newline at end of file +cp workflow/report/*.Rmd ${PREFIX}/bin/ diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index 616da31c08dfc..f5a78e0b92088 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.0" %} -{% set sha256 = "6062ece4701b6de964d1f25fc6e9e0d6b6525f3b04f9ca22d8b90191c7767928" %} +{% set version = "0.5.0" %} +{% set sha256 = "77ba116665fd00a945b65072b86b4c54f672b1b74912309709f580f7329b4adf" %} package: name: harpy @@ -12,63 +12,50 @@ source: build: skip: True # [osx] number: 0 + missing_dso_whitelist: + - /lib64/libstdc++.so.6 + - /lib64/libc.so.6 run_exports: - {{ pin_subpackage('harpy', max_pin="x.x") }} requirements: host: - - python =3.9 + - python =3.10 + - pip run: - - bcftools - - bioconductor-complexheatmap - - bwa - - fastp - - fastqc - - hapcut2 - - icu - - libzlib - - leviathan - - llvm-openmp + - bcftools =1.19 - multiqc - - naibr-plus - - python =3.9 - - pysam - - r-base - - r-circlize - - r-dplyr - - r-dt - - r-ggplot2 - - r-ggridges - - r-knitr - - r-magrittr - - r-plotly - - r-rmarkdown - - r-stitch - - r-tidyr - - r-viridislite + - pandas + - pysam =0.22 + - python =3.10 - rich-click - - snakemake >=7 - - sambamba + - snakemake-minimal - samtools - seqtk - tabix - - xz test: commands: - "snakemake --version" - - "R --version" - "harpy --version" + about: home: "https://github.com/pdimens/harpy/" - license: MIT + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE summary: "Process raw haplotagging data, from raw sequences to phased haplotypes." + description: | + Harpy is a command-line tool to easily process haplotag or 10x linked-read data. It uses + Snakemake under the hood to execute different workflows (quality control, trimming, + alignment, variant calling, phasing, etc.), but the user is rarely, if ever, exposed + to Snakemake directly. With an emphasis on user-friendliness, parallelization, transparency, + and reproducibility, Harpy aims to quickly handle data processing so that you can focus more + on analyzing your data. doc_url: https://pdimens.github.io/harpy/ dev_url: https://github.com/pdimens/harpy extra: - container: - extended-base: True recipe-maintainers: - pdimens skip-lints: From c78943b5a6fdbf68feec68da9b15a903790525ee Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 14:24:36 -0500 Subject: [PATCH 2039/2173] Update amdirt to 1.5.0 (#45813) * Update amdirt to 1.5.0 * Fix run export linting --------- Co-authored-by: James A. Fellows Yates --- recipes/amdirt/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/amdirt/meta.yaml b/recipes/amdirt/meta.yaml index 897c231a4e148..32fcaf104f35f 100644 --- a/recipes/amdirt/meta.yaml +++ b/recipes/amdirt/meta.yaml @@ -1,5 +1,5 @@ {% set name = "amdirt" %} -{% set version = "1.4.6" %} +{% set version = "1.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/AMDirT-{{ version }}.tar.gz - sha256: dc099a28c68996ea7e8ca087856598e693fa5f780eec166ee9fcac8780b1f930 + sha256: f52028b539767e7d8ae357aa0716716b7b18ee0231612ffc9c4d4a2eb1e74f24 build: entry_points: @@ -15,6 +15,8 @@ build: noarch: python script: {{ PYTHON }} -m pip install . -vv number: 0 + run_exports: + - {{ pin_subpackage("amdirt", max_pin="x.x") }} requirements: host: From 49a357046ed650b8da74c5348fca153b52d99498 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 14:53:00 -0500 Subject: [PATCH 2040/2173] Update sercol to 1.0.0 (#45792) * Update sercol to 1.0.0 * add run_exports --------- Co-authored-by: mencian --- recipes/sercol/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/sercol/meta.yaml b/recipes/sercol/meta.yaml index 47cefcfa8bf95..cedf8663759d9 100644 --- a/recipes/sercol/meta.yaml +++ b/recipes/sercol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sercol" %} -{% set version = "0.1.4" %} +{% set version = "1.0.0" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: eab962cf60bccb3c500b0eac7f51e865efefc4203d0323da3c4d5414e0b4e577 + sha256: 6507f5efcee4596eb77c45f1580ff562533ef5d115918a6a28bc4eac09ec191c build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('sercol', max_pin="x") }} requirements: host: @@ -30,7 +32,8 @@ test: about: home: "https://github.com/openvax/sercol" - license: Apache Software + license: Apache-2.0 + license_file: LICENSE license_family: APACHE summary: "Rich collection class with grouping and filtering helpers" From 4b1ca1312b8c58065bdfa97bd8419b4081d98038 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 18:25:46 -0500 Subject: [PATCH 2041/2173] Update snakemake-executor-plugin-googlebatch to 0.3.0 (#45819) --- recipes/snakemake-executor-plugin-googlebatch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml index 2b428cb274a58..1cc605247f4ba 100644 --- a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml +++ b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-googlebatch" %} -{% set version = "0.2.0" %} +{% set version = "0.3.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_googlebatch-{{ version }}.tar.gz - sha256: 3cccef6db07f47d53c0863db960c36d24c6336caabbea2b7fd3f2fc42c95edc4 + sha256: b143fcaeffceec682bc0f7e3f13eece3596a5d6faaf41fab94977f4a93948c16 build: noarch: python From 63fff9da4d54d618e9cc65050901dda95ed69108 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 18:25:56 -0500 Subject: [PATCH 2042/2173] Update snakemake-storage-plugin-s3 to 0.2.9 (#45820) --- recipes/snakemake-storage-plugin-s3/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-storage-plugin-s3/meta.yaml b/recipes/snakemake-storage-plugin-s3/meta.yaml index 9bc32ac5fff7f..f846ede5119a0 100644 --- a/recipes/snakemake-storage-plugin-s3/meta.yaml +++ b/recipes/snakemake-storage-plugin-s3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-s3" %} -{% set version = "0.2.8" %} +{% set version = "0.2.9" %} package: name: {{ name|lower }} @@ -7,12 +7,12 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_s3-{{ version }}.tar.gz - sha256: 4006be9cec5113aaead77a0c9f362be4f3af5409a5da1a3a0f7d69675b222605 + sha256: 41cb23326f37dc576d4a1deac15b3f5a647e26ca957a69ae06b128c044ba2f32 build: noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 1 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} From d902bcbb23dfe920fd32080e6272d0bde57578a7 Mon Sep 17 00:00:00 2001 From: lspindler2509 <83402447+lspindler2509@users.noreply.github.com> Date: Fri, 16 Feb 2024 01:00:06 +0100 Subject: [PATCH 2043/2173] Add recipe for biodigest (#45751) * added recipe for biodigest * added missing properties * corrected name * add graphtools * graphtool import * add install * correct name * different install * different import * addressed changes from review * unnecessary info deleted * clean up recipe --------- Co-authored-by: mencian --- recipes/biodigest/meta.yaml | 49 +++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/biodigest/meta.yaml diff --git a/recipes/biodigest/meta.yaml b/recipes/biodigest/meta.yaml new file mode 100644 index 0000000000000..1f5455223cb84 --- /dev/null +++ b/recipes/biodigest/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "biodigest" %} +{% set version = "0.2.16" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 7618cedf40fedd6dd60aa2fbf8635fb4af0a2c0ae16c01ef9741d30729b6e8bc + +build: + number: 0 + script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" + noarch: python + run_exports: + - {{ pin_subpackage('biodigest', max_pin="x.x") }} + +requirements: + host: + - pip + - python >=3.7 + run: + - biothings_client ==0.2.6 + - gseapy ==0.10.5 + - graph-tool + - numpy ==1.24.3 + - pandas ==1.5.2 + - psutil ==5.9.0 + - pycairo >=1.21.0 + - python >=3.7 + - requests ==2.28.2 + - scipy ==1.8.0 + - seaborn ==0.12.2 + + +test: + imports: + - biodigest + - biodigest.evaluation + - biodigest.evaluation.d_utils + - biodigest.evaluation.mappers + +about: + home: "http://pypi.python.org/pypi/biodigest/" + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: "In silico Validation of Disease and Gene Sets, Clusterings or Subnetworks (DIGEST)" From 519853686328e1a8089e67a9ab212e4f2019a425 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 15 Feb 2024 18:43:35 -0600 Subject: [PATCH 2044/2173] Add recipe for genbank v0.110 (#45822) --- recipes/genbank/meta.yaml | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 recipes/genbank/meta.yaml diff --git a/recipes/genbank/meta.yaml b/recipes/genbank/meta.yaml new file mode 100644 index 0000000000000..d5a0c8f267aad --- /dev/null +++ b/recipes/genbank/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "genbank" %} +{% set version = "0.110" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/genbank-{{ version }}.tar.gz + sha256: f9a6ba243d62934e9e5ed283d8b475ab3dd9a3760ba329a054d5f6df54a8ec45 + +build: + number: 0 + skip: True # [py < 36] + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('genbank', max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + host: + - python + - pip + run: + - python + +test: + imports: + - genbank + +about: + home: https://github.com/deprekate/genbank + summary: Code to work with Genbank files + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE From 2e947209623826862724e2705273f9ea33383a94 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 15 Feb 2024 19:41:20 -0600 Subject: [PATCH 2045/2173] Update peptide-shaker to 3.0.6 (#45823) --- recipes/peptide-shaker/meta.yaml | 4 ++-- recipes/peptide-shaker/peptide-shaker.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/peptide-shaker/meta.yaml b/recipes/peptide-shaker/meta.yaml index 677a59a7abc65..3c16f06cf6d56 100644 --- a/recipes/peptide-shaker/meta.yaml +++ b/recipes/peptide-shaker/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the peptide-shaker.py file {% set name = "PeptideShaker" %} -{% set version = "3.0.4" %} -{% set sha256 = "e1317b51dda3e10348f74e544832169340939f056576d2f01ed13988e56e8214" %} +{% set version = "3.0.6" %} +{% set sha256 = "9356fb98d8d70bde35d3b37b0de24b5b76943ae9103a1af250018c0204062951" %} package: name: peptide-shaker diff --git a/recipes/peptide-shaker/peptide-shaker.py b/recipes/peptide-shaker/peptide-shaker.py index 98a22145a4cda..54aedb2ae0e6f 100755 --- a/recipes/peptide-shaker/peptide-shaker.py +++ b/recipes/peptide-shaker/peptide-shaker.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'PeptideShaker-3.0.4.jar' +jar_file = 'PeptideShaker-3.0.6.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] From 9a6510f495e7f2fedda691e03acfe95ebb17e139 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 22:31:54 -0500 Subject: [PATCH 2046/2173] Update phanotate to 1.6.4 (#45809) * Update phanotate to 1.6.4 * add run_exports * add genbank --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/phanotate/meta.yaml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/recipes/phanotate/meta.yaml b/recipes/phanotate/meta.yaml index 00d8dc1cede86..7965786cd5199 100644 --- a/recipes/phanotate/meta.yaml +++ b/recipes/phanotate/meta.yaml @@ -1,5 +1,5 @@ {% set name = "phanotate" %} -{% set version = "1.5.1" %} +{% set version = "1.6.4" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "1c3b241d59b801f9023946ef3ba1090e4fc32a4ff5bd06ba0144320ae9693de6" + sha256: "315524223515c88a00b13104c91c1b85f8187e8eec5459bdf66046c30ff1e23f" build: - number: 1 - skip: True # [py27] - script: "{{ PYTHON }} -m pip install . --no-deps -vv " + number: 0 + skip: True # [py < 36] + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + run_exports: + - {{ pin_subpackage('phanotate', max_pin="x") }} requirements: build: @@ -21,6 +23,7 @@ requirements: - pip - python run: + - python - fastpath - matplotlib-base - scipy @@ -28,8 +31,8 @@ requirements: - statsmodels - backports.tempfile - textwrap3 - - setuptools - trnascan-se + - genbank test: commands: From 3b66f2c71b6922713d4de3715dabdc3f6a089c5d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 15 Feb 2024 23:05:15 -0500 Subject: [PATCH 2047/2173] Update primer3-py to 2.0.3 (#45825) --- recipes/primer3-py/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/primer3-py/meta.yaml b/recipes/primer3-py/meta.yaml index f9a31011d0db2..7eec666088e21 100644 --- a/recipes/primer3-py/meta.yaml +++ b/recipes/primer3-py/meta.yaml @@ -1,5 +1,5 @@ {% set name = "primer3-py" %} -{% set version = "2.0.2" %} +{% set version = "2.0.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/primer3-py-{{ version }}.tar.gz - sha256: 1fa140cab651a2841ec71f3e29ef347e6546f644884e3cac1fe536c4feb8eb5c + sha256: 1ec6ce99ea149b1c82361c654a0eab824e698ce32d5f9ed2dd8f8f37564b3f5f build: number: 0 From f814437ed3f9e4545fadc8b3e2281727e588e3dd Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 15 Feb 2024 22:56:09 -0600 Subject: [PATCH 2048/2173] Update searchgui to 4.3.6 (#45824) * Update searchgui to 4.3.6 * restore build variable --- recipes/searchgui/meta.yaml | 4 ++-- recipes/searchgui/searchgui.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index 6108e9779ef2a..5f489c4eb2479 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the searchgui.py file {% set name = "SearchGUI" %} -{% set version = "4.3.5" %} -{% set sha256 = "51458d20745f83c88fe1041d0e3ff64b148538c63795a0b548c1aa3f7ca8f67d" %} +{% set version = "4.3.6" %} +{% set sha256 = "76c3662165e929a82d49408d344409b62057cb0c0cf6a4834b54585a756cf894" %} {% set build = "0" %} package: diff --git a/recipes/searchgui/searchgui.py b/recipes/searchgui/searchgui.py index f697c358d602e..c6c3cfb7c386d 100755 --- a/recipes/searchgui/searchgui.py +++ b/recipes/searchgui/searchgui.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'SearchGUI-4.3.5.jar' +jar_file = 'SearchGUI-4.3.6.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] From 4b820c03f4f4457b7fcf82c063d623c56565b457 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 00:58:54 -0500 Subject: [PATCH 2049/2173] Update pbsim3 to 3.0.2 (#45827) --- recipes/pbsim3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pbsim3/meta.yaml b/recipes/pbsim3/meta.yaml index 5a166dcaeb058..8b4d4a835b177 100644 --- a/recipes/pbsim3/meta.yaml +++ b/recipes/pbsim3/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pbsim3" %} -{% set version = "3.0.1" %} -{% set sha256 = "4d2d0cabc1adfd1ade0cde983fb37f7e8af477c0fd7b09ef3e753742b89cc541" %} +{% set version = "3.0.2" %} +{% set sha256 = "db938d58bbe3003f36b0b6f9fdc5a190816ff1c30e1d7da53b87e0fb6aee4795" %} package: name: {{ name }} From 9100aaa68bd572f00ebea6487f8fcc982e05e31d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 03:39:53 -0500 Subject: [PATCH 2050/2173] Update insilicoseq to 2.0.0 (#45816) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update insilicoseq to 2.0.0 * add run_exports * update checksums --------- Co-authored-by: mencian Co-authored-by: Hadrien Gourlé --- recipes/insilicoseq/checksums.md5 | 4 ++-- recipes/insilicoseq/meta.yaml | 12 +++++++++--- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/recipes/insilicoseq/checksums.md5 b/recipes/insilicoseq/checksums.md5 index 62eea9823d41f..d0cfecf9e2afb 100644 --- a/recipes/insilicoseq/checksums.md5 +++ b/recipes/insilicoseq/checksums.md5 @@ -1,2 +1,2 @@ -80319ebef7bd8f98c3d589c42ba852da bogus-reads_R1.fastq -f883f153efbbc1a1519c21f4829ba8dd bogus-reads_R2.fastq +9aeb0f7da8af96b9ce20270a50b20aec bogus-reads_R1.fastq +638e4fe4e8470feeb40e359995d803db bogus-reads_R2.fastq diff --git a/recipes/insilicoseq/meta.yaml b/recipes/insilicoseq/meta.yaml index 7270ab4cc77fe..d212e177e6070 100644 --- a/recipes/insilicoseq/meta.yaml +++ b/recipes/insilicoseq/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.6.0" %} -{% set sha256 = "4cbd8e30a17e9591899be42aaa776e0748907709ac56db8133050335f24d35e5" %} +{% set version = "2.0.0" %} +{% set sha256 = "1eb851ea345aaf46d8a5924516bbd55c8f957bb83ada8e9a995c1aae001d5d2a" %} package: name: insilicoseq @@ -13,8 +13,10 @@ build: noarch: python entry_points: - iss = iss.app:main - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv number: 0 + run_exports: + - {{ pin_subpackage('insilicoseq', max_pin="x") }} requirements: host: @@ -33,6 +35,8 @@ requirements: test: imports: - iss + commands: + - iss --help files: - bogus-genome.fasta.gz - checksums.md5 @@ -41,8 +45,10 @@ about: home: https://github.com/HadrienG/InSilicoSeq license: MIT license_family: MIT + license_file: LICENSE summary: A sequencing simulator. dev_url: https://github.com/HadrienG/InSilicoSeq + doc_url: https://insilicoseq.readthedocs.io/en/latest/ extra: recipe-maintainers: From 7160ca0de0f55663a26482df58b91944d05aba9c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 09:24:11 -0500 Subject: [PATCH 2051/2173] Update badread to 0.4.1 (#45826) * Update badread to 0.4.1 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/badread/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/badread/meta.yaml b/recipes/badread/meta.yaml index 00bef0af70ac4..f787041f5d582 100644 --- a/recipes/badread/meta.yaml +++ b/recipes/badread/meta.yaml @@ -1,5 +1,5 @@ -{% set version='0.4.0' %} -{% set sha256='1920f1efc1eae7b17f1fd9c6878795b5ba8d7fd910c933999aad349672a994b0' %} +{% set version='0.4.1' %} +{% set sha256='236dee5ac99b8d0c1997c482df5b805908b0c34f75277ef706e897af71db1f9a' %} package: name: badread @@ -10,9 +10,11 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 noarch: python script: {{ PYTHON }} -m pip install . --no-deps -vv + run_exports: + - {{ pin_subpackage('badread', max_pin='x.x') }} requirements: host: From 4f01bc350f098590cd9388e82cb27cc3ec8996fc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 10:15:31 -0500 Subject: [PATCH 2052/2173] Update bigscape to 1.1.9 (#45829) --- recipes/bigscape/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bigscape/meta.yaml b/recipes/bigscape/meta.yaml index 7915ed0a1a506..0809408af242a 100644 --- a/recipes/bigscape/meta.yaml +++ b/recipes/bigscape/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.8" %} -{% set sha256 = "9a9c256cb0464ca23408fe5a1738db21b8818b487216fb939d7aef037339a598" %} +{% set version = "1.1.9" %} +{% set sha256 = "ef0ddb5b433e0b1467ae5f96037fd6d23ebcba6bc08201d1421eba35d072e534" %} package: name: bigscape From 2f2123fadd65d6d5de5d43acd7ec0657ceea7033 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 11:39:00 -0500 Subject: [PATCH 2053/2173] Update pyhmmer to 0.10.5 (#45833) --- recipes/pyhmmer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index 65622ccd0e60d..314fea094cdc4 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.4" %} +{% set version = "0.10.5" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 08bc02aadf0f113df2b2912478bb02be9daf5d322df9c72bcd07fa01fe53a87b + sha256: 1c9c6bb5600b96eb3386c524b24bf6eb1f51610017e82b585fe0f3b3c7cdbe03 build: number: 0 From b79ebf9a78959292453ec0cfc367c6835d339851 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 12:13:37 -0500 Subject: [PATCH 2054/2173] Update deeplcretrainer to 0.2.11 (#45831) * Update deeplcretrainer to 0.2.9 * Update deeplcretrainer to 0.2.10 * Update deeplcretrainer to 0.2.11 --- recipes/deeplcretrainer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/deeplcretrainer/meta.yaml b/recipes/deeplcretrainer/meta.yaml index 5d602ecfa1aa3..e3ad13723e94d 100644 --- a/recipes/deeplcretrainer/meta.yaml +++ b/recipes/deeplcretrainer/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DeepLCRetrainer" %} -{% set version = "0.2.8" %} -{% set sha256 = "73a9052d186921df42cfefce6215ee50f2a0abb3c4b1cef4a67126a59dfa7c9b" %} +{% set version = "0.2.11" %} +{% set sha256 = "99b1b2f41abb8d79638cc0731095e4b12bb7ca07ab1d64d87923e6b00154996b" %} package: name: {{ name|lower }} From dec0eff4da3ff862bef7687482e7545d720a5b55 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 15:41:55 -0500 Subject: [PATCH 2055/2173] Update ucsc-cell-browser to 1.2.5 (#45841) --- recipes/ucsc-cell-browser/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ucsc-cell-browser/meta.yaml b/recipes/ucsc-cell-browser/meta.yaml index a86e0702e4f9c..1dfd309f10ef8 100644 --- a/recipes/ucsc-cell-browser/meta.yaml +++ b/recipes/ucsc-cell-browser/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.2.4' %} +{% set version = '1.2.5' %} {% set name = "cellbrowser" %} package: @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "9c7414dd377ce36c290b1eef0763d0e9d0b8fa9ddc697f6bcfd1e2efa49e67f9" + sha256: "76757ff00f806f48d47831b0bd9df82aa9e170e4ce96629993a0e8ea5f539bf5" build: number: 0 From 0717980b20d4137a4d704b609cf34573c1dd6552 Mon Sep 17 00:00:00 2001 From: tlacroix Date: Fri, 16 Feb 2024 22:56:47 +0100 Subject: [PATCH 2056/2173] Update icescreen v1.3.2 (#45839) --- recipes/icescreen/meta.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/recipes/icescreen/meta.yaml b/recipes/icescreen/meta.yaml index a1d4fdde1d551..09c46a851ab4f 100644 --- a/recipes/icescreen/meta.yaml +++ b/recipes/icescreen/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ICEscreen" %} -{% set version = "1.3.1" %} +{% set version = "1.3.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/archive/v{{ version }}/icescreen-v{{ version }}.tar.gz - sha256: 283fb2bf95eb9066a535a25f7df94f6ec9d4b78083d62bd5237f801e94ac02d5 + sha256: f8d691891bd92e2dc4a72b14a5404645d26f30d3fbe09d407b45c548d37f2ca3 build: number: 0 @@ -23,11 +23,11 @@ requirements: run: - python - pandas >=2.1.0 - - snakemake-minimal >=7.32 - - biopython =1.81 - - bcbio-gff =0.7.0 - - blast =2.12 - - hmmer =3.3.2 + - snakemake-minimal >=8.4 + - biopython =1.83 + - blast =2.15 + - hmmer =3.4 + - pyarrow test: commands: @@ -38,7 +38,7 @@ about: license: AGPL-3.0-or-later license_family: AGPL summary: "ICEscreen detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes." - doc_url: icescreen.migale.inrae.fr + doc_url: https://icescreen.migale.inrae.fr extra: recipe-maintainers: From 6fd6397f22b50ff86460041ce8fd72314ae5b298 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 16 Feb 2024 16:57:43 -0500 Subject: [PATCH 2057/2173] Update ncbi-datasets-pylib to 16.4.8 (#45838) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index adb9708118530..dcd72174fd033 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.7" %} -{% set sha256 = "6d637d0b730426a35fa89f8107ada4573abe374214a1c93f9bafdb265986c9f4" %} +{% set version = "16.4.8" %} +{% set sha256 = "5c08fc546170079034be19f53468667114d0695ab348bb2c04794141a9a6ed3c" %} package: name: {{ name|lower }} From 19541a69e0e3321f716116675edf1879d442a1a2 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Fri, 16 Feb 2024 22:58:18 +0100 Subject: [PATCH 2058/2173] fix: pin gffutils python to <3.12 (#45828) * fix: pin gffutils python to <3.12 * fix: add run_exports following best practices from docs * do as I'm told... --- recipes/gffutils/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/gffutils/meta.yaml b/recipes/gffutils/meta.yaml index f1f35d06d9903..30f72adae5628 100644 --- a/recipes/gffutils/meta.yaml +++ b/recipes/gffutils/meta.yaml @@ -12,8 +12,10 @@ source: build: noarch: python - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: @@ -23,7 +25,7 @@ requirements: - argcomplete >=1.9.4 - argh >=0.26.2 - pyfaidx >=0.5.5.2 - - python + - python <3.12 - simplejson - six >=1.12.0 From 5650967910eedcd06068a3f64b5ce68e3d3f4dbe Mon Sep 17 00:00:00 2001 From: SantaMcCloud <100047964+SantaMcCloud@users.noreply.github.com> Date: Fri, 16 Feb 2024 22:58:30 +0100 Subject: [PATCH 2059/2173] Update bigscape to 1.1.9 (#45836) * update bigscape to the newest version * Update bigscape to 1.1.8 * Update bigscape recipe From f4885c4bfaa0130bc5e34a8ed39e7db948b6a6ab Mon Sep 17 00:00:00 2001 From: gennadyFauna <153561808+gennadyFauna@users.noreply.github.com> Date: Fri, 16 Feb 2024 13:58:38 -0800 Subject: [PATCH 2060/2173] Update/fix kb-python (#45808) * kb python compatibility kb build fails due to obscure pysam incompatibilities on python 3.9. * Update meta.yaml --- recipes/kb-python/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/kb-python/meta.yaml b/recipes/kb-python/meta.yaml index 23a0ad79fcaaa..840469c6ff8be 100644 --- a/recipes/kb-python/meta.yaml +++ b/recipes/kb-python/meta.yaml @@ -11,7 +11,7 @@ source: patches: config.py.patch build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" entry_points: @@ -21,10 +21,10 @@ build: requirements: host: - - python >=3.7 + - python >=3.7, <3.9 - pip run: - - python >=3.7 + - python >=3.7, <3.9 - anndata >=0.6.22.post1 - h5py >=2.10.0 - jinja2 >2.10.1 From 181debb6a6eda6b9a3bd2aa46b2c93b52214e028 Mon Sep 17 00:00:00 2001 From: Ryan James Kennedy <67742838+ryanjameskennedy@users.noreply.github.com> Date: Fri, 16 Feb 2024 22:58:48 +0100 Subject: [PATCH 2061/2173] Add git to serotypefinder (#45837) --- recipes/serotypefinder/build.sh | 8 ++++---- recipes/serotypefinder/meta.yaml | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/serotypefinder/build.sh b/recipes/serotypefinder/build.sh index 448adcd673160..bdcf3a4a8221e 100644 --- a/recipes/serotypefinder/build.sh +++ b/recipes/serotypefinder/build.sh @@ -5,10 +5,6 @@ mkdir -p ${PREFIX}/bin chmod +x serotypefinder.py cp serotypefinder.py ${PREFIX}/bin/serotypefinder -# copy script to download database -chmod +x ${RECIPE_DIR}/update-serotypefinder-db.sh -cp ${RECIPE_DIR}/update-serotypefinder-db.sh ${PREFIX}/bin/update-serotypefinder-db - # create folder for database download target=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION} mkdir -p ${target}/db/ @@ -18,6 +14,10 @@ touch ${target}/db/.empty cp ${RECIPE_DIR}/download-db.sh ${PREFIX}/bin chmod +x ${PREFIX}/bin/download-db.sh +# copy script to download database +chmod +x ${RECIPE_DIR}/update-serotypefinder-db.sh +cp ${RECIPE_DIR}/update-serotypefinder-db.sh ${PREFIX}/bin/update-serotypefinder-db + # set SEROTYPEFINDER_DB variable on env activation mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d cat <> ${PREFIX}/etc/conda/activate.d/serotypefinder.sh diff --git a/recipes/serotypefinder/meta.yaml b/recipes/serotypefinder/meta.yaml index 6fb2ab6ca1434..9bbaafbbaa65d 100644 --- a/recipes/serotypefinder/meta.yaml +++ b/recipes/serotypefinder/meta.yaml @@ -12,7 +12,7 @@ source: - database_path.patch build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('serotypefinder', max_pin="x") }} @@ -27,7 +27,7 @@ requirements: - kma - python >=3.8 - tabulate >=0.8.9 - + - git test: commands: From 7c56552f60dc62a8b4254dccf50261cd458c2912 Mon Sep 17 00:00:00 2001 From: "Pavel V. Dimens" <19176506+pdimens@users.noreply.github.com> Date: Fri, 16 Feb 2024 17:01:44 -0500 Subject: [PATCH 2062/2173] Update harpy build to use smaller release instead of source (#45843) * Update harpy build to use smaller release instead of source * add license to tarball --- recipes/harpy/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index f5a78e0b92088..83fd39527998c 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,17 +1,17 @@ {% set version = "0.5.0" %} -{% set sha256 = "77ba116665fd00a945b65072b86b4c54f672b1b74912309709f580f7329b4adf" %} +{% set sha256 = "58d407059057f6f3aa6213e2bbb00bf9d920b405fe435baf88837d60b5cc0d08" %} package: name: harpy version: '{{ version }}' source: - url: https://github.com/pdimens/harpy/archive/{{ version }}.tar.gz + url: https://github.com/pdimens/harpy/releases/download/{{ version }}/harpy.{{ version }}.tar.gz sha256: '{{ sha256 }}' build: skip: True # [osx] - number: 0 + number: 1 missing_dso_whitelist: - /lib64/libstdc++.so.6 - /lib64/libc.so.6 From e30e1bf7015d4c4d32ba7f474ec6e50063273fce Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Fri, 16 Feb 2024 23:05:52 +0000 Subject: [PATCH 2063/2173] added recipe for tracegroomer (#45814) * added recipe for tracegroomer * added home and summary --- recipes/tracegroomer/meta.yaml | 59 ++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 recipes/tracegroomer/meta.yaml diff --git a/recipes/tracegroomer/meta.yaml b/recipes/tracegroomer/meta.yaml new file mode 100644 index 0000000000000..d6ea7f2606309 --- /dev/null +++ b/recipes/tracegroomer/meta.yaml @@ -0,0 +1,59 @@ +{% set name = "tracegroomer" %} +{% set version = "0.1.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/tracegroomer-{{ version }}.tar.gz + sha256: 87728daf011976062eabb7967b3b286d7905b4cd5b92387bc1b3f07abfd6cf16 + +build: + entry_points: + - tracegroomer = tracegroomer.__main__:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('tracegroomer', max_pin="x") }} + +requirements: + host: + - python >=3.10,<4.0 + - poetry-core + - pip + run: + - python >=3.10.0,<4.0.0 + - sphinx >=7.2.6,<8.0.0 + - click >=8.1.7,<9.0.0 + - matplotlib-base >=3.8.2,<4.0.0 + - mypy >=1.8.0,<2.0.0 + - numpy >=1.26.4,<2.0.0 + - pandas >=2.2.0,<3.0.0 + - scipy >=1.12.0,<2.0.0 + - scikit-learn >=1.4.0,<2.0.0 + - seaborn >=0.13.2,<0.14.0 + - openpyxl >=3.1.2,<4.0.0 + - pyyaml >=6.0.1,<7.0.0 + - python-dotenv >=1.0.1,<2.0.0 + - pydantic >=1.10.8,<2.0.0 + +test: + imports: + - tracegroomer + commands: + - pip check + - tracegroomer --help + requires: + - pip + +about: + summary: 'Format and normalise tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet analysis.' + license: MIT + license_file: LICENSE + home: 'https://github.com/cbib/TraceGroomer' + +extra: + recipe-maintainers: + - hechth From 7d9d2104c1f4b64027aff085bcc4b8c172f971f6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 17 Feb 2024 02:48:43 -0500 Subject: [PATCH 2064/2173] Update viralmsa to 1.1.44 (#45850) --- recipes/viralmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/viralmsa/meta.yaml b/recipes/viralmsa/meta.yaml index 8c476c2293244..7f8cf82f1cbac 100644 --- a/recipes/viralmsa/meta.yaml +++ b/recipes/viralmsa/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.43" %} +{% set version = "1.1.44" %} package: name: viralmsa @@ -12,7 +12,7 @@ build: source: url: https://github.com/niemasd/ViralMSA/archive/refs/tags/{{ version }}.tar.gz - sha256: 15adaed42f65e2b6a0ba7e6db498fd67f3227b4658f555313194d5b73234ed89 + sha256: a3f90307b86e6171beadc61bfc09309570d51d9b21085a6c74054b86a8991026 requirements: run: From b17aa7e7da1bfdac67de11c693c33fecd2a8dff7 Mon Sep 17 00:00:00 2001 From: Nextstrain bot <78992647+nextstrain-bot@users.noreply.github.com> Date: Sat, 17 Feb 2024 10:11:25 -0800 Subject: [PATCH 2065/2173] Update nextclade to 3.2.1 (#45853) Co-authored-by: nextstrain-bot --- recipes/nextclade/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nextclade/meta.yaml b/recipes/nextclade/meta.yaml index b53743caebf7f..174aad8dc0c36 100644 --- a/recipes/nextclade/meta.yaml +++ b/recipes/nextclade/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nextclade" %} -{% set version = "3.2.0" %} +{% set version = "3.2.1" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-unknown-linux-gnu # [linux64] - sha256: 392f5b980f291f1580cfc09abc51779955c83811aa0537f6dba7d755e03c8fa9 # [linux64] + sha256: 797d9dab371dad8fcd65d6fe8347f8e3caa21243a930b0b422cb0e68f2039b57 # [linux64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: deabdd06b1e6b6052c0ae50985b36db9839dfd8393de3a8d44b812b4b8b52cf6 # [osx and x86_64] + sha256: 9be0cca8dcf580bed2aa1746d8117a29711b72c96029ac960ca29e715f51abf3 # [osx and x86_64] - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/{{ name }}-aarch64-apple-darwin # [arm64] - sha256: 3b6185ff3741da4f15bd382f2f3c9cefb342e8add90a29be6050e20e4b3e66d2 # [arm64] + sha256: e2dbf3d2fa624f8926068dee7a678d867bfbe607fa2efefe7ca0d2f478f8df1a # [arm64] build: number: 0 From c523a236a4e3452292c6ebb962d7a1f75dc2205b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 17 Feb 2024 13:27:17 -0500 Subject: [PATCH 2066/2173] Update harpy to 0.6.0 (#45844) --- recipes/harpy/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index 83fd39527998c..f51726858a1c8 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.5.0" %} -{% set sha256 = "58d407059057f6f3aa6213e2bbb00bf9d920b405fe435baf88837d60b5cc0d08" %} +{% set version = "0.6.0" %} +{% set sha256 = "3b7010054c3cafb19ae6973154015e17cd4688966237af90f5584d933eec86b3" %} package: name: harpy @@ -11,7 +11,7 @@ source: build: skip: True # [osx] - number: 1 + number: 0 missing_dso_whitelist: - /lib64/libstdc++.so.6 - /lib64/libc.so.6 From a8778052fab9819009e5c25c7d4222f92d8bd180 Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Sat, 17 Feb 2024 13:57:40 -0500 Subject: [PATCH 2067/2173] Create build.sh (#45849) * Create build.sh * Create meta.yaml * Update meta.yaml * add oarfish * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml Add dash --- recipes/oarfish/build.sh | 7 +++++++ recipes/oarfish/meta.yaml | 30 ++++++++++++++++++++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 recipes/oarfish/build.sh create mode 100644 recipes/oarfish/meta.yaml diff --git a/recipes/oarfish/build.sh b/recipes/oarfish/build.sh new file mode 100644 index 0000000000000..3c3929c054e07 --- /dev/null +++ b/recipes/oarfish/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash -euo +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . diff --git a/recipes/oarfish/meta.yaml b/recipes/oarfish/meta.yaml new file mode 100644 index 0000000000000..d571d3d5e4b3f --- /dev/null +++ b/recipes/oarfish/meta.yaml @@ -0,0 +1,30 @@ +{% set version = "0.2.0" %} + +package: + name: oarfish + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("oarfish", max_pin="x.x") }} + +source: + url: https://github.com/COMBINE-lab/oarfish/archive/v{{ version }}.tar.gz + sha256: 47e9ad6ae8af5f96eac16f294052319948a25892a9554c36ac5fe73646f20c2e + +requirements: + build: + - {{ compiler('rust') }} + host: + run: + +test: + commands: + - oarfish --help + +about: + home: https://github.com/COMBINE-lab/oarfish + license: BSD-3-Clause + license_file: LICENSE + summary: oarfish is a tool for fast, accurate and versatile transcript quantification from long-read RNA-seq data From fe57e51d6a7428073482d22a6ca6d7369f69305a Mon Sep 17 00:00:00 2001 From: pirovc <4673375+pirovc@users.noreply.github.com> Date: Sun, 18 Feb 2024 09:28:40 +0100 Subject: [PATCH 2068/2173] Update ganon to 2.1.0 (#45760) * ganon version 2.1.0 * add dep. test * add dep. test * Update meta.yaml * Update meta.yaml --------- Co-authored-by: James A. Fellows Yates --- recipes/ganon/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/ganon/meta.yaml b/recipes/ganon/meta.yaml index 3f42b377f4284..8138ce24f94e8 100755 --- a/recipes/ganon/meta.yaml +++ b/recipes/ganon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ganon" %} -{% set version = "2.0.1" %} +{% set version = "2.1.0" %} package: name: "{{ name|lower }}" @@ -8,7 +8,7 @@ package: source: - folder: ganon url: https://github.com/pirovc/{{ name }}/archive/{{ version }}.tar.gz - sha256: e8050f9522e35fe41abd5425ebe35a292081ff179a6a42cd285002ba0ef89f5f + sha256: bba93f9c45c922d6d309fcb81dfeddac6ef5439852ff1c48a1e6fed299e29f8b - folder: robin-hood-hashing url: https://github.com/martinus/robin-hood-hashing/archive/refs/tags/3.11.3.tar.gz sha256: dcf2b7fa9ef9dd0c67102d94c28e8df3effbe1845e0ed1f31f4772ca5e857fc4 @@ -30,7 +30,7 @@ requirements: - catch2 ==2.* - cxxopts >=2.2.0 - python - - pandas >=1.1.0 + - pandas >=1.2.0 - multitax >=1.3.1 - genome_updater >=0.6.3 - grep @@ -38,10 +38,12 @@ requirements: - curl - diffutils - zlib + - parameterized >=0.9.0 + - raptor ==3.* run: - bzip2 - python - - pandas >=1.1.0 + - pandas >=1.2.0 - multitax >=1.3.1 - genome_updater >=0.6.3 - grep @@ -49,7 +51,7 @@ requirements: - curl - diffutils - zlib - - raptor ==3.0.1 + - raptor ==3.* test: commands: From f5b9c3a7f6fbbe5fd856a3e23f4137da7d5d587d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 03:29:02 -0500 Subject: [PATCH 2069/2173] Update tsebra to 1.1.2.3 (#45854) --- recipes/tsebra/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tsebra/meta.yaml b/recipes/tsebra/meta.yaml index d0c23407dc092..025b3cec0dc83 100644 --- a/recipes/tsebra/meta.yaml +++ b/recipes/tsebra/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.1.2.2" %} +{% set version = "1.1.2.3" %} {% set name = "tsebra" %} -{% set sha256 = "e055efea29d3b73a6202c56fb9256bf6006005ef54c8a5de83b9aa0377fff27c" %} +{% set sha256 = "bdba8f114a75bd822e7af475f09bc433d1b673902ec09e1ed1f735d21ea80222" %} package: name: "{{ name }}" From 3953434d3c8d56682c7cfe00e35c10dbfbb2aaef Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 03:29:42 -0500 Subject: [PATCH 2070/2173] Update braker3 to 3.0.8 (#45856) --- recipes/braker3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/braker3/meta.yaml b/recipes/braker3/meta.yaml index cbf46b0d20506..174a5deb011ec 100644 --- a/recipes/braker3/meta.yaml +++ b/recipes/braker3/meta.yaml @@ -1,6 +1,6 @@ {% set name = "BRAKER3" %} -{% set version = "3.0.7" %} -{% set sha256 = "578b51538e9d18c6f4d8892452d05d59b9126dcfbb6a32a1fe6f70c210370c96" %} +{% set version = "3.0.8" %} +{% set sha256 = "f2623290c3007a3e42719a0bb2713bec7226db222bfef742895a9d5d0b4ee526" %} package: name: "{{ name|lower }}" From 39be0b445f47a14bfd651b7b6d81e17d26f6b9a5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 04:03:55 -0500 Subject: [PATCH 2071/2173] Update f5c to 1.4 (#45857) --- recipes/f5c/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/f5c/meta.yaml b/recipes/f5c/meta.yaml index 55b96f9534adf..5b8c3e4ee649d 100644 --- a/recipes/f5c/meta.yaml +++ b/recipes/f5c/meta.yaml @@ -1,5 +1,5 @@ {% set name = "f5c" %} -{% set version = "1.3" %} +{% set version = "1.4" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/hasindu2008/f5c/releases/download/v{{ version }}/f5c-v{{ version }}-release.tar.gz - sha256: 5688016fe92c8dc6dc5124d4d81bf2ad0ed5fcd78ea0d0a1995f5c868ea1f819 + sha256: 9336b35caf6486f9fffc791591ef7b40bea9156ecfb1d315fe222b6e9957d632 build: number: 0 From c16bfb19cf6548355dafc21a5f559230c51a0e70 Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Sun, 18 Feb 2024 04:04:25 -0500 Subject: [PATCH 2072/2173] add piscem-infer (#45852) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * add piscem-infer * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Rename build.sh to build.sh * Update meta.yaml * Update meta.yaml * Update build.sh * Update build.sh * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/piscem-infer/build.sh | 8 ++++++++ recipes/piscem-infer/meta.yaml | 31 +++++++++++++++++++++++++++++++ 2 files changed, 39 insertions(+) create mode 100644 recipes/piscem-infer/build.sh create mode 100644 recipes/piscem-infer/meta.yaml diff --git a/recipes/piscem-infer/build.sh b/recipes/piscem-infer/build.sh new file mode 100644 index 0000000000000..fd9c0897999fd --- /dev/null +++ b/recipes/piscem-infer/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash -euo +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" + +# build statically linked binary with Rust +RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path . + diff --git a/recipes/piscem-infer/meta.yaml b/recipes/piscem-infer/meta.yaml new file mode 100644 index 0000000000000..01b9ea8560cea --- /dev/null +++ b/recipes/piscem-infer/meta.yaml @@ -0,0 +1,31 @@ +{% set version = "0.5.2" %} + +package: + name: piscem-infer + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("piscem-infer", max_pin="x.x") }} + +source: + url: https://github.com/COMBINE-lab/piscem-infer/archive/v{{ version }}.tar.gz + sha256: 95bdab6724428ebb05dc7459ea717857e2c90fb3fe1065d131858a70273a16c5 + +requirements: + build: + - rust >=1.75 + - {{ compiler('rust') }} + host: + run: + +test: + commands: + - piscem-infer --help + +about: + home: https://github.com/COMBINE-lab/piscem-infer + license: BSD-3-Clause + license_file: LICENSE + summary: piscem-infer is a flexible tool to perform target quantification from bulk-sequencing data From 6d3c7e09f3f03a4098245272535cc87e0a3b9011 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 04:05:03 -0500 Subject: [PATCH 2073/2173] Update tracegroomer to 0.1.2 (#45848) --- recipes/tracegroomer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tracegroomer/meta.yaml b/recipes/tracegroomer/meta.yaml index d6ea7f2606309..5b435366e63af 100644 --- a/recipes/tracegroomer/meta.yaml +++ b/recipes/tracegroomer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tracegroomer" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/tracegroomer-{{ version }}.tar.gz - sha256: 87728daf011976062eabb7967b3b286d7905b4cd5b92387bc1b3f07abfd6cf16 + sha256: a1b951583f6016d96799a270def0472b6b7a93c5fe94e685fb30916f73d32662 build: entry_points: From 394e8cede3c538c0acd7619aef4fbf88f5362895 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 04:05:16 -0500 Subject: [PATCH 2074/2173] Update augur to 24.2.2 (#45847) --- recipes/augur/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index acab680fa5d8b..ab32c10e43f51 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "24.2.1" %} +{% set version = "24.2.2" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: c1fe7c357357d9b73dd614db7641695bbd780d884bebe2fb6082f19a28bb0f3b + sha256: f15359e193163ce397a2bc056d0f495fbddb223544af1b5956204cf135b79c11 build: number: 0 From 07816aa39f68eaf927a71dfe9649d5c9d2ee0b45 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 11:13:10 -0500 Subject: [PATCH 2075/2173] Update snakemake to 8.4.9 (#45858) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 9fc08ce4c7cbd..a226a8f3ff36b 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.8" %} +{% set version = "8.4.9" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: ab64a4f402f78ec252f211d9cc900344fdc2a000dadcec91833efb5fd0f275e7 + sha256: 6bd24c39110a8d6744d09aab5ca71bde0c4559542ec7f58e52a6c4d360120171 build: number: 0 From 97660a91e790f8f3b8e08c839fdf5aeb95b2441f Mon Sep 17 00:00:00 2001 From: Tim Dunn <13918078+TimD1@users.noreply.github.com> Date: Sun, 18 Feb 2024 11:26:32 -0500 Subject: [PATCH 2076/2173] Add vcfdist package (#45815) * First vcfdist recipe build attempt. * Added pin_subpackage() * Added 'cd src' * Update build.sh Added 'cd src' * Updated vcfdist version with more compatible Makefile. * Add BASH path exports * C++ version of path variables * Updated vcfdist source to v2.4.0 * Update meta.yaml --- recipes/vcfdist/build.sh | 9 ++++++ recipes/vcfdist/conda_build_config.yaml | 4 +++ recipes/vcfdist/meta.yaml | 42 +++++++++++++++++++++++++ 3 files changed, 55 insertions(+) create mode 100644 recipes/vcfdist/build.sh create mode 100644 recipes/vcfdist/conda_build_config.yaml create mode 100644 recipes/vcfdist/meta.yaml diff --git a/recipes/vcfdist/build.sh b/recipes/vcfdist/build.sh new file mode 100644 index 0000000000000..ba9402cf841f3 --- /dev/null +++ b/recipes/vcfdist/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +export CPATH="${PREFIX}/include" +export CPLUS_INCLUDE_PATH="${PREFIX}/include" +export LD_LIBRARY_PATH="${PREFIX}/lib" + +cd src && make +install -d "${PREFIX}/bin" +install vcfdist "${PREFIX}/bin" diff --git a/recipes/vcfdist/conda_build_config.yaml b/recipes/vcfdist/conda_build_config.yaml new file mode 100644 index 0000000000000..50a90b77e33c2 --- /dev/null +++ b/recipes/vcfdist/conda_build_config.yaml @@ -0,0 +1,4 @@ +htslib: + - 1.17 +pin_run_as_build: + htslib: x.x diff --git a/recipes/vcfdist/meta.yaml b/recipes/vcfdist/meta.yaml new file mode 100644 index 0000000000000..bd4e85ad61cf7 --- /dev/null +++ b/recipes/vcfdist/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "2.4.0" %} +{% set sha256 = "bdb1bc84229f2bb81c9a4b5ee005b4f586895c320f504fbd1f983a0ef1cd6bb6" %} + +package: + name: vcfdist + version: {{ version }} + +source: + url: https://github.com/TimD1/vcfdist/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("vcfdist", max_pin="x.x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + host: + - htslib + run: + - htslib + +test: + commands: + - vcfdist --version + +about: + summary: 'vcfdist: benchmarking phased germline variant calls in VCF format' + home: https://github.com/TimD1/vcfdist + license: GPL-3.0-only + license_family: GPL3 + license_file: LICENSE + doc_url: https://github.com/TimD1/vcfdist/wiki + +extra: + maintainers: + - TimD1 + identifiers: + - doi:10.5281/zenodo.8368282 From 054da765f1dce4d10d1a22949d86d0f935e7a82f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 14:49:46 -0500 Subject: [PATCH 2077/2173] Update r-pscbs to 0.67.0 (#45855) * Update r-pscbs to 0.67.0 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-pscbs/meta.yaml | 51 +++++++++++++++++++++------------------ 1 file changed, 27 insertions(+), 24 deletions(-) diff --git a/recipes/r-pscbs/meta.yaml b/recipes/r-pscbs/meta.yaml index dba0c9851e2ea..6b9486d7121bf 100644 --- a/recipes/r-pscbs/meta.yaml +++ b/recipes/r-pscbs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.66.0' %} +{% set version = '0.67.0' %} package: name: r-pscbs @@ -8,48 +8,51 @@ source: url: - {{ cran_mirror }}/src/contrib/PSCBS_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/PSCBS/PSCBS_{{ version }}.tar.gz - sha256: 58805636e55e0fd3f57bd4a0e296a8bb3d57a7bdd0fdd5868a73ddc83d173a93 + sha256: 2695d18d197a3bd729cca0940248ddc1880e4f54da95b9ecc5eda002a715cdbe build: noarch: generic - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-pscbs', max_pin="x") }} requirements: host: - r-base - - bioconductor-dnacopy - - r-r.cache >=0.13.0 - - r-r.methodss3 >=1.7.1 - - r-r.oo >=1.22.0 - - r-r.utils >=2.8.0 - - bioconductor-aroma.light - - r-future >=1.12.0 - - r-listenv >=0.7.0 - - r-matrixstats >=0.54.0 + - bioconductor-dnacopy >=1.42.0 + - r-r.cache >=0.16.0 + - r-r.methodss3 >=1.8.2 + - r-r.oo >=1.25.0 + - r-r.utils >=2.12.0 + - bioconductor-aroma.light >=2.4.0 + - r-future >=1.28.0 + - r-listenv >=0.8.0 + - r-matrixstats >=0.62.0 run: - r-base - - bioconductor-dnacopy - - r-r.cache >=0.13.0 - - r-r.methodss3 >=1.7.1 - - r-r.oo >=1.22.0 - - r-r.utils >=2.8.0 - - bioconductor-aroma.light - - r-future >=1.12.0 - - r-listenv >=0.7.0 - - r-matrixstats >=0.54.0 + - bioconductor-dnacopy >=1.42.0 + - r-r.cache >=0.16.0 + - r-r.methodss3 >=1.8.2 + - r-r.oo >=1.25.0 + - r-r.utils >=2.12.0 + - bioconductor-aroma.light >=2.4.0 + - r-future >=1.28.0 + - r-listenv >=0.8.0 + - r-matrixstats >=0.62.0 test: commands: - - $R -e "library('PSCBS')" # [not win] - - "\"%R%\" -e \"library('PSCBS')\"" # [win] + - $R -e "library('PSCBS')" about: home: https://github.com/HenrikBengtsson/PSCBS - license: GPL (>= 2) + license: GPL-2.0-or-later summary: Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported. license_family: GPL3 + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' From e3e1d1b80f10b5ebd2a9c72d3174eb2533ca1304 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 18 Feb 2024 15:50:38 -0500 Subject: [PATCH 2078/2173] Update panaroo to 1.4.1 (#45863) --- recipes/panaroo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/panaroo/meta.yaml b/recipes/panaroo/meta.yaml index 8d83ad1beb7c2..a85cb44af1e88 100644 --- a/recipes/panaroo/meta.yaml +++ b/recipes/panaroo/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.0" %} +{% set version = "1.4.1" %} {% set name = "panaroo" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/gtonkinhill/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 651a11c9326bf885709ad555722ffefc5f67a365dce8a6475c09cd8d3537a89c + sha256: 5ff88a48b339083bcbf843e84eeff3be5f9eda3808394da436386ce0cdfc0111 build: number: 0 From 04ce77aa45dbf7ca3e9f00587088e4f0d15c5314 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 05:58:18 -0500 Subject: [PATCH 2079/2173] Update clipkit to 2.2.2 (#45864) --- recipes/clipkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clipkit/meta.yaml b/recipes/clipkit/meta.yaml index 63fb201258cb4..7c62e3cce5c85 100644 --- a/recipes/clipkit/meta.yaml +++ b/recipes/clipkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "clipkit" %} -{% set version = "2.2.0" %} +{% set version = "2.2.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7f973cec1842a3066c1478752b8692012174f5a58df870c1518a56cd37264605 + sha256: 76e13db515a951490e9ed6a86955c6207fae3292fb62b6d8adef7ac4a235077a build: number: 0 From e1f2b45a8cae5c9bb12d7dd4a4de9ec9a44e87d7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 06:02:50 -0500 Subject: [PATCH 2080/2173] Update r-aroma.affymetrix to 3.2.2 (#45866) * Update r-aroma.affymetrix to 3.2.2 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-aroma.affymetrix/meta.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/r-aroma.affymetrix/meta.yaml b/recipes/r-aroma.affymetrix/meta.yaml index b28a7de9263f0..c8237d9eb4f99 100644 --- a/recipes/r-aroma.affymetrix/meta.yaml +++ b/recipes/r-aroma.affymetrix/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '3.2.1' %} +{% set version = '3.2.2' %} package: name: r-aroma.affymetrix @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/aroma.affymetrix_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/aroma.affymetrix/aroma.affymetrix_{{ version }}.tar.gz - sha256: 7aefbbddf94f6fc0ee2dec261f0caa6ca28d5f36aa7f7534ffb5f4e10ec4f5fb + sha256: 18e1c9479e3e41bdfff06769d0ff2d85fcae16042cfd0eefa4dbcd0c4f3c9c40 build: noarch: generic - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-aroma.affymetrix', max_pin="x.x") }} requirements: host: @@ -60,3 +62,5 @@ about: Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006. license_family: LGPL + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' From 25491a58faf1303a34b040c53f64bb31cecc4cb1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 19 Feb 2024 12:28:12 +0100 Subject: [PATCH 2081/2173] add snakemake-interface-report-plugins (#45871) --- .../meta.yaml | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 recipes/snakemake-interface-report-plugins/meta.yaml diff --git a/recipes/snakemake-interface-report-plugins/meta.yaml b/recipes/snakemake-interface-report-plugins/meta.yaml new file mode 100644 index 0000000000000..16c4632e6a84d --- /dev/null +++ b/recipes/snakemake-interface-report-plugins/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "snakemake-interface-report-plugins" %} +{% set version = "1.0.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_report_plugins-{{ version }}.tar.gz + sha256: 02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage("snakemake-interface-report-plugins", max_pin="x") }} + +requirements: + host: + - python >=3.11,<4.0 + - poetry-core + - pip + run: + - python >=3.11.0,<4.0.0 + - snakemake-interface-common >=1.16.0,<2.0.0 + +test: + imports: + - snakemake_interface_report_plugins + commands: + - pip check + requires: + - pip + +about: + summary: This package provides a stable interface for interactions between Snakemake and its report plugins. + home: https://github.com/snakemake/snakemake-interface-report-plugins + license: MIT + license_file: LICENSE + +extra: + recipe-maintainers: + - koesterlab From 84267edb77003e8da06b42bce7dab66d1f5d28fa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:15:12 -0500 Subject: [PATCH 2082/2173] Update genoboo to 0.4.13 (#45620) * Update genoboo to 0.4.13 * fix build * fix osx --------- Co-authored-by: Anthony Bretaudeau --- recipes/genoboo/build.sh | 7 +++++-- recipes/genoboo/meta.yaml | 4 ++-- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/genoboo/build.sh b/recipes/genoboo/build.sh index 76a76236e8b16..d42cfaa60bf28 100644 --- a/recipes/genoboo/build.sh +++ b/recipes/genoboo/build.sh @@ -11,17 +11,20 @@ export ARCH=$(uname -m) export HOME="$(mktemp -d)" # Install meteor here (instead of in npm run bundle) because we need to patch the install script -curl "https://install.meteor.com/?release=2.8.0" > meteor.sh +curl "https://install.meteor.com/?release=2.13.3" > meteor.sh chmod a+x meteor.sh sed -i.bak 's|PREFIX=|#PREFIX=|' meteor.sh ./meteor.sh +sed -i.bak 's/"preinstall".*/"preinstall":"",/g' package.json + npm install --unsafe-perm export PATH=$PATH:"$HOME/.meteor" # Now run the normal gnb install -METEOR_ALLOW_SUPERUSER=1 METEOR_DISABLE_OPTIMISTIC_CACHING=1 npm run bundle + +TOOL_NODE_FLAGS="--max-old-space-size=2048" METEOR_ALLOW_SUPERUSER=1 METEOR_DISABLE_OPTIMISTIC_CACHING=1 npm run bundle cp -R genoboo_v${PKG_VERSION}/* $outdir diff --git a/recipes/genoboo/meta.yaml b/recipes/genoboo/meta.yaml index 1ea6112da89ba..5a1a8efef34fd 100644 --- a/recipes/genoboo/meta.yaml +++ b/recipes/genoboo/meta.yaml @@ -1,6 +1,6 @@ {% set name = 'genoboo' %} -{% set version = '0.4.12' %} -{% set sha256 = 'd8c280a174360c03ad4be4292e628ccf416a170771a369aa4bf32a5cebf1085e' %} +{% set version = '0.4.13' %} +{% set sha256 = '7a300f2cc9d885e2c5bf51ddcbdd9c952ef3f74d5801918e0f9114cdc3991b41' %} package: name: {{ name|lower }} From 0196c640a0a9316994760f844ee537cc91788a7a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:26:23 -0500 Subject: [PATCH 2083/2173] Update last to 1542 (#45868) --- recipes/last/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 9298623f84248..8c7b6b9fae609 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -1,5 +1,5 @@ {% set name = "LAST" %} -{% set version = "1541" %} +{% set version = "1542" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip - sha256: 80165ad97bd651b038ca187cc990c930ec96a0a9f5715a2179b5b75304ed64f9 + sha256: ee26e762fe76d167241f7e85b5e72ef8d17ed243c405e38dbbd06de97003596a build: number: 0 From 8046679b8b4ee5c527f73182574676c683905aef Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:26:29 -0500 Subject: [PATCH 2084/2173] Update pybiolib to 1.1.1749 (#45870) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 4d20a5881de64..1b55ef019fc9c 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1747" %} +{% set version = "1.1.1749" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: b6e014d302e0551db14697ec438ec07fecbf7bdd3634ccd22a47c4410a7a7839 + sha256: ec24fc1418b84918ffa85a9bf7a251e102e3dd025eb9460745ba19ba32600bf3 build: noarch: python From 512a35fd8c13c6cc8a504aff39d0e6cd8417bcab Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:26:42 -0500 Subject: [PATCH 2085/2173] Update snakemake-interface-storage-plugins to 3.1.0 (#45874) --- recipes/snakemake-interface-storage-plugins/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-storage-plugins/meta.yaml b/recipes/snakemake-interface-storage-plugins/meta.yaml index f3ebb462501db..8ca9b30fbc900 100644 --- a/recipes/snakemake-interface-storage-plugins/meta.yaml +++ b/recipes/snakemake-interface-storage-plugins/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-storage-plugins" %} -{% set version = "3.0.0" %} +{% set version = "3.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_storage_plugins-{{ version }}.tar.gz - sha256: f20d85ee7e86a1e2ffa3f72e2385dd5abb17fa7b58a26cba8ba59096872fe169 + sha256: 26e95be235ef2a9716b890ea96c3a9a2e62061c5d72fbb89c2fad2afada87304 build: noarch: python From 48a41b0ca07e975f73ceb95596d560800b2a92fc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:27:06 -0500 Subject: [PATCH 2086/2173] Update reframed to 1.5.1 (#45875) --- recipes/reframed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/reframed/meta.yaml b/recipes/reframed/meta.yaml index 5bc8f8eec8325..257bf77160da5 100644 --- a/recipes/reframed/meta.yaml +++ b/recipes/reframed/meta.yaml @@ -1,5 +1,5 @@ {% set name = "reframed" %} -{% set version = "1.5.0" %} +{% set version = "1.5.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/reframed-{{ version }}.tar.gz - sha256: 2f40e631080be7aa8f2ea1c1f4b1ffa5cf52e87e4279978b6c72c7bb690dc1c1 + sha256: cded8ba31fa1dcddb358f79122cbe5d1f4562a538a4058045d462b50d7fc71c8 build: noarch: python From 35c62d900fc381f99730aa2e6a24ffba93249026 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:27:19 -0500 Subject: [PATCH 2087/2173] Update snakemake-interface-common to 1.17.0 (#45876) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index f7298deb2e3a2..38e66d2a7ae0f 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.16.0" %} +{% set version = "1.17.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: b0780b9c3525435031815fd1f01079828d55c83fef18b5a0b05caa965408046b + sha256: d1f0cb83611f24f62ec5af852cee1cef429dd4e86c55bf373092fc682acac133 build: noarch: python From 6ea9c6a6e2f357db75ae6baad458eb5b237181a0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:28:41 -0500 Subject: [PATCH 2088/2173] Update nanomotif to 0.1.19 (#45878) --- recipes/nanomotif/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanomotif/meta.yaml b/recipes/nanomotif/meta.yaml index afe275f534641..8620e63a0f280 100644 --- a/recipes/nanomotif/meta.yaml +++ b/recipes/nanomotif/meta.yaml @@ -1,5 +1,5 @@ {% set name = "nanomotif" %} -{% set version = "0.1.18" %} +{% set version = "0.1.19" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nanomotif-{{ version }}.tar.gz - sha256: a8a4e7bfe21617c51003ae9d0ed056b1a5380d7df83b3d115cd079d06e8cd116 + sha256: e62cc67dc23bc185aa9af77420e53be0d820fa70880d1b048c522d646def75ef build: entry_points: From 93bc89f896081f096e0cdd1c60575dc6cb104e0e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 12:29:23 -0500 Subject: [PATCH 2089/2173] Update harpy to 0.6.1 (#45885) --- recipes/harpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index f51726858a1c8..8ceac942c5b01 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6.0" %} -{% set sha256 = "3b7010054c3cafb19ae6973154015e17cd4688966237af90f5584d933eec86b3" %} +{% set version = "0.6.1" %} +{% set sha256 = "82841865d78362b084f76031329b30ff82521160d7ebdfb64386bfd32dac131c" %} package: name: harpy From 11d36ce9be50a4f6f62380b5c80ca26980715f30 Mon Sep 17 00:00:00 2001 From: Christian Atallah <34323164+chrisAta@users.noreply.github.com> Date: Mon, 19 Feb 2024 18:50:27 +0000 Subject: [PATCH 2090/2173] Add mgnify-pipelines-toolkit recipe (#45872) * initial mgnify-pipelines-toolkit bioconda commit * fix lint by adding homepage and run_exports * fix argv error with new release of toolkit * update sha256 --- recipes/mgnify-pipelines-toolkit/meta.yaml | 70 ++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 recipes/mgnify-pipelines-toolkit/meta.yaml diff --git a/recipes/mgnify-pipelines-toolkit/meta.yaml b/recipes/mgnify-pipelines-toolkit/meta.yaml new file mode 100644 index 0000000000000..424f194a0dfc0 --- /dev/null +++ b/recipes/mgnify-pipelines-toolkit/meta.yaml @@ -0,0 +1,70 @@ +{% set name = "mgnify-pipelines-toolkit" %} +{% set version = "0.0.9" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgnify_pipelines_toolkit-{{ version }}.tar.gz + sha256: 6140dd322824086169cebd6ba2a22c9be9276920f3ea04c6fe6e96c7848c3d1d + +build: + entry_points: + - get_subunits = mgnify_pipelines_toolkit.analysis.shared.get_subunits:main + - get_subunits_coords = mgnify_pipelines_toolkit.analysis.shared.get_subunits_coords:main + - mapseq2biom = mgnify_pipelines_toolkit.analysis.shared.mapseq2biom:main + - are_there_primers = mgnify_pipelines_toolkit.analysis.amplicon.are_there_primers:main + - assess_inflection_point_mcp = mgnify_pipelines_toolkit.analysis.amplicon.assess_inflection_point_mcp:main + - assess_mcp_proportions = mgnify_pipelines_toolkit.analysis.amplicon.assess_mcp_proportions:main + - classify_var_regions = mgnify_pipelines_toolkit.analysis.amplicon.classify_var_regions:main + - find_mcp_inflection_points = mgnify_pipelines_toolkit.analysis.amplicon.find_mcp_inflection_points:main + - make_asv_count_table = mgnify_pipelines_toolkit.analysis.amplicon.make_asv_count_table:main + - remove_ambiguous_reads = mgnify_pipelines_toolkit.analysis.amplicon.remove_ambiguous_reads:main + - rev_comp_se_primers = mgnify_pipelines_toolkit.analysis.amplicon.rev_comp_se_primers:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('mgnify-pipelines-toolkit', max_pin="x.x") }} + +requirements: + host: + - python >=3.9 + - setuptools >=61.0 + - pip + run: + - python >=3.9 + - biopython ==1.82 + - numpy ==1.26.0 + - pandas ==2.0.2 + - regex ==2023.12.25 + +test: + imports: + - mgnify_pipelines_toolkit + commands: + - pip check + - get_subunits --help + - get_subunits_coords --help + - mapseq2biom --help + - are_there_primers --help + - assess_inflection_point_mcp --help + - assess_mcp_proportions --help + - classify_var_regions --help + - find_mcp_inflection_points --help + - make_asv_count_table --help + - remove_ambiguous_reads --help + - rev_comp_se_primers --help + requires: + - pip + +about: + home: https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit + summary: Collection of scripts and tools for MGnify pipelines + license: Apache-2.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - chrisAta From 9defd434e805f0709e45a1e2fb5fc763f5f63e8f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:24:58 -0500 Subject: [PATCH 2091/2173] Update snakemake to 8.4.11 (#45882) * Update snakemake to 8.4.10 * Update snakemake to 8.4.11 --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index a226a8f3ff36b..d25d92a34cfe4 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.9" %} +{% set version = "8.4.11" %} package: name: snakemake @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 6bd24c39110a8d6744d09aab5ca71bde0c4559542ec7f58e52a6c4d360120171 + sha256: 6c176d2f3e9cb163a81d1b0e9876b2178c6d8187971d95c9ac2be3470d94d246 build: number: 0 From a1a673290e9e0c804c3779f1dc3eb254e4bf6b08 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:25:34 -0500 Subject: [PATCH 2092/2173] Update mirmachine to 0.2.13 (#45877) * Update mirmachine to 0.2.13 * Update mirmachine meta.yaml (#45879) * Update mirmachine meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Sinan U. Umu --- recipes/mirmachine/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/mirmachine/meta.yaml b/recipes/mirmachine/meta.yaml index 0d9b2844285c3..aeb3d30ca4d51 100644 --- a/recipes/mirmachine/meta.yaml +++ b/recipes/mirmachine/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MirMachine" %} -{% set version = "0.2.12" %} +{% set version = "0.2.13" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 5e55e5d4358d44e5f59f610476f1420a565c1bb916d1de1323d984d02313232c + sha256: 0a2d7d466a391b07a358ee543c34814974f8273cd42ce37f5ccb757169649411 build: noarch: python number: 0 script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_compatible("MirMachine", max_pin="x.x") }} requirements: host: From 88b80b585d027f8490ff61e9fac030f575d4e5da Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:41:48 -0500 Subject: [PATCH 2093/2173] Update r-aroma.core to 3.3.1 (#45873) * Update r-aroma.core to 3.3.1 * add run_exports --------- Co-authored-by: mencian --- recipes/r-aroma.core/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/r-aroma.core/meta.yaml b/recipes/r-aroma.core/meta.yaml index c2ec781553729..5d9c36cd653b2 100644 --- a/recipes/r-aroma.core/meta.yaml +++ b/recipes/r-aroma.core/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '3.3.0' %} +{% set version = '3.3.1' %} package: name: r-aroma.core @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/aroma.core_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/aroma.core/aroma.core_{{ version }}.tar.gz - sha256: 7b6ab7cc6079f6783b0eaa2c10a29492e53cfb3f05b7a298588491b35a472188 + sha256: fa26bca509750eb44e85cae2d78b03870c003d4f7e0360977e924a7838805e44 build: noarch: generic - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-aroma.core', max_pin="x") }} requirements: host: @@ -54,10 +56,11 @@ test: - $R -e "library('aroma.core')" about: - home: https://github.com/HenrikBengtsson/aroma.core, http://www.aroma-project.org/ + home: https://www.aroma-project.org/ license: LGPL-2.1-or-later summary: Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'. + dev_url: https://github.com/HenrikBengtsson/aroma.core license_family: LGPL license_file: - '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' From 773173c14f0cf3d4ace20c3f860dd32538dfe015 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:41:55 -0500 Subject: [PATCH 2094/2173] Update tissuumaps to 3.2.0.5 (#45834) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/tissuumaps/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tissuumaps/meta.yaml b/recipes/tissuumaps/meta.yaml index 5f81144cf6ced..50e6992dce10d 100644 --- a/recipes/tissuumaps/meta.yaml +++ b/recipes/tissuumaps/meta.yaml @@ -4,7 +4,7 @@ # - add pyqt6 (or possibly pyqt>=6) dependency # Until then, only the "tissuumaps_server" script is available, not "tissuumaps" -{% set version = "3.2.0.4" %} +{% set version = "3.2.0.5" %} package: name: tissuumaps @@ -12,7 +12,7 @@ package: source: url: https://github.com/TissUUmaps/TissUUmaps/archive/refs/tags/{{ version }}.tar.gz - sha256: 02ce7e575075fd5b401c322ade25ed9f52cc4b7af944a9c29441c1784506a1ed + sha256: 2d0cefff0aa54a8f9bb040cf5537a77c5fec2a40954b8c1b2b2af8a07bb181d9 build: number: 0 From b35c3c8a8bed1c28e1910410cb709dab09c2a1d4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:43:47 -0500 Subject: [PATCH 2095/2173] Update snakemake-storage-plugin-s3 to 0.2.10 (#45835) * Update snakemake-storage-plugin-s3 to 0.2.10 * retrigger CI --------- Co-authored-by: mencian --- recipes/snakemake-storage-plugin-s3/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake-storage-plugin-s3/meta.yaml b/recipes/snakemake-storage-plugin-s3/meta.yaml index f846ede5119a0..55783267920c3 100644 --- a/recipes/snakemake-storage-plugin-s3/meta.yaml +++ b/recipes/snakemake-storage-plugin-s3/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-s3" %} -{% set version = "0.2.9" %} +{% set version = "0.2.10" %} package: name: {{ name|lower }} @@ -7,11 +7,11 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_s3-{{ version }}.tar.gz - sha256: 41cb23326f37dc576d4a1deac15b3f5a647e26ca957a69ae06b128c044ba2f32 + sha256: a4554d170b5621751aba20ee08e6357090471a0a68b173525b118580c287a12e build: noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -40,7 +40,9 @@ about: summary: A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.) home: https://github.com/snakemake/snakemake-storage-plugin-s3 license: MIT + license_family: MIT license_file: LICENSE + doc_url: https://snakemake.github.io/snakemake-plugin-catalog/plugins/storage/s3.html extra: recipe-maintainers: From ea8dff77ed9b9f305e13871253932d48bfd930fc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:52:04 -0500 Subject: [PATCH 2096/2173] Update vcf2parquet to 0.5.0 (#45881) * Update vcf2parquet to 0.5.0 * add run_exports --------- Co-authored-by: mencian --- recipes/vcf2parquet/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/vcf2parquet/meta.yaml b/recipes/vcf2parquet/meta.yaml index f5b5e47b394db..ad6addc3938bc 100644 --- a/recipes/vcf2parquet/meta.yaml +++ b/recipes/vcf2parquet/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.1" %} -{% set sha256 = "c0eb32658e4ec05433b265c78c158e216e2e464a15174615c1e6d39380019a46" %} +{% set version = "0.5.0" %} +{% set sha256 = "61cba26e418d33af994bc85c4e5174ed115fc15bcf94f4f54e14a31ab839c82f" %} package: name: vcf2parquet @@ -11,17 +11,18 @@ source: build: number: 0 + run_exports: + - {{ pin_subpackage('vcf2parquet', max_pin="x.x") }} requirements: build: - {{ compiler("c") }} - - rust + - {{ compiler("rust") }} - pkg-config # [osx] host: - xz - zlib - bzip2 - run: test: commands: From 9464b71cd56ecda1588d7555e006034aac49f2b0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:56:17 -0500 Subject: [PATCH 2097/2173] Update anglerfish to 0.6.1 (#45830) * Update anglerfish to 0.6.1 * add requirements.txt * copy requirements.txt to SRC_DIR --------- Co-authored-by: Brandon Seah Co-authored-by: mencian --- recipes/anglerfish/meta.yaml | 10 ++++++---- recipes/anglerfish/requirements.txt | 6 ++++++ 2 files changed, 12 insertions(+), 4 deletions(-) create mode 100644 recipes/anglerfish/requirements.txt diff --git a/recipes/anglerfish/meta.yaml b/recipes/anglerfish/meta.yaml index ee4d25f033fc1..d15537aa287a2 100644 --- a/recipes/anglerfish/meta.yaml +++ b/recipes/anglerfish/meta.yaml @@ -1,5 +1,5 @@ {% set name = "anglerfish" %} -{% set version = "0.6.0" %} +{% set version = "0.6.1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,12 @@ package: source: url: "https://pypi.io/packages/source/b/bio-{{ name }}/bio-{{ name }}-{{ version }}.tar.gz" - sha256: b67a0c77680f85ebdf88622382bb271655e807c60dc3bdcd01997d336e6574fa + sha256: 91a62cbbc388009bd503df0d3f64441c0e86ab377da46f721f5fcf82b9cce331 build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + script: "cp ${RECIPE_DIR}/requirements.txt ${SRC_DIR} && {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" entry_points: - anglerfish=anglerfish.anglerfish:anglerfish run_exports: @@ -24,11 +24,13 @@ requirements: - python >=3.7 run: - biopython + - click + - minimap2 - numpy + - pandas - python >=3.7 - python-levenshtein - pyyaml - - minimap2 test: imports: diff --git a/recipes/anglerfish/requirements.txt b/recipes/anglerfish/requirements.txt new file mode 100644 index 0000000000000..db39464867253 --- /dev/null +++ b/recipes/anglerfish/requirements.txt @@ -0,0 +1,6 @@ +biopython==1.83 +click==8.1.7 +levenshtein==0.23.0 +numpy==1.26.3 +pandas==2.1.4 +pyyaml==6.0.1 \ No newline at end of file From ffe575f4e3687b080a2a5c17efbe9e2e98dcba87 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 15:23:33 -0500 Subject: [PATCH 2098/2173] Update snakemake-storage-plugin-fs to 0.2.0 (#45884) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/snakemake-storage-plugin-fs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-storage-plugin-fs/meta.yaml b/recipes/snakemake-storage-plugin-fs/meta.yaml index 2f0f622a761d0..996d529132ccb 100644 --- a/recipes/snakemake-storage-plugin-fs/meta.yaml +++ b/recipes/snakemake-storage-plugin-fs/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-storage-plugin-fs" %} -{% set version = "0.1.5" %} +{% set version = "0.2.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_storage_plugin_fs-{{ version }}.tar.gz - sha256: f1a54248008b6c65102a1fde2064e3b66aadd9f6795522bacb452deecfe181ad + sha256: cad1859036cbf429ea6fdb97f242567ec54a36d0b6ff900ce0d3ecfb6a824ae7 build: noarch: python From c49831bb17f5fd6bff42d6283944b310c89c3269 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:52:10 -0600 Subject: [PATCH 2099/2173] Add recipe for sctriangulate v0.13.0 (#45889) * Add recipe for sctriangulate v0.13.0 * edit dependencies --- recipes/sctriangulate/LICENSE | 21 +++++++++++++++++ recipes/sctriangulate/meta.yaml | 41 +++++++++++++++++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 recipes/sctriangulate/LICENSE create mode 100644 recipes/sctriangulate/meta.yaml diff --git a/recipes/sctriangulate/LICENSE b/recipes/sctriangulate/LICENSE new file mode 100644 index 0000000000000..f8836ff0edea6 --- /dev/null +++ b/recipes/sctriangulate/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2021 Guangyuan(Frank) Li + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/recipes/sctriangulate/meta.yaml b/recipes/sctriangulate/meta.yaml new file mode 100644 index 0000000000000..9d3d2eb7a402a --- /dev/null +++ b/recipes/sctriangulate/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "sctriangulate" %} +{% set version = "0.13.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sctriangulate-{{ version }}.tar.gz + sha256: dc24a47c912c15d06465ea6ec87599e5bcdf06d18955d964f96eebce445a7bc2 + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation + run_exports: + - {{ pin_subpackage('sctriangulate', max_pin="x.x") }} + +requirements: + host: + - python >=3.7 + - pip + run: + - python >=3.7 + - squidpy + - gseapy ==0.10.4 + - scrublet ==0.2.3 + - yattag + - anytree + - mygene ==3.2.2 + +test: + imports: + - sctriangulate + +about: + home: https://github.com/frankligy/scTriangulate + summary: A Python package to mix-and-match conflicting clustering results in single cell analysis, and generate reconciled clustering solutions. + license: MIT + license_family: MIT + license_file: LICENSE From 83cd0a214d93c0e7fd07afd4e71e914a56690fd8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 17:14:12 -0500 Subject: [PATCH 2100/2173] Update jbrowse2 to 2.10.2 (#45890) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index 48774c686d68b..49ca9eeb5caee 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.10.1" %} +{% set version = "2.10.2" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 9495e73d98e4eb287c8a48d8d4a61f2523755a4582681ce4e8e09b9e0fbef291 + sha256: 06e6054086ae0a1aa3bcd55ed6fe475fc23b5960a9907c25c0d3cadfab2c6db7 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From 0ebb57a8c74febd1703fbb1f0892de21c8c9d822 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 19 Feb 2024 17:14:19 -0500 Subject: [PATCH 2101/2173] Update oakvar to 2.9.88 (#45891) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 2054f16001ab9..8e67b03ac181a 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.87" %} -{% set sha256 = "3ee4c24b0d1f8995b7f41ec2ba2c6948c9bd6bed4166715a1fe3b0e4436fba44" %} +{% set version = "2.9.88" %} +{% set sha256 = "ebb19910d3c3b0eff179430ea175072c21a658557b72b11dc5c5d45ddddab7c2" %} package: name: {{ name|lower }} From 89f4f6432d6b438aa7a62292e3832fb0498a7a1e Mon Sep 17 00:00:00 2001 From: Christian Atallah <34323164+chrisAta@users.noreply.github.com> Date: Mon, 19 Feb 2024 23:09:16 +0000 Subject: [PATCH 2102/2173] Update mgnify-pipelines-toolkit package to add missing alias for standard_primer_matching script (#45893) * add missing alias for standard_primer_matching * add description --- recipes/mgnify-pipelines-toolkit/meta.yaml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/recipes/mgnify-pipelines-toolkit/meta.yaml b/recipes/mgnify-pipelines-toolkit/meta.yaml index 424f194a0dfc0..180d73ca19264 100644 --- a/recipes/mgnify-pipelines-toolkit/meta.yaml +++ b/recipes/mgnify-pipelines-toolkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mgnify-pipelines-toolkit" %} -{% set version = "0.0.9" %} +{% set version = "0.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgnify_pipelines_toolkit-{{ version }}.tar.gz - sha256: 6140dd322824086169cebd6ba2a22c9be9276920f3ea04c6fe6e96c7848c3d1d + sha256: ec70929a119207c866b2eeb92323a30d82998a983ef0364ecaf288d5994dfb00 build: entry_points: @@ -22,6 +22,7 @@ build: - make_asv_count_table = mgnify_pipelines_toolkit.analysis.amplicon.make_asv_count_table:main - remove_ambiguous_reads = mgnify_pipelines_toolkit.analysis.amplicon.remove_ambiguous_reads:main - rev_comp_se_primers = mgnify_pipelines_toolkit.analysis.amplicon.rev_comp_se_primers:main + - standard_primer_matching = mgnify_pipelines_toolkit.analysis.amplicon.standard_primer_matching:main noarch: python script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 @@ -56,12 +57,16 @@ test: - make_asv_count_table --help - remove_ambiguous_reads --help - rev_comp_se_primers --help + - standard_primer_matching --help requires: - pip about: home: https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit summary: Collection of scripts and tools for MGnify pipelines + description: | + This package contains a collection of scripts used by MGnify + pipelines license: Apache-2.0 license_file: LICENSE From d399eb91d5ade278838b248cd91e9d171e962adf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 04:07:54 -0500 Subject: [PATCH 2103/2173] Update gxf2bed to 0.2.0 (#45900) --- recipes/gxf2bed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gxf2bed/meta.yaml b/recipes/gxf2bed/meta.yaml index 0104d86e074a6..b95b9777d8ddb 100644 --- a/recipes/gxf2bed/meta.yaml +++ b/recipes/gxf2bed/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gxf2bed" %} -{% set version = "0.1.0" %} +{% set version = "0.2.0" %} package: name: gxf2bed @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 75aa006736b7e03a16bf7cb1dd1e2a7fef87a5cc9d114b2ea603df79042cd2a9 + sha256: 5bd42033a2b72fe8e4a6dd467fb97ca3cd4ebd71d2f4466467cec384c5acbf9c build: number: 0 From ca55f5eee3b69ff4ad09ba2f3fe41a6bf167cb28 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 04:13:26 -0500 Subject: [PATCH 2104/2173] Update decoupler to 1.6.0 (#45888) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update decoupler to 1.6.0 * clean up recipe * Delete recipes/decoupler/meta.yaml --------- Co-authored-by: mencian Co-authored-by: Björn Grüning --- recipes/decoupler/meta.yaml | 52 ------------------------------------- 1 file changed, 52 deletions(-) delete mode 100644 recipes/decoupler/meta.yaml diff --git a/recipes/decoupler/meta.yaml b/recipes/decoupler/meta.yaml deleted file mode 100644 index d8c9c0a826d9f..0000000000000 --- a/recipes/decoupler/meta.yaml +++ /dev/null @@ -1,52 +0,0 @@ -{% set name = "decoupler" %} -{% set version = "1.5.0" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/decoupler-{{ version }}.tar.gz - sha256: 1278b0912df0eb22618b720a7c862e6babd874472290e7c81c27dcf65c5bd48a - -build: - noarch: python - script: {{ PYTHON }} -m pip install . -vv - number: 0 - run_exports: - - {{ pin_subpackage(name, max_pin="x") }} - -requirements: - host: - - python >=3.6 - - pip - run: - - python >=3.6 - - numba - - tqdm - - anndata - - typing-extensions - - seaborn - - skranger - - scikit-learn - - omnipath - - adjusttext - - scanpy - -test: - imports: - - decoupler - commands: - - pip check - requires: - - pip - -about: - home: https://github.com/saezlab/decoupler-py - summary: Ensemble of methods to infer biological activities from omics data - license: GPL-3.0 - license_file: LICENSE - -extra: - recipe-maintainers: - - pcm32 From e6fbd9be24ed2139d6149c4aa9c9c3aefceed7eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 20 Feb 2024 12:04:11 +0100 Subject: [PATCH 2105/2173] fix: snakemake dependencies (#45903) --- recipes/snakemake/meta.yaml | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index d25d92a34cfe4..b5e3f12330276 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,3 +1,5 @@ +# Attention: when upgrading the version, please compare below dependencies with +# https://github.com/snakemake/snakemake/blob/{version}/setup.cfg {% set version = "8.4.11" %} package: @@ -9,7 +11,7 @@ source: sha256: 6c176d2f3e9cb163a81d1b0e9876b2178c6d8187971d95c9ac2be3470d94d246 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage("snakemake", max_pin="x") }} @@ -81,16 +83,14 @@ outputs: run: # Keep in sync with snakemake/setup.cfg - python >=3.11,<3.13 - - immutables - appdirs - - conda-inject >=1.3.1,<2.0 + - immutables - configargparse - connection_pool >=0.0.3 - datrie - docutils - gitpython - humanfriendly - - immutables - jinja2 >=3.0,<4.0 - jsonschema - nbformat @@ -100,17 +100,18 @@ outputs: - pyyaml - requests >=2.8.1 - reretry - - smart_open >=3.0 + - smart_open >=3.0,<4.0 - snakemake-interface-executor-plugins >=8.1.3,<9.0 - - snakemake-interface-common >=1.15.0,<2.0 - - snakemake-interface-storage-plugins >=3.0.0,<4.0 + - snakemake-interface-common >=1.17.0,<2.0 + - snakemake-interface-storage-plugins >=3.1.0,<4.0 - stopit - tabulate - throttler - - toposort >=1.10 - - yte >=1.5.1,<2.0 + - toposort >=1.10,<2.0 - wrapt + - yte >=1.5.1,<2.0 - dpath >=2.1.6,<3.0.0 + - conda-inject >=1.3.1,<2.0 test: imports: From b81545e0987e0bbdff3125bcc6a47a1b0c55191f Mon Sep 17 00:00:00 2001 From: George Bouras <84495559+gbouras13@users.noreply.github.com> Date: Wed, 21 Feb 2024 00:59:36 +1030 Subject: [PATCH 2106/2173] fix phanotate to lower than 1.6.4 (#45906) --- recipes/pharokka/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pharokka/meta.yaml b/recipes/pharokka/meta.yaml index fad8abba9cbc1..21fb6adf06685 100644 --- a/recipes/pharokka/meta.yaml +++ b/recipes/pharokka/meta.yaml @@ -8,7 +8,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-build-isolation --use-pep517 --no-deps -vvv" run_exports: @@ -26,7 +26,7 @@ requirements: - python >=3.5 - bcbio-gff >=0.7.0 - biopython >=1.78,<1.82 - - phanotate >=1.5.0 + - phanotate >=1.5.0,<1.6.4 - mmseqs2 ==13.45111 - trnascan-se >=2.0.9 - minced >=0.4.2 From ef597c955cb1fe84cada48ca097374eae1ce5c56 Mon Sep 17 00:00:00 2001 From: mwaldl Date: Tue, 20 Feb 2024 17:01:07 +0100 Subject: [PATCH 2107/2173] Add initial RRIkinDP recipe (#45821) * add initial RRIkinDP recipes * add run export section * use matplotlib-base instead of matplotlib in dependencies * fix typo in test/commands * add boost and openmp as run requirement * debugging boost location * use compiler flags to solve issue of not found boost lib * add compiler flags to make call * switch to release that supports passing of CXXFLAGS and LDFLAGS when running make * define path to output executable * switch to lower case name space for python module * use $PYTHON instead of python in build.sh * update to source release with license file * Change bin installation path * change source release to fix return value of RRIkinDP --version --------- Co-authored-by: Sebastian Will --- recipes/rrikindp/build.sh | 8 +++++ recipes/rrikindp/meta.yaml | 71 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 recipes/rrikindp/build.sh create mode 100644 recipes/rrikindp/meta.yaml diff --git a/recipes/rrikindp/build.sh b/recipes/rrikindp/build.sh new file mode 100644 index 0000000000000..0f8e3cfde1a94 --- /dev/null +++ b/recipes/rrikindp/build.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +$PYTHON -m pip install . --no-deps --ignore-installed -vv + +cd src/rrikindp + +make -j ${CPU_COUNT} CXXFLAGS+="-I${CONDA_PREFIX}/include" LDFLAGS+="-L${CONDA_PREFIX}/lib" +install RRIkinDP "${PREFIX}/bin" diff --git a/recipes/rrikindp/meta.yaml b/recipes/rrikindp/meta.yaml new file mode 100644 index 0000000000000..18246c4e9a938 --- /dev/null +++ b/recipes/rrikindp/meta.yaml @@ -0,0 +1,71 @@ + +{% set name = "RRIkinDP" %} +{% set version = "0.0.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/mwaldl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 75f6f0dd0c993796423ca812ab4926225c44d718ab3bbe90c0be856aa5d83d2f + +build: + number: 0 + run_exports: + - {{ pin_subpackage('rrikindp', max_pin="x.x,x") }} + +requirements: + build: + - python + - pip + - make + - {{ compiler('cxx') }} + host: + - python + - boost-cpp + - viennarna >=2.6.0 + - intarna + - llvm-openmp + run: + - boost-cpp + - llvm-openmp + - python >=3.6 + - intarna + - viennarna >=2.6.0 + - matplotlib-base >=3.7.0 + - seaborn >=0.12.0 + - pandas >=2.0.0 + + +output: + files: + - src/RRIkinDP/RRIkinDP + py_modules: + - rrikindp + +test: + commands: + - RRIkinDP --version + imports: + - rrikindp + +about: + home: "https://github.com/mwaldl/RRIkinDP" + license: "GPL-3.0-only" + license_family: GPL + license_file: COPYING + summary: 'Evaluation of thermodynamic and kinetic features of RNA-RNA interactions.' + description: | + RRIkinDP evaluated thermodynamic and kinetic features of RNA-RNA interactions. As input, two RNA + sequences as well as their interaction structure is provided. The tool generates the state space of + all intermediate interactions from single base pair interactions to the full input interaction. + On top of this state space it computes the barrier energy for the best direct path from a given + start interaction to the full input interaction. + doc_url: https://doi.org/10.1101/2023.07.28.548983 + dev_url: https://github.com/mwaldl/RRIkinDP + +extra: + recipe-maintainers: + - mwaldl + - s-will From 8f9a05614dcebbd0a3591149b5045c973c76e90a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 11:50:46 -0500 Subject: [PATCH 2108/2173] Update nf-core to 2.13 (#45912) --- recipes/nf-core/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml index bdfc0e175394a..af43d2adb35cf 100644 --- a/recipes/nf-core/meta.yaml +++ b/recipes/nf-core/meta.yaml @@ -1,6 +1,6 @@ {% set name = "nf-core" %} -{% set version = "2.12.1" %} -{% set sha256 = "29503365111d5f760fe178cb0db317f9196af5340e649e68e345eb06c95be211" %} +{% set version = "2.13" %} +{% set sha256 = "7e0eb09bd56b2dd2861ea162204c6c0b2c966be29cacde2bb758831423ce7c81" %} package: name: {{ name|lower }} From 711c611700e989c3904b2991e3fe71cb29c22de6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 12:36:07 -0500 Subject: [PATCH 2109/2173] Update annosine2 to 2.0.7 (#45901) --- recipes/annosine2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annosine2/meta.yaml b/recipes/annosine2/meta.yaml index 8e3f769b95e18..e3e0c6c3e22fc 100644 --- a/recipes/annosine2/meta.yaml +++ b/recipes/annosine2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "annosine2" %} -{% set version = "1.0.5" %} +{% set version = "2.0.7" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4b51d569f064657d31ad70893723ce1809e0be22d9be0fa23bb4c9924645a423 + sha256: 94387b895e2b011125211039598b8c426124aa43be6915697243497eefb7fff8 build: number: 0 From ccad747405247b5a7696dc49d96977601004196e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 12:36:43 -0500 Subject: [PATCH 2110/2173] Update biocommons.seqrepo to 0.6.9 (#45898) * Update biocommons.seqrepo to 0.6.8 * Update biocommons.seqrepo to 0.6.9 --- recipes/biocommons.seqrepo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biocommons.seqrepo/meta.yaml b/recipes/biocommons.seqrepo/meta.yaml index 190a81d3545ba..0009a20f469c5 100644 --- a/recipes/biocommons.seqrepo/meta.yaml +++ b/recipes/biocommons.seqrepo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biocommons.seqrepo" %} -{% set version = "0.6.7" %} +{% set version = "0.6.9" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/biocommons.seqrepo-{{ version }}.tar.gz - sha256: 2c3f982c1ed3adb1971a0dd2e7a554d096a1c5801075e384a62dd3f73d5e8c81 + sha256: b08d616c6ab5c4bc8e1ef5e09e94c5c274c6da41f75a435323eddc716c9b5575 build: number: 0 From 7097d3fad7ddf75e168d381dd4b170e3fb10207a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 12:41:01 -0500 Subject: [PATCH 2111/2173] Update sevenbridges-python to 2.10.3 (#45907) --- recipes/sevenbridges-python/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index 34b191fef1cfc..346b24f70a44f 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.10.2" %} -{% set sha256 = "4402b7b874f97532c5156a68b45ebb9554a774ffd182ef346876cca83db791a9" %} +{% set version = "2.10.3" %} +{% set sha256 = "eb49e2300eaba7d4f50d07cfb10e9706079741a7964e36f9158c2f4efa3ea3c4" %} package: name: sevenbridges-python From 42b4594a9e96c74eca9ad4da00878cd6a2cff986 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 15:14:31 -0500 Subject: [PATCH 2112/2173] Update pyfastani to 0.5.1 (#45908) * Update pyfastani to 0.5.1 * run_exports --------- Co-authored-by: Thanh Lee --- recipes/pyfastani/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/pyfastani/meta.yaml b/recipes/pyfastani/meta.yaml index 7f8c1496bd166..d85b7057c9ad7 100644 --- a/recipes/pyfastani/meta.yaml +++ b/recipes/pyfastani/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyfastani" %} -{% set version = "0.4.1" %} +{% set version = "0.5.1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,14 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 44d86cbe8581d4891748ebe9851ae0a0c27489bb9f77728131415ed6b90cc35a + sha256: ad6c28303290a2389c29ed20db8266bbc4bf89a5b1bf64a7514d1bc9c6ba2d92 build: - number: 3 + number: 0 skip: True #[py2k] script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: build: From 1ecdd4b8189519cb23722eb93627b67153b08b70 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 20 Feb 2024 15:20:14 -0500 Subject: [PATCH 2113/2173] Update snakemake to 8.4.12 (#45911) --- recipes/snakemake/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index b5e3f12330276..a2220d2f22c9b 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.4.11" %} +{% set version = "8.4.12" %} package: name: snakemake @@ -8,10 +8,10 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 6c176d2f3e9cb163a81d1b0e9876b2178c6d8187971d95c9ac2be3470d94d246 + sha256: 1320590f24d3ef08d63ac91f1b3f634b27e4cfef21c7bbb3f267a79d75327621 build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_subpackage("snakemake", max_pin="x") }} From eb1f0084f58f8e7d77491b5ef3fd07bc92104d7a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 03:47:11 -0500 Subject: [PATCH 2114/2173] Update annotsv to 3.4 (#45916) --- recipes/annotsv/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annotsv/meta.yaml b/recipes/annotsv/meta.yaml index c729ada9c6038..8b2d6880cc386 100644 --- a/recipes/annotsv/meta.yaml +++ b/recipes/annotsv/meta.yaml @@ -1,6 +1,6 @@ {% set name = "annotsv" %} -{% set version = "3.3.9" %} -{% set sha256 = "698db38f70aaf7e839fbe090fc647b5dd7584c71a9b6397e38bf5af83a4e4c44" %} +{% set version = "3.4" %} +{% set sha256 = "98dcdbaf93525380e6c9c9dd0d501bf1af21b68155f635e4422a955970ca8f83" %} package: name: {{ name }} From e3a6bb2c4440893b393c3241d6d0c94dfdd54c37 Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Wed, 21 Feb 2024 10:51:23 +0000 Subject: [PATCH 2115/2173] Update scanpy-scripts to 1.9.301 (#45913) --- recipes/scanpy-scripts/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index 6cad46ec670b5..990206e2e559f 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -1,14 +1,13 @@ {% set name = "scanpy-scripts" %} -{% set version = "1.9.0" %} +{% set version = "1.9.301" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - # - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - - url: https://github.com/ebi-gene-expression-group/scanpy-scripts/archive/refs/heads/develop.tar.gz - sha256: 669fb6f12e23a689e2e889d160c3f4f09d05d33068bef36a88bb94f9053c7b9c + - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: c681d9cf5670d8b771b7327684f19d52f9661ee31e685241af4d960220a5d63b folder: scanpy-scripts build: From 239accc760dc264a194f9699fbb169e15c67def6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 06:17:39 -0500 Subject: [PATCH 2116/2173] Update mehari to 0.23.0 (#45928) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index e410ddacac824..f198f9be47627 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.22.0" %} -{% set sha256 = "1240ac7d026eebfa6a4396548f748848501fd0128e3ca81cc890ee70faf33fac" %} +{% set version = "0.23.0" %} +{% set sha256 = "296ba1df8bfa2bd7ce6efe4d109af9214f1b6ac921563ab537c87ade827e01ad" %} package: name: mehari From 7b925f1a4873ed9e54b6a5fa896cc4a33e6e69e2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 06:21:08 -0500 Subject: [PATCH 2117/2173] Update r-ontologyplot to 1.7 (#45920) * Update r-ontologyplot to 1.7 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-ontologyplot/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/r-ontologyplot/meta.yaml b/recipes/r-ontologyplot/meta.yaml index 8b6b1b81d83ed..94c88333bac20 100644 --- a/recipes/r-ontologyplot/meta.yaml +++ b/recipes/r-ontologyplot/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.6' %} +{% set version = '1.7' %} package: name: r-ontologyplot @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/ontologyPlot_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/ontologyPlot/ontologyPlot_{{ version }}.tar.gz - sha256: 41a601e2201f32673c6830adc770a877be1ba4003b7352d4c09c8c50a3e8a158 + sha256: d508b861cfd596555f1b7bea681de71c9674fa7b708bb00b7a55744fb2cfd61b build: - number: 4 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-ontologyplot', max_pin="x") }} requirements: host: @@ -35,7 +37,8 @@ test: about: home: https://CRAN.R-project.org/package=ontologyPlot - license: GPL (>= 2) + license: GPL-2.0-or-later summary: Functions for visualising sets of ontological terms using the 'graphviz' layout system. license_family: GPL3 - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' From b1a27087054963d751f0791d3b19b23dfb93ee69 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 06:43:37 -0500 Subject: [PATCH 2118/2173] Update metaphlan to 4.1.0 (#45926) * Update metaphlan to 4.1.0 * Update meta.yaml * Fixing strainphlan -h --------- Co-authored-by: Francesco Asnicar --- recipes/metaphlan/meta.yaml | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/recipes/metaphlan/meta.yaml b/recipes/metaphlan/meta.yaml index 26ea15ee0a30e..362577e6f15ae 100644 --- a/recipes/metaphlan/meta.yaml +++ b/recipes/metaphlan/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metaphlan" %} -{% set version = "4.0.6" %} +{% set version = "4.1.0" %} package: name: {{ name }} @@ -7,13 +7,15 @@ package: source: url: https://github.com/biobakery/MetaPhlAn/archive/{{version}}.tar.gz - sha256: f69e9499056a259829a50f4eb5ab8e62e76f57852df921784d66fb5d7c4379a4 + sha256: 7552ee617a1ca7d862cc07bbb4f238ab0a8872f2702fb49192bee0461264d376 build: noarch: python number: 0 script: {{ PYTHON }} -m pip install -vv --no-deps . + run_exports: + - {{ pin_subpackage('metaphlan', max_pin='x.x') }} requirements: host: @@ -24,10 +26,9 @@ requirements: run: - python >=3.7 - bowtie2 >=2.3.0 - - cmseq - - phylophlan - dendropy - numpy + - phylophlan >=3.1 - biom-format - matplotlib-base - biopython @@ -39,7 +40,15 @@ requirements: - pysam - raxml >=8.2.10 - samtools >=1.9 - + - r-base >=4 + - r-essentials + - r-optparse + - r-rbiom + - r-ape + - r-compositions + - r-biocmanager + - bioconductor-microbiome + - hclust2 test: commands: - metaphlan -v @@ -51,6 +60,12 @@ test: - plot_tree_graphlan.py -h - sample2markers.py -h - strain_transmission.py -h + - sgb_to_gtdb_profile.py -h + - metaphlan2krona.py -h + - hclust2.py -h + - run_treeshrink.py -h + - treeshrink.py -h + - create_toy_database.py -h - bowtie2-align-s --help about: From a4ac8e1cf81346cbc070af6d659abcc660089896 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 07:54:29 -0500 Subject: [PATCH 2119/2173] Update snakemake-interface-common to 1.17.1 (#45930) --- recipes/snakemake-interface-common/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-interface-common/meta.yaml b/recipes/snakemake-interface-common/meta.yaml index 38e66d2a7ae0f..5d1078964b88a 100644 --- a/recipes/snakemake-interface-common/meta.yaml +++ b/recipes/snakemake-interface-common/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-interface-common" %} -{% set version = "1.17.0" %} +{% set version = "1.17.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_interface_common-{{ version }}.tar.gz - sha256: d1f0cb83611f24f62ec5af852cee1cef429dd4e86c55bf373092fc682acac133 + sha256: 555c8218d9b68ddc1046f94a517e7d0f22e15bdc839d6ce149608d8ec137b9ae build: noarch: python From 18bacb073f7104e47eb1c27c1cdf03930cd272c0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 12:19:33 -0500 Subject: [PATCH 2120/2173] Update cramino to 0.14.3 (#45935) --- recipes/cramino/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cramino/meta.yaml b/recipes/cramino/meta.yaml index 5647f84ea1049..d7ba67ed1e831 100644 --- a/recipes/cramino/meta.yaml +++ b/recipes/cramino/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.14.1" %} +{% set version = "0.14.3" %} package: name: cramino @@ -12,7 +12,7 @@ build: source: url: https://github.com/wdecoster/cramino/archive/v{{ version }}.tar.gz - sha256: 57e15afb113808c327a4ec843ae1677f37c35f692e04927cfcc3823affac6cff + sha256: 10bf8574892077915b314422c18690ec141d8c934e8446502761601f4ab78303 requirements: build: From c8756f044a217b46c1d95114c0d83d4dd8b0403c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 12:48:39 -0500 Subject: [PATCH 2121/2173] Update ngs-chew to 0.9.4 (#45934) * Update ngs-chew to 0.9.3 * Update meta.yaml * Update ngs-chew to 0.9.4 --------- Co-authored-by: Manuel Holtgrewe --- recipes/ngs-chew/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/ngs-chew/meta.yaml b/recipes/ngs-chew/meta.yaml index 70a556610a8a9..f6df359de7c2e 100644 --- a/recipes/ngs-chew/meta.yaml +++ b/recipes/ngs-chew/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.9.2" %} -{% set sha256 = "5220182a9b2e6d2c2adf8ca6053c5a8ebf917942c6486eeee19aa2ccc6bea561" %} +{% set version = "0.9.4" %} +{% set sha256 = "7ea102e92268d9db07f9361735da6da1ebf433dbd5bff0766f8a9aaf6b93c279" %} package: name: ngs-chew @@ -37,6 +37,7 @@ requirements: - vcfpy - bcftools - samtools + - pyarrow test: commands: From e4c4a1afc33ea974e84d72a676440ff4d5f25e15 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 13:41:28 -0500 Subject: [PATCH 2122/2173] Update trtools to 6.0.0 (#45915) * Update trtools to 6.0.0 * Update trtools to 6.0.0 (#45894) * sync dependency version constraints with pyproject.toml https://github.com/gymrek-lab/TRTools/blob/daaa0271e052248dcbbe594b1c4c08a69db9d353/pyproject.toml#L34-L44 * add poetry-core as a build dependency * add patch * remove script entry points which are only valid in pyproject.toml and not meta.yaml recipes --------- Co-authored-by: mencian --------- Co-authored-by: Arya Massarat <23412689+aryarm@users.noreply.github.com> Co-authored-by: mencian --- recipes/trtools/meta.yaml | 35 +++++++++++++++------------ recipes/trtools/test_trtools.sh.patch | 13 ++++++++++ 2 files changed, 33 insertions(+), 15 deletions(-) create mode 100644 recipes/trtools/test_trtools.sh.patch diff --git a/recipes/trtools/meta.yaml b/recipes/trtools/meta.yaml index f0431f6c1f2ec..7e885105b91e8 100644 --- a/recipes/trtools/meta.yaml +++ b/recipes/trtools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trtools" %} -{% set version = "5.1.1" %} +{% set version = "6.0.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,9 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: e3b107d3d4a2ba2f0df49c382df911ab79bfbdf04aa15c84d3093bed67e4220d + sha256: afb0337a27aab41a9974ce3390e5d3d0932f5740631db8a91f7cb3c3c10ad148 + patches: + - test_trtools.sh.patch build: noarch: python @@ -27,20 +29,20 @@ build: requirements: host: - - python >=3.5 - - pip >=20.1.1 + - python >=3.7.1 + - poetry-core >=1.0.0 + - pip >=20.3 run: - - cyvcf2 >=0.30.1 - - matplotlib-base >=3.2.2 - - numpy >=1.18.5 - - pandas >=1.0.5 - - pybedtools >=0.8.1 - - pysam >=0.16.0.1 - - python >=3.5 + - python >=3.7.1,<4.0 + - cyvcf2 >=0.30.4 + - matplotlib-base >=3.1.2 + - numpy >=1.17.3,<2.0 + - pandas >=1.2.0 + - pysam >=0.15.4 - scikit-learn >=0.23.1 - - scipy >=1.4.1 - - statsmodels >=0.13.5 - - pyfaidx >=0.5.3 + - scipy >=1.3.3 + - statsmodels >=0.10.2 + - pyfaidx >=0.5.6 - ART >=2016.06.05 test: @@ -71,7 +73,7 @@ test: - simTR --help about: - home: http://github.com/gymreklab/TRTools + home: https://github.com/gymreklab/TRTools license: MIT license_family: MIT license_file: LICENSE.txt @@ -83,3 +85,6 @@ extra: recipe-maintainers: - LiterallyUniqueLogin - aryarm + identifiers: + - biotools:trtools + - doi:10.1093/bioinformatics/btaa736 diff --git a/recipes/trtools/test_trtools.sh.patch b/recipes/trtools/test_trtools.sh.patch new file mode 100644 index 0000000000000..b4c6bf6b3f284 --- /dev/null +++ b/recipes/trtools/test_trtools.sh.patch @@ -0,0 +1,13 @@ +diff --git a/trtools/testsupport/test_trtools.sh b/trtools/testsupport/test_trtools.sh +index 67eb46d5..09e1bf3b 100755 +--- a/trtools/testsupport/test_trtools.sh ++++ b/trtools/testsupport/test_trtools.sh +@@ -15,7 +15,7 @@ if [ ! -d "$TMP" ] ; then + echo "Downloading test data ..." + mkdir $TMP + pushd $TMP +- git clone -b v$(dumpSTR --version) https://github.com/gymrek-lab/TRTools.git ++ git clone -b v$(dumpSTR --version) https://github.com/gymrek-lab/TRTools.git . + popd + echo "Download done" + else From 72a757299d2b830da3df6a106011e0ffa31738b2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 13:56:16 -0500 Subject: [PATCH 2123/2173] Update pytrf to 1.3.0 (#45932) --- recipes/pytrf/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pytrf/meta.yaml b/recipes/pytrf/meta.yaml index 14cbbf40ed6d3..209d0d802eb4b 100644 --- a/recipes/pytrf/meta.yaml +++ b/recipes/pytrf/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pytrf" %} -{% set version = "1.2.1" %} -{% set sha256 = "47d201d0cb2dad705f9a4e6030d374878c4b6e30762eefd08f159c28db7402df" %} +{% set version = "1.3.0" %} +{% set sha256 = "624497536b4e9a5cb8bbddb7ead7a2253a89b27ccf872178e9a8d975e21695f6" %} package: name: "{{ name|lower }}" @@ -11,7 +11,7 @@ source: sha256: "{{ sha256 }}" build: - number: 1 + number: 0 skip: True # [py < 36] script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" run_exports: From eae3ea85a790db0af2ecf1c1010609f055f34faa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 13:59:55 -0500 Subject: [PATCH 2124/2173] Update earlgrey to 4.1.0 (#45927) --- recipes/earlgrey/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml index e53bf3657fabd..f7fcf4ea41de7 100644 --- a/recipes/earlgrey/meta.yaml +++ b/recipes/earlgrey/meta.yaml @@ -1,6 +1,6 @@ {% set name = "EarlGrey" %} -{% set version = "4.0.8" %} -{% set sha256 = "ae68c9bc464320d07ee026079c7fc2819d5768f29b7742224fc481fd03c46615" %} +{% set version = "4.1.0" %} +{% set sha256 = "682fe5115294b48ac663c3ebe3260811d490d011565f4ad876218ca0417a33cd" %} package: name: {{ name|lower }} From 7d0612aefdd67dd4f2dabef3263d6f18d6453f31 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 14:00:01 -0500 Subject: [PATCH 2125/2173] Update ncbi-datasets-pylib to 16.4.9 (#45918) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index dcd72174fd033..8f1be91eac4f5 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.8" %} -{% set sha256 = "5c08fc546170079034be19f53468667114d0695ab348bb2c04794141a9a6ed3c" %} +{% set version = "16.4.9" %} +{% set sha256 = "7a6973469573d8b029f89a52d4f3f6a9612f4bd28c1d8975ba03640fbcf9f1bd" %} package: name: {{ name|lower }} From 159bc328f4e33963760689f860b34490cc6d32b7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 14:00:26 -0500 Subject: [PATCH 2126/2173] Update ampcombi to 0.2.0 (#45909) * Update ampcombi to 0.2.0 * run_exports * lowercase software name --------- Co-authored-by: Thanh Lee --- recipes/ampcombi/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ampcombi/meta.yaml b/recipes/ampcombi/meta.yaml index 463325c2d636f..dd27f1ed0b8e9 100644 --- a/recipes/ampcombi/meta.yaml +++ b/recipes/ampcombi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "AMPcombi" %} -{% set version = "0.1.7" %} +{% set version = "0.2.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a73ab40cc80670f403aa629d1c1d7318ce21cc952618fdc1eba0ef667fae3578 + sha256: 96ddff5067279d3da05a662d627e793b040764560c6b6a6464bfe01a0768a27b build: noarch: python @@ -15,6 +15,8 @@ build: entry_points: - ampcombi = ampcombi:main script: "{{ PYTHON }} -m pip install . -vv" + run_exports: + - {{ pin_subpackage("ampcombi", max_pin="x.x") }} requirements: host: From a3be23f0cf826a4c0c55a399476473d71f3e89a1 Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren Date: Wed, 21 Feb 2024 14:01:28 -0500 Subject: [PATCH 2127/2173] Update bed2gff v.0.1.4 (#45923) * new: gtfsort recipe * new: bed2gtf recipe * new: bed2gff recipe * fix: clean recipe * feat: add build.sh * fix: clean recipe; add build.sh * fix: delete other recipes already in PRs * fix spacing * Update meta.yaml * feat: bed2gff v.0.1.4 * feat: bed2gff v.0.1.4 --------- Co-authored-by: mencian --- recipes/bed2gff/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bed2gff/meta.yaml b/recipes/bed2gff/meta.yaml index 8dd9a3b9338c3..f7e17ea6ec0dd 100644 --- a/recipes/bed2gff/meta.yaml +++ b/recipes/bed2gff/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bed2gff" %} -{% set version = "0.1.3" %} +{% set version = "0.1.4" %} package: name: bed2gff @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz - sha256: c278185aba8c352ec2b14cc7db6eb08afb5b81e000b0acb9330bfccdad10506c + sha256: 171c4e334faf50bd7a75d47faaf7e0adda52b820f9af02db282b185af000a0a0 build: number: 0 From 8d2631c3fe9bf5ebef05a55a7277e53bf43d7ae1 Mon Sep 17 00:00:00 2001 From: miguelteixeira <92163520+lhtxa@users.noreply.github.com> Date: Wed, 21 Feb 2024 20:08:32 +0100 Subject: [PATCH 2128/2173] CarveMe recipe (#45799) * CarveMe recipe * carveme recipe * carveme recipe * fk * updated recipe and license * asd * relax pinning * relax pinning * scip fix * fix reframed scip dependencies * reframed version * missing requests --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/carveme/LICENSE.txt | 16 +++++++++ recipes/carveme/meta.yaml | 65 +++++++++++++++++++++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 recipes/carveme/LICENSE.txt create mode 100644 recipes/carveme/meta.yaml diff --git a/recipes/carveme/LICENSE.txt b/recipes/carveme/LICENSE.txt new file mode 100644 index 0000000000000..e9b0f54ede839 --- /dev/null +++ b/recipes/carveme/LICENSE.txt @@ -0,0 +1,16 @@ + +Apache Software License 2.0 + +Copyright (c) 2017, Daniel Machado + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + +http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. diff --git a/recipes/carveme/meta.yaml b/recipes/carveme/meta.yaml new file mode 100644 index 0000000000000..3a9692325ff17 --- /dev/null +++ b/recipes/carveme/meta.yaml @@ -0,0 +1,65 @@ +{% set name = "carveme" %} +{% set version = "1.6.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: 3f58e2519af378b15b7e0d175aefa94566793503e32856d690720213a1a9d478 + +build: + number: 0 + entry_points: + - build_universe=carveme.cli.build_universe:main + - curate_universe=carveme.cli.curate_universe:main + - carve=carveme.cli.carve:main + - gapfill=carveme.cli.gapfill:main + - merge_community=carveme.cli.merge_community:main + - benchmark=carveme.cli.benchmark:main + script: "{{ PYTHON }} -m pip install --use-pep517 . -vv" + noarch: python + build: + run_exports: + - {{ pin_subpackage('carveme', max_pin="x.x.x") }} + +requirements: + host: + - python >=3.8 + - pip + run: + - pandas + - python >=3.8 + - reframed >=1.5.1 + - diamond + - pyscipopt + - scip + - numpy + - requests +test: + imports: + - carveme + - carveme.cli + - carveme.reconstruction + - carveme.universe + - tests + commands: + - build_universe --help + - curate_universe --help + - carve --help + - gapfill --help + - merge_community --help + - benchmark --help + +about: + home: "https://github.com/cdanielmachado/carveme" + license: Apache-2.0 + license_family: APACHE + license_file: LICENSE.txt + summary: "CarveMe: automated genome-scale metabolic model reconstruction" + +extra: + recipe-maintainers: + - lhtxa + - cdanielmachado From 0d56752f4b8c209c8d16cc4c9ec3436bb73f4f83 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 14:11:37 -0500 Subject: [PATCH 2129/2173] Update bed2gtf to 1.9.1 (#45925) --- recipes/bed2gtf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bed2gtf/meta.yaml b/recipes/bed2gtf/meta.yaml index 9ce15cb1fe6a5..90543d51d327f 100644 --- a/recipes/bed2gtf/meta.yaml +++ b/recipes/bed2gtf/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bed2gtf" %} -{% set version = "1.9.0" %} +{% set version = "1.9.1" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz - sha256: ae09861fa3474b3298a0469ad6d58bced91667792b5a20fdafe7b0dde6a05351 + sha256: 7acf7dff631a4d724420110a7a4e28a8324ae9040311567c0feeeec6a33fe661 build: number: 0 From 66425b28347ec0bd9d420ee09ebf8008ed080c03 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 14:12:18 -0500 Subject: [PATCH 2130/2173] Update pcaone to 0.4.2 (#45937) --- recipes/pcaone/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml index 3f67d9dbac7c4..78f7aad64ada9 100644 --- a/recipes/pcaone/meta.yaml +++ b/recipes/pcaone/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.1" %} -{% set sha256 = "03f8afa9870507e03aa90a349a00f70f56bbf202b05a4d3d648148f3c30b6518" %} +{% set version = "0.4.2" %} +{% set sha256 = "94d8d41b251dbe2f1dab2aaa80e96ebf51753033ba01a43aae995069554c5a82" %} package: From 86a0823303d1ff7af0c10bf19ce117f7d41c4621 Mon Sep 17 00:00:00 2001 From: Guy Assa <78320514+theAguy@users.noreply.github.com> Date: Wed, 21 Feb 2024 21:30:57 +0200 Subject: [PATCH 2131/2173] ver 2.0.8 (#45862) * ver 2.0.8 * Pin python, biopython typing.Protocol introduced in python 3.8 Bio.SubsMat removed in biopython 1.80 --------- Co-authored-by: Brandon Seah --- recipes/crispector2/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/crispector2/meta.yaml b/recipes/crispector2/meta.yaml index 8b47e82f104df..cf882e1b1ee03 100644 --- a/recipes/crispector2/meta.yaml +++ b/recipes/crispector2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.7" %} +{% set version = "2.0.8" %} package: name: crispector2 @@ -15,15 +15,15 @@ build: source: url: https://github.com/theAguy/crispector2/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3531fd5cad957c046a54355a18552453bf1dac7141b3e7b7c13b40ccf5599a86 + sha256: 9ca7823cbd4decdd3b1bbe3bd4bb7c77e87142ce4d1df21f06565ee9ee465177 requirements: host: - - python 3.7 + - python >=3.8 - pip run: - - python 3.7 - - biopython >=1.74 + - python >=3.8 + - biopython >=1.74, <=1.79 # Bio.SubsMat - fastp - python-edlib - click >=7.0 From da42844b21b129f7fd129ba90f7a63c62ba306ed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 14:43:25 -0500 Subject: [PATCH 2132/2173] Update pronto to 2.5.6 (#45936) * Update pronto to 2.5.6 * add run_exports --------- Co-authored-by: mencian --- recipes/pronto/meta.yaml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/recipes/pronto/meta.yaml b/recipes/pronto/meta.yaml index ed42fc4d9781c..4651abcbc0bd9 100644 --- a/recipes/pronto/meta.yaml +++ b/recipes/pronto/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pronto" %} -{% set version = "2.5.5" %} +{% set version = "2.5.6" %} package: name: "{{ name }}" @@ -7,12 +7,14 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8f9a0917156248b2cce05d238c5d76a7b49ee07619f2bce3c73796bff82d5b4f + sha256: eacdaa9b629042d1a07c59470241576c111751229ac052a05bfce8180df33bf8 build: noarch: python number: 0 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-deps -vvv + run_exports: + - {{ pin_subpackage('pronto', max_pin="x") }} requirements: host: @@ -35,10 +37,13 @@ test: - pronto.serializers about: - home: http://github.com/althonos/pronto + home: https://github.com/althonos/pronto license: MIT summary: 'Python frontend to ontologies' license_family: MIT + license_file: COPYING + doc_url: https://pronto.readthedocs.io/en/stable/ + dev_url: https://github.com/althonos/pronto extra: recipe-maintainers: From 68cab44a4c64ccb5d69726648a9af4d960ded15d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 15:25:21 -0500 Subject: [PATCH 2133/2173] Update r-metacoder to 0.3.7 (#45904) * Update r-metacoder to 0.3.7 * add run_exports --------- Co-authored-by: mencian --- recipes/r-metacoder/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/r-metacoder/meta.yaml b/recipes/r-metacoder/meta.yaml index d4dcb0e8b2ae0..82b9450e80aaf 100644 --- a/recipes/r-metacoder/meta.yaml +++ b/recipes/r-metacoder/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.3.6' %} +{% set version = '0.3.7' %} package: name: r-metacoder @@ -8,10 +8,12 @@ source: url: - {{ cran_mirror }}/src/contrib/metacoder_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/metacoder/metacoder_{{ version }}.tar.gz - sha256: a2ab9675e1b08f4bf7027a74c4e7a1777e71850420e0a901784da0ddbdc5f896 + sha256: a48bf05b526cc3125605fcb221e96f55c74fd18d535c1a0e55982e3cbf3ffe38 build: - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage('r-metacoder', max_pin="x.x") }} rpaths: - lib/R/lib/ - lib/ @@ -73,7 +75,8 @@ test: - $R -e "library('metacoder')" about: - home: https://grunwaldlab.github.io/metacoder_documentation/ + home: https://github.com/grunwaldlab/metacoder + doc_url: https://grunwaldlab.github.io/metacoder_documentation/ license: GPL-2 | GPL-3 summary: A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy). From 9ee9dfe3292ec5dde7469de63d4cbcb2ba9c6ba8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 16:22:21 -0500 Subject: [PATCH 2134/2173] Update ncbi-datasets-pylib to 16.5.0 (#45938) --- recipes/ncbi-datasets-pylib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ncbi-datasets-pylib/meta.yaml b/recipes/ncbi-datasets-pylib/meta.yaml index 8f1be91eac4f5..ca968a0c85017 100644 --- a/recipes/ncbi-datasets-pylib/meta.yaml +++ b/recipes/ncbi-datasets-pylib/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ncbi-datasets-pylib" %} -{% set version = "16.4.9" %} -{% set sha256 = "7a6973469573d8b029f89a52d4f3f6a9612f4bd28c1d8975ba03640fbcf9f1bd" %} +{% set version = "16.5.0" %} +{% set sha256 = "df952921dac4244df9e40d467bd441169f95c2435846b1ab55f2ccfcce805acc" %} package: name: {{ name|lower }} From adf37faf72e92bc8785301ecb943f3a622a0cf92 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 18:26:53 -0500 Subject: [PATCH 2135/2173] Update humid to 1.0.4 (#45704) * Update humid to 1.0.3 * add run_exports * edit license_file line * Update humid to 1.0.4 --------- Co-authored-by: mencian Co-authored-by: Redmar van den Berg <15814544+Redmar-van-den-Berg@users.noreply.github.com> --- recipes/humid/meta.yaml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/humid/meta.yaml b/recipes/humid/meta.yaml index bbc1e7ba47dc4..77f3ae3e1d436 100644 --- a/recipes/humid/meta.yaml +++ b/recipes/humid/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.0.2" %} +{% set version = "1.0.4" %} package: name: humid @@ -6,10 +6,12 @@ package: source: url: https://github.com/jfjlaros/HUMID/releases/download/v{{ version }}/humid-v{{ version }}.tar.gz - sha256: 3e35f663884cb47b089740629a61537e56536479c0c9b560819e599fd047d34e + sha256: 5da8a2a95514304b7a32a6525bb6047bae16b96e56a9737a57a745470eac7733 build: - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage('humid', max_pin="x") }} requirements: build: @@ -17,7 +19,6 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} - isa-l - - libdeflate host: - isa-l - libdeflate @@ -32,4 +33,6 @@ test: about: home: https://github.com/jfjlaros/HUMID license: MIT + license_family: MIT summary: HUMID -- High-performance UMI Deduplicator + doc_url: https://humid.readthedocs.io/en/latest/usage.html From 8818735ee6e20ca145498589acb61d4d9f2f60c8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 21 Feb 2024 19:06:06 -0500 Subject: [PATCH 2136/2173] Update trtools to 6.0.1 (#45940) * Update trtools to 6.0.1 * remove patch --------- Co-authored-by: mencian --- recipes/trtools/meta.yaml | 6 ++---- recipes/trtools/test_trtools.sh.patch | 13 ------------- 2 files changed, 2 insertions(+), 17 deletions(-) delete mode 100644 recipes/trtools/test_trtools.sh.patch diff --git a/recipes/trtools/meta.yaml b/recipes/trtools/meta.yaml index 7e885105b91e8..9cd7d82dec675 100644 --- a/recipes/trtools/meta.yaml +++ b/recipes/trtools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trtools" %} -{% set version = "6.0.0" %} +{% set version = "6.0.1" %} package: name: "{{ name|lower }}" @@ -7,9 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: afb0337a27aab41a9974ce3390e5d3d0932f5740631db8a91f7cb3c3c10ad148 - patches: - - test_trtools.sh.patch + sha256: 915e5f1e2ee490ad2e78294014da71cb103182277fc075ee0ccc1d27aab8bece build: noarch: python diff --git a/recipes/trtools/test_trtools.sh.patch b/recipes/trtools/test_trtools.sh.patch deleted file mode 100644 index b4c6bf6b3f284..0000000000000 --- a/recipes/trtools/test_trtools.sh.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/trtools/testsupport/test_trtools.sh b/trtools/testsupport/test_trtools.sh -index 67eb46d5..09e1bf3b 100755 ---- a/trtools/testsupport/test_trtools.sh -+++ b/trtools/testsupport/test_trtools.sh -@@ -15,7 +15,7 @@ if [ ! -d "$TMP" ] ; then - echo "Downloading test data ..." - mkdir $TMP - pushd $TMP -- git clone -b v$(dumpSTR --version) https://github.com/gymrek-lab/TRTools.git -+ git clone -b v$(dumpSTR --version) https://github.com/gymrek-lab/TRTools.git . - popd - echo "Download done" - else From d2e778dfe7dc9342bf5048b12434c59ab2812955 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 22 Feb 2024 13:11:24 +1300 Subject: [PATCH 2137/2173] Added ltr_harvest_parallel (#45867) * Added ltr_harvest_parallel * Fixed pin_subpackage * Removed version for perl --- recipes/ltr_harvest_parallel/build.sh | 15 ++++++++++ recipes/ltr_harvest_parallel/meta.yaml | 41 ++++++++++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 recipes/ltr_harvest_parallel/build.sh create mode 100644 recipes/ltr_harvest_parallel/meta.yaml diff --git a/recipes/ltr_harvest_parallel/build.sh b/recipes/ltr_harvest_parallel/build.sh new file mode 100644 index 0000000000000..ebadfe1bb70e0 --- /dev/null +++ b/recipes/ltr_harvest_parallel/build.sh @@ -0,0 +1,15 @@ +#!/bin/sh +set -x -e + +LTR_HARVEST_PARALLEL_DIR=${PREFIX}/share/LTR_HARVEST_parallel + +mkdir -p ${PREFIX}/bin +mkdir -p ${LTR_HARVEST_PARALLEL_DIR} +cp -r bin/LTR_HARVEST_parallel/* ${LTR_HARVEST_PARALLEL_DIR} + +cat <>${PREFIX}/bin/LTR_HARVEST_parallel +#!/bin/bash +perl ${LTR_HARVEST_PARALLEL_DIR}/LTR_HARVEST_parallel \$@ +END + +chmod a+x ${PREFIX}/bin/LTR_HARVEST_parallel diff --git a/recipes/ltr_harvest_parallel/meta.yaml b/recipes/ltr_harvest_parallel/meta.yaml new file mode 100644 index 0000000000000..0c0366ea3aca4 --- /dev/null +++ b/recipes/ltr_harvest_parallel/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "LTR_HARVEST_parallel" %} +{% set version = "1.1" %} +{% set edta_version = "2.2.0" %} +{% set sha256 = "3515667804437f749f0bb934812ca83b23ec5472c221786f6e5a0d4b613a1a7a" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/oushujun/EDTA/archive/v{{ edta_version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('ltr_harvest_parallel', max_pin='x') }} + +requirements: + run: + - perl + - genometools-genometools ==1.6.5 + +test: + commands: + - LTR_HARVEST_parallel -check_dependencies > /dev/null + +about: + home: https://github.com/oushujun/EDTA/tree/8980f498f05ad63dbffa3241842d3d38e939531b/bin/LTR_HARVEST_parallel + license: MIT + license_family: MIT + license_file: LICENSE + summary: Perl wrapper for parallel execution of LTR_harvest + dev_url: https://github.com/oushujun/EDTA/tree/8980f498f05ad63dbffa3241842d3d38e939531b/bin/LTR_HARVEST_parallel + doc_url: https://github.com/oushujun/EDTA/tree/8980f498f05ad63dbffa3241842d3d38e939531b/bin/LTR_HARVEST_parallel + +extra: + identifiers: + - doi:10.1186/s13059-019-1905-y + - doi:10.1101/2022.10.09.511471 From 87b39f1c53cb93f927252f845664bbc196fbf40e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 22 Feb 2024 02:56:34 -0500 Subject: [PATCH 2138/2173] Update mehari to 0.23.1 (#45947) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index f198f9be47627..2357b0b532a06 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.23.0" %} -{% set sha256 = "296ba1df8bfa2bd7ce6efe4d109af9214f1b6ac921563ab537c87ade827e01ad" %} +{% set version = "0.23.1" %} +{% set sha256 = "fd025d56c0d13c6e48c4fcfff799bace96ec267317993c255bfbbfe8bb7dafac" %} package: name: mehari From ad5aedd466773e591151daebb2710b9615f07596 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 22 Feb 2024 09:47:50 -0500 Subject: [PATCH 2139/2173] Update varlociraptor to 8.4.5 (#45950) --- recipes/varlociraptor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varlociraptor/meta.yaml b/recipes/varlociraptor/meta.yaml index 98b3bb7d447fc..c7c24a4b76bf6 100644 --- a/recipes/varlociraptor/meta.yaml +++ b/recipes/varlociraptor/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "8.4.4" %} +{% set version = "8.4.5" %} package: name: varlociraptor @@ -11,7 +11,7 @@ build: source: url: https://github.com/varlociraptor/varlociraptor/archive/v{{ version }}.tar.gz - sha256: e95294fb7dcefc1f61e26fac3fceedb8355138ff386e5ffd76236f3aea083cb3 + sha256: 96141350ba0eeaf57731f654f2c33b7044a3b64a433d863e6c659b82d1ca3526 requirements: build: From 0f8cc809a2ef5cfee6e8aa3822d0998d78cb9cfe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 22 Feb 2024 09:51:53 -0500 Subject: [PATCH 2140/2173] Update ppanggolin to 2.0.3 (#45951) --- recipes/ppanggolin/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ppanggolin/meta.yaml b/recipes/ppanggolin/meta.yaml index 16e09e9ca169c..85280b93ba3e0 100644 --- a/recipes/ppanggolin/meta.yaml +++ b/recipes/ppanggolin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.2" %} +{% set version = "2.0.3" %} package: name: ppanggolin @@ -6,7 +6,7 @@ package: source: url: https://github.com/labgem/PPanGGOLiN/archive/{{ version }}.tar.gz - sha256: a655b378b05da41c5d2b7e8e8269af722681854c5d6c7c9589d01bea636035a1 + sha256: 0cd44aa30868387fb3617c52658674e57d9bd73efab636e7d8690f5d1a144c5f build: number: 0 From 73b819eaef4ddbc2430dfd09bce80514efd6d856 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 22 Feb 2024 09:55:46 -0500 Subject: [PATCH 2141/2173] Update mehari to 0.23.2 (#45956) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 2357b0b532a06..9273c9e42a05b 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.23.1" %} -{% set sha256 = "fd025d56c0d13c6e48c4fcfff799bace96ec267317993c255bfbbfe8bb7dafac" %} +{% set version = "0.23.2" %} +{% set sha256 = "d6b25df465fd6da7423c54b254b8506bfb39f647a45378b3cd1d6221db8040cd" %} package: name: mehari From 5c34c199d9dee8ecd303a054543888ce9e9ff438 Mon Sep 17 00:00:00 2001 From: pirovc <4673375+pirovc@users.noreply.github.com> Date: Thu, 22 Feb 2024 19:48:19 +0100 Subject: [PATCH 2142/2173] Update dudes to 0.10.0 (#45959) * dudes v0.10.0 * python310 * matplotlib-base * poetry * license --- recipes/dudes/meta.yaml | 45 ++++++++++++++++++++++++++++------------- 1 file changed, 31 insertions(+), 14 deletions(-) diff --git a/recipes/dudes/meta.yaml b/recipes/dudes/meta.yaml index af2174caed477..31bf5937c52ae 100644 --- a/recipes/dudes/meta.yaml +++ b/recipes/dudes/meta.yaml @@ -1,30 +1,47 @@ +{% set name = "dudes" %} +{% set version = "0.10.0" %} + package: - name: dudes - version: "0.08" + name: "{{ name|lower }}" + version: "{{ version }}" source: - url: https://github.com/pirovc/dudes/archive/dudes_v0.08.tar.gz - md5: b569094e73ad2d40dccac7a26554a839 + url: https://github.com/pirovc/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: cb53be14da0c9d40e4ac758a6de7fe98e494c5bff3847d5aa6568a1ea8781180 build: noarch: python - number: 2 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + number: 0 + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed --no-cache-dir -vvv . + run_exports: + - {{ pin_subpackage(name, max_pin="x") }} requirements: host: - - python >=3 + - python >=3.10 - pip + - poetry run: - - python >=3 - - numpy - - pandas + - python >=3.10 + - matplotlib-base >=3.5.1 + - numpy >=1.21.0 + - pandas >=1.4.1 test: commands: - - DUDes.py -h 2>&1 | echo $? + - dudes -h + - dudesdb -h about: - home: https://github.com/pirovc/dudes/ - license: The MIT License (MIT) - summary: 'DUDes: a top-down taxonomic profiler for metagenomics' + home: https://github.com/pirovc/dudes + summary: "DUDes: a top-down taxonomic profiler for metagenomics and metaproteomics" + license: MIT License + license_family: MIT + license_file: LICENSE.md + +extra: + identifiers: + - doi:10.1093/bioinformatics/btw150 + recipe-maintainers: + - pirovc + - rababerladuseladim From 039c73d579227cee1bf4c072e453becd745f9b5d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 04:08:54 -0500 Subject: [PATCH 2143/2173] Update fasten to 0.8.3 (#45962) --- recipes/fasten/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fasten/meta.yaml b/recipes/fasten/meta.yaml index 79537796084c4..07b12a9b9b61f 100644 --- a/recipes/fasten/meta.yaml +++ b/recipes/fasten/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.1" %} -{% set sha256 = "35314fa8b6c8d2139338ed070f1c171b06bb7760efecf3e06064bc521399e2cd" %} +{% set version = "0.8.3" %} +{% set sha256 = "ae4d56cb81ae1e5ead734aaf3727ae595bb6c8703707f408915b992ee6ba08f1" %} package: name: fasten From b409ac68639a39895da0480cfe8914779b0c9772 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 05:51:13 -0500 Subject: [PATCH 2144/2173] Update cramino to 0.14.4 (#45972) --- recipes/cramino/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cramino/meta.yaml b/recipes/cramino/meta.yaml index d7ba67ed1e831..dedfeb0ffcfa5 100644 --- a/recipes/cramino/meta.yaml +++ b/recipes/cramino/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.14.3" %} +{% set version = "0.14.4" %} package: name: cramino @@ -12,7 +12,7 @@ build: source: url: https://github.com/wdecoster/cramino/archive/v{{ version }}.tar.gz - sha256: 10bf8574892077915b314422c18690ec141d8c934e8446502761601f4ab78303 + sha256: b07a40180dae4d413ba1cb3ea1307bcf5208634cab38ede352e70e8edd84e6ba requirements: build: From 1bc8d10a24dbc07d3a9c1066cbb75ddda9d3dc6b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 05:52:10 -0500 Subject: [PATCH 2145/2173] Update insilicoseq to 2.0.1 (#45971) --- recipes/insilicoseq/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/insilicoseq/meta.yaml b/recipes/insilicoseq/meta.yaml index d212e177e6070..9839e23b74ac0 100644 --- a/recipes/insilicoseq/meta.yaml +++ b/recipes/insilicoseq/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.0.0" %} -{% set sha256 = "1eb851ea345aaf46d8a5924516bbd55c8f957bb83ada8e9a995c1aae001d5d2a" %} +{% set version = "2.0.1" %} +{% set sha256 = "a1b452fbb6781c5c04bad269836893bf8d2103215e8d131c37baa95a74b2cbaa" %} package: name: insilicoseq From 51bbb6ec4a51cdfd1680a36123ca8010d1cd537a Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 23 Feb 2024 15:14:05 +0100 Subject: [PATCH 2146/2173] Bump multiqc to do another build (#45969) See https://github.com/MultiQC/MultiQC/issues/2283 --- recipes/multiqc/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index cb8edecf3f5a4..2f3097c7e9847 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 46e01394ee4c213eee3c14fde01afcb0da3e87a29b09a119e5aaeabf2817313d build: - number: 1 + number: 2 entry_points: - multiqc=multiqc.__main__:run_multiqc noarch: python From 1a9c18273737c87d4f87e1feea778cf66b250b31 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 09:34:19 -0500 Subject: [PATCH 2147/2173] Update pydeseq2 to 0.4.5 (#45970) * Update pydeseq2 to 0.4.5 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/pydeseq2/meta.yaml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/recipes/pydeseq2/meta.yaml b/recipes/pydeseq2/meta.yaml index 5086ace06d91f..c66af03900ccf 100644 --- a/recipes/pydeseq2/meta.yaml +++ b/recipes/pydeseq2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pydeseq2" %} -{% set version = "0.4.4" %} +{% set version = "0.4.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pydeseq2-{{ version }}.tar.gz - sha256: ebd978d51d4d66b40e6dce8826029d9551fec9946c2a75793e75eb748cc3b207 + sha256: 51b32980f1959bb14c8830b151f60493fff7d8c5e0a1774889ef09de5aa194f1 build: noarch: python @@ -18,18 +18,17 @@ build: requirements: host: - - python >=3.8 + - python >=3.9 - pip run: - - python >=3.8 + - python >=3.9 - anndata >=0.8.0 - jupyter - ipython - numpy >=1.23.0 - pandas >=1.4.0 - scikit-learn >=1.1.0 - - scipy >=1.8.0 - - statsmodels + - scipy >=1.11.0 - matplotlib-base >=3.6.2 test: From fa18703a2b04ed1741cb195cb861696bf5c256ed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 10:52:01 -0500 Subject: [PATCH 2148/2173] Update panaroo to 1.4.2 (#45978) --- recipes/panaroo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/panaroo/meta.yaml b/recipes/panaroo/meta.yaml index a85cb44af1e88..5fbf153632352 100644 --- a/recipes/panaroo/meta.yaml +++ b/recipes/panaroo/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.4.1" %} +{% set version = "1.4.2" %} {% set name = "panaroo" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/gtonkinhill/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: 5ff88a48b339083bcbf843e84eeff3be5f9eda3808394da436386ce0cdfc0111 + sha256: 7f3e06d19dfc8b65e761ea0199e0a1363ee8b708bab327679000e770de9f3af3 build: number: 0 From f73c561bb61a0f335526525f6e98c4b340987a03 Mon Sep 17 00:00:00 2001 From: Reid Wagner <74672860+reid-wagner@users.noreply.github.com> Date: Fri, 23 Feb 2024 10:24:04 -0600 Subject: [PATCH 2149/2173] Add IonQuant recipe. (#45126) * Add IonQuant recipe. * Add maintainer field. Co-authored-by: M Bernt --------- Co-authored-by: M Bernt --- recipes/ionquant/academic_install.py | 74 ++++++++++++++++++++++++ recipes/ionquant/build.sh | 33 +++++++++++ recipes/ionquant/ionquant.py | 86 ++++++++++++++++++++++++++++ recipes/ionquant/meta.yaml | 50 ++++++++++++++++ 4 files changed, 243 insertions(+) create mode 100755 recipes/ionquant/academic_install.py create mode 100644 recipes/ionquant/build.sh create mode 100755 recipes/ionquant/ionquant.py create mode 100644 recipes/ionquant/meta.yaml diff --git a/recipes/ionquant/academic_install.py b/recipes/ionquant/academic_install.py new file mode 100755 index 0000000000000..fb4adafac6868 --- /dev/null +++ b/recipes/ionquant/academic_install.py @@ -0,0 +1,74 @@ +#!/usr/bin/env python3 + +# Automates accepting the academic license agreements in order to download IonQuant. A user of this package is then expected to accept the terms themselves when they download a license key from the IonQuant site, which is enforced by the wrapper script and IonQuant jar file. + +import argparse +import hashlib +import os +import re +import sys +import urllib.request +import urllib.parse + +IONQUANT_URL = 'http://msfragger-upgrader.nesvilab.org/ionquant/upgrade_download.php' +DOWNLOAD_READ_SIZE = 1000000 + +def download_url(url, post_dict, dest): + data = urllib.parse.urlencode(post_dict).encode('ascii') + with open(dest, 'wb') as wh: + size = 0 + m = hashlib.sha256() + with urllib.request.urlopen(url, data) as f: + while True: + seg = f.read(DOWNLOAD_READ_SIZE) + m.update(seg) + bytes_read = len(seg) + if bytes_read < 1: + break + size += bytes_read + wh.write(seg) + + return m.hexdigest() + +def parse_version(version_string): + version_pattern = '([\\d.]+)' + m = re.search(version_pattern, version_string.strip()) + if m: + return m.groups()[0] + return None + +parser = argparse.ArgumentParser( + description="Download IonQuant zip file." +) +parser.add_argument( + '-n', '--name', help='user name' +) +parser.add_argument( + '-e', '--email', help='email' +) +parser.add_argument( + '-o', '--organization', help='institutional organization' +) +parser.add_argument( + '-i', '--ionquant_version', help='IonQuant version', required=True +) +parser.add_argument( + '-p', '--path', default='.', help='path in which to install' +) +parser.add_argument( + '--hash', default='.', help='SHA256 hash of downloaded zip' +) + +args = parser.parse_args() +iq_ver = parse_version(args.ionquant_version) +if iq_ver == None: + print(f'Could not find version: {args.ionquant_version}', file=sys.stderr) + sys.exit(1) + +iq_zip = iq_ver + '$zip' +dest = os.path.join(args.path, 'IonQuant-' + iq_ver + '.zip') +data = {'transfer': 'academic', 'agreement1': 'true', 'name': args.name, 'email' : args.email, 'organization' : args.organization, 'download': iq_zip} + +if download_url(IONQUANT_URL, data, dest) != args.hash: + print('Invalid hash calculated.', file=sys.stderr) + sys.exit(1) diff --git a/recipes/ionquant/build.sh b/recipes/ionquant/build.sh new file mode 100644 index 0000000000000..9a487d861c802 --- /dev/null +++ b/recipes/ionquant/build.sh @@ -0,0 +1,33 @@ +#!/bin/bash + +# These values are submitted to the IonQuant site when downloading the application zip. +if [[ -z "$NAME" ]]; then + NAME="${USERNAME:-bioconda}"; +fi +if [[ -z "$EMAIL" ]]; then + EMAIL="${NAME}@${HOSTNAME:-bioconda.org}"; +fi +if [[ -z "$INSTITUTION" ]]; then + INSTITUTION="${HOSTNAME:-bioconda.org}"; +fi + +# Create directories +TARGET="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +mkdir -p "$TARGET" + +# Add wrapper python script and link to unprefixed name. +cp "$RECIPE_DIR/ionquant.py" "$TARGET" +ln -s "$TARGET/ionquant.py" "$PREFIX/bin/ionquant" +chmod 0755 "${PREFIX}/bin/ionquant" + +# This script automates accepting the academic license agreements in order to download the software and build the package. A user of this package is then expected to accept the terms themselves when they download a license key from the IonQuant site, which is enforced by the wrapper script and IonQuant jar file. +"${RECIPE_DIR}/academic_install.py" -n galaxy -e "$EMAIL" -o "$INSTITUTION" -i "$PKG_VERSION" -p "$TARGET" --hash "$SHA256SUM" +if [[ $? -ne 0 ]]; then + echo "Problem downloading jar file." > /dev/stderr + exit 1; +fi + +# Unzip and link jar. +cd "$TARGET" +unzip "IonQuant-$PKG_VERSION.zip" +ln -s "IonQuant-$PKG_VERSION/IonQuant-$PKG_VERSION.jar" "IonQuant.jar" diff --git a/recipes/ionquant/ionquant.py b/recipes/ionquant/ionquant.py new file mode 100755 index 0000000000000..b9de0803001e1 --- /dev/null +++ b/recipes/ionquant/ionquant.py @@ -0,0 +1,86 @@ +#!/usr/bin/env python +# +# Wrapper script for Java Conda packages that ensures that the java runtime +# is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128). +# + +import os +import sys +import subprocess +from os import access, getenv, X_OK + +jar_file = os.path.join(os.path.dirname(__file__), "IonQuant.jar") + +default_jvm_mem_opts = ['-Xms512m', '-Xmx1g'] + +license_agreement_text = ''' +Please provide pass a license key with the --key argument. You may obtain a key by agreeing to the terms at https://msfragger.arsci.com/ionquant/. +''' + +def real_dirname(path): + """Return the symlink-resolved, canonicalized directory-portion of path.""" + return os.path.dirname(os.path.realpath(path)) + + +def java_executable(): + """Return the executable name of the Java interpreter.""" + java_home = getenv('JAVA_HOME') + java_bin = os.path.join('bin', 'java') + + if java_home and access(os.path.join(java_home, java_bin), X_OK): + return os.path.join(java_home, java_bin) + else: + return 'java' + + +def jvm_opts(argv): + """Construct list of Java arguments based on our argument list. + + The argument list passed in argv must not include the script name. + The return value is a 3-tuple lists of strings of the form: + (memory_options, prop_options, passthrough_options) + """ + mem_opts = [] + prop_opts = [] + pass_args = [] + + for arg in argv: + if arg.startswith('-D'): + prop_opts.append(arg) + elif arg.startswith('-XX'): + prop_opts.append(arg) + elif arg.startswith('-Xm'): + mem_opts.append(arg) + else: + pass_args.append(arg) + + # In the original shell script the test coded below read: + # if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ] + # To reproduce the behaviour of the above shell code fragment + # it is important to explictly check for equality with None + # in the second condition, so a null envar value counts as True! + + if mem_opts == [] and getenv('_JAVA_OPTIONS') == None: + mem_opts = default_jvm_mem_opts + + return (mem_opts, prop_opts, pass_args) + + +def main(): + java = java_executable() + jar_dir = real_dirname(sys.argv[0]) + jar_path = os.path.join(jar_dir, jar_file) + jar_arg = '-jar' + + (mem_opts, prop_opts, pass_args) = jvm_opts(sys.argv[1:]) + + if '--key' not in sys.argv: + print(license_agreement_text) + sys.exit(1) + + java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args + + sys.exit(subprocess.call(java_args)) + +if __name__ == '__main__': + main() diff --git a/recipes/ionquant/meta.yaml b/recipes/ionquant/meta.yaml new file mode 100644 index 0000000000000..3b87b49eeac8c --- /dev/null +++ b/recipes/ionquant/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.10.12" %} + +# This key was generated ONLY for the testing of this bioconda package. +# Users must generate their own key by agreeing to the terms at https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf. +{% set academic_use_only_key = "47cb2953-b4bf7726-2c96f5fe-8f1013aa" %} +{% set sha256sum = "861a633ab815a34ea54e6e26f318e19b510b25cb8955f3daeb83d6d10c6938ea" %} + +package: + name: ionquant + version: {{ version }} + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage('ionquant', max_pin="x.x") }} + script_env: + - SHA256SUM={{ sha256sum }} + +requirements: + host: + - python >=3.9 + - unzip + run: + - openjdk >=11 + - python >=3.8 + +test: + commands: + - ionquant --key {{ academic_use_only_key }} -Xms512m -Xmx1g --help 2>&1 | grep 'IonQuant' + +about: + home: https://github.com/Nesvilab/IonQuant + license: Academic License (https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf) + summary: A label free quantification tool + description: | + IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. + It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). + It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. + + IonQuant is available freely for academic research and educational purposes only, in accordance with the terms at https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf. + +extra: + recipe-maintainers: + - reid-wagner + notes: | + The "ionquant" command runs the IonQuant java program. + identifiers: + - biotools:fragpipe + - doi:10.1074/mcp.TIR120.002048 From e804570e8afb92b202924fd374d37a25605010b3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 11:34:17 -0500 Subject: [PATCH 2150/2173] Update chewbbaca to 3.3.3 (#45975) --- recipes/chewbbaca/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index fae78e05f24ed..770e27d49c701 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -1,5 +1,5 @@ {% set name = 'chewBBACA' %} -{% set version = '3.3.2' %} +{% set version = '3.3.3' %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4e282320ce8b6b3b6e71d2db8961911c523d970f8b06e16c7c42b2aff0ae5f03 + sha256: c29e34bdca769b38f8e9c7f7bd3547563f9e1e1effe5266e7b00674d9a7ca12a build: number: 0 From f50482bb5da9126343b460f70ae370319faa9cc9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 11:52:46 -0500 Subject: [PATCH 2151/2173] Update defense-finder to 1.2.2 (#45960) --- recipes/defense-finder/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/defense-finder/meta.yaml b/recipes/defense-finder/meta.yaml index 3bb41bf1ac853..8b03555254ce6 100644 --- a/recipes/defense-finder/meta.yaml +++ b/recipes/defense-finder/meta.yaml @@ -1,5 +1,5 @@ {% set name = "defense-finder" %} -{% set version = "1.2.1" %} +{% set version = "1.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/mdmparis/defense-finder/archive/v{{ version }}.tar.gz - sha256: bff50fce7442e1bcc7fb7dd9ed202176662e5e02205551eee5ca05e4172cd2cd + sha256: e34e59cf1329e26c9cb6e42bb5cb6a7a051e09ca4bf981b9334f73a08d354625 # patches: 0001-fix-no-results.patch build: From e59d869880ba8eff84fbcdfcba927e9849e56dd9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 12:42:01 -0500 Subject: [PATCH 2152/2173] Update oakvar to 2.9.89 (#45981) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 8e67b03ac181a..a8f76bc238221 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.88" %} -{% set sha256 = "ebb19910d3c3b0eff179430ea175072c21a658557b72b11dc5c5d45ddddab7c2" %} +{% set version = "2.9.89" %} +{% set sha256 = "1c55c4d0bf7b849c14deaaa213591ca825ff33f8cb5d4b17b787e49bb60f11a3" %} package: name: {{ name|lower }} From c5f0b4fc30c2b29e90ce60ab5e5b51a190b38a21 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 12:42:10 -0500 Subject: [PATCH 2153/2173] Update bionumpy to 1.0.4 (#45977) --- recipes/bionumpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bionumpy/meta.yaml b/recipes/bionumpy/meta.yaml index e150ab834eebc..eb79aa91be613 100644 --- a/recipes/bionumpy/meta.yaml +++ b/recipes/bionumpy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.2" %} +{% set version = "1.0.4" %} package: name: bionumpy @@ -6,7 +6,7 @@ package: source: url: https://github.com/bionumpy/bionumpy/archive/refs/tags/v{{ version }}.tar.gz - sha256: 0052120fb3c07a83d5064b680246b2b8ddf251dac526ac60d6d1c18f4ee944eb + sha256: 88d84fd1f18c4406c79bc492963267e837673d961af2dfceb45f65ef27430823 build: noarch: python From d81930511ba6fafa36755032e80ccee425a9d785 Mon Sep 17 00:00:00 2001 From: Benjamin Linard <22132778+blinard-BIOINFO@users.noreply.github.com> Date: Fri, 23 Feb 2024 19:15:42 +0100 Subject: [PATCH 2154/2173] Add recipe epik (#45973) * Adds recipe for epik --------- Co-authored-by: Benjamin Linard --- recipes/epik/build.sh | 24 +++++++++++++++++++++++ recipes/epik/meta.yaml | 42 ++++++++++++++++++++++++++++++++++++++++ recipes/epik/run_test.sh | 36 ++++++++++++++++++++++++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 recipes/epik/build.sh create mode 100644 recipes/epik/meta.yaml create mode 100644 recipes/epik/run_test.sh diff --git a/recipes/epik/build.sh b/recipes/epik/build.sh new file mode 100644 index 0000000000000..7bdd89211df09 --- /dev/null +++ b/recipes/epik/build.sh @@ -0,0 +1,24 @@ +#!/bin/bash +set -ex + +export CPLUS_INCLUDE_PATH=${PREFIX}/include +export CPP_INCLUDE_PATH=${PREFIX}/include +export CXX_INCLUDE_PATH=${PREFIX}/include + +#to ensure zlib location +export CFLAGS="$CFLAGS -I$PREFIX/include" +export LDFLAGS="$LDFLAGS -L$PREFIX/lib" + +mkdir -p $PREFIX/bin +mkdir -p $PREFIX/lib + +cmake -B build -DBUILD_SHARED_LIBS=ON --install-prefix=$PREFIX +cmake --build build --target all +cmake --install build + +ls $PREFIX/bin +ls $PREFIX/lib + +chmod +x $PREFIX/bin/epik-aa +chmod +x $PREFIX/bin/epik-dna +chmod +x $PREFIX/bin/epik.py diff --git a/recipes/epik/meta.yaml b/recipes/epik/meta.yaml new file mode 100644 index 0000000000000..438e50ab8cc17 --- /dev/null +++ b/recipes/epik/meta.yaml @@ -0,0 +1,42 @@ +{% set name = "EPIK" %} +{% set version = "0.2.0" %} +{% set sha256 = "33db0a0fec8e89950110ea8c910947e00e224117dcba2a78d9347f61da4fe1cb" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/phylo42/{{ name|lower }}/releases/download/v{{ version }}/EPIK-v{{ version }}_src_for_bioconda.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('epik', max_pin="x.x") }} + +requirements: + build: + - make + - {{ compiler('cxx') }} + - cmake + - llvm-openmp # [osx] + host: + - boost-cpp >=1.67 + - zlib + - rapidjson + run: + - boost-cpp >=1.67 + - llvm-openmp # [osx] + - python + - click + + +about: + home: https://github.com/phylo42/epik + license: MIT + license_family: MIT + license_file: LICENSE + summary: "EPIK is a tool for fast alignement-free phylogenetic placements." + description: "EPIK uses pre-computed phylo-k-mers indexes (see package IPK) to rapidly place large amounts of sequences on a fixed phylogenetic tree. Please cite: doi.org/10.1093/bioinformatics/btad692" + diff --git a/recipes/epik/run_test.sh b/recipes/epik/run_test.sh new file mode 100644 index 0000000000000..d35e1baf13fad --- /dev/null +++ b/recipes/epik/run_test.sh @@ -0,0 +1,36 @@ +#!/usr/bin/env bash + +PASS=true + +# A +echo "test A" +command -v epik-dna +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + +# B +echo "test B" +command -v epik-aa +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + +# C +echo "test C" +epik-dna 2>&1 | grep "Evolutionary Placement with Informative K-mers" +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + +#D +echo "test D" +epik.py place --help +if [ $? -ne 0 ]; then + echo "failed" + PASS=false +fi + From bdb3a5104a58d1f874bb9d264177320c08f0f0d3 Mon Sep 17 00:00:00 2001 From: Qiyun Zhu Date: Fri, 23 Feb 2024 11:19:06 -0700 Subject: [PATCH 2155/2173] Update Woltka to 0.1.6 (#45967) * Update Woltka to 0.1.6 * Update Woltka to 0.1.6 * Update Woltka to 0.1.6 * Update Woltka to 0.1.6 * updated license --- recipes/woltka/meta.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/woltka/meta.yaml b/recipes/woltka/meta.yaml index 0eb7ddeaedf5b..f5fdbff852898 100644 --- a/recipes/woltka/meta.yaml +++ b/recipes/woltka/meta.yaml @@ -1,5 +1,5 @@ {% set name = "woltka" %} -{% set version = "0.1.5" %} +{% set version = "0.1.6" %} package: name: "{{ name|lower }}" @@ -7,14 +7,16 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e97f84ba5044aec8aae7f54dc42a4172c0972a3ca008e4cf7909d364496fa16d + sha256: d1ffe069515284f6350e3129b5fa3a65b4a583105282c5af0a3997c30b7f8e99 build: number: 0 noarch: python entry_points: - woltka=woltka.cli:cli - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + run_exports: + - {{ pin_subpackage("woltka", max_pin="x.x") }} requirements: host: @@ -37,9 +39,9 @@ test: about: home: "https://github.com/qiyunzhu/woltka" - license: BSD + license: BSD-3-Clause license_family: BSD - license_file: + license_file: LICENSE summary: "versatile meta-omic data classifier" doc_url: dev_url: From 9529eb237b4f97acc0445dc4c823154a87abded1 Mon Sep 17 00:00:00 2001 From: Marc Sturm Date: Fri, 23 Feb 2024 19:23:21 +0100 Subject: [PATCH 2156/2173] Update of ngs-bits to version 2024_02 (#45961) * Updated ngs-bits to version 2018_10 * Updated ngs-bits to version 2024_02 --- recipes/ngs-bits/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ngs-bits/meta.yaml b/recipes/ngs-bits/meta.yaml index 5fa12dddf0aa1..36577f5655986 100755 --- a/recipes/ngs-bits/meta.yaml +++ b/recipes/ngs-bits/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2023_11" %} +{% set version = "2024_02" %} package: name: ngs-bits @@ -11,7 +11,7 @@ build: source: url: https://github.com/imgag/ngs-bits/releases/download/{{ version }}/ngs-bits-{{ version }}.tgz - sha256: bb994eb9a74043fa173a3b0ee6b9eafdf3e7b1aeb1ebcc2ba3e73888e1e61fa4 + sha256: 29f95f6e4e5c1cd57e463730312464bb2b632758c46abd5e1531a1d75a26a782 requirements: build: From ecf319b76ba774f1be03e4fcaefad7a4b1638639 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 14:47:06 -0500 Subject: [PATCH 2157/2173] Update hmftools-mark-dups to 1.1.1 (#45968) --- recipes/hmftools-mark-dups/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-mark-dups/meta.yaml b/recipes/hmftools-mark-dups/meta.yaml index c1fc3b06c02b4..e85200d715b60 100644 --- a/recipes/hmftools-mark-dups/meta.yaml +++ b/recipes/hmftools-mark-dups/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1" %} -{% set sha256 = "f2939d64ef5d96c638264074cf28eaf140d85ff5a21b537dbb156b54ab142047" %} +{% set version = "1.1.1" %} +{% set sha256 = "053440f3aac22a6bd627795bd5968180c0e6b7dcce43e45dab1a5536e1220abd" %} package: name: hmftools-mark-dups From f05f6b837b1807c0b9042cc3eb77214fdf524292 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 23 Feb 2024 17:17:33 -0500 Subject: [PATCH 2158/2173] Update pyhmmer to 0.10.6 (#45931) --- recipes/pyhmmer/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index 314fea094cdc4..38c369f3a8ce2 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmer" %} -{% set version = "0.10.5" %} +{% set version = "0.10.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1c9c6bb5600b96eb3386c524b24bf6eb1f51610017e82b585fe0f3b3c7cdbe03 + sha256: 47e017ccc523046400312afc937d4d68306f6ca0ed82e313deb3697d4fd8ccff build: number: 0 From 33996c7b6043b6c996eaaf1431d84f08f1a9f437 Mon Sep 17 00:00:00 2001 From: Leonid Kostrykin Date: Sat, 24 Feb 2024 08:38:39 +0100 Subject: [PATCH 2159/2173] Update segmetrics to 1.4.1 (#45964) * Bump segmetrics to 1.4.1 * minor consistency changes --------- Co-authored-by: Robert A. Petit III --- recipes/segmetrics/meta.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/recipes/segmetrics/meta.yaml b/recipes/segmetrics/meta.yaml index 73bb5a142078f..085a15459bbea 100644 --- a/recipes/segmetrics/meta.yaml +++ b/recipes/segmetrics/meta.yaml @@ -1,20 +1,20 @@ {% set name = "segmetrics" %} -{% set version = "1.4" %} -{% set repo_url = "https://github.com/BMCV/segmetrics.py" %} -{% set docs_url = "https://segmetrics.readthedocs.io" %} +{% set version = "1.4.1" %} package: name: "{{ name }}" version: "{{ version }}" source: - url: "{{ repo_url }}/archive/refs/tags/{{ version }}.zip" - sha256: 65fce3cd45c4f1fa0f83013a3f7c245e8ea2698ed94a75454b5f5dc833c97ad5 + url: "https://github.com/BMCV/segmetrics/archive/refs/tags/{{ version }}.zip" + sha256: a9c2eec155cc3cc3028fed4e9cf97d08fe1ef666100bb50f251f2b63b8377616 build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv " + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} requirements: host: @@ -39,11 +39,11 @@ test: - python -m segmetrics.cli --help about: - home: "{{ repo_url }}" + home: "https://github.com/BMCV/segmetrics" license: MIT summary: "A Python package implementing image segmentation and object detection performance measures, for biomedical image analysis and beyond." - dev_url: "{{ repo_url }}" - doc_url: "{{ docs_url }}" + dev_url: "https://github.com/BMCV/segmetrics" + doc_url: "https://segmetrics.readthedocs.io" extra: recipe-maintainers: From b802c61a9c547c59da7cee1bcf991424d790cf66 Mon Sep 17 00:00:00 2001 From: Dillon Roach Date: Sat, 24 Feb 2024 01:30:11 -0800 Subject: [PATCH 2160/2173] Delete recipes/r-harmony directory for transfer to conda-forge (#45982) Adding the package to CF in this PR: https://github.com/conda-forge/staged-recipes/pull/25268 --- recipes/r-harmony/build.sh | 1 - recipes/r-harmony/meta.yaml | 59 ------------------------------------- 2 files changed, 60 deletions(-) delete mode 100644 recipes/r-harmony/build.sh delete mode 100644 recipes/r-harmony/meta.yaml diff --git a/recipes/r-harmony/build.sh b/recipes/r-harmony/build.sh deleted file mode 100644 index 5bf492ab9fc06..0000000000000 --- a/recipes/r-harmony/build.sh +++ /dev/null @@ -1 +0,0 @@ -$R CMD INSTALL --build . diff --git a/recipes/r-harmony/meta.yaml b/recipes/r-harmony/meta.yaml deleted file mode 100644 index 2fde7c768fbde..0000000000000 --- a/recipes/r-harmony/meta.yaml +++ /dev/null @@ -1,59 +0,0 @@ -{% set version = '0.1' %} - -package: - name: r-harmony - version: {{ version }} - -source: - url: https://github.com/immunogenomics/harmony/archive/{{ version }}.tar.gz - sha256: 1243bec2c9cd96d32ee48cafc74795bf18c3b50789e388ef8d80e4440940ae2b - -build: - # https://github.com/immunogenomics/harmony/issues/180 - skip: True # [osx] - number: 6 - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - build: - - {{ compiler('cxx') }} - host: - - r-base - - r-rcpp - - r-dplyr - - r-cowplot - - r-tidyr - - r-ggplot2 - - r-irlba - - r-matrix - - r-tibble - - bioconductor-singlecellexperiment - - r-rlang - - r-rcpparmadillo - - r-rcppprogress - run: - - r-base - - r-dplyr - - r-cowplot - - r-tidyr - - r-ggplot2 - - r-irlba - - r-matrix - - r-tibble - - bioconductor-singlecellexperiment - - r-rlang - - r-rcpparmadillo - - r-rcppprogress - -test: - commands: - - $R -e "library('harmony')" - -about: - home: https://github.com/immunogenomics/harmony - dev_url: https://github.com/immunogenomics/harmony - license: GPL-3.0-only - license_file: LICENSE - summary: Fast, sensitive and accurate integration of single-cell data with Harmony From 6fed1aa80fce3ff4e63d73041c85f69218ff7cbe Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 04:39:24 -0500 Subject: [PATCH 2161/2173] Update snakemake-executor-plugin-slurm to 0.3.2 (#45991) --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 38c4d83d70a5c..0e3d1706f16d2 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.3.1" %} +{% set version = "0.3.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 3c45605515f73020d437872e6003de661ddd17a09e2e60780b2d19a5668f0eb5 + sha256: 3912f2895eab1270d7a42959a2e221ce53428dfffb847e03ec6bc4eead88e30b build: noarch: python From 56e0fc48dd4af38f6f99a0f1c470b863e354a330 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 06:00:06 -0500 Subject: [PATCH 2162/2173] Update snakemake to 8.5.1 (#45993) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update snakemake to 8.5.1 * Update meta.yaml --------- Co-authored-by: Johannes Köster --- recipes/snakemake/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index a2220d2f22c9b..60287b09c96b7 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.4.12" %} +{% set version = "8.5.1" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 1320590f24d3ef08d63ac91f1b3f634b27e4cfef21c7bbb3f267a79d75327621 + sha256: 1cfc81901047b831aa322a22fe86f3a2191b721a8deeb28d6448ae4eb0a5bc70 build: number: 0 @@ -104,6 +104,7 @@ outputs: - snakemake-interface-executor-plugins >=8.1.3,<9.0 - snakemake-interface-common >=1.17.0,<2.0 - snakemake-interface-storage-plugins >=3.1.0,<4.0 + - snakemake-interface-report-plugins >=1.0.0,<2.0.0 - stopit - tabulate - throttler From 10eec08e636b283471be8dc0431dd8c0067da8bd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:50:05 -0500 Subject: [PATCH 2163/2173] Update snakemake to 8.5.2 (#45994) --- recipes/snakemake/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 60287b09c96b7..ab1c0e27635e0 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,6 +1,6 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg -{% set version = "8.5.1" %} +{% set version = "8.5.2" %} package: name: snakemake @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: 1cfc81901047b831aa322a22fe86f3a2191b721a8deeb28d6448ae4eb0a5bc70 + sha256: cc94876263182277e4a429e5d371c867400eeddc791c114dfd090d1bb3158975 build: number: 0 From cd7a7ffb1e86bd99cc27804f761c0d9b2e746a5a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:50:13 -0500 Subject: [PATCH 2164/2173] Update fiji-simple_omero_client to 5.17.0 (#45990) --- recipes/fiji-simple_omero_client/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fiji-simple_omero_client/meta.yaml b/recipes/fiji-simple_omero_client/meta.yaml index 1a71aba5be3a5..cf97f12237bf0 100644 --- a/recipes/fiji-simple_omero_client/meta.yaml +++ b/recipes/fiji-simple_omero_client/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fiji-simple_omero_client" %} -{% set version = "5.16.0" %} +{% set version = "5.17.0" %} package: name: {{ name | lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/GReD-Clermont/simple-omero-client/releases/download/{{ version }}/simple-omero-client-{{ version }}.jar - sha256: 577a1edcea00a4f3ad50360e8e53c0f25474b44ae21ffc20afbc757cc6c6c9d3 + sha256: 4dd058185368fb7511e538112bd8edc382409495ce2127ab19405c2b3dcef55a build: number: 0 From 98bc07f4e88787ad9e08da2648763b65207a0e59 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:50:25 -0500 Subject: [PATCH 2165/2173] Update isospecpy to 2.2.2 (#45986) --- recipes/isospecpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/isospecpy/meta.yaml b/recipes/isospecpy/meta.yaml index a40f7264077e9..a162dafa99b55 100644 --- a/recipes/isospecpy/meta.yaml +++ b/recipes/isospecpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "isospecpy" %} -{% set version = "2.2.1" %} +{% set version = "2.2.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/IsoSpecPy-{{ version }}.tar.gz - sha256: 5426cd5ff70835b9d6b54de60b8d7b850eb63758c7443378bcb6d84601a69075 + sha256: ca838870d31c4879f7e8d0ff782876858888532b6eb0d501fb9650bf5395578e build: script: {{ PYTHON }} -m pip install . -vv From 24ea6bf6a1f0649191c3dfd1f447d43c6268ac84 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:50:35 -0500 Subject: [PATCH 2166/2173] Update augur to 24.2.3 (#45983) --- recipes/augur/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml index ab32c10e43f51..afe0aac0b2035 100644 --- a/recipes/augur/meta.yaml +++ b/recipes/augur/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "24.2.2" %} +{% set version = "24.2.3" %} package: name: augur @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nextstrain-augur/nextstrain-augur-{{ version }}.tar.gz - sha256: f15359e193163ce397a2bc056d0f495fbddb223544af1b5956204cf135b79c11 + sha256: 67f21f0de7d5cbf8e7f95d01f27d6a42d0e8e0c63e373969609d879c5f4785d0 build: number: 0 From 01a2341d3944014db4162009102e748fdabb5f91 Mon Sep 17 00:00:00 2001 From: Marcel Martin Date: Sat, 24 Feb 2024 13:50:55 +0100 Subject: [PATCH 2167/2173] Update minute to 0.6.0 (#45976) --- recipes/minute/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/minute/meta.yaml b/recipes/minute/meta.yaml index ea573baaaef3b..7de1dc0076d35 100644 --- a/recipes/minute/meta.yaml +++ b/recipes/minute/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "0.4.0" %} +{% set version = "0.6.0" %} package: name: minute version: {{ version }} source: - url: https://github.com/NBISweden/minute/archive/v{{ version }}.tar.gz - sha256: 38156262a2d105774c93f2732ded5af866965a57552969540f29cfe5d03ba62a + url: https://github.com/NBISweden/minute/archive/refs/tags/v{{ version }}.tar.gz + sha256: 168077b9bc369d8e4bbda51133d00a344dc33716e2a070311cfacaf792b131d7 build: number: 0 From bb5bc0ca61ec3d244cbee620cc3a403296977adf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:51:02 -0500 Subject: [PATCH 2168/2173] Update pcaone to 0.4.3 (#45974) --- recipes/pcaone/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml index 78f7aad64ada9..427ea5b26e300 100644 --- a/recipes/pcaone/meta.yaml +++ b/recipes/pcaone/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.4.2" %} -{% set sha256 = "94d8d41b251dbe2f1dab2aaa80e96ebf51753033ba01a43aae995069554c5a82" %} +{% set version = "0.4.3" %} +{% set sha256 = "91467feef2fa90f168aa2b7d4f4e9b2ec21e255af21c3191bfc9c96a241126c0" %} package: From db05f886a3faf89b2105f38f196cf0cdc127df5f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:51:13 -0500 Subject: [PATCH 2169/2173] Update synapseclient to 4.1.0 (#45965) --- recipes/synapseclient/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/synapseclient/meta.yaml b/recipes/synapseclient/meta.yaml index 58be08dcd1ec8..fa49bf12a5f38 100644 --- a/recipes/synapseclient/meta.yaml +++ b/recipes/synapseclient/meta.yaml @@ -1,5 +1,5 @@ {% set name = "synapseclient" %} -{% set version = "4.0.0" %} +{% set version = "4.1.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/synapseclient-{{ version }}.tar.gz - sha256: 9b1acfa4fc9d76c3d69fab3a362e80a4f3cb8dbd60cea0dd6ab34fbb120a9b34 + sha256: a3a3bb581a5424d4d57408a6c81505b0c50907b7b88ad1cea59f62bf9ee8919e build: noarch: python From c109bd6e2af2b99f022a09baf63ba8c0ee1249bc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 07:51:23 -0500 Subject: [PATCH 2170/2173] Update fgpyo to 0.1.3 (#45963) --- recipes/fgpyo/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fgpyo/meta.yaml b/recipes/fgpyo/meta.yaml index a92669798697a..2082d162ec3a6 100644 --- a/recipes/fgpyo/meta.yaml +++ b/recipes/fgpyo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fgpyo" %} -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/fulcrumgenomics/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: e305049a2961a400519de2426f6b06bac00cd0216ab68e7966ea24420593ab37 + sha256: fbf58a5bb936a7b817c61cd3fb905f7daf48326b9b642a96e16310c14d236715 build: noarch: python From c0569ec5d41c936439cc424ad731f3573c7064f8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 24 Feb 2024 14:58:07 +0100 Subject: [PATCH 2171/2173] add libpdf support to EMBOSS (#45992) * add libpdf support * add run_exports --- recipes/emboss/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/emboss/meta.yaml b/recipes/emboss/meta.yaml index 6d391404b6993..f0dc4935fe501 100644 --- a/recipes/emboss/meta.yaml +++ b/recipes/emboss/meta.yaml @@ -3,8 +3,10 @@ package: version: "6.6.0" build: - number: 7 + number: 8 skip: True # [osx] + run_exports: + - {{ pin_subpackage("emboss", max_pin="x.x") }} source: url: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz @@ -19,10 +21,12 @@ requirements: - zlib - libgd - libpng + - libharu run: - zlib - libgd - libpng + - libharu about: home: http://emboss.open-bio.org/ From 157efe02938639f5858a2d2b48d7c2065295f0c0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 24 Feb 2024 18:14:09 -0500 Subject: [PATCH 2172/2173] Update mgnify-pipelines-toolkit to 0.1.1 (#45949) --- recipes/mgnify-pipelines-toolkit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mgnify-pipelines-toolkit/meta.yaml b/recipes/mgnify-pipelines-toolkit/meta.yaml index 180d73ca19264..00a8968f37bce 100644 --- a/recipes/mgnify-pipelines-toolkit/meta.yaml +++ b/recipes/mgnify-pipelines-toolkit/meta.yaml @@ -1,5 +1,5 @@ {% set name = "mgnify-pipelines-toolkit" %} -{% set version = "0.1.0" %} +{% set version = "0.1.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mgnify_pipelines_toolkit-{{ version }}.tar.gz - sha256: ec70929a119207c866b2eeb92323a30d82998a983ef0364ecaf288d5994dfb00 + sha256: 925b5b154d2858289fc83339fedeb09e58019c0a319edf20d822bc658ff8825b build: entry_points: From 9b0642864104b27bac046f15c25e5db4ce4f7dc9 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sat, 24 Feb 2024 22:06:47 -0500 Subject: [PATCH 2173/2173] use circleci as artifact source (but only for packages) --- .circleci/config.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 141443ed4a1f0..7020f97145379 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -135,7 +135,8 @@ jobs: # a basic unit of work in a run bioconda-utils handle-merged-pr recipes config.yml \ --repo bioconda/bioconda-recipes \ --git-range ${CIRCLE_SHA1}~1 ${CIRCLE_SHA1} \ - --fallback build + --fallback build \ + --artifact-source circleci bulk_build: parameters: